From 8394619baceb118df92e355377fd543bb1aa501a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 13 Dec 2021 17:18:24 +0100 Subject: gnu: Simplify package inputs. This commit was obtained by running: ./pre-inst-env guix style without any additional argument. --- gnu/packages/bioconductor.scm | 7570 ++++++++++++++++++++--------------------- 1 file changed, 3617 insertions(+), 3953 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 44bf5c7d24..17d15c06c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -73,7 +73,7 @@ `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") (synopsis "Genome wide annotation for E coli strain K12") (description @@ -103,7 +103,7 @@ analysis.") (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.Bt.eg.db") (synopsis "Genome wide annotation for Bovine") (description @@ -125,7 +125,7 @@ based on mapping using Entrez Gene identifiers.") (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/reactome.db/") (synopsis "Annotation maps for reactome") (description @@ -148,7 +148,7 @@ database, assembled using data from REACTOME.") `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") @@ -171,7 +171,7 @@ taurus (UCSC version bosTau8).") `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") (synopsis "Full genome sequences for Worm") @@ -196,7 +196,7 @@ objects.") `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") (synopsis "Full genome sequences for Worm") @@ -221,7 +221,7 @@ objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") (synopsis "Full genome sequences for Fly") @@ -246,7 +246,7 @@ objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") (synopsis "Full genome sequences for Fly") @@ -271,9 +271,7 @@ Biostrings objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-dmelanogaster-ucsc-dm3" - ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") (synopsis "Full masked genome sequences for Fly") (description @@ -301,7 +299,7 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11") (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)") (description @@ -324,7 +322,7 @@ as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") (synopsis "Full genome sequences for Homo sapiens") @@ -347,7 +345,7 @@ as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) (build-system r-build-system) - (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) + (propagated-inputs (list r-bsgenome)) (home-page "https://bioconductor.org/packages/release/data/annotation/html/\ BSgenome.Hsapiens.NCBI.GRCh38.html") @@ -372,9 +370,7 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" - ,r-bsgenome-hsapiens-ucsc-hg19))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19)) (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") (synopsis "Full masked genome sequences for Homo sapiens") (description @@ -403,7 +399,7 @@ default.") `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") (synopsis "Full genome sequences for Mouse") @@ -427,9 +423,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-mmusculus-ucsc-mm9" - ,r-bsgenome-mmusculus-ucsc-mm9))) + (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9)) (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") (synopsis "Full masked genome sequences for Mouse") (description @@ -458,7 +452,7 @@ default." ) `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") (synopsis "Full genome sequences for Mouse") @@ -501,7 +495,7 @@ ID and species. It is used by functions in the GenomeInfoDb package.") `((upstream-name . "GO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/GO.db") (synopsis "Annotation maps describing the entire Gene Ontology") (description @@ -523,12 +517,12 @@ information about the latest version of the Gene Ontologies.") `((upstream-name . "Homo.sapiens"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures + r-go-db + r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene + r-organismdbi + r-annotationdbi)) (home-page "https://bioconductor.org/packages/Homo.sapiens/") (synopsis "Annotation package for the Homo.sapiens object") (description @@ -550,13 +544,12 @@ several related annotation packages.") (properties `((upstream-name . "Mus.musculus"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-mm-eg-db" ,r-org-mm-eg-db) - ("r-organismdbi" ,r-organismdbi) - ("r-txdb-mmusculus-ucsc-mm10-knowngene" - ,r-txdb-mmusculus-ucsc-mm10-knowngene))) + (list r-annotationdbi + r-genomicfeatures + r-go-db + r-org-mm-eg-db + r-organismdbi + r-txdb-mmusculus-ucsc-mm10-knowngene)) (home-page "https://bioconductor.org/packages/Mus.musculus") (synopsis "Annotation package for the Mus.musculus object") (description @@ -578,7 +571,7 @@ from several related annotation packages.") `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") (synopsis "Genome wide annotation for Worm") (description @@ -600,7 +593,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") (synopsis "Genome wide annotation for Fly") (description @@ -622,7 +615,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") (synopsis "Annotation for Zebrafish") (description @@ -644,7 +637,7 @@ based on mapping using Entrez Gene identifiers.") `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description @@ -666,7 +659,7 @@ on mapping using Entrez Gene identifiers.") `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") (synopsis "Genome wide annotation for Mouse") (description @@ -689,7 +682,7 @@ annotations for the genome of the model mouse Mus musculus.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") (synopsis "Full genome sequences for Homo sapiens") @@ -713,7 +706,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") @@ -737,7 +730,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") `((upstream-name . "EnsDb.Hsapiens.v75"))) (build-system r-build-system) (propagated-inputs - `(("r-ensembldb" ,r-ensembldb))) + (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") (synopsis "Ensembl based annotation package") (description @@ -760,8 +753,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene") (synopsis "Annotation package for TxDb object(s)") @@ -785,7 +777,7 @@ exposing these as TxDb objects.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -810,7 +802,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -835,8 +827,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") @@ -861,9 +852,7 @@ database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-bsgenome r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") @@ -890,8 +879,7 @@ based on the knownGene track.") `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") (synopsis "Annotation package for C elegans TxDb objects") (description @@ -914,11 +902,8 @@ by exposing these as TxDb objects.") `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") (description @@ -942,7 +927,7 @@ annotations.") `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) (build-system r-build-system) (propagated-inputs - `(("r-minfi" ,r-minfi))) + (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") (synopsis "Manifest for Illumina's EPIC methylation arrays") (description @@ -963,7 +948,7 @@ annotations.") `((upstream-name . "DO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/DO.db/") (synopsis "Annotation maps describing the entire Disease Ontology") (description @@ -985,7 +970,7 @@ Disease Ontology.") (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/PFAM.db") (synopsis "Set of protein ID mappings for PFAM") (description @@ -1009,12 +994,12 @@ using data from public repositories.") `((upstream-name . "phastCons100way.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors)) (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") (synopsis "UCSC phastCons conservation scores for hg19") (description @@ -1040,7 +1025,7 @@ species.") `((upstream-name . "ABAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/ABAData/") (synopsis "Gene expression in human brain regions from Allen Brain Atlas") (description @@ -1087,29 +1072,29 @@ All datasets are restricted to protein coding genes.") "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-aneufinderdata" ,r-aneufinderdata) - ("r-ecp" ,r-ecp) - ("r-foreach" ,r-foreach) - ("r-doparallel" ,r-doparallel) - ("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-bamsignals" ,r-bamsignals) - ("r-dnacopy" ,r-dnacopy) - ("r-biostrings" ,r-biostrings) - ("r-genomicalignments" ,r-genomicalignments) - ("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2) - ("r-ggdendro" ,r-ggdendro) - ("r-ggrepel" ,r-ggrepel) - ("r-reordercluster" ,r-reordercluster) - ("r-mclust" ,r-mclust) - ("r-cowplot" ,r-cowplot))) + (list r-knitr)) + (propagated-inputs + (list r-genomicranges + r-aneufinderdata + r-ecp + r-foreach + r-doparallel + r-biocgenerics + r-s4vectors + r-genomeinfodb + r-iranges + r-rsamtools + r-bamsignals + r-dnacopy + r-biostrings + r-genomicalignments + r-ggplot2 + r-reshape2 + r-ggdendro + r-ggrepel + r-reordercluster + r-mclust + r-cowplot)) (home-page "https://bioconductor.org/packages/AneuFinder/") (synopsis "Copy number variation analysis in single-cell-sequencing data") (description "This package implements functions for copy number variant @@ -1152,10 +1137,8 @@ from Illumina 450k methylation arrays.") `((upstream-name . "biscuiteerData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-curl" ,r-curl) - ("r-experimenthub" ,r-experimenthub))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationhub r-curl r-experimenthub)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biscuiteerData") (synopsis "Data package for Biscuiteer") (description @@ -1222,8 +1205,7 @@ GenomicRanges Bioconductor package.") `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) (propagated-inputs - `(("r-rtracklayer" ,r-rtracklayer) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-rtracklayer r-genomicfeatures)) (home-page "https://bioconductor.org/packages/geneLenDataBase/") (synopsis "Lengths of mRNA transcripts for a number of genomes") (description @@ -1248,7 +1230,7 @@ genomes and gene ID formats, largely based on the UCSC table browser.") ;; make sense to build substitutes. (arguments `(#:substitutable? #f)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Experimental data for use with the genomation package") (description @@ -1271,10 +1253,7 @@ downloaded from Encode.") "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-dexseq" ,r-dexseq) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-biocstyle r-dexseq r-knitr r-rmarkdown)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts @@ -1325,7 +1304,7 @@ resulting in a complete gene expression profile for each cell.") (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase))) + (list r-biobase)) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description @@ -1350,7 +1329,7 @@ the form of an @code{exprSet} object.") (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy))) + (list r-affy)) (home-page "https://bioconductor.org/packages/affydata/") (synopsis "Affymetrix data for demonstration purposes") (description @@ -1400,12 +1379,12 @@ yeast are also included.") `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-experimenthub" ,r-experimenthub) - ("r-hdf5array" ,r-hdf5array) - ("r-multiassayexperiment" ,r-multiassayexperiment) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-annotationhub + r-experimenthub + r-hdf5array + r-multiassayexperiment + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description @@ -1473,12 +1452,12 @@ packages.") "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rsamtools" ,r-rsamtools))) + (list r-s4vectors + r-iranges + r-genomicranges + r-genomicalignments + r-rtracklayer + r-rsamtools)) (home-page "https://bioconductor.org/packages/CoverageView/") (synopsis "Coverage visualization package for R") (description "This package provides a framework for the visualization of @@ -1500,16 +1479,16 @@ how the coverage distributed across the genome.") "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fastcluster" ,r-fastcluster) - ("r-ggplot2" ,r-ggplot2) - ("r-gviz" ,r-gviz) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-fastcluster + r-ggplot2 + r-gviz + r-plyr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/cummeRbund/") (synopsis "Analyze Cufflinks high-throughput sequencing data") (description "This package allows for persistent storage, access, @@ -1560,12 +1539,12 @@ set analyses, and can deal with repeated or longitudinal data.") "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-dbi + r-iranges + r-rsqlite + r-s4vectors + r-xvector)) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing @@ -1585,15 +1564,15 @@ biological sequences.") (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-vgam" ,r-vgam))) + (list r-biostrings + r-genomicranges + r-iranges + r-rhtslib + r-summarizedexperiment + r-variantannotation + r-vgam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gerstung-lab/deepSNV/") (synopsis "Detection of subclonal SNVs in deep sequencing data") (description @@ -1622,13 +1601,10 @@ bases such as COSMIC.") `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) + (list r-biocgenerics r-s4vectors r-iranges r-matrix + r-matrixgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DelayedArray") (synopsis "Delayed operations on array-like objects") (description @@ -1654,11 +1630,9 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs - `(("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-iranges r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/leekgroup/derfinderHelper") (synopsis "Helper for derfinder") (description @@ -1681,17 +1655,17 @@ calculation in parallel.") (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-edger + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-mass + r-reshape2 + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DRIMSeq") (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") (description @@ -1716,15 +1690,15 @@ results.") (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs - `(("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-cluster" ,r-cluster) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocneighbors + r-biocparallel + r-cluster + r-igraph + r-matrix + r-rcpp + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily @@ -1745,12 +1719,12 @@ and evaluate clustering results.") "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-genomeinfodb" ,r-genomeinfodb))) + (list r-biobase + r-iranges + r-genomicranges + r-rcolorbrewer + r-rtracklayer + r-genomeinfodb)) (home-page "https://bioconductor.org/packages/IdeoViz/") (synopsis "Plots data along a chromosomal ideogram") (description "This package provides functions to plot data associated with @@ -1771,8 +1745,7 @@ arbitrary genomic intervals along chromosomal ideogram.") `((upstream-name . "IRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (home-page "https://bioconductor.org/packages/IRanges") (synopsis "Infrastructure for manipulating intervals on sequences") (description @@ -1799,37 +1772,37 @@ possible.") (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-dexseq" ,r-dexseq) - ("r-dplyr" ,r-dplyr) - ("r-drimseq" ,r-drimseq) - ("r-edger" ,r-edger) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcurl" ,r-rcurl) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tximeta" ,r-tximeta) - ("r-tximport" ,r-tximport) - ("r-venndiagram" ,r-venndiagram) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-dexseq + r-dplyr + r-drimseq + r-edger + r-futile-logger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-limma + r-magrittr + r-plyr + r-rcolorbrewer + r-rcurl + r-readr + r-reshape2 + r-rtracklayer + r-stringr + r-tibble + r-tximeta + r-tximport + r-venndiagram + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/") (synopsis "Analyze alternative splicing in RNA-seq data") (description @@ -1853,11 +1826,7 @@ Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description @@ -1881,10 +1850,9 @@ absolute GSEA.") (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) + (list r-biobase r-limsolve)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type @@ -1911,10 +1879,8 @@ relative abundances across samples.") `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-reshape2" ,r-reshape2))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb + r-reshape2)) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the @@ -1938,25 +1904,25 @@ closely reconstructs the mutational profile.") (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-bigmemory" ,r-bigmemory) ; suggested - ("r-synchronicity" ,r-synchronicity) ; suggested - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-pkgmaker" ,r-pkgmaker) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-registry" ,r-registry) - ("r-reshape2" ,r-reshape2) - ("r-rngtools" ,r-rngtools) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cluster + r-biobase + r-biocmanager + r-bigmemory ; suggested + r-synchronicity ; suggested + r-colorspace + r-digest + r-doparallel + r-foreach + r-ggplot2 + r-gridbase + r-pkgmaker + r-rcolorbrewer + r-registry + r-reshape2 + r-rngtools + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "http://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description @@ -1981,14 +1947,14 @@ performing parallel computations on multicore machines.") "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-preprocesscore + r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description @@ -2009,7 +1975,7 @@ analysis.") "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/affycomp/") (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") (description @@ -2032,9 +1998,7 @@ measures for Affymetrix Oligonucleotide Arrays.") `((upstream-name . "AffyCompatible"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml))) + (list r-biostrings r-rcurl r-xml)) (home-page "https://bioconductor.org/packages/AffyCompatible/") (synopsis "Work with Affymetrix GeneChip files") (description @@ -2059,9 +2023,7 @@ Command Console} (AGCC)-compatible sample annotation files.") (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affydata" ,r-affydata) - ("r-biobase" ,r-biobase))) + (list r-affy r-affydata r-biobase)) (home-page "https://bioconductor.org/packages/affyContam/") (synopsis "Structured corruption of Affymetrix CEL file data") (description @@ -2084,27 +2046,27 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-edger" ,r-edger) - ("r-gcrma" ,r-gcrma) - ("r-glimma" ,r-glimma) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gplots" ,r-gplots) - ("r-hwriter" ,r-hwriter) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-oligoclasses" ,r-oligoclasses) - ("r-reportingtools" ,r-reportingtools) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xtable" ,r-xtable))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-edger + r-gcrma + r-glimma + r-ggplot2 + r-gostats + r-gplots + r-hwriter + r-lattice + r-limma + r-oligoclasses + r-reportingtools + r-rsqlite + r-s4vectors + r-xtable)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description @@ -2125,9 +2087,9 @@ to streamline the more common analyses that a Biostatistician might see.") "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) (build-system r-build-system) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + (list r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/bmbolstad/affyio") (synopsis "Tools for parsing Affymetrix data files") (description @@ -2177,13 +2139,13 @@ structure.") "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-httr" ,r-httr) - ("r-xml" ,r-xml) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-httr + r-xml + r-xtable)) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") @@ -2205,15 +2167,15 @@ microarrays.") `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-keggrest" ,r-keggrest) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-dbi + r-keggrest + r-iranges + r-rsqlite + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description @@ -2235,10 +2197,9 @@ annotation data packages using SQLite data storage.") `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) + (list r-genomicranges r-lazyeval)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -2262,16 +2223,16 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") `((upstream-name . "AnnotationForge"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-rcurl + r-rsqlite + r-s4vectors + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -2293,21 +2254,21 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biocversion + r-curl + r-dplyr + r-httr + r-interactivedisplaybase + r-rappdirs + r-rsqlite + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -2334,10 +2295,7 @@ by the user, helping with quick and reproducible access.") (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/aroma.light") (synopsis "Methods for normalization and visualization of microarray data") (description @@ -2360,14 +2318,14 @@ classes.") "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-rcpp + r-rhtslib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -2391,7 +2349,7 @@ paired-end data.") `((upstream-name . "Biobase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/Biobase") (synopsis "Base functions for Bioconductor") (description @@ -2413,17 +2371,17 @@ on Bioconductor or which replace R functions.") `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) + (list r-annotationdbi + r-biocfilecache + r-digest + r-httr + r-progress + r-rappdirs + r-stringr + r-xml + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") (description @@ -2479,11 +2437,9 @@ powerful online queries from gene annotation to database mining.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) + (list r-futile-logger r-snow r-bh)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -2506,12 +2462,12 @@ objects.") `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-crayon + r-genomeinfodb + r-iranges + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description @@ -2534,25 +2490,25 @@ biological sequences or sets of sequences.") (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-annotationdbi + r-annotationfilter + r-biocgenerics + r-biostrings + r-dichromat + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-hmisc + r-iranges + r-rcolorbrewer + r-rlang + r-rsamtools + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/biovizBase") (synopsis "Basic graphic utilities for visualization of genomic data") (description @@ -2576,16 +2532,16 @@ effort and encourages consistency.") `((upstream-name . "BSgenome"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/BSgenome") (synopsis "Infrastructure for Biostrings-based genome data packages") (description @@ -2607,16 +2563,16 @@ genome data packages and support for efficient SNP representation.") (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-graph" ,r-graph) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix) - ("r-rbgl" ,r-rbgl) - ("r-dbi" ,r-dbi))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-genefilter + r-graph + r-gseabase + r-matrix + r-rbgl + r-dbi)) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -2636,28 +2592,27 @@ analysis.") "1nr5p1h9131rvbpnh2kizzx9q6f4ycq6rzxy1yqg2pczqcg7hy4x")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-boot" ,r-boot) - ("r-enrichplot" ,r-enrichplot) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-dplyr" ,r-dplyr) - ("r-plotrix" ,r-plotrix) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" - ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-knitr)) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-boot + r-enrichplot + r-iranges + r-genomeinfodb + r-genomicranges + r-genomicfeatures + r-ggplot2 + r-gplots + r-gtools + r-dplyr + r-plotrix + r-dplyr + r-magrittr + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://www.bioconductor.org/packages/ChIPseeker/") (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization") (description "This package implements functions to retrieve the nearest @@ -2684,12 +2639,12 @@ annotation, distance to TSS, and overlap of peaks or genes.") "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-lattice + r-s4vectors + r-shortread)) (home-page "https://bioconductor.org/packages/chipseq") (synopsis "Package for analyzing ChIPseq data") (description @@ -2712,20 +2667,20 @@ experiments.") `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-clue + r-colorspace + r-digest + r-doparallel + r-foreach + r-getoptlong + r-globaloptions + r-iranges + r-matrixstats + r-png + r-rcolorbrewer)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -2750,20 +2705,20 @@ self-defined annotation graphics.") (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel + r-chipseq + r-copyhelper + r-data-table + r-dnacopy + r-futile-logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gtools + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors)) (home-page "https://github.com/PeeperLab/CopywriteR") (synopsis "Copy number information from targeted sequencing") (description @@ -2790,14 +2745,14 @@ number detection tools.") (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-biocgenerics + r-genefilter + r-geneplotter + r-lattice + r-locfit + r-mass + r-rcolorbrewer)) (home-page "https://www-huber.embl.de/users/anders/DESeq/") (synopsis "Differential gene expression analysis") (description @@ -2821,21 +2776,21 @@ distribution.") (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-genefilter + r-geneplotter + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-rcpp + r-rcpparmadillo + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -2859,25 +2814,25 @@ distribution.") (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-deseq2 + r-genefilter + r-geneplotter + r-genomicranges + r-hwriter + r-iranges + r-rcolorbrewer + r-rsamtools + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -2905,11 +2860,9 @@ exploration of the results.") `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/DirichletMultinomial") (synopsis "Dirichlet-Multinomial mixture models for microbiome data") (description @@ -2933,20 +2886,20 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-aroma-light + r-biobase + r-biocgenerics + r-biocmanager + r-biomart + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -2972,10 +2925,7 @@ global-scaling and full-quantile normalization.") (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp + (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of @@ -3000,24 +2950,24 @@ CAGE.") "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-curl + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-protgenerics + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -3045,11 +2995,8 @@ chromosome region or transcript models of lincRNA genes.") "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase r-biocgenerics r-genomicranges r-iranges + r-s4vectors)) (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") (synopsis "Fast segmentation algorithm for genetic sequencing data") (description @@ -3075,10 +3022,7 @@ microarrays or GRanges for sequencing data.") "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) + (list r-annotationdbi r-go-db r-graph r-keggrest)) (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" "articles/10.1186/1471-2105-10-161")) (synopsis "Generally applicable gene-set enrichment for pathway analysis") @@ -3106,14 +3050,10 @@ analysis using other methods.") "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-survival" ,r-survival))) + (list r-annotate r-annotationdbi r-biobase r-biocgenerics + r-survival)) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description @@ -3133,8 +3073,7 @@ high-throughput sequencing experiments.") "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gplots" ,r-gplots))) + (list r-rcolorbrewer r-gplots)) (home-page "https://www.bioconductor.org/packages/GeneOverlap/") (synopsis "Test and visualize gene overlaps") (description "This package can be used to test two sets of gene lists @@ -3153,28 +3092,28 @@ and visualize the results.") "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridbase + r-impute + r-iranges + r-matrixstats + r-plotrix + r-plyr + r-rcpp + r-readr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqpattern)) + (native-inputs + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -3202,13 +3141,10 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodbdata" ,r-genomeinfodbdata) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomeInfoDb") (synopsis "Utilities for manipulating chromosome identifiers") (description @@ -3232,15 +3168,15 @@ names in their natural, rather than lexicographic, order.") `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GenomicAlignments") (synopsis "Representation and manipulation of short genomic alignments") (description @@ -3265,23 +3201,23 @@ alignments.") `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocio + r-biomart + r-biostrings + r-dbi + r-genomeinfodb + r-genomicranges + r-iranges + r-rcurl + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicFeatures") (synopsis "Tools for working with transcript centric annotations") (description @@ -3309,18 +3245,18 @@ extracting the desired features in a convenient format.") (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixgenerics + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/GenomicFiles") (synopsis "Distributed computing by file or by range") (description @@ -3343,13 +3279,9 @@ provide added flexibility for data combination and manipulation.") `((upstream-name . "GenomicRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -3374,15 +3306,15 @@ manipulating genomic intervals and variables defined along a genome.") (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-annotationforge" ,r-annotationforge) - ("r-biobase" ,r-biobase) - ("r-category" ,r-category) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rbgl" ,r-rbgl))) + (list r-annotate + r-annotationdbi + r-annotationforge + r-biobase + r-category + r-go-db + r-graph + r-rgraphviz + r-rbgl)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") (description @@ -3405,14 +3337,14 @@ testing and other simple calculations.") (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-graph + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -3433,7 +3365,7 @@ Enrichment Analysis} (GSEA).") "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -3457,12 +3389,10 @@ the Human Protein Atlas project.") ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) + (list curl zlib ; packages using rhtslib need to link with zlib + r-zlibbioc)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -3482,7 +3412,7 @@ of other R packages who wish to make use of HTSlib.") (base32 "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/impute") (synopsis "Imputation for microarray data") @@ -3506,11 +3436,9 @@ microarray data, using nearest neighbor averaging.") `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) + (list r-biocgenerics r-dt r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -3532,11 +3460,9 @@ Shiny-based display methods for Bioconductor objects.") (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) + (list r-biostrings r-httr r-png)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -3576,27 +3502,27 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-data-table + r-emdbook + r-fastseg + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-kernsmooth + r-limma + r-mclust + r-mgcv + r-qvalue + r-r-utils + r-rcpp + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-zlibbioc)) + (native-inputs + (list r-knitr)) ; for vignettes (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") @@ -3624,12 +3550,12 @@ TAB-Seq.") (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-iranges + r-seqlogo + r-xvector)) (home-page "https://bioconductor.org/packages/motifRG") (synopsis "Discover motifs in high throughput sequencing data") (description @@ -3650,7 +3576,7 @@ throughput genetic sequencing data sets using regression methods.") "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) @@ -3697,30 +3623,30 @@ in SNV base substitution data.") (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mscoreutils" ,r-mscoreutils) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-biobase + r-biocgenerics + r-biocparallel + r-digest + r-ggplot2 + r-impute + r-iranges + r-lattice + r-maldiquant + r-mass + r-mscoreutils + r-mzid + r-mzr + r-pcamethods + r-plyr + r-protgenerics + r-rcpp + r-s4vectors + r-scales + r-vsn + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -3747,32 +3673,32 @@ of mass spectrometry based proteomics data.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-annotationhub + r-biobase + r-biocgenerics + r-biocstyle + r-biostrings + r-data-table + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-iterators + r-msnbase + r-msmstests + r-mzid + r-mzr + r-protgenerics + r-purrr + r-r-cache + r-rcpp + r-reshape2 + r-rlang + r-runit + r-stringr + r-tibble + r-xtable)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description @@ -3799,14 +3725,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) + (list r-doparallel + r-foreach + r-iterators + r-plyr + r-protgenerics + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -3848,20 +3774,20 @@ specific parser.") -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.28.0. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list ;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.28.0. + boost-for-mysql ; use this instead of the bundled boost sources + zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-ncdf4 + r-protgenerics + r-rcpp + r-rhdf5lib + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -3887,17 +3813,17 @@ previously been used in XCMS.") (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-dbi + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-s4vectors)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several @@ -3919,10 +3845,7 @@ the fact that each of these packages implements a select methods.") (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-biocgenerics r-mass r-rcpp)) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") (description @@ -3969,8 +3892,7 @@ proteomics packages.") (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-graph" ,r-graph))) + (list r-bh r-graph)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description @@ -3991,35 +3913,35 @@ the graph algorithms contained in the Boost library.") (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-data-table + r-dt + r-genomation + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gprofiler2 + r-iranges + r-knitr + r-pbapply + r-pheatmap + r-plotly + r-plotrix + r-proxy + r-ranger + r-rsqlite + r-rtracklayer + r-rmarkdown + r-s4vectors + pandoc)) + (native-inputs + (list r-knitr)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -4042,16 +3964,16 @@ library implementing most of the pipeline's features.") (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-memoise + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -4074,27 +3996,27 @@ region sets and other genomic features.") `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-category" ,r-category) - ("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gseabase" ,r-gseabase) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-pfam-db" ,r-pfam-db) - ("r-r-utils" ,r-r-utils) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-category + r-deseq2 + r-edger + r-ggbio + r-ggplot2 + r-gostats + r-gseabase + r-hwriter + r-iranges + r-knitr + r-lattice + r-limma + r-pfam-db + r-r-utils + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -4121,10 +4043,9 @@ browser.") "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5filters r-rhdf5lib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -4151,11 +4072,11 @@ the available RAM.") (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5lib)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/grimbough/rhdf5filters") (synopsis "HDF5 compression filters") (description @@ -4186,16 +4107,16 @@ HDF5 datasets.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bitops + r-genomeinfodb + r-genomicranges + r-iranges + r-rhtslib + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") (description @@ -4221,11 +4142,7 @@ tab-delimited (tabix) files.") (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) + (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description @@ -4253,24 +4170,24 @@ tab-delimited (tabix) files.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-restfulr" ,r-restfulr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-biocio + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rcurl + r-restfulr + r-rsamtools + r-s4vectors + r-xml + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description @@ -4296,13 +4213,13 @@ as well as query and modify the browser state, such as the current viewport.") (properties `((upstream-name . "samr"))) (build-system r-build-system) (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-gsa + r-impute + r-matrixstats + r-openxlsx + r-shiny + r-shinyfiles)) + (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/SAM/") (synopsis "Significance analysis of Microarrays") (description @@ -4324,23 +4241,23 @@ differential expression analysis, RNAseq data and related problems.") (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-xgboost" ,r-xgboost))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-igraph + r-mass + r-matrix + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) (home-page "https://github.com/plger/scDblFinder") (synopsis "Detect multiplets in single-cell RNA sequencing data") (description @@ -4365,7 +4282,7 @@ comprehensive scDblFinder method.") (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description @@ -4388,11 +4305,7 @@ Stephens (1990).") `((upstream-name . "seqPattern"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) + (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix)) (home-page "https://bioconductor.org/packages/seqPattern") (synopsis "Visualising oligonucleotide patterns and motif occurrences") (description @@ -4415,24 +4328,24 @@ reference point and sorted by a user defined feature.") (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-rhtslib + r-hwriter + r-iranges + r-lattice + r-latticeextra + r-rsamtools + r-s4vectors + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/ShortRead") (synopsis "FASTQ input and manipulation tools") (description @@ -4459,22 +4372,22 @@ ungapped alignment formats.") `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-cluster" ,r-cluster) - ("r-complexheatmap" ,r-complexheatmap) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-matrix" ,r-matrix) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-proxyc" ,r-proxyc) - ("r-slam" ,r-slam) - ("r-tm" ,r-tm))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-circlize + r-clue + r-cluster + r-complexheatmap + r-digest + r-getoptlong + r-go-db + r-gosemsim + r-matrix + r-org-hs-eg-db + r-proxyc + r-slam + r-tm)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/simplifyEnrichment") (synopsis "Simplify functional enrichment results") (description "This package provides a new clustering algorithm, binary @@ -4498,12 +4411,9 @@ and comparing the clusterings.") `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-igraph r-matrix r-s4vectors r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/TrajectoryUtils") (synopsis "Single-cell trajectory analysis utilities") (description @@ -4525,15 +4435,15 @@ structures to hold pseudotime inference results.") "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrixstats" ,r-matrixstats) - ("r-princurve" ,r-princurve) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-trajectoryutils" ,r-trajectoryutils))) + (list r-igraph + r-matrixstats + r-princurve + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-trajectoryutils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/slingshot") (synopsis "Tools for ordering single-cell sequencing") (description "This package provides functions for inferring continuous, @@ -4558,15 +4468,15 @@ graph construction.") (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-hash" ,r-hash) - ("r-igraph" ,r-igraph) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcurl" ,r-rcurl) - ("r-sqldf" ,r-sqldf))) + (list r-gplots + r-hash + r-igraph + r-plotrix + r-plyr + r-png + r-rcolorbrewer + r-rcurl + r-sqldf)) (home-page "https://git.bioconductor.org/packages/STRINGdb") (synopsis "Search tool for the retrieval of interacting proteins database") (description @@ -4590,22 +4500,22 @@ that integrates the various evidences.") (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") (synopsis "R package designed to simplify structural variant analysis") (description @@ -4629,17 +4539,17 @@ involving two separate genomic loci encoded as GRanges objects.") `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-delayedarray + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-matrixgenerics + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -4662,12 +4572,12 @@ samples.") "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) + (list r-edger + r-genefilter + r-mgcv + r-biocparallel + r-matrixstats + r-limma)) (home-page "https://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -4694,21 +4604,21 @@ unmodeled, or latent sources of noise.") (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-crayon" ,r-crayon) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-ggplot2 + r-htmlwidgets + r-magrittr + r-rsamtools + r-s4vectors + r-shortread + r-stringr + r-summarizedexperiment + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -4737,15 +4647,15 @@ annotation infrastructure.") `((upstream-name . "topGO"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) + (list r-annotationdbi + r-dbi + r-biobase + r-biocgenerics + r-go-db + r-graph + r-lattice + r-matrixstats + r-sparsem)) (home-page "https://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") (description @@ -4768,7 +4678,7 @@ dependencies between GO terms can be implemented and applied.") "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description @@ -4793,24 +4703,24 @@ of gene-level counts.") (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrixgenerics + r-summarizedexperiment + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector + r-zlibbioc)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") @@ -4831,13 +4741,9 @@ coding changes and predict coding outcomes.") "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) + (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description @@ -4867,14 +4773,14 @@ and specific in detecting differential transcription.") (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs - `(("r-alluvial" ,r-alluvial) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-mclust" ,r-mclust) - ("r-plyr" ,r-plyr) - ("r-stringdb" ,r-stringdb))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-alluvial + r-ggplot2 + r-gridextra + r-igraph + r-mclust + r-plyr + r-stringdb)) + (native-inputs (list r-knitr)) (home-page "https://git.bioconductor.org/packages/XINA") (synopsis "Identifying proteins that exhibit similar patterns") (description @@ -4941,11 +4847,9 @@ describing each of the graphs.") (("import\\(zlibbioc\\)") "")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/XVector") (synopsis "Representation and manpulation of external sequences") (description @@ -4985,15 +4889,15 @@ libraries for systems that do not have these available via other means.") (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk" ,r-basilisk) - ("r-cli" ,r-cli) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-reticulate" ,r-reticulate) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk + r-cli + r-delayedarray + r-matrix + r-reticulate + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://github.com/theislab/zellkonverter") (synopsis "Conversion between AnnData and single-cell experiments objects") (description @@ -5017,12 +4921,12 @@ saving AnnData objects to disk.") "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-lattice" ,r-lattice) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-lattice + r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/geneplotter") (synopsis "Graphics functions for genomic data") (description @@ -5043,19 +4947,19 @@ saving AnnData objects to disk.") (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-biostrings + r-dbi + r-ff + r-foreach + r-genomicranges + r-iranges + r-rsqlite + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/oligoClasses/") (synopsis "Classes for high-throughput arrays") (description @@ -5077,21 +4981,21 @@ packages.") "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-affxparser" ,r-affxparser) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-affxparser + r-affyio + r-biobase + r-biocgenerics + r-biostrings + r-dbi + r-ff + r-oligoclasses + r-preprocesscore + r-rsqlite + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -5113,10 +5017,9 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description @@ -5168,13 +5071,13 @@ integration with @code{Rcpp}.") (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs - `(("r-emdbook" ,r-emdbook) - ("r-genomicranges" ,r-genomicranges) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppnumerical" ,r-rcppnumerical) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-emdbook + r-genomicranges + r-rcpp + r-rcppeigen + r-rcppnumerical + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for @@ -5195,14 +5098,14 @@ posterior for individual coefficients.") (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-mass" ,r-mass) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-mass + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high @@ -5223,29 +5126,29 @@ signal in the input, that lead to spurious peaks during peak calling.") (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apeglm" ,r-apeglm) - ("r-ashr" ,r-ashr) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gplots" ,r-gplots) - ("r-greylistchip" ,r-greylistchip) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcolorbrewer" , r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-systempiper" ,r-systempiper))) + (list r-amap + r-apeglm + r-ashr + r-biocparallel + r-deseq2 + r-dplyr + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gplots + r-greylistchip + r-iranges + r-lattice + r-limma + r-locfit + r-rcolorbrewer + r-rcpp + r-rhtslib + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-systempiper)) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description @@ -5268,13 +5171,13 @@ occupancy (overlap) analysis and plotting functions.") (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rsamtools" ,r-rsamtools) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-s4vectors + r-iranges + r-genomicranges + r-summarizedexperiment + r-rsamtools + r-genomicalignments + r-rtracklayer)) (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") @@ -5299,20 +5202,20 @@ processing to visualization and annotation.") "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-benchmarkme" ,r-benchmarkme) - ("r-biocparallel" ,r-biocparallel) - ("r-clusterr" ,r-clusterr) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-knitr)) + (propagated-inputs + (list r-beachmat + r-benchmarkme + r-biocparallel + r-clusterr + r-delayedarray + r-matrix + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/mbkmeans") (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") (description "This package implements the mini-batch k-means algorithm for @@ -5332,10 +5235,7 @@ large datasets, including support for on-disk data representation.") "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-survival r-biocgenerics r-biobase r-mass)) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description @@ -5369,7 +5269,7 @@ expressed genes in DNA microarray experiments.") "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description @@ -5391,8 +5291,7 @@ expressed genes in DNA microarray experiments.") (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-igraph" ,r-igraph))) + (list r-graph r-igraph)) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description @@ -5415,9 +5314,7 @@ fitting of some classes of graphical Markov models.") (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-limma" ,r-limma) - ("r-rbgl" ,r-rbgl))) + (list r-graph r-limma r-rbgl)) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description @@ -5441,9 +5338,7 @@ a given recall, F-score for single and multiple classes are available.") (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-codetools r-graph r-xml)) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description @@ -5469,33 +5364,33 @@ determining dependencies between variables, code improvement suggestions.") (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-matrixstats" ,r-matrixstats) - ("r-multtest" ,r-multtest) - ("r-rbgl" ,r-rbgl) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biomart + r-biostrings + r-dbi + r-dplyr + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-graph + r-interactionset + r-iranges + r-keggrest + r-matrixstats + r-multtest + r-rbgl + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -5523,7 +5418,7 @@ enrichedGO (addGeneIDs).") `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats))) + (list r-matrixstats)) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description @@ -5547,7 +5442,7 @@ incompatibilities.") (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma))) + (list r-limma)) (home-page "https://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted @@ -5567,8 +5462,7 @@ normalization and quality checking.") (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-marray" ,r-marray))) + (list r-biobase r-marray)) (home-page "https://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5587,11 +5481,7 @@ the @code{arrayCGH} packages.") (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-impute" ,r-impute) - ("r-dnacopy" ,r-dnacopy) - ("r-snowfall" ,r-snowfall))) + (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall)) (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5610,16 +5500,16 @@ the @code{arrayCGH} packages.") (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-cghcall" ,r-cghcall) - ("r-dnacopy" ,r-dnacopy) - ("r-future-apply" ,r-future-apply) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-r-utils" ,r-r-utils) - ("r-rsamtools" ,r-rsamtools))) + (list r-biobase + r-cghbase + r-cghcall + r-dnacopy + r-future-apply + r-genomicranges + r-iranges + r-matrixstats + r-r-utils + r-rsamtools)) (home-page "https://bioconductor.org/packages/QDNAseq") (synopsis "Quantitative DNA sequencing for chromosomal aberrations") (description "The genome is divided into non-overlapping fixed-sized bins, @@ -5644,9 +5534,7 @@ respectively.") (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges))) + (list r-abind r-edger r-genomicranges)) (home-page "https://bioconductor.org/packages/baySeq/") (synopsis "Bayesian analysis of differential expression patterns in count data") (description @@ -5670,16 +5558,16 @@ more complex hypotheses) via empirical Bayesian methods.") (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics + r-bsgenome-hsapiens-ucsc-hg19 + r-bsgenome-mmusculus-ucsc-mm9 + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description @@ -5704,24 +5592,24 @@ datasets.") (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sqldf" ,r-sqldf))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-plyr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-sqldf)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -5745,13 +5633,13 @@ assessment, principal component analysis on codon coverage.") (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bayseq" ,r-bayseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-seqlogo" ,r-seqlogo))) + (list r-abind + r-bayseq + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-seqlogo)) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description @@ -5774,16 +5662,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.") `((upstream-name . "InteractionSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -5808,24 +5696,24 @@ experiments.") `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-gviz + r-igraph + r-interactionset + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") (synopsis "R package for handling genomic interaction data") (description @@ -5846,7 +5734,7 @@ information and producing various plots and statistics.") (base32 "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) (build-system r-build-system) - (propagated-inputs `(("r-amap" ,r-amap))) + (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") (synopsis "Cluster and tree conversion") (description @@ -5867,12 +5755,12 @@ trees and clusters to other programs.") "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biasedurn" ,r-biasedurn) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genelendatabase" ,r-genelendatabase) - ("r-go-db" ,r-go-db) - ("r-mgcv" ,r-mgcv))) + (list r-annotationdbi + r-biasedurn + r-biocgenerics + r-genelendatabase + r-go-db + r-mgcv)) (home-page "https://bioconductor.org/packages/goseq/") (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") (description @@ -5894,15 +5782,15 @@ defined categories which are over/under represented in RNA-seq data.") (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-deseq2 + r-edger + r-htmlwidgets + r-jsonlite + r-limma + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -5927,8 +5815,7 @@ information.") (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-rcpp)) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description @@ -5950,8 +5837,7 @@ in omics data.") "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-biobase r-mass)) (home-page "http://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description @@ -5976,30 +5862,29 @@ genes or proteins in these datasets.") (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-desolve" ,r-desolve) - ("r-gdata" ,r-gdata) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plgem" ,r-plgem) - ("r-proc" ,r-proc) - ("r-rootsolve" ,r-rootsolve) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-txdb-mmusculus-ucsc-mm9-knowngene" - ,r-txdb-mmusculus-ucsc-mm9-knowngene))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-deseq2 + r-desolve + r-gdata + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-kernsmooth + r-plgem + r-proc + r-rootsolve + r-rsamtools + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment + r-txdb-mmusculus-ucsc-mm9-knowngene)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -6023,11 +5908,9 @@ modeling the rates that determines changes in mature mRNA levels.") (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description @@ -6052,12 +5935,9 @@ demultiplexed, i.e. assigned to their original reference barcode.") (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edaseq" ,r-edaseq) - ("r-edger" ,r-edger) - ("r-mass" ,r-mass))) + (list r-biobase r-edaseq r-edger r-mass)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description @@ -6080,13 +5960,9 @@ samples.") (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -6112,10 +5988,8 @@ achieved for all methods using the BiocParallel framework.") (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-delayedarray r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/LTLA/ScaledMatrix") (synopsis "Create a DelayedMatrix of scaled and centered values") (description @@ -6140,14 +6014,14 @@ multiplication.") (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidytree" ,r-tidytree))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-dplyr + r-jsonlite + r-magrittr + r-rlang + r-tibble + r-tidytree)) + (native-inputs (list r-knitr)) (home-page "https://github.com/YuLab-SMU/treeio") (synopsis "Base classes and functions for Phylogenetic tree input and output") (description @@ -6172,20 +6046,20 @@ platform for merging tree with associated data and converting file formats.") (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-aplot" ,r-aplot) - ("r-dplyr" ,r-dplyr) - ("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyr" ,r-tidyr) - ("r-tidytree" ,r-tidytree) - ("r-treeio" ,r-treeio) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-aplot + r-dplyr + r-ggfun + r-ggplot2 + r-magrittr + r-purrr + r-rlang + r-scales + r-tidyr + r-tidytree + r-treeio + r-yulab-utils)) + (native-inputs (list r-knitr)) (home-page "https://yulab-smu.top/treedata-book/") (synopsis "R package for visualization of trees and annotation data") (description @@ -6209,9 +6083,9 @@ data.") (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/metapod") (synopsis "Meta-analyses on p-values of differential analyses") (description @@ -6238,18 +6112,18 @@ missing values and weighting where appropriate.") (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rsvd" ,r-rsvd) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-irlba + r-matrix + r-rcpp + r-rsvd + r-s4vectors + r-scaledmatrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -6272,30 +6146,30 @@ possible, parallelization is achieved using the BiocParallel framework.") "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ggplot-multistats" ,r-ggplot-multistats) - ("r-ggplot2" ,r-ggplot2) - ("r-ggthemes" ,r-ggthemes) - ("r-irlba" ,r-irlba) - ("r-knn-covertree" ,r-knn-covertree) - ("r-matrix" ,r-matrix) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-rspectra" ,r-rspectra) - ("r-scales" ,r-scales) - ("r-scatterplot3d" ,r-scatterplot3d) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-smoother" ,r-smoother) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vim" ,r-vim))) - (native-inputs - `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes + (list r-biobase + r-biocgenerics + r-ggplot-multistats + r-ggplot2 + r-ggthemes + r-irlba + r-knn-covertree + r-matrix + r-pcamethods + r-proxy + r-rcpp + r-rcppeigen + r-rcpphnsw + r-rspectra + r-scales + r-scatterplot3d + r-singlecellexperiment + r-smoother + r-summarizedexperiment + r-tidyr + r-tidyselect + r-vim)) + (native-inputs + (list r-nbconvertr)) ; for vignettes (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -6317,11 +6191,7 @@ maps.") (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) + (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml)) (home-page "https://github.com/bcalder/savR") (synopsis "Parse and analyze Illumina SAV files") (description @@ -6343,25 +6213,25 @@ Viewer (SAV) files, access data, and generate QC plots.") (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biovizbase" ,r-biovizbase) - ("r-broom" ,r-broom) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-biovizbase + r-broom + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-hexbin + r-iranges + r-rcolorbrewer + r-rmarkdown + r-rsamtools + r-s4vectors + r-scales + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -6381,10 +6251,7 @@ sequencing data.") "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) (home-page "https://bioconductor.org/packages/copynumber") (synopsis "Segmentation of single- and multi-track copy number data") (description @@ -6405,7 +6272,7 @@ penalized least squares regression method.") "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/DNAcopy") (synopsis "DNA copy number data analysis") (description @@ -6430,9 +6297,7 @@ abnormal copy number.") (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs - `(("r-capushe" ,r-capushe) - ("r-edger" ,r-edger) - ("r-plotrix" ,r-plotrix))) + (list r-capushe r-edger r-plotrix)) (home-page "https://cran.r-project.org/web/packages/HTSCluster") (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") (description @@ -6484,7 +6349,7 @@ and summarizing a set of statistics using a weighted distance approach.") (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-qvalue" ,r-qvalue))) + (list r-qvalue)) (home-page "https://cran.r-project.org/web/packages/NBPSeq") (synopsis "Negative binomial models for RNA-Seq data") (description @@ -6506,9 +6371,7 @@ and regression inferences from RNA-sequencing data.") (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-blockmodeling" ,r-blockmodeling) - ("r-gplots" ,r-gplots) - ("r-testthat" ,r-testthat))) + (list r-blockmodeling r-gplots r-testthat)) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description @@ -6528,23 +6391,23 @@ gene and isoform level using RNA-seq data") "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-bamsignals" ,r-bamsignals) - ("r-bezier" ,r-bezier) - ("r-biovizbase" ,r-biovizbase) - ("r-digest" ,r-digest) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-bamsignals + r-bezier + r-biovizbase + r-digest + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-memoise + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -6567,10 +6430,9 @@ coordinates.") "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -6598,12 +6460,9 @@ to install interface to SYMPHONY.") (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-fdrtool" ,r-fdrtool) - ("r-lpsymphony" ,r-lpsymphony) - ("r-slam" ,r-slam))) + (list r-biocgenerics r-fdrtool r-lpsymphony r-slam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -6630,19 +6489,19 @@ independent of the p-value under the null hypothesis.") (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-limma" ,r-limma) - ("r-reshape2" ,r-reshape2) - ("r-rocr" ,r-rocr) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-shinydashboard" ,r-shinydashboard) - ("r-upsetr" ,r-upsetr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-dt + r-ggplot2 + r-limma + r-reshape2 + r-rocr + r-scales + r-shiny + r-shinybs + r-shinydashboard + r-upsetr)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -6667,11 +6526,9 @@ interactive exploration of results.") `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-delayedarray r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/ResidualMatrix") (synopsis "Create a DelayedMatrix of regression residuals") (description @@ -6697,23 +6554,23 @@ multiplication and calculation of row/column sums or means.") (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-residualmatrix" ,r-residualmatrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-igraph + r-matrix + r-rcpp + r-residualmatrix + r-s4vectors + r-scaledmatrix + r-scuttle + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/batchelor") (synopsis "Single-Cell Batch Correction Methods") (description @@ -6740,20 +6597,20 @@ the numbers of cells across batches.") (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-abind + r-biobase + r-biocgenerics + r-data-table + r-ggplot2 + r-plyr + r-progress + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -6774,38 +6631,38 @@ single cell assay data.") "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocviews" ,r-biocviews) - ("r-cluster" ,r-cluster) - ("r-combinat" ,r-combinat) - ("r-ddrtree" ,r-ddrtree) - ("r-densityclust" ,r-densityclust) - ("r-dplyr" ,r-dplyr) - ("r-fastica" ,r-fastica) - ("r-ggplot2" ,r-ggplot2) - ("r-hsmmsinglecell" ,r-hsmmsinglecell) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-proxy" ,r-proxy) - ("r-qlcmatrix" ,r-qlcmatrix) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-slam" ,r-slam) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-vgam" ,r-vgam) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocviews + r-cluster + r-combinat + r-ddrtree + r-densityclust + r-dplyr + r-fastica + r-ggplot2 + r-hsmmsinglecell + r-igraph + r-irlba + r-limma + r-mass + r-matrix + r-matrixstats + r-pheatmap + r-plyr + r-proxy + r-qlcmatrix + r-rann + r-rcpp + r-reshape2 + r-rtsne + r-slam + r-stringr + r-tibble + r-vgam + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -6837,11 +6694,11 @@ qPCR data, but could be used with other types as well.") (properties `((upstream-name . "leidenbase"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "https://github.com/cole-trapnell-lab/leidenbase") (synopsis "R and C wrappers to run the Leiden find_partition function") (description @@ -6870,11 +6727,7 @@ several functions from the R igraph package.") "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) (build-system r-build-system) (propagated-inputs - `(("r-generics" ,r-generics) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://pneuvial.github.io/sanssouci") (synopsis "Post Hoc multiple testing inference") (description @@ -6899,50 +6752,50 @@ user-defined and/or data-driven sets of hypotheses.") "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-batchelor" ,r-batchelor) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-grr" ,r-grr) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-leidenbase" ,r-leidenbase) - ("r-limma" ,r-limma) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrix-utils" ,r-matrix-utils) - ("r-pbapply" ,r-pbapply) - ("r-pbmcapply" ,r-pbmcapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-pryr" ,r-pryr) - ("r-proxy" ,r-proxy) - ("r-pscl" ,r-pscl) - ("r-purrr" ,r-purrr) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel) - ("r-reshape2" ,r-reshape2) - ("r-reticulate" ,r-reticulate) - ("r-rhpcblasctl" ,r-rhpcblasctl) - ("r-rsample" ,r-rsample) - ("r-rtsne" ,r-rtsne) - ("r-shiny" ,r-shiny) - ("r-slam" ,r-slam) - ("r-spdep" ,r-spdep) - ("r-speedglm" ,r-speedglm) - ("r-stringr" ,r-stringr) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-uwot" ,r-uwot) - ("r-viridis" ,r-viridis))) + (list r-assertthat + r-batchelor + r-biobase + r-biocgenerics + r-delayedmatrixstats + r-dplyr + r-ggplot2 + r-ggrepel + r-grr + r-htmlwidgets + r-igraph + r-irlba + r-leidenbase + r-limma + r-lmtest + r-mass + r-matrix + r-matrix-utils + r-pbapply + r-pbmcapply + r-pheatmap + r-plotly + r-pryr + r-proxy + r-pscl + r-purrr + r-rann + r-rcpp + r-rcppparallel + r-reshape2 + r-reticulate + r-rhpcblasctl + r-rsample + r-rtsne + r-shiny + r-slam + r-spdep + r-speedglm + r-stringr + r-singlecellexperiment + r-tibble + r-tidyr + r-uwot + r-viridis)) (home-page "https://github.com/cole-trapnell-lab/monocle3") (synopsis "Analysis toolkit for single-cell RNA-Seq data") (description @@ -6963,8 +6816,7 @@ user-defined and/or data-driven sets of hypotheses.") (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-matrix" ,r-matrix))) + (list r-biobase r-matrix)) (home-page "https://bioconductor.org/packages/NOISeq") (synopsis "Exploratory analysis and differential expression for RNA-seq data") (description @@ -6990,19 +6842,19 @@ assumptions.") (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs - `(("r-arm" ,r-arm) - ("r-biocparallel" ,r-biocparallel) - ("r-ebseq" ,r-ebseq) - ("r-fields" ,r-fields) - ("r-ggplot2" ,r-ggplot2) - ("r-mclust" ,r-mclust) - ("r-outliers" ,r-outliers) - ("r-s4vectors" ,r-s4vectors) - ("r-scran" ,r-scran) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-arm + r-biocparallel + r-ebseq + r-fields + r-ggplot2 + r-mclust + r-outliers + r-s4vectors + r-scran + r-singlecellexperiment + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description @@ -7027,29 +6879,29 @@ distributions.") "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) (build-system r-build-system) (propagated-inputs - `(("r-aroma-light" ,r-aroma-light) - ("r-biocparallel" ,r-biocparallel) - ("r-boot" ,r-boot) - ("r-class" ,r-class) - ("r-cluster" ,r-cluster) - ("r-compositions" ,r-compositions) - ("r-diptest" ,r-diptest) - ("r-edger" ,r-edger) - ("r-fpc" ,r-fpc) - ("r-gplots" ,r-gplots) - ("r-hexbin" ,r-hexbin) - ("r-limma" ,r-limma) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-mixtools" ,r-mixtools) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rhdf5" ,r-rhdf5) - ("r-ruvseq" ,r-ruvseq) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aroma-light + r-biocparallel + r-boot + r-class + r-cluster + r-compositions + r-diptest + r-edger + r-fpc + r-gplots + r-hexbin + r-limma + r-matrixgenerics + r-matrixstats + r-mixtools + r-rarpack + r-rcolorbrewer + r-rhdf5 + r-ruvseq + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -7072,18 +6924,18 @@ high-throughput analyses.") (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) + (list r-biobase + r-data-table + r-dplyr + r-httr + r-limma + r-magrittr + r-r-utils + r-readr + r-tidyr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -7106,7 +6958,7 @@ the bridge between GEO and BioConductor.") "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) (build-system r-build-system) (propagated-inputs - `(("r-base64" ,r-base64))) + (list r-base64)) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description @@ -7127,9 +6979,7 @@ files, including IDAT.") "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multtest" ,r-multtest) - ("r-scrime" ,r-scrime))) + (list r-biobase r-multtest r-scrime)) (home-page "https://bioconductor.org/packages/siggenes/") (synopsis "Multiple testing using SAM and Efron's empirical Bayes approaches") @@ -7153,19 +7003,19 @@ Bayes Analyses of Microarrays} (EBAM).") "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dorng" ,r-dorng) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biocgenerics + r-dorng + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-iterators + r-limma + r-locfit + r-matrixstats + r-s4vectors)) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description @@ -7187,37 +7037,37 @@ studies.") "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bumphunter" ,r-bumphunter) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-geoquery" ,r-geoquery) - ("r-hdf5array" ,r-hdf5array) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-nlme" ,r-nlme) - ("r-nor1mix" ,r-nor1mix) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quadprog" ,r-quadprog) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-s4vectors" ,r-s4vectors) - ("r-siggenes" ,r-siggenes) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bumphunter + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genefilter + r-genomeinfodb + r-genomicranges + r-geoquery + r-hdf5array + r-illuminaio + r-iranges + r-lattice + r-limma + r-mass + r-mclust + r-nlme + r-nor1mix + r-preprocesscore + r-quadprog + r-rcolorbrewer + r-reshape + r-s4vectors + r-siggenes + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -7238,27 +7088,27 @@ methylation arrays.") "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-minfi" ,r-minfi) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-fdb-infiniummethylation-hg19 + r-genefilter + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-illuminaio + r-iranges + r-lattice + r-matrixstats + r-minfi + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description @@ -7285,21 +7135,21 @@ and Infinium HD arrays are also included.") "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-methylumi" ,r-methylumi) - ("r-mgcv" ,r-mgcv) - ("r-nleqslv" ,r-nleqslv) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite))) + (list r-affy + r-annotate + r-annotationdbi + r-biobase + r-dbi + r-genomicfeatures + r-genomicranges + r-kernsmooth + r-lattice + r-mass + r-methylumi + r-mgcv + r-nleqslv + r-preprocesscore + r-rsqlite)) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description @@ -7325,26 +7175,26 @@ especially Illumina Infinium methylation microarrays.") (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apcluster" ,r-apcluster) - ("r-ellipse" ,r-ellipse) - ("r-fastcluster" ,r-fastcluster) - ("r-fpc" ,r-fpc) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rtsne" ,r-rtsne) - ("r-statmod" ,r-statmod) - ("r-vegan" ,r-vegan) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-amap + r-apcluster + r-ellipse + r-fastcluster + r-fpc + r-ggdendro + r-ggplot2 + r-gmodels + r-igraph + r-limma + r-mass + r-mclust + r-rcpp + r-rcpparmadillo + r-rtsne + r-statmod + r-vegan + r-zoo)) + (native-inputs + (list r-knitr)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -7386,21 +7236,21 @@ evaluation of DEG analysis methods.") (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bit64" ,r-bit64) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-rhdf5" ,r-rhdf5) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bit64 + r-dplyr + r-ggplot2 + r-magrittr + r-rhdf5 + r-shortread + r-stringr + r-tibble + r-tidyr + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -7427,10 +7277,7 @@ surface of a flowcell.") (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs - `(("r-multcomp" ,r-multcomp) - ("r-multtest" ,r-multtest) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plotrix" ,r-plotrix))) + (list r-multcomp r-multtest r-mvtnorm r-plotrix)) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description @@ -7455,10 +7302,7 @@ are standardized and usable by the accompanying mutossGUI package.") "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mutoss" ,r-mutoss) - ("r-rdpack" ,r-rdpack) - ("r-tfisher" ,r-tfisher))) + (list r-lattice r-mutoss r-rdpack r-tfisher)) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description @@ -7481,28 +7325,28 @@ published results; and a routine for graphical display.") "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mgcv" ,r-mgcv) - ("r-pbapply" ,r-pbapply) - ("r-princurve" ,r-princurve) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-slingshot" ,r-slingshot) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-trajectoryutils" ,r-trajectoryutils) - ("r-viridis" ,r-viridis))) + (list r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-igraph + r-magrittr + r-mass + r-matrix + r-matrixstats + r-mgcv + r-pbapply + r-princurve + r-rcolorbrewer + r-s4vectors + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-tibble + r-trajectoryutils + r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://statomics.github.io/tradeSeq/index.html") (synopsis "Trajectory-based differential expression analysis") (description @@ -7529,9 +7373,7 @@ performs inference on the parameters of the GAM.") "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-yaml" ,r-yaml))) + (list r-biocgenerics r-iranges r-yaml)) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description @@ -7554,20 +7396,20 @@ peak definition in combination with known profile characteristics.") (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description @@ -7594,7 +7436,7 @@ gmapR.") (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description @@ -7619,11 +7461,9 @@ information about samples and features can be added to the plot.") (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-rcpp" ,r-rcpp))) + (list r-annotationdbi r-go-db r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description @@ -7647,8 +7487,7 @@ sets of GO terms, gene products and gene clusters.") "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) (build-system r-build-system) (propagated-inputs - `(("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue))) + (list r-multtest r-qvalue)) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description @@ -7700,15 +7539,15 @@ phenotype of interest.") (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-doparallel + r-foreach + r-genomicranges + r-iranges + r-plyr + r-rtracklayer + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/fcScan") (synopsis "Detect clusters of coordinates with user defined options") (description @@ -7733,16 +7572,16 @@ presence of additional sites within the allowed window size.") "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-fastmatch" ,r-fastmatch) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh + r-biocparallel + r-data-table + r-fastmatch + r-ggplot2 + r-gridextra + r-matrix + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -7766,16 +7605,16 @@ to multiple hypothesis correction.") (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocparallel" ,r-biocparallel) - ("r-do-db" ,r-do-db) - ("r-fgsea" ,r-fgsea) - ("r-ggplot2" ,r-ggplot2) - ("r-gosemsim" ,r-gosemsim) - ("r-qvalue" ,r-qvalue) - ("r-reshape2" ,r-reshape2))) + (list r-annotationdbi + r-biocparallel + r-do-db + r-fgsea + r-ggplot2 + r-gosemsim + r-qvalue + r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description @@ -7800,23 +7639,23 @@ data.") "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) (build-system r-build-system) (propagated-inputs - `(("r-aplot" ,r-aplot) - ("r-dose" ,r-dose) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-ggtree" ,r-ggtree) - ("r-gosemsim" ,r-gosemsim) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-scatterpie" ,r-scatterpie) - ("r-shadowtext" ,r-shadowtext) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aplot + r-dose + r-ggplot2 + r-ggraph + r-ggtree + r-gosemsim + r-igraph + r-magrittr + r-plyr + r-purrr + r-rcolorbrewer + r-reshape2 + r-scatterpie + r-shadowtext + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -7840,21 +7679,21 @@ All the visualization methods are developed based on ggplot2 graphics.") `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-downloader" ,r-downloader) - ("r-dplyr" ,r-dplyr) - ("r-enrichplot" ,r-enrichplot) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-qvalue" ,r-qvalue) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-dose + r-downloader + r-dplyr + r-enrichplot + r-go-db + r-gosemsim + r-magrittr + r-plyr + r-qvalue + r-rlang + r-tidyr + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -7874,33 +7713,33 @@ profiles (GO and KEGG) of gene and gene clusters.") "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocsingular" ,r-biocsingular) - ("r-cluster" ,r-cluster) - ("r-delayedarray" ,r-delayedarray) - ("r-edger" ,r-edger) - ("r-hdf5array" ,r-hdf5array) - ("r-howmany" ,r-howmany) - ("r-kernlab" ,r-kernlab) - ("r-limma" ,r-limma) - ("r-locfdr" ,r-locfdr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mbkmeans" ,r-mbkmeans) - ("r-nmf" ,r-nmf) - ("r-phylobase" ,r-phylobase) - ("r-pracma" ,r-pracma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-zinbwave" ,r-zinbwave))) + (list r-knitr)) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocsingular + r-cluster + r-delayedarray + r-edger + r-hdf5array + r-howmany + r-kernlab + r-limma + r-locfdr + r-matrix + r-matrixstats + r-mbkmeans + r-nmf + r-phylobase + r-pracma + r-rcolorbrewer + r-rcpp + r-s4vectors + r-scales + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-zinbwave)) (home-page "https://bioconductor.org/packages/clusterExperiment/") (synopsis "Compare clusterings for single-cell sequencing") (description "This package provides functionality for running and comparing @@ -7922,26 +7761,26 @@ expression data sets.") (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fpc" ,r-fpc) - ("r-gbm" ,r-gbm) - ("r-gdata" ,r-gdata) - ("r-genefilter" ,r-genefilter) - ("r-ggvis" ,r-ggvis) - ("r-hwriter" ,r-hwriter) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-mlbench" ,r-mlbench) - ("r-pls" ,r-pls) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rpart" ,r-rpart) - ("r-sfsmisc" ,r-sfsmisc) - ("r-shiny" ,r-shiny) - ("r-threejs" ,r-threejs))) + (list r-annotate + r-biobase + r-biocgenerics + r-cluster + r-fpc + r-gbm + r-gdata + r-genefilter + r-ggvis + r-hwriter + r-magrittr + r-mass + r-mlbench + r-pls + r-rcolorbrewer + r-rcpp + r-rpart + r-sfsmisc + r-shiny + r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description @@ -7970,11 +7809,7 @@ data in R and Bioconductor containers.") (substitute* "DESCRIPTION" ((", KEGG.db") ""))))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-go-db" ,r-go-db))) + (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db)) (home-page "https://bioconductor.org/packages/annaffy/") (synopsis "Annotation tools for Affymetrix biological metadata") (description @@ -8000,10 +7835,9 @@ It allows searching of biological metadata using various criteria.") (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet))) + (list r-biobase r-glmnet)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Core") (synopsis "Automated Affymetrix array analysis core package") (description @@ -8025,15 +7859,15 @@ arrays.") (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet) - ("r-pamr" ,r-pamr) - ("r-rocr" ,r-rocr) - ("r-varselrf" ,r-varselrf))) + (list r-a4core + r-a4preproc + r-biobase + r-glmnet + r-pamr + r-rocr + r-varselrf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Classif/") (synopsis "Automated Affymetrix array analysis classification package") (description @@ -8055,10 +7889,9 @@ Affymetrix arrays.") (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-biobase r-biocgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Preproc/") (synopsis "Automated Affymetrix array analysis preprocessing package") (description @@ -8080,9 +7913,9 @@ is used for preprocessing the arrays.") (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs - `(("r-xtable" ,r-xtable))) + (list r-xtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Reporting/") (synopsis "Automated Affymetrix array analysis reporting package") (description @@ -8104,16 +7937,16 @@ provides reporting features.") (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-genefilter" ,r-genefilter) - ("r-glmnet" ,r-glmnet) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-mpm" ,r-mpm) - ("r-multtest" ,r-multtest))) + (list r-a4core + r-a4preproc + r-annaffy + r-biobase + r-genefilter + r-glmnet + r-gplots + r-limma + r-mpm + r-multtest)) (home-page "https://bioconductor.org/packages/a4Base/") (synopsis "Automated Affymetrix array analysis base package") (description @@ -8134,11 +7967,7 @@ Affymetrix arrays.") "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) (build-system r-build-system) (propagated-inputs - `(("r-a4base" ,r-a4base) - ("r-a4classif" ,r-a4classif) - ("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-a4reporting" ,r-a4reporting))) + (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) (home-page "https://bioconductor.org/packages/a4/") (synopsis "Automated Affymetrix array analysis umbrella package") (description @@ -8160,28 +7989,28 @@ Affymetrix arrays.") (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-circlize" ,r-circlize) - ("r-flexdashboard" ,r-flexdashboard) - ("r-ggcorrplot" ,r-ggcorrplot) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-knitr" ,r-knitr) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rmarkdown" ,r-rmarkdown) - ("r-stringr" ,r-stringr) - ("r-vegan" ,r-vegan) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-biocparallel + r-biocstyle + r-circlize + r-flexdashboard + r-ggcorrplot + r-ggdendro + r-ggplot2 + r-gridextra + r-knitr + r-plotly + r-plyr + r-png + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-stringr + r-vegan + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -8207,11 +8036,9 @@ further downstream analysis on its output.") "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-ellipse" ,r-ellipse) - ("r-ggplot2" ,r-ggplot2))) + (list r-biocparallel r-ellipse r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bacon/") (synopsis "Controlling bias and inflation in association studies") (description @@ -8235,11 +8062,7 @@ fitting a three-component normal mixture on z-scores.") (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo))) + (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo)) (home-page "https://bioconductor.org/packages/rGADEM/") (synopsis "De novo sequence motif discovery") (description @@ -8261,15 +8084,15 @@ genomic sequence data.") (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-rgadem" ,r-rgadem) - ("r-s4vectors" ,r-s4vectors))) + (list gsl)) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-lattice + r-rgadem + r-s4vectors)) (home-page "https://bioconductor.org/packages/MotIV/") (synopsis "Motif identification and validation") (description @@ -8291,15 +8114,15 @@ distributions, modules and filter motifs.") (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-splitstackshape" ,r-splitstackshape))) + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-splitstackshape)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -8318,26 +8141,26 @@ frequency matrices from nine public sources, for multiple organisms.") (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-grimport" ,r-grimport) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-motifdb" ,r-motifdb) - ("r-motifstack" ,r-motifstack) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-grimport + r-gviz + r-iranges + r-matrixstats + r-motifdb + r-motifstack + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tfmpvalue + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place @@ -8371,13 +8194,9 @@ Bioconductor.") (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-xml" ,r-xml))) + (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -8402,22 +8221,22 @@ type and symbol colors.") (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biobase + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biostrings + r-delayedarray + r-genomeinfodb + r-genomicranges + r-hdf5array + r-iranges + r-rhdf5 + r-s4vectors + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -8439,26 +8258,26 @@ position-specific scores within R and Bioconductor.") (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-chippeakanno" ,r-chippeakanno) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-motifstack" ,r-motifstack) - ("r-preseqr" ,r-preseqr) - ("r-randomforest" ,r-randomforest) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-chippeakanno + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-genomicscores + r-iranges + r-kernsmooth + r-limma + r-motifstack + r-preseqr + r-randomforest + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ATACseqQC/") (synopsis "ATAC-seq quality control") (description @@ -8486,15 +8305,15 @@ footprints.") (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-mapplots" ,r-mapplots) - ("r-rcpp" ,r-rcpp) - ("r-vioplot" ,r-vioplot))) + (list r-annotationdbi + r-genomicranges + r-gtools + r-iranges + r-mapplots + r-rcpp + r-vioplot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description @@ -8535,14 +8354,14 @@ annotations and ontologies.") (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-abadata" ,r-abadata) - ("r-data-table" ,r-data-table) - ("r-gofuncr" ,r-gofuncr) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-rcpp" ,r-rcpp))) + (list r-abadata + r-data-table + r-gofuncr + r-gplots + r-gtools + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -8568,8 +8387,7 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi))) + (list r-annotationdbi r-dbi)) (home-page "https://www.iysik.com/r/annotationfuncs") (synopsis "Annotation translation functions") (description @@ -8592,7 +8410,7 @@ different identifieres using the Biocore Data Team data-packages (e.g. (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/annotationTools/") (synopsis "Annotate microarrays and perform gene expression analyses") (description @@ -8618,27 +8436,27 @@ text files).") `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-nlme" ,r-nlme) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gridextra + r-gviz + r-iranges + r-lattice + r-latticeextra + r-nlme + r-rsamtools + r-s4vectors + r-seqinr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -8660,16 +8478,16 @@ investigation using RNA-seq data.") (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-gseabase" ,r-gseabase) - ("r-mixtools" ,r-mixtools) - ("r-r-utils" ,r-r-utils) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-gseabase + r-mixtools + r-r-utils + r-s4vectors + r-shiny + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -8699,18 +8517,18 @@ needed.") (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fftwtools" ,r-fftwtools) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jpeg" ,r-jpeg) - ("r-locfit" ,r-locfit) - ("r-png" ,r-png) - ("r-rcurl" ,r-rcurl) - ("r-tiff" ,r-tiff))) + (list r-abind + r-biocgenerics + r-fftwtools + r-htmltools + r-htmlwidgets + r-jpeg + r-locfit + r-png + r-rcurl + r-tiff)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/aoles/EBImage") (synopsis "Image processing and analysis toolbox for R") (description @@ -8737,18 +8555,17 @@ visualization with image data.") "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ebimage" ,r-ebimage) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-mzr" ,r-mzr) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" - ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-ebimage + r-iranges + r-limma + r-matrix + r-mzr + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -8771,12 +8588,9 @@ analysis.") "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges))) + (list r-circlize r-genomicranges r-getoptlong r-iranges)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -8802,21 +8616,21 @@ genomic categories and to add self-defined graphics in the plot.") `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-nmf" ,r-nmf) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-nmf + r-pcamethods + r-proxy + r-reshape2 + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -8840,31 +8654,31 @@ decomposition algorithms.") (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-corrplot" ,r-corrplot) - ("r-dendextend" ,r-dendextend) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtrellis" ,r-gtrellis) - ("r-keggrest" ,r-keggrest) - ("r-limsolve" ,r-limsolve) - ("r-magrittr" ,r-magrittr) - ("r-pmcmr" ,r-pmcmr) - ("r-pracma" ,r-pracma) - ("r-reshape2" ,r-reshape2) - ("r-somaticsignatures" ,r-somaticsignatures) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-circlize + r-complexheatmap + r-corrplot + r-dendextend + r-doparallel + r-dplyr + r-genomeinfodb + r-genomicranges + r-getoptlong + r-ggbeeswarm + r-ggplot2 + r-gridextra + r-gtrellis + r-keggrest + r-limsolve + r-magrittr + r-pmcmr + r-pracma + r-reshape2 + r-somaticsignatures + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -8888,12 +8702,12 @@ provided.") "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-xvector" ,r-xvector))) + (list r-affy + r-affyio + r-biobase + r-biocmanager + r-biostrings + r-xvector)) (home-page "https://bioconductor.org/packages/gcrma/") (synopsis "Background adjustment using sequence information") (description @@ -8924,11 +8738,7 @@ gene-specific binding is expected.") "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gcrma" ,r-gcrma) - ("r-genefilter" ,r-genefilter))) + (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter)) (home-page "https://bioconductor.org/packages/simpleaffy/") (synopsis "Very simple high level analysis of Affymetrix data") (description @@ -8952,7 +8762,7 @@ generating high resolution journal figures.") "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (build-system r-build-system) (propagated-inputs - `(("r-simpleaffy" ,r-simpleaffy))) + (list r-simpleaffy)) (home-page "https://bioconductor.org/packages/yaqcaffy/") (synopsis "Affymetrix quality control and reproducibility analysis") (description @@ -8974,15 +8784,15 @@ chips with the MAQC reference datasets.") "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-minfi" ,r-minfi) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-doparallel + r-foreach + r-ggplot2 + r-iterators + r-minfi + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -9007,19 +8817,19 @@ groups.") "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biomart" ,r-biomart) - ("r-downloader" ,r-downloader) - ("r-edger" ,r-edger) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quantro" ,r-quantro) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-readr" ,r-readr))) + (list r-biobase + r-biomart + r-downloader + r-edger + r-gplots + r-limma + r-matrixstats + r-preprocesscore + r-quantro + r-rcolorbrewer + r-readr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -9044,14 +8854,14 @@ large RNA-seq experiments.") "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description @@ -9074,17 +8884,17 @@ sites and alignments obtained from standard RNA-seq experiments.") (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-locfit" ,r-locfit) - ("r-magrittr" ,r-magrittr) - ("r-matrixstats" ,r-matrixstats) - ("r-pracma" ,r-pracma) - ("r-roar" ,r-roar))) + (list r-biobase + r-deseq2 + r-dplyr + r-ggplot2 + r-locfit + r-magrittr + r-matrixstats + r-pracma + r-roar)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -9114,7 +8924,7 @@ genes.") `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) (propagated-inputs - `(("r-waveslim" ,r-waveslim))) + (list r-waveslim)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description @@ -9136,25 +8946,25 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-massspecwavelet" ,r-massspecwavelet) - ("r-mscoreutils" ,r-mscoreutils) - ("r-msfeatures" ,r-msfeatures) - ("r-msnbase" ,r-msnbase) - ("r-mzr" ,r-mzr) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-robustbase" ,r-robustbase) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-iranges + r-lattice + r-massspecwavelet + r-mscoreutils + r-msfeatures + r-msnbase + r-mzr + r-plyr + r-protgenerics + r-rann + r-rcolorbrewer + r-robustbase + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -9178,11 +8988,9 @@ data for high-throughput, untargeted analyte profiling.") (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats))) + (list r-limma r-locfit r-matrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description @@ -9203,18 +9011,18 @@ that arising from 16s metagenomic surveys.") "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-purrr" ,r-purrr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-assertthat + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-purrr + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -9258,17 +9066,16 @@ widgets in R.") "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) (build-system r-build-system) (inputs - `(("netpbm" ,netpbm) - ("perl" ,perl))) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-gcrma" ,r-gcrma) - ("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue) - ("r-vsn" ,r-vsn))) + (list netpbm perl)) + (propagated-inputs + (list r-affy + r-annaffy + r-biobase + r-biocmanager + r-gcrma + r-multtest + r-qvalue + r-vsn)) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description @@ -9291,15 +9098,15 @@ Currently only Affymetrix oligonucleotide analysis is supported.") "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-matrix" ,r-matrix) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-softimpute" ,r-softimpute) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocparallel + r-edger + r-genefilter + r-matrix + r-singlecellexperiment + r-softimpute + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-inflated negative binomial model for RNA-seq data") (description "This package implements a general and flexible zero-inflated @@ -9325,13 +9132,9 @@ the data.") (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description @@ -9354,13 +9157,11 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rsamtools" ,r-rsamtools))) + (list r-magrittr r-rsamtools)) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))) + (list samtools zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -9382,14 +9183,14 @@ rapid adapter trimming, identification, and read merging.") "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -9413,7 +9214,7 @@ expression\".") (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) - (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) + (propagated-inputs (list r-arrmdata)) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description @@ -9436,16 +9237,16 @@ Infinium HumanMethylation 450k assay.") (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-dbplyr" ,r-dbplyr) - ("r-dplyr" ,r-dplyr) - ("r-filelock" ,r-filelock) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite))) + (list r-curl + r-dbi + r-dbplyr + r-dplyr + r-filelock + r-httr + r-rappdirs + r-rsqlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description @@ -9468,7 +9269,7 @@ and data files used across sessions.") "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description @@ -9499,7 +9300,7 @@ Gaussian distributions.") (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description @@ -9522,22 +9323,22 @@ alignment tool.") (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-igraph + r-iranges + r-rsamtools + r-rtracklayer + r-runit + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -9577,11 +9378,9 @@ interpretation.") (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-sgseq" ,r-sgseq))) + (list r-genomicfeatures r-genomicranges r-sgseq)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -9605,25 +9404,25 @@ index.") (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rbowtie" ,r-rbowtie) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-iranges + r-rbowtie + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -9647,26 +9446,26 @@ quantification of genomic regions of interest.") (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biocstyle + r-biostrings + r-biovizbase + r-genomicalignments + r-genomicfiles + r-ggplot2 + r-iranges + r-knitr + r-markdown + r-plyr + r-rcpp + r-reshape2 + r-rsamtools + r-s4vectors + r-shiny + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -9690,10 +9489,7 @@ graphics.") (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-slam" ,r-slam) - ("r-tsne" ,r-tsne))) + (list r-igraph r-matrix r-slam r-tsne)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -9718,9 +9514,7 @@ routines to analyse the resulting networks and their natural projections.") "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass))) + (list r-biobase r-limma r-mass)) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description @@ -9748,18 +9542,18 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-qqman" ,r-qqman) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-ggrepel + r-iranges + r-limma + r-qqman + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -9784,10 +9578,9 @@ packages.") "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multidataset" ,r-multidataset))) + (list r-biobase r-multidataset)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description @@ -9822,13 +9615,9 @@ coefficients).") "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-multidataset" ,r-multidataset) - ("r-randomforest" ,r-randomforest) - ("r-ropls" ,r-ropls))) + (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description @@ -9855,21 +9644,21 @@ datasets.") "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-regioner" ,r-regioner) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-readr + r-regioner + r-reshape2 + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -9896,9 +9685,9 @@ annotations.") "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description @@ -9923,12 +9712,12 @@ and to both short and long sequence reads.") (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-flowcore" ,r-flowcore) - ("r-graph" ,r-graph) - ("r-runit" ,r-runit) - ("r-xml" ,r-xml))) + (list r-biobase + r-corpcor + r-flowcore + r-graph + r-runit + r-xml)) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description @@ -9950,9 +9739,7 @@ and to both short and long sequence reads.") `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs - `(("r-all" ,r-all) - ("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster))) + (list r-all r-biobase r-cluster)) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description @@ -9974,14 +9761,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib))) + (list r-bh + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rhdf5lib + r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description @@ -10003,17 +9790,17 @@ interact with gated cytometry data.") (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors))) + (list r-bh + r-biobase + r-biocgenerics + r-cytolib + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rprotobuflib + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -10035,10 +9822,7 @@ with flow cytometry data.") (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-feature" ,r-feature) - ("r-flowcore" ,r-flowcore) - ("r-rrcov" ,r-rrcov))) + (list r-biobase r-feature r-flowcore r-rrcov)) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description @@ -10061,16 +9845,16 @@ change point detection.") (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-flowcore" ,r-flowcore) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-bh + r-biobase + r-biocgenerics + r-flowcore + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -10092,19 +9876,19 @@ manipulation of flow cytometry data.") (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-data-table + r-flowcore + r-flowworkspace + r-ggplot2 + r-gridextra + r-hexbin + r-ncdfflow + r-plyr + r-rcolorbrewer + r-rlang + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description @@ -10129,17 +9913,17 @@ statistics to the plot.") (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-flowcore" ,r-flowcore) - ("r-hexbin" ,r-hexbin) - ("r-idpmisc" ,r-idpmisc) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-flowcore + r-hexbin + r-idpmisc + r-kernsmooth + r-lattice + r-latticeextra + r-mass + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -10163,20 +9947,19 @@ statistics to the plot.") `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-corpcor" ,r-corpcor) - ("r-ellipse" ,r-ellipse) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-graph" ,r-graph) - ("r-mnormt" ,r-mnormt))) + (list r-biobase + r-biocgenerics + r-clue + r-corpcor + r-ellipse + r-flowcore + r-flowviz + r-graph + r-mnormt)) (inputs - `(("gsl" ,gsl))) + (list gsl)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -10207,7 +9990,7 @@ model with Box-Cox transformation.") (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description @@ -10229,35 +10012,35 @@ for other R packages to compile and link against.") (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs - `(("r-aws-s3" ,r-aws-s3) - ("r-aws-signature" ,r-aws-signature) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aws-s3 + r-aws-signature + r-bh + r-biobase + r-biocgenerics + r-cytolib + r-data-table + r-delayedarray + r-digest + r-dplyr + r-flowcore + r-ggplot2 + r-graph + r-lattice + r-latticeextra + r-matrixstats + r-ncdfflow + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-s4vectors + r-scales + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -10283,20 +10066,20 @@ matches the flowJo analysis.") (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fda" ,r-fda) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-kernsmooth" ,r-kernsmooth) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rrcov" ,r-rrcov))) + (list r-biobase + r-biocgenerics + r-cluster + r-fda + r-flowcore + r-flowviz + r-flowworkspace + r-kernsmooth + r-ks + r-lattice + r-mass + r-ncdfflow + r-rcolorbrewer + r-rrcov)) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description @@ -10319,29 +10102,29 @@ package.") (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-data-table" ,r-data-table) - ("r-flowclust" ,r-flowclust) - ("r-flowcore" ,r-flowcore) - ("r-flowstats" ,r-flowstats) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-graph" ,r-graph) - ("r-gtools" ,r-gtools) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-r-utils" ,r-r-utils) - ("r-rbgl" ,r-rbgl) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-clue + r-data-table + r-flowclust + r-flowcore + r-flowstats + r-flowviz + r-flowworkspace + r-graph + r-gtools + r-ks + r-lattice + r-mass + r-ncdfflow + r-plyr + r-r-utils + r-rbgl + r-rcolorbrewer + r-rcpp + r-rrcov)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -10363,38 +10146,37 @@ sequential way to mimic the manual gating strategy.") (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs - `(("libxml2" ,libxml2) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggcyto" ,r-ggcyto) - ("r-graph" ,r-graph) - ("r-jsonlite" ,r-jsonlite) - ("r-lattice" ,r-lattice) - ("r-opencyto" ,r-opencyto) - ("r-plyr" ,r-plyr) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-runit" ,r-runit) - ("r-tibble" ,r-tibble) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list libxml2 zlib)) + (propagated-inputs + (list r-base64enc + r-bh + r-biobase + r-corpcor + r-cytolib + r-data-table + r-dplyr + r-flowcore + r-flowworkspace + r-ggcyto + r-graph + r-jsonlite + r-lattice + r-opencyto + r-plyr + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-runit + r-tibble + r-xml + r-xml2 + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description @@ -10416,28 +10198,28 @@ standard to exchange gated cytometry data with other software platforms.") (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-colorramps" ,r-colorramps) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cytoml" ,r-cytoml) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggforce" ,r-ggforce) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpointdensity" ,r-ggpointdensity) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-scattermore" ,r-scattermore) - ("r-tidyr" ,r-tidyr) - ("r-xml" ,r-xml))) + (list r-biocgenerics + r-colorramps + r-consensusclusterplus + r-cytoml + r-dplyr + r-flowcore + r-flowworkspace + r-ggforce + r-ggnewscale + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggrepel + r-igraph + r-magrittr + r-pheatmap + r-rcolorbrewer + r-rlang + r-rtsne + r-scattermore + r-tidyr + r-xml)) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description @@ -10459,23 +10241,23 @@ self-organizing map clustering and minimal spanning trees.") (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-corpcor" ,r-corpcor) - ("r-dplyr" ,r-dplyr) - ("r-ellipse" ,r-ellipse) - ("r-ggrepel" ,r-ggrepel) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-corpcor + r-dplyr + r-ellipse + r-ggrepel + r-ggplot2 + r-gridextra + r-igraph + r-lattice + r-mass + r-matrixstats + r-rarpack + r-rcolorbrewer + r-reshape2 + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description @@ -10505,25 +10287,25 @@ delete entire rows with missing data.") (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-mixomics" ,r-mixomics) - ("r-moments" ,r-moments) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-reshape2" ,r-reshape2) - ("r-robustbase" ,r-robustbase) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-gmodels + r-gplots + r-mass + r-matrixstats + r-mixomics + r-moments + r-rcpp + r-rcppeigen + r-reshape2 + r-robustbase + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description @@ -10551,20 +10333,20 @@ data, to only emphasize the data that actually matters.") (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs - `(("r-arrow" ,r-arrow) - ("r-aucell" ,r-aucell) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-feather" ,r-feather) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gseabase" ,r-gseabase) - ("r-r-utils" ,r-r-utils) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-arrow + r-aucell + r-biocgenerics + r-data-table + r-dplyr + r-feather + r-genomeinfodb + r-genomicranges + r-gseabase + r-r-utils + r-summarizedexperiment + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -10593,12 +10375,8 @@ genes in the gene-set that are ranked above the leading edge).") (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-delaporte" ,r-delaporte) - ("r-hmisc" ,r-hmisc) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description @@ -10618,30 +10396,30 @@ genes in the gene-set that are ranked above the leading edge).") "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-glasso" ,r-glasso) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-monocle" ,r-monocle) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vgam" ,r-vgam))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-fnn + r-genomicranges + r-ggplot2 + r-glasso + r-gviz + r-igraph + r-iranges + r-matrix + r-monocle + r-plyr + r-reshape2 + r-s4vectors + r-stringi + r-stringr + r-tibble + r-tidyr + r-vgam)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description @@ -10668,9 +10446,9 @@ accessibility data.") (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs - `(("r-monocle3" ,r-monocle3) - ,@(alist-delete "r-monocle" - (package-propagated-inputs r-cicero))))))) + (modify-inputs (package-propagated-inputs r-cicero) + (delete "r-monocle") + (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package @@ -10687,31 +10465,31 @@ accessibility data.") `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gwascat" ,r-gwascat) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-universalmotif" ,r-universalmotif))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-deseq2 + r-dplyr + r-edger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gwascat + r-iranges + r-magrittr + r-r-utils + r-readr + r-reshape2 + r-rlang + r-rtracklayer + r-s4vectors + r-seqinr + r-stringi + r-stringr + r-universalmotif)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis @@ -10740,22 +10518,22 @@ analysis, evolutionary conservation, biogenesis to functional analysis.") (base32 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) - (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-dosnow" ,r-dosnow) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (propagated-inputs + (list r-aucell + r-data-table + r-dplyr + r-dosnow + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description @@ -10788,24 +10566,24 @@ cisTopics and explore the nature and regulatory proteins driving them.") "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . "cisTopic"))) (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-text2vec" ,r-text2vec))) + (list r-aucell + r-data-table + r-dosnow + r-dplyr + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors + r-text2vec)) (native-inputs - `(("r-knitr" ,r-knitr)))))) + (list r-knitr))))) (define-public r-genie3 (package @@ -10821,10 +10599,9 @@ cisTopics and explore the nature and regulatory proteins driving them.") (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-reshape2" ,r-reshape2))) + (list r-dplyr r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -10846,7 +10623,7 @@ regulatory networks from expression data.") (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description @@ -10871,7 +10648,7 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) (build-system r-build-system) - (propagated-inputs `(("r-minfi" ,r-minfi))) + (propagated-inputs (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") (synopsis "Annotation for Illumina's 450k methylation arrays") @@ -10894,17 +10671,16 @@ data.") (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-illuminahumanmethylation450kanno-ilmn12-hg19" - ,r-illuminahumanmethylation450kanno-ilmn12-hg19) - ("r-illuminaio" ,r-illuminaio) - ("r-limma" ,r-limma) - ("r-lumi" ,r-lumi) - ("r-matrixstats" ,r-matrixstats) - ("r-methylumi" ,r-methylumi) - ("r-roc" ,r-roc))) + (list r-biobase + r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminaio + r-limma + r-lumi + r-matrixstats + r-methylumi + r-roc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description @@ -10955,11 +10731,9 @@ metrics, with methods for objects produced by the @code{methylumi} and (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs - `(("lz4" ,lz4) - ("xz" ,xz) - ("zlib" ,zlib))) + (list lz4 xz zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -10991,14 +10765,14 @@ with multiple R processes supported by the package @code{parallel}.") (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gdsfmt" ,r-gdsfmt) - ("r-geoquery" ,r-geoquery) - ("r-illuminaio" ,r-illuminaio) - ("r-methylumi" ,r-methylumi) - ("r-minfi" ,r-minfi) - ("r-watermelon" ,r-watermelon))) + (list r-biobase + r-biocgenerics + r-gdsfmt + r-geoquery + r-illuminaio + r-methylumi + r-minfi + r-watermelon)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -11020,9 +10794,7 @@ with multiple R processes supported by the package @code{parallel}.") (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib))) + (list r-biostrings r-genomicranges r-rhtslib)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description @@ -11048,13 +10820,13 @@ genome sequence.") ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-bsgenome" ,r-bsgenome) - ("r-biostrings" ,r-biostrings))) + (list r-biocgenerics + r-s4vectors + r-iranges + r-genomeinfodb + r-genomicranges + r-bsgenome + r-biostrings)) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") @@ -11084,9 +10856,7 @@ injected in that sequence).") (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs - `(("r-rjava" ,r-rjava) - ("r-rsamtools" ,r-rsamtools) - ("r-seqbias" ,r-seqbias))) + (list r-rjava r-rsamtools r-seqbias)) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description @@ -11109,22 +10879,22 @@ format.") (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-foreach" ,r-foreach) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-mclust" ,r-mclust) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-foreach + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-mclust + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqinr + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description @@ -11157,23 +10927,23 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-proxy" ,r-proxy) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vegan" ,r-vegan) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-deseq2 + r-dplyr + r-dynamictreecut + r-edger + r-ggplot2 + r-hmisc + r-limma + r-magrittr + r-proxy + r-s4vectors + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description @@ -11198,30 +10968,30 @@ provides methods for retrieving enriched pathways.") `((upstream-name . "VariantFiltering"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-graph" ,r-graph) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-shinythemes" ,r-shinythemes) - ("r-shinytree" ,r-shinytree) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-xvector" ,r-xvector))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-genomicscores + r-graph + r-gviz + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-shiny + r-shinyjs + r-shinythemes + r-shinytree + r-summarizedexperiment + r-variantannotation + r-xvector)) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description @@ -11244,7 +11014,7 @@ populations, splice site strength, conservation, etc.") (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart))) + (list r-biomart)) (home-page "https://bioconductor.org/packages/GenomeGraphs/") (synopsis "Plotting genomic information from Ensembl") (description @@ -11272,16 +11042,16 @@ same genome coordinate system.") (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomegraphs" ,r-genomegraphs) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-oligo" ,r-oligo) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-waveslim" ,r-waveslim))) + (list r-affy + r-biobase + r-biostrings + r-genomegraphs + r-genomicranges + r-iranges + r-oligo + r-oligoclasses + r-preprocesscore + r-waveslim)) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description @@ -11304,25 +11074,25 @@ arrays based on fast wavelet-based functional models.") `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-lme4" ,r-lme4) - ("r-lmertest" ,r-lmertest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-pbkrtest" ,r-pbkrtest) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocparallel + r-doparallel + r-foreach + r-ggplot2 + r-gplots + r-iterators + r-limma + r-lme4 + r-lmertest + r-mass + r-matrix + r-pbkrtest + r-progress + r-reshape2 + r-rlang + r-scales)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -11348,11 +11118,7 @@ measures.") (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer)) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") @@ -11383,8 +11149,7 @@ features (e.g. genes, microRNAs).") `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-htqpcr" ,r-htqpcr))) + (list r-biocgenerics r-htqpcr)) (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description @@ -11415,18 +11180,18 @@ data.") (substitute* "src/Makevars" (("/usr/bin/strip") (which "strip")))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcppthread" ,r-rcppthread) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-mass + r-rcpp + r-rcppthread + r-rlang + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/universalmotif/") (synopsis @@ -11458,15 +11223,15 @@ motifs, and others.") `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description @@ -11493,10 +11258,9 @@ using whole genome sequencing data.") `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2))) + (list r-data-table r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description @@ -11521,7 +11285,7 @@ cellular organization in health and disease.") (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth))) + (list r-kernsmooth)) (home-page "https://bioconductor.org/packages/BGmix/") (synopsis "Bayesian models for differential gene expression") (description @@ -11543,10 +11307,7 @@ gene expression.") (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gcrma" ,r-gcrma) - ("r-rcpp" ,r-rcpp))) + (list r-affy r-biobase r-gcrma r-rcpp)) (home-page "https://bioconductor.org/packages/bgx/") (synopsis "Bayesian gene expression") (description @@ -11594,9 +11355,7 @@ algorithm which is more efficient for larger data sets.") (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-gseabase" ,r-gseabase) - ("r-multtest" ,r-multtest))) + (list r-biobase r-gseabase r-multtest)) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description @@ -11618,10 +11377,9 @@ results.") (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-poibin" ,r-poibin))) + (list r-genomicranges r-poibin)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -11648,12 +11406,11 @@ the read count and GC content bias.") (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs - `(("libsbml" ,libsbml))) + (list libsbml)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph))) + (list r-biocgenerics r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.sbml.org") (synopsis "R support for SBML") (description @@ -11675,7 +11432,7 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (home-page "https://bioconductor.org/packages/hypergraph") (synopsis "Hypergraph data structures") (description @@ -11696,11 +11453,9 @@ manipulating hypergraphs.") "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) - (inputs `(("graphviz" ,graphviz))) + (inputs (list graphviz)) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-hypergraph" ,r-hypergraph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-graph r-hypergraph r-rgraphviz)) (home-page "https://bioconductor.org/packages/hyperdraw") (synopsis "Visualizing hypergraphs") (description @@ -11721,12 +11476,12 @@ manipulating hypergraphs.") (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs - `(("r-hyperdraw" ,r-hyperdraw) - ("r-hypergraph" ,r-hypergraph) - ("r-lim" ,r-lim) - ("r-limsolve" ,r-limsolve) - ("r-rsbml" ,r-rsbml) - ("r-stringr" ,r-stringr))) + (list r-hyperdraw + r-hypergraph + r-lim + r-limsolve + r-rsbml + r-stringr)) (home-page "https://bioconductor.org/packages/BiGGR/") (synopsis "Constraint based modeling using metabolic reconstruction databases") (description @@ -11752,9 +11507,9 @@ networks and estimated fluxes can be visualized with hypergraphs.") `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory))) + (list r-bigmemory)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -11785,26 +11540,26 @@ a file-backed matrix with factor properties.") (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-dplyr" ,r-dplyr) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-hmisc" ,r-hmisc) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-shiny" ,r-shiny) - ("r-shinycssloaders" ,r-shinycssloaders) - ("r-shinydashboard" ,r-shinydashboard) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-delayedarray + r-dplyr + r-ggally + r-ggplot2 + r-gridextra + r-hexbin + r-hmisc + r-htmlwidgets + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-shiny + r-shinycssloaders + r-shinydashboard + r-stringr + r-summarizedexperiment + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description @@ -11828,23 +11583,23 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-jsonlite" ,r-jsonlite) - ("r-png" ,r-png) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-rsvg" ,r-rsvg) - ("r-stringi" ,r-stringi))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-bh + r-biocgenerics + r-dbi + r-digest + r-dt + r-ggplot2 + r-gridextra + r-jsonlite + r-png + r-rcpp + r-rcurl + r-rjson + r-rsvg + r-stringi)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -11870,10 +11625,8 @@ structures.") (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-runit" ,r-runit))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics r-chemminer r-runit)) + (native-inputs (list r-knitr)) (home-page "https://github.com/girke-lab/fmcsR") (synopsis "Mismatch tolerant maximum common substructure searching") (description @@ -11902,15 +11655,15 @@ searching and clustering.") (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-dbi" ,r-dbi) - ("r-matrix" ,r-matrix) - ("r-rjson" ,r-rjson) - ("r-rsqlite" ,r-rsqlite) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-chemminer + r-dbi + r-matrix + r-rjson + r-rsqlite + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/girke-lab/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description @@ -11937,12 +11690,9 @@ available bioactivity data.") (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-tidyr" ,r-tidyr))) + (list r-biobase r-broom r-dplyr r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -11969,11 +11719,7 @@ visualize bioinformatics analyses.") (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-checkmate" ,r-checkmate) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs))) + (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -11996,16 +11742,16 @@ symbols).") (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-enrichplot" ,r-enrichplot) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-graphite" ,r-graphite) - ("r-igraph" ,r-igraph) - ("r-reactome-db" ,r-reactome-db))) + (list r-annotationdbi + r-dose + r-enrichplot + r-ggplot2 + r-ggraph + r-graphite + r-igraph + r-reactome-db)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -12028,9 +11774,7 @@ enrichment analysis and several functions for visualization.") (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster) - ("r-lattice" ,r-lattice))) + (list r-biobase r-cluster r-lattice)) (home-page "https://bioconductor.org/packages/EBarrays/") (synopsis "Gene clustering and differential expression identification") (description @@ -12052,7 +11796,7 @@ microarray data.") (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/BiocCaseStudies") (synopsis "Support for the case studies monograph") (description @@ -12074,16 +11818,16 @@ monograph.") `((upstream-name . "BiocCheck"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) + (list r-codetools + r-graph + r-httr + r-knitr + r-optparse + r-biocmanager + r-biocviews + r-stringdist)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -12104,10 +11848,7 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-geneplotter" ,r-geneplotter) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biocgenerics r-geneplotter r-graph r-rgraphviz)) (home-page "https://bioconductor.org/packages/biocGraph/") (synopsis "Graph examples and use cases in Bioinformatics") (description @@ -12129,13 +11870,9 @@ different graph related packages produced by Bioconductor.") `((upstream-name . "BiocStyle"))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-bookdown" ,r-bookdown) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) + (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -12157,13 +11894,13 @@ functionality.") `((upstream-name . "biocViews"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-graph" ,r-graph) - ("r-rbgl" ,r-rbgl) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml) - ("r-runit" ,r-runit))) + (list r-biobase + r-biocmanager + r-graph + r-rbgl + r-rcurl + r-xml + r-runit)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -12185,15 +11922,15 @@ also known as views, in a controlled vocabulary.") (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-curl" ,r-curl) - ("r-rappdirs" ,r-rappdirs) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationhub + r-biocfilecache + r-biocgenerics + r-biocmanager + r-curl + r-rappdirs + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description @@ -12219,13 +11956,13 @@ access.") (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs - `(("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-mass + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/Kraus-Lab/groHMM") (synopsis "GRO-seq analysis pipeline") (description @@ -12247,15 +11984,15 @@ access.") `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -12281,30 +12018,30 @@ rownames.") (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs - `(("r-bigrquery" ,r-bigrquery) - ("r-car" ,r-car) - ("r-complexheatmap" ,r-complexheatmap) - ("r-curatedtcgadata" ,r-curatedtcgadata) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-bigrquery + r-car + r-complexheatmap + r-curatedtcgadata + r-dbi + r-dplyr + r-dt + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-graph + r-httr + r-iranges + r-magrittr + r-plyr + r-rgraphviz + r-rjson + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description @@ -12326,11 +12063,9 @@ tools for genome-scale analysis of cancer studies.") (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix))) + (list r-biocparallel r-gseabase r-matrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -12355,30 +12090,30 @@ gene selection, testing relationships, and so on.") (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-gh" ,r-gh) - ("r-graph" ,r-graph) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rbgl" ,r-rbgl) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-biocmanager + r-biocviews + r-dplyr + r-dt + r-gh + r-graph + r-htmltools + r-htmlwidgets + r-httr + r-igraph + r-jsonlite + r-magrittr + r-rbgl + r-readr + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description @@ -12403,18 +12138,18 @@ analytics on packages.") (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocio" ,r-biocio) - ("r-dplyr" ,r-dplyr) - ("r-keggrest" ,r-keggrest) - ("r-ontologyindex" ,r-ontologyindex) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-annotationdbi + r-biocio + r-dplyr + r-keggrest + r-ontologyindex + r-plyr + r-rlang + r-s4vectors + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -12442,17 +12177,17 @@ accessing web references for elements/sets are also available in BiocSet.") `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-bookdown" ,r-bookdown) - ("r-git2r" ,r-git2r) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringr" ,r-stringr) - ("r-usethis" ,r-usethis))) + (list r-biocstyle + r-bookdown + r-git2r + r-httr + r-knitr + r-rmarkdown + r-rstudioapi + r-stringr + r-usethis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") (synopsis "Tools to aid the development of Bioconductor Workflow packages") (description @@ -12474,8 +12209,7 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-biobase r-kernsmooth)) (home-page "https://bioconductor.org/packages/bioDist/") (synopsis "Different distance measures") (description @@ -12497,21 +12231,21 @@ distance measures.") (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-cowplot" ,r-cowplot) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocparallel + r-biocsingular + r-cowplot + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-ggplot2 + r-ggrepel + r-lattice + r-matrix + r-rcpp + r-reshape2)) + (native-inputs (list r-knitr)) (home-page "https://github.com/kevinblighe/PCAtools") (synopsis "PCAtools: everything Principal Components Analysis") (description @@ -12543,12 +12277,8 @@ dimensional mass cytometry data.") (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") (description @@ -12571,17 +12301,17 @@ user's input and automatically retrieving results from GREAT web server.") (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-corpcor" ,r-corpcor) - ("r-doparallel" ,r-doparallel) - ("r-dosnow" ,r-dosnow) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-matrixcalc" ,r-matrixcalc) - ("r-rtsne" ,r-rtsne) - ("r-umap" ,r-umap))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-cluster + r-corpcor + r-doparallel + r-dosnow + r-foreach + r-ggplot2 + r-matrix + r-matrixcalc + r-rtsne + r-umap)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/M3C") (synopsis "Monte Carlo reference-based consensus clustering") (description @@ -12604,7 +12334,7 @@ hypothesis @code{K=1}.") (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (home-page "https://bioconductor.org/packages/Icens") (synopsis "NPMLE for censored and truncated data") (description @@ -12629,10 +12359,7 @@ truncated data.") (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs - `(("r-icens" ,r-icens) - ("r-mlecens" ,r-mlecens) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-icens r-mlecens r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/interval/") (synopsis "Weighted Logrank tests and NPMLE for interval censored data") (description @@ -12656,11 +12383,7 @@ plot them, and perform logrank or Wilcoxon type tests.") (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs - `(("r-interval" ,r-interval) - ("r-kmsurv" ,r-kmsurv) - ("r-mass" ,r-mass) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-interval r-kmsurv r-mass r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/FHtest/") (synopsis "Tests for survival data based on the Fleming-Harrington class") (description @@ -12689,23 +12412,23 @@ with: (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-deseq2 + r-fda + r-genomicalignments + r-genomicranges + r-ggbio + r-ggplot2 + r-gtools + r-lsd + r-matrix + r-reshape2 + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") (synopsis "Analysis of multiplexed 4C sequencing data") @@ -12755,7 +12478,7 @@ routines.") `((upstream-name . "S4Vectors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/S4Vectors") (synopsis "S4 implementation of vectors and lists") (description @@ -12784,18 +12507,18 @@ S4Vectors package itself.") (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore))) + (list r-annotationdbi + r-doparallel + r-dynamictreecut + r-fastcluster + r-foreach + r-go-db + r-hmisc + r-impute + r-rcpp + r-survival + r-matrixstats + r-preprocesscore)) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") @@ -12834,11 +12557,11 @@ data manipulation and visualization.") ;; FIXME: Rgraphviz bundles the sources of an older variant of ;; graphviz. It does not build with the latest version of graphviz, so ;; we do not add graphviz to the inputs. - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://bioconductor.org/packages/Rgraphviz") (synopsis "Plotting capabilities for R graph objects") (description @@ -12859,11 +12582,9 @@ objects from the @code{graph} package.") (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) + (list r-data-table r-fdrtool r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -12885,13 +12606,13 @@ assays such as Hi-C.") (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcolorbrewer + r-rtracklayer)) (home-page "https://bioconductor.org/packages/HiTC") (synopsis "High throughput chromosome conformation capture analysis") (description @@ -12915,16 +12636,16 @@ provided.") (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-delayedarray + r-iranges + r-matrix + r-rhdf5 + r-rhdf5filters + r-rhdf5lib + r-s4vectors)) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") (description "This package provides an array-like container for convenient @@ -13004,8 +12725,7 @@ block processing.") (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - `(("hdf5" ,hdf5-1.10) - ("zlib" ,zlib))) + (list hdf5-1.10 zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) @@ -13028,12 +12748,9 @@ packages.") "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -13056,29 +12773,29 @@ matrices.") (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-powerlaw" ,r-powerlaw) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-annotate + r-biocgenerics + r-biostrings + r-dbi + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-go-db + r-iranges + r-keggrest + r-powerlaw + r-r-utils + r-readr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ge11232002/CNEr") (synopsis "CNE Detection and Visualization") (description @@ -13106,27 +12823,27 @@ advanced visualization of sets of conserved noncoding elements.") (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-catools" ,r-catools) - ("r-cner" ,r-cner) - ("r-dbi" ,r-dbi) - ("r-dirichletmultinomial" ,r-dirichletmultinomial) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqlogo" ,r-seqlogo) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-catools + r-cner + r-dbi + r-dirichletmultinomial + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-rsqlite + r-rtracklayer + r-s4vectors + r-seqlogo + r-tfmpvalue + r-xml + r-xvector)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ge11232002/TFBSTools") (synopsis "Transcription factor binding site (TFBS) analysis") (description @@ -13152,19 +12869,19 @@ provides a wrapper of de novo motif discovery software.") (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/motifmatchr") (synopsis "Fast motif matching in R") (description @@ -13185,29 +12902,29 @@ This package wraps C++ code from the MOODS motif calling library.") (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-nabor" ,r-nabor) - ("r-plotly" ,r-plotly) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-matrix + r-miniui + r-nabor + r-plotly + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rsamtools + r-rtsne + r-s4vectors + r-shiny + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") (synopsis "Determine chromatin variation across regions") (description @@ -13234,13 +12951,10 @@ sequence (@code{DNAse-seq}) experiments.") `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomicranges" ,r-genomicranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -13264,18 +12978,18 @@ libraries.") (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomicranges" ,r-genomicranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-matrix + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/scuttle") (synopsis "Single-cell RNA-Seq analysis utilities") (description @@ -13297,28 +13011,28 @@ of other packages.") "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-ggbeeswarm + r-ggplot2 + r-ggrepel + r-gridextra + r-matrix + r-rcolorbrewer + r-rlang + r-rtsne + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -13339,28 +13053,28 @@ quality control.") "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-metapod" ,r-metapod) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-igraph + r-limma + r-matrix + r-metapod + r-rcpp + r-s4vectors + r-scuttle + r-singlecellexperiment + r-statmod + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -13384,11 +13098,8 @@ variable and significantly correlated genes.") `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-matrix r-matrixgenerics r-matrixstats r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/sparseMatrixStats/") (synopsis "Summary statistics for rows and columns of sparse matrices") (description @@ -13412,15 +13123,15 @@ data in the column sparse format.") `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors) - ("r-sparsematrixstats" ,r-sparsematrixstats))) + (list r-delayedarray + r-iranges + r-matrix + r-matrixgenerics + r-matrixstats + r-s4vectors + r-sparsematrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -13447,12 +13158,9 @@ memory usage and processing time is minimized.") (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-clue" ,r-clue) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-clue r-mass r-rcpp r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") (synopsis "Core utils for mass spectrometry data") (description @@ -13478,11 +13186,9 @@ within the R for Mass Spectrometry packages.") (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-mscoreutils" ,r-mscoreutils) - ("r-protgenerics" ,r-protgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-mscoreutils r-protgenerics r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsFeatures") (synopsis "Functionality for mass spectrometry features") (description @@ -13511,10 +13217,9 @@ the respective packages (such as e.g. @code{xcms}).") (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocIO") (synopsis "Standard input and output for Bioconductor packages") (description @@ -13545,10 +13250,7 @@ as well as local access. Developers can register a file extension, e.g., (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-msnbase" ,r-msnbase) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-gplots r-mass r-msnbase r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/msmsEDA") (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") @@ -13571,10 +13273,7 @@ experiments, and visualize de influence of the involved factors.") (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-msmseda" ,r-msmseda) - ("r-msnbase" ,r-msnbase) - ("r-qvalue" ,r-qvalue))) + (list r-edger r-msmseda r-msnbase r-qvalue)) (home-page "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") @@ -13603,34 +13302,34 @@ relevant, and the minimum expression of the most abundant condition.") (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-drc" ,r-drc) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-nnls" ,r-nnls) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-complexheatmap + r-consensusclusterplus + r-cowplot + r-data-table + r-dplyr + r-drc + r-flowcore + r-flowsom + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-magrittr + r-matrix + r-matrixstats + r-nnls + r-purrr + r-rcolorbrewer + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") @@ -13660,22 +13359,22 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicfiles + r-genomicranges + r-ggplot2 + r-homo-sapiens + r-iranges + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -13710,35 +13409,35 @@ by Ernst and Kellis.") (("fechable") "fetchable")) #t))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-biovizbase + r-bsgenome + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggally + r-ggplot2 + r-gridextra + r-gtable + r-hmisc + r-iranges + r-organismdbi + r-reshape2 + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -13776,21 +13475,21 @@ interval to data view, mismatch pileup, and several splicing summaries.") (("importFrom\\(ff,.*") "import(ff)\n")) #t))))) (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-batchjobs + r-bbmisc + r-biocgenerics + r-bit + r-doparallel + r-ff + r-ffbase + r-foreach + r-genomicfiles + r-genomicranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -13813,38 +13512,38 @@ and more.") (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-batchjobs + r-bbmisc + r-beeswarm + r-biobase + r-biocgenerics + r-doparallel + r-dplyr + r-erma + r-ffbase + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-ggbeeswarm + r-ggplot2 + r-gqtlbase + r-hardyweinberg + r-homo-sapiens + r-iranges + r-limma + r-mgcv + r-plotly + r-reshape2 + r-s4vectors + r-shiny + r-snpstats + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -13869,30 +13568,30 @@ family of feature/genome hypotheses.") (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-biovizbase + r-bsgenome + r-digest + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-lattice + r-latticeextra + r-matrixstats + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -13917,20 +13616,20 @@ with your data.") "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-s4vectors" ,r-s4vectors) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-readr + r-s4vectors + r-snpstats + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -13951,10 +13650,7 @@ EMBL-EBI GWAS catalog.") (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-rcurl" ,r-rcurl) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-graph r-rcurl r-rgraphviz r-xml)) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description @@ -13978,18 +13674,18 @@ functionalities including parsing, graph operation, visualization and etc.") "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-ensdb-hsapiens-v75 + r-ensembldb + r-genomeinfodb + r-genomicfiles + r-httr + r-matrix + r-rsamtools + r-snpstats + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -14015,9 +13711,7 @@ defining LD blocks.") (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-genetics" ,r-genetics) - ("r-rcpp" ,r-rcpp) - ("r-snpstats" ,r-snpstats))) + (list r-genetics r-rcpp r-snpstats)) (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description @@ -14042,14 +13736,14 @@ on the plot.") "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjags" ,r-rjags))) + (list gsl)) + (propagated-inputs + (list r-lme4 + r-nnet + r-rcpp + r-rcpparmadillo + r-rgraphviz + r-rjags)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -14079,12 +13773,9 @@ statistical dependencies in messy, complex data.") "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-catools" ,r-catools) - ("r-rcpp" ,r-rcpp) - ("r-rsamtools" ,r-rsamtools))) + (list r-bh r-catools r-rcpp r-rsamtools)) (home-page "https://cran.r-project.org/web/packages/spp/") (synopsis "ChIP-Seq processing pipeline") (description "This package provides tools for analysis of ChIP-seq and @@ -14104,14 +13795,14 @@ other functional sequencing data.") (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-graph" ,r-graph) - ("r-kegggraph" ,r-kegggraph) - ("r-keggrest" ,r-keggrest) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-png" ,r-png) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-graph + r-kegggraph + r-keggrest + r-org-hs-eg-db + r-png + r-rgraphviz + r-xml)) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description @@ -14138,12 +13829,9 @@ large-scale and fully automated analysis.") "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics r-matrix r-survival r-zlibbioc)) (home-page "https://bioconductor.org/packages/snpStats") (synopsis "Methods for SNP association studies") (description @@ -14166,21 +13854,21 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs - `(("r-bamsignals" ,r-bamsignals) - ("r-biocgenerics" ,r-biocgenerics) - ("r-chromstardata" ,r-chromstardata) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-bamsignals + r-biocgenerics + r-chromstardata + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-mvtnorm + r-reshape2 + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ataudt/chromstaR") (synopsis "Chromatin state analysis for ChIP-Seq data") (description @@ -14204,16 +13892,16 @@ analyses.") (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-annotationdbi + r-dplyr + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-knitr + r-magrittr + r-rtracklayer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Guitar") (synopsis "Visualize genomic features") (description @@ -14235,8 +13923,7 @@ starting site, start codon, stop codon and transcription ending site.") (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) + (list r-biomart r-zoo)) (home-page "https://bioconductor.org/packages/Sushi") (synopsis "Tools for visualizing genomics data") (description @@ -14258,17 +13945,17 @@ visualizations for publication-quality multi-panel figures.") (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sva" ,r-sva))) + (list r-biobase + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-sva)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ballgown") (synopsis "Flexible, isoform-level differential expression analysis") (description @@ -14291,17 +13978,17 @@ to annotation.") "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) - (inputs `(("megadepth" ,megadepth))) + (inputs (list megadepth)) (propagated-inputs - `(("r-cmdfun" ,r-cmdfun) - ("r-dplyr" ,r-dplyr) - ("r-fs" ,r-fs) - ("r-genomicranges" ,r-genomicranges) - ("r-magrittr" ,r-magrittr) - ("r-readr" ,r-readr) - ("r-xfun" ,r-xfun))) + (list r-cmdfun + r-dplyr + r-fs + r-genomicranges + r-magrittr + r-readr + r-xfun)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LieberInstitute/megadepth") (synopsis "BigWig and BAM related utilities") (description @@ -14325,16 +14012,16 @@ regions or annotations of your choice from BigWig files.") (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-futile-logger" ,r-futile-logger) - ("r-matrix" ,r-matrix) - ("r-outliers" ,r-outliers) - ("r-rcpp" ,r-rcpp) - ("r-rdpack" ,r-rdpack))) + (list r-abind + r-biocparallel + r-data-table + r-futile-logger + r-matrix + r-outliers + r-rcpp + r-rdpack)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/uds-helms/BEclear") (synopsis "Correction of batch effects in DNA methylation data") (description @@ -14358,19 +14045,19 @@ real numbers.") (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs - `(("kallisto" ,kallisto) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-jsonlite" ,r-jsonlite) - ("r-rhdf5" ,r-rhdf5) - ("r-rslurm" ,r-rslurm) - ("r-rtracklayer" ,r-rtracklayer) - ("r-sjmisc" ,r-sjmisc) - ("r-tximport" ,r-tximport))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list kallisto + r-biomart + r-biostrings + r-data-table + r-dplyr + r-genomicfeatures + r-jsonlite + r-rhdf5 + r-rslurm + r-rtracklayer + r-sjmisc + r-tximport)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeCall") (synopsis "RNA-Seq present/absent gene expression calls generation") (description @@ -14394,18 +14081,18 @@ all RNA-Seq libraries of each species integrated in Bgee.") (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-curl" ,r-curl) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-graph" ,r-graph) - ("r-r-utils" ,r-r-utils) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-tidyr" ,r-tidyr) - ("r-topgo" ,r-topgo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-curl + r-data-table + r-digest + r-dplyr + r-graph + r-r-utils + r-rcurl + r-rsqlite + r-tidyr + r-topgo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeDB_R") (synopsis "Annotation and gene expression data retrieval from Bgee database") (description @@ -14428,11 +14115,8 @@ anatomical terms, mapped to genes by expression patterns.") (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-stringi" ,r-stringi))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-httpuv r-httr r-jsonlite r-stringi)) + (native-inputs (list r-knitr)) (home-page "https://github.com/tamerh/biobtreeR") (synopsis "Use biobtree tool from R") (description @@ -14455,7 +14139,7 @@ mappings functionalities.") (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs - `(("r-infotheo" ,r-infotheo))) + (list r-infotheo)) (home-page "http://minet.meyerp.com") (synopsis "Mutual information networks") (description @@ -14478,10 +14162,7 @@ information networks from data.") `((upstream-name . "geNetClassifier"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-ebarrays" ,r-ebarrays) - ("r-minet" ,r-minet))) + (list r-biobase r-e1071 r-ebarrays r-minet)) (home-page "https://www.cicancer.org") (synopsis "Classify diseases and build gene networks using expression profiles") (description @@ -14504,8 +14185,8 @@ interface to query the classifier.") "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) - (propagated-inputs `(("r-filelock" ,r-filelock))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-filelock)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/dir.expiry") (synopsis "Managing expiration for cache directories") (description @@ -14530,8 +14211,8 @@ eliminating obsolete caches generated by old versions of packages.") `((upstream-name . "basilisk.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-dir-expiry" ,r-dir-expiry))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dir-expiry)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk.utils") (synopsis "Basilisk installation utilities") (description @@ -14553,10 +14234,8 @@ package, primarily for creation of the underlying Conda instance.") (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk-utils" ,r-basilisk-utils) - ("r-dir-expiry" ,r-dir-expiry) - ("r-reticulate" ,r-reticulate))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk-utils r-dir-expiry r-reticulate)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk") (synopsis "Freeze Python dependencies inside Bioconductor packages") (description @@ -14586,13 +14265,13 @@ Python environments in a single R session.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-styler" ,r-styler) - ("r-usethis" ,r-usethis))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocmanager + r-fs + r-glue + r-rlang + r-styler + r-usethis)) + (native-inputs (list r-knitr)) (home-page "https://github.com/lcolladotor/biocthis") (synopsis "Automate package and project setup for Bioconductor packages") (description @@ -14616,13 +14295,13 @@ Bioconductor-friendly.") `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) (propagated-inputs - `(("docker" ,docker) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-memoise" ,r-memoise) - ("r-readr" ,r-readr) - ("r-whisker" ,r-whisker))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list docker + r-dplyr + r-httr + r-memoise + r-readr + r-whisker)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocDockerManager") (synopsis "Access and manage Bioconductor Docker images") (description @@ -14645,25 +14324,25 @@ the Bioconductor project.") (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-chk" ,r-chk) - ("r-jsonlite" ,r-jsonlite) - ("r-lgr" ,r-lgr) - ("r-lifecycle" ,r-lifecycle) - ("r-openssl" ,r-openssl) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-stringr" ,r-stringr) - ("r-testthat" ,r-testthat) - ("r-withr" ,r-withr) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-chk + r-jsonlite + r-lgr + r-lifecycle + r-openssl + r-plyr + r-progress + r-r6 + r-rappdirs + r-rcpp + r-rcurl + r-rsqlite + r-stringr + r-testthat + r-withr + r-xml + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biodb") (synopsis "Library for connecting to chemical and biological databases") (description @@ -14690,11 +14369,8 @@ separate published packages.") (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rhdf5" ,r-rhdf5))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-jsonlite r-matrix r-plyr r-rhdf5)) + (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/biomformat/") (synopsis "Interface package for the BIOM file format") (description @@ -14742,10 +14418,7 @@ design.") (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-mvcclass" ,r-mvcclass) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biobase r-graph r-mvcclass r-rgraphviz)) (home-page "https://bioconductor.org/packages/BioMVCClass") (synopsis "Model-View-Controller (MVC) classes that use Biobase") (description @@ -14767,10 +14440,7 @@ design.") (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-genomicranges r-gviz r-iranges r-mvtnorm)) (home-page "https://bioconductor.org/packages/biomvRCNS") (synopsis "Copy number study and segmentation for multivariate biological data") (description @@ -14795,28 +14465,28 @@ using aCGH or sequencing.") (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-complexheatmap" ,r-complexheatmap) - ("r-deseq2" ,r-deseq2) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-genie3" ,r-genie3) - ("r-ggnetwork" ,r-ggnetwork) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-igraph" ,r-igraph) - ("r-intergraph" ,r-intergraph) - ("r-matrixstats" ,r-matrixstats) - ("r-minet" ,r-minet) - ("r-netrep" ,r-netrep) - ("r-networkd3" ,r-networkd3) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-sva" ,r-sva) - ("r-wgcna" ,r-wgcna))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-complexheatmap + r-deseq2 + r-dynamictreecut + r-genie3 + r-ggnetwork + r-ggnewscale + r-ggplot2 + r-ggpubr + r-igraph + r-intergraph + r-matrixstats + r-minet + r-netrep + r-networkd3 + r-rcolorbrewer + r-reshape2 + r-summarizedexperiment + r-sva + r-wgcna)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/almeidasilvaf/BioNERO") (synopsis "Biological network reconstruction omnibus") (description @@ -14851,11 +14521,7 @@ networks.") (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-igraph" ,r-igraph) - ("r-rbgl" ,r-rbgl))) + (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl)) (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html") (synopsis "Functional analysis of biological networks") (description @@ -14884,26 +14550,26 @@ scoring subnetwork.") (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-pathview" ,r-pathview) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-psych" ,r-psych) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rjsonio" ,r-rjsonio) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-whisker" ,r-whisker) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-dt + r-ggplot2 + r-hmisc + r-igraph + r-knitr + r-markdown + r-pathview + r-pheatmap + r-plyr + r-psych + r-rcolorbrewer + r-rjsonio + r-rmarkdown + r-shiny + r-shinybs + r-whisker + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jardimViniciusC/BioNetStat") (synopsis "Biological network analysis") (description @@ -14926,11 +14592,9 @@ network and metabolic pathways view.") (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edger" ,r-edger) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-edger r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://accio.github.io/BioQC/") (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") (description @@ -14954,15 +14618,15 @@ optimised for high performance.") (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-psych" ,r-psych) - ("r-stringr" ,r-stringr))) + (list r-cluster + r-genomicranges + r-hmisc + r-igraph + r-mass + r-psych + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/xyang2uchicago/BioTIP") (synopsis "R package for characterization of biological tipping-point") (description @@ -14984,20 +14648,20 @@ help unravel disease regulatory trajectory.") (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-dplyr" ,r-dplyr) - ("r-drtmle" ,r-drtmle) - ("r-ggplot2" ,r-ggplot2) - ("r-ggsci" ,r-ggsci) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-superheat" ,r-superheat) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biocparallel + r-dplyr + r-drtmle + r-ggplot2 + r-ggsci + r-limma + r-s4vectors + r-summarizedexperiment + r-superheat + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://code.nimahejazi.org/biotmle/") (synopsis "Targeted learning with moderated statistics for biomarker discovery") (description @@ -15026,31 +14690,31 @@ ensemble machine learning for the estimation of nuisance functions.") (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-permute" ,r-permute) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-iranges + r-limma + r-locfit + r-permute + r-r-utils + r-rcpp + r-rhdf5 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/bsseq") (synopsis "Analyze, manage and store bisulfite sequencing data") (description @@ -15072,25 +14736,25 @@ visualizing bisulfite sequencing data.") (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-annotatr" ,r-annotatr) - ("r-biocparallel" ,r-biocparallel) - ("r-bsseq" ,r-bsseq) - ("r-bumphunter" ,r-bumphunter) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-nlme" ,r-nlme) - ("r-outliers" ,r-outliers) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-annotatr + r-biocparallel + r-bsseq + r-bumphunter + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-matrixstats + r-nlme + r-outliers + r-rcolorbrewer + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/dmrseq") (synopsis "Detection and inference of differentially methylated regions") (description @@ -15122,30 +14786,30 @@ interest on transformed methylation proportions.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-crayon" ,r-crayon) - ("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-later" ,r-later) - ("r-logger" ,r-logger) - ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) - ("r-purrr" ,r-purrr) - ("r-rappdirs" ,r-rappdirs) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://saezlab.github.io/OmnipathR/") (synopsis "OmniPath web service client and more") (description @@ -15170,34 +14834,34 @@ for ligand activity prediction from transcriptomics data.") (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biscuiteerdata" ,r-biscuiteerdata) - ("r-bsseq" ,r-bsseq) - ("r-data-table" ,r-data-table) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dmrseq" ,r-dmrseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-impute" ,r-impute) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mus-musculus" ,r-mus-musculus) - ("r-qdnaseq" ,r-qdnaseq) - ("r-qualv" ,r-qualv) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biscuiteerdata + r-bsseq + r-data-table + r-delayedmatrixstats + r-dmrseq + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-homo-sapiens + r-impute + r-matrix + r-matrixstats + r-mus-musculus + r-qdnaseq + r-qualv + r-r-utils + r-readr + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/trichelab/biscuiteer") (synopsis "Convenience functions for the Biscuit package") (description @@ -15221,23 +14885,23 @@ estimates, etc.") (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tximport" ,r-tximport))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-ensembldb + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-jsonlite + r-matrix + r-s4vectors + r-summarizedexperiment + r-tibble + r-tximport)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description @@ -15261,24 +14925,24 @@ reproducibility.") (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomformat" ,r-biomformat) - ("r-biostrings" ,r-biostrings) - ("r-cluster" ,r-cluster) - ("r-data-table" ,r-data-table) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-multtest" ,r-multtest) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-vegan" ,r-vegan))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-ade4 + r-ape + r-biobase + r-biocgenerics + r-biomformat + r-biostrings + r-cluster + r-data-table + r-foreach + r-ggplot2 + r-igraph + r-multtest + r-plyr + r-reshape2 + r-scales + r-vegan)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description -- cgit v1.2.3 From e3196755e60ba7f1ed9d432e73f26a85e0c8893c Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 13 Dec 2021 22:15:07 +0100 Subject: gnu: Further simplify package inputs. This is the result of running: ./pre-inst-env guix style --input-simplification=safe and manually undoing changes on a dozen of packages to reduce rebuilds (derivations for emacs, icecat, and libreoffice are unchanged.) --- gnu/packages/admin.scm | 46 +- gnu/packages/algebra.scm | 7 +- gnu/packages/assembly.scm | 18 +- gnu/packages/astronomy.scm | 10 +- gnu/packages/audio.scm | 71 +-- gnu/packages/bioconductor.scm | 64 +- gnu/packages/check.scm | 27 +- gnu/packages/cinnamon.scm | 34 +- gnu/packages/compression.scm | 12 +- gnu/packages/cran.scm | 26 +- gnu/packages/databases.scm | 16 +- gnu/packages/debian.scm | 5 +- gnu/packages/documentation.scm | 3 +- gnu/packages/easyrpg.scm | 3 +- gnu/packages/education.scm | 4 +- gnu/packages/emacs-xyz.scm | 103 ++-- gnu/packages/enchant.scm | 12 +- gnu/packages/esolangs.scm | 2 +- gnu/packages/fcitx5.scm | 5 +- gnu/packages/file-systems.scm | 18 +- gnu/packages/finance.scm | 10 +- gnu/packages/flashing-tools.scm | 4 +- gnu/packages/fontutils.scm | 16 +- gnu/packages/freedesktop.scm | 26 +- gnu/packages/ftp.scm | 4 +- gnu/packages/game-development.scm | 5 +- gnu/packages/games.scm | 64 +- gnu/packages/geo.scm | 6 +- gnu/packages/glib.scm | 18 +- gnu/packages/gnome-xyz.scm | 12 +- gnu/packages/gnome.scm | 346 +++++------ gnu/packages/gnunet.scm | 6 +- gnu/packages/graphics.scm | 4 +- gnu/packages/gstreamer.scm | 37 +- gnu/packages/guile-xyz.scm | 29 +- gnu/packages/hardware.scm | 3 +- gnu/packages/haskell-check.scm | 19 +- gnu/packages/haskell-web.scm | 4 +- gnu/packages/haskell-xyz.scm | 30 +- gnu/packages/image-processing.scm | 62 +- gnu/packages/image-viewers.scm | 8 +- gnu/packages/image.scm | 6 +- gnu/packages/jose.scm | 4 +- gnu/packages/julia-xyz.scm | 6 +- gnu/packages/kde-frameworks.scm | 46 +- gnu/packages/kde-internet.scm | 126 ++-- gnu/packages/kde-multimedia.scm | 54 +- gnu/packages/kde-pim.scm | 54 +- gnu/packages/kde-utils.scm | 48 +- gnu/packages/kde.scm | 3 +- gnu/packages/libusb.scm | 3 +- gnu/packages/linux.scm | 4 +- gnu/packages/lisp-check.scm | 45 +- gnu/packages/lisp-xyz.scm | 1165 +++++++++++++++-------------------- gnu/packages/lxde.scm | 2 +- gnu/packages/machine-learning.scm | 7 +- gnu/packages/mail.scm | 28 +- gnu/packages/mate.scm | 218 +++---- gnu/packages/maths.scm | 8 +- gnu/packages/messaging.scm | 6 +- gnu/packages/monitoring.scm | 5 +- gnu/packages/music.scm | 61 +- gnu/packages/nano.scm | 3 +- gnu/packages/networking.scm | 22 +- gnu/packages/ocaml.scm | 6 +- gnu/packages/openbox.scm | 22 +- gnu/packages/package-management.scm | 7 +- gnu/packages/pdf.scm | 11 +- gnu/packages/perl.scm | 35 +- gnu/packages/photo.scm | 7 +- gnu/packages/plotutils.scm | 2 +- gnu/packages/pulseaudio.scm | 3 +- gnu/packages/python-check.scm | 3 +- gnu/packages/python-web.scm | 19 +- gnu/packages/python-xyz.scm | 54 +- gnu/packages/qt.scm | 2 +- gnu/packages/radio.scm | 5 +- gnu/packages/ruby.scm | 6 +- gnu/packages/sawfish.scm | 7 +- gnu/packages/spice.scm | 4 +- gnu/packages/statistics.scm | 36 +- gnu/packages/textutils.scm | 2 +- gnu/packages/version-control.scm | 4 +- gnu/packages/video.scm | 38 +- gnu/packages/virtualization.scm | 22 +- gnu/packages/vpn.scm | 4 +- gnu/packages/web.scm | 20 +- gnu/packages/wm.scm | 34 +- gnu/packages/wv.scm | 6 +- gnu/packages/xdisorg.scm | 14 +- gnu/packages/xfce.scm | 78 +-- gnu/packages/xiph.scm | 5 +- gnu/packages/xml.scm | 30 +- gnu/packages/xorg.scm | 12 +- 94 files changed, 1544 insertions(+), 2077 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 4ed1f1abf3..de2f67f238 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -206,13 +206,13 @@ simplicity in mind.") (native-inputs (list bison flex)) (inputs - `(("libgcrypt" ,libgcrypt) - ("libgpg-error" ,libgpg-error) - ("libmhash" ,libmhash) - ("pcre:static" ,pcre "static") - ("pcre" ,pcre) - ("zlib:static" ,zlib "static") - ("zlib" ,zlib))) + (list libgcrypt + libgpg-error + libmhash + `(,pcre "static") + pcre + `(,zlib "static") + zlib)) (synopsis "File and directory integrity checker") (description "AIDE (Advanced Intrusion Detection Environment) is a file and directory @@ -645,9 +645,7 @@ console.") (inputs (list ncurses)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("python" ,python-minimal-wrapper))) ; for scripts/MakeHeader.py + (list autoconf automake python-minimal-wrapper)) ; for scripts/MakeHeader.py (home-page "https://htop.dev") (synopsis "Interactive process viewer") (description @@ -2303,14 +2301,14 @@ characters can be replaced as well, as can UTF-8 characters.") "1zlh44w67py416hkvw6nrfmjickc2d43v51vcli5p374d5sw84ql")))) (build-system gnu-build-system) (inputs - `(("ntfs-3g" ,ntfs-3g) - ("util-linux" ,util-linux "lib") - ("openssl" ,openssl) - ;; FIXME: add reiserfs. - ("zlib" ,zlib) - ("e2fsprogs" ,e2fsprogs) - ("libjpeg" ,libjpeg-turbo) - ("ncurses" ,ncurses))) + (list ntfs-3g + `(,util-linux "lib") + openssl + ;; FIXME: add reiserfs. + zlib + e2fsprogs + libjpeg-turbo + ncurses)) (home-page "https://www.cgsecurity.org/wiki/TestDisk") (synopsis "Data recovery tool") (description @@ -3918,12 +3916,12 @@ late.") #t)))) (build-system gnu-build-system) (inputs - `(("mpi" ,openmpi) - ("munge" ,munge) - ("boost" ,boost) - ("libelf" ,libelf) - ("libgcrypt" ,libgcrypt) - ("libgpg-error" ,libgpg-error))) + (list openmpi + munge + boost + libelf + libgcrypt + libgpg-error)) (synopsis "Infrastructue for large scale tool daemon launching") (description "LaunchMON is a software infrastructure that enables HPC run-time diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 6717a2ce2e..2c9674fdb4 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -214,11 +214,8 @@ the real span of the lattice.") (inputs (list fplll gmp mpfr pari-gp)) (propagated-inputs - `(("cysignals" ,python-cysignals) - ("cython" ,python-cython) - ("flake8" ,python-flake8) - ("numpy" ,python-numpy) - ("pytest" ,python-pytest))) + (list python-cysignals python-cython python-flake8 python-numpy + python-pytest)) (home-page "https://github.com/fplll/fpylll") (synopsis "Python interface for fplll") (description "fpylll is a Python wrapper for fplll.") diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm index bcb42a083f..51bf840bee 100644 --- a/gnu/packages/assembly.scm +++ b/gnu/packages/assembly.scm @@ -271,15 +271,15 @@ assembler, a C compiler and a linker. The assembler uses Intel syntax "0p6wklslkkp3s4aisj3w5a53bagqn5fy4m6088ppd4fcfxgqkrcd")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("bison" ,bison) - ("flex" ,flex) - ("help2man" ,help2man) - ("gettext" ,gettext-minimal) - ("libtool" ,libtool) - ("makeinfo" ,texinfo) - ("pkg-config" ,pkg-config))) + (list autoconf + automake + bison + flex + help2man + gettext-minimal + libtool + texinfo + pkg-config)) (home-page "https://www.gnu.org/software/libjit/") (synopsis "Just-In-Time compilation library") (description diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 0a1c556b85..d88a0ef739 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -200,10 +200,7 @@ for reading and writing.") (base32 "0nh12dr7gk4ki55lz95pkm4fpf7kazirra3zax9pab6v4qql4hlw")))) (build-system gnu-build-system) (native-inputs - `(("automake" ,automake) - ("autoreconf" ,autoconf) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list automake autoconf libtool pkg-config)) (home-page "https://github.com/liberfa/erfa") (synopsis "Essential Routines for Fundamental Astronomy") (description @@ -1224,10 +1221,9 @@ functions, so that they can be called with scalar or array inputs.") (base32 "0wxdqn92q1grv8k7xi7h88ac6wnznw4xh5bdlz1vz6za2dgsyj4m")))) (build-system python-build-system) (native-inputs - `(("cython" ,python-cython) - ("pytest" ,python-pytest))) + (list python-cython python-pytest)) (inputs - `(("numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://github.com/kbarbary/sep") (synopsis "Astronomical source extraction and photometry library") (description diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index eeae55efcb..2181b8e907 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -985,16 +985,16 @@ plugins are provided.") "17x4hylgq4dn9qycsdacfxy64f5cv57n2qgkvsdp524gnqzw4az3")))) (build-system gnu-build-system) (inputs - `(("fluidsynth" ,fluidsynth) - ("expat" ,expat) - ("glib" ,glib) - ("gtk" ,gtk+-2) - ("cairo" ,cairo) - ("lash" ,lash) - ("jack" ,jack-1) - ("lv2" ,lv2) - ("ladspa" ,ladspa) - ("fftw" ,fftw))) + (list fluidsynth + expat + glib + gtk+-2 + cairo + lash + jack-1 + lv2 + ladspa + fftw)) (native-inputs (list pkg-config)) (native-search-paths @@ -1140,13 +1140,13 @@ synchronized with the server to play synced audio.") (base32 "1c98z2xxz9pgcb4dg99gz8qrylh5cnag0j18a52d88ifsy24isvq")))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) ;for autopoint - ("libtool" ,libtool) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("which" ,which))) + (list autoconf + automake + gettext-minimal ;for autopoint + libtool + perl + pkg-config + which)) (inputs (list fftwf perl-xml-parser)) (build-system gnu-build-system) @@ -1315,10 +1315,7 @@ object library.") (base32 "1sr9knfhbm2m0wpkjq2l5n471vnl51wy4p6j4m95zqybimzb4s2j")))) (build-system cmake-build-system) (native-inputs - `(("bison" ,bison) - ("flex" ,flex) - ("gettext" ,gettext-minimal) - ("zlib" ,zlib))) + (list bison flex gettext-minimal zlib)) (inputs (list alsa-lib boost @@ -1994,21 +1991,21 @@ auto-wah.") #t)))) (build-system gnu-build-system) (inputs - `(("alsa-utils" ,alsa-utils) - ("fltk" ,fltk) - ("libx11" ,libx11) - ("libxext" ,libxext) - ("libxfixes" ,libxfixes) - ("libxft" ,libxft) - ("libxrender" ,libxrender) - ("libxpm" ,libxpm) - ("fontconfig" ,fontconfig) - ("freetype" ,freetype) - ("jack" ,jack-1) - ("alsa-lib" ,alsa-lib) - ("libsndfile" ,libsndfile) - ("libsamplerate" ,libsamplerate) - ("zlib" ,zlib))) + (list alsa-utils + fltk + libx11 + libxext + libxfixes + libxft + libxrender + libxpm + fontconfig + freetype + jack-1 + alsa-lib + libsndfile + libsamplerate + zlib)) (home-page "http://rakarrack.sourceforge.net/") (synopsis "Audio effects processor") (description @@ -3417,7 +3414,7 @@ stretching and pitch scaling of audio. This package contains the library.") (base32 "1623kirmxhmvmhx7f8lbzk0f18w2hrhwlkzl8l4aa906lfqffdp2")))) (build-system cmake-build-system) (native-inputs - `(("catch" ,catch-framework2))) + (list catch-framework2)) (inputs (list fftw)) (home-page "https://mixxxdj.github.io/libkeyfinder/") diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 17d15c06c5..e4b01170e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1510,14 +1510,14 @@ used visualizations.") "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-kernsmooth" ,r-kernsmooth) - ("r-matrixstats" ,r-matrixstats) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-statmod" ,r-statmod) - ("r-survey" ,r-survey) - ("r-viridislite" ,r-kernsmooth))) + (list r-ggplot2 + r-kernsmooth + r-matrixstats + r-patchwork + r-pbapply + r-statmod + r-survey + r-kernsmooth)) (home-page "https://github.com/borishejblum/dearseq") (synopsis "DEA for RNA-seq data through a robust variance component test") (description @@ -3578,30 +3578,30 @@ throughput genetic sequencing data sets using regression methods.") (native-inputs (list r-knitr)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biostrings + r-bsgenome + ;; These two packages are suggested packages + r-bsgenome-hsapiens-1000genomes-hs37d5 + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggalluvial + r-ggdendro + r-ggplot2 + r-iranges + r-magrittr + r-nmf + r-pracma + r-purrr + r-rcolorbrewer + r-s4vectors + r-stringr + r-tibble + r-tidyr + r-variantannotation)) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") (description "This package provides an extensive toolset for the diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 5368de3356..0a90a3b167 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -103,9 +103,7 @@ (base32 "0lsg791x6n95pxg6vif8qfc46nqcamhjq3g0dl5xqf6imy7n3acd")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("clang" ,clang) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper))) + (list clang pkg-config python-wrapper)) (inputs (list glib)) (synopsis "Code checker for C") @@ -435,7 +433,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.") "100r0kmra8jmra2hv92lzvwcmphpaiccwvq3lpdsa5b7hailhach")))) (build-system cmake-build-system) (inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (synopsis "Automated test framework for C++ and Objective-C") (description "Catch2 stands for C++ Automated Test Cases in Headers and is a multi-paradigm automated test framework for C++ and Objective-C.") @@ -1619,8 +1617,7 @@ testresources package instead.") (list python-pbr)) (arguments '()) (native-inputs - `(("python-fixtures" ,python-fixtures) - ("python-testtols" ,python-testtools))) + (list python-fixtures python-testtools)) (description "Testresources is an extension to Python's unittest to allow declarative use of resources by test cases."))) @@ -1638,12 +1635,10 @@ use of resources by test cases."))) "0j0ymmnc5nfxi1qzvy59j27viqca7l7xd0y9x29g7yr0h693j804")))) (build-system python-build-system) (propagated-inputs - `(("python-extras" ,python-extras) - ("python-testtools" ,python-testtools-bootstrap))) + (list python-extras python-testtools-bootstrap)) (native-inputs - `(("python-fixtures" ,python-fixtures-bootstrap) - ("python-hypothesis" ,python-hypothesis) - ("python-testscenarios" ,python-testscenarios-bootstrap))) + (list python-fixtures-bootstrap python-hypothesis + python-testscenarios-bootstrap)) (home-page "https://launchpad.net/subunit") (synopsis "Python implementation of the subunit protocol") (description @@ -2108,9 +2103,7 @@ seamlessly into your existing Python unit testing work flow.") "02j101m5grjrbvrgjap17jsxd1hgawkylmyswcn33vf42mxh9zzr")))) (build-system python-build-system) (propagated-inputs - `(("python-hypothesis" ,python-hypothesis) - ("python-lark-parser" ,python-lark-parser) - ("python-libcst" ,python-libcst-minimal))) + (list python-hypothesis python-lark-parser python-libcst-minimal)) (home-page "https://github.com/Zac-HD/hypothesmith") (synopsis "Strategies for generating Python programs") (description @@ -2318,7 +2311,7 @@ recognize TestCases.") "0gf2dpahpl5igb7jh1sr9acj3z3gp7zahqdqb69nk6wx01c8kc1g")))) (build-system python-build-system) (propagated-inputs - `(("pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/fschulze/pytest-warnings") (synopsis "Pytest plugin to list Python warnings in pytest report") (description @@ -2347,7 +2340,7 @@ pytest report.") "038049nyjl7di59ycnxvc9nydivc5m8np3hqq84j2iirkccdbs5n")))) (build-system python-build-system) (propagated-inputs - `(("pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://bitbucket.org/memedough/pytest-capturelog/overview") (synopsis "Pytest plugin to catch log messages") (description @@ -2372,7 +2365,7 @@ pytest report.") (native-inputs (list unzip)) (propagated-inputs - `(("pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/eisensheng/pytest-catchlog") (synopsis "Pytest plugin to catch log messages") (description diff --git a/gnu/packages/cinnamon.scm b/gnu/packages/cinnamon.scm index e1c9d7b614..fe33e797e4 100644 --- a/gnu/packages/cinnamon.scm +++ b/gnu/packages/cinnamon.scm @@ -53,24 +53,24 @@ (build-system gnu-build-system) ;; TODO: package 'libgsystem'. (inputs - `(("accountsservice" ,accountsservice) - ("gtk+" ,gtk+) - ("glib" ,glib) - ("gobject-introspection" ,gobject-introspection) - ("gnome-common" ,gnome-common) - ("libxkbfile" ,libxkbfile) - ("libxrandr" ,libxrandr) - ("python-2" ,python-2) - ("pulseaudio" ,pulseaudio) - ("xkeyboard-config" ,xkeyboard-config))) + (list accountsservice + gtk+ + glib + gobject-introspection + gnome-common + libxkbfile + libxrandr + python-2 + pulseaudio + xkeyboard-config)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("glib" ,glib "bin") ; glib-gettextize - ("intltool" ,intltool) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf + automake + gettext-minimal + `(,glib "bin") ; glib-gettextize + intltool + libtool + pkg-config)) (home-page "https://github.com/linuxmint/cinnamon-desktop/") (synopsis "Library for the Cinnamon Desktop") (description diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 17f6c276b4..1a3c639884 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1896,11 +1896,8 @@ timestamps in the file header with a fixed time (1 January 2008). (native-inputs (list perl pkg-config)) (inputs - `(("gnutls" ,gnutls) - ("liblzma" ,xz) - ("openssl" ,openssl) - ("zlib" ,zlib) - ("zstd:lib" ,zstd "lib"))) + (list gnutls xz openssl zlib + `(,zstd "lib"))) (build-system cmake-build-system) (home-page "https://libzip.org") (synopsis "C library for reading, creating, and modifying zip archives") @@ -2463,10 +2460,7 @@ file compression algorithm.") (base32 "00adrjpxqlaccrwjf65w3vhxfswdj0as8aj263c6f9b85llypc5v")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("intltool" ,intltool) - ("libxslt" ,libxslt) - ("pkg-config" ,pkg-config))) + (list gettext-minimal intltool libxslt pkg-config)) (inputs (list adwaita-icon-theme ; hard-coded theme gtk+)) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0c224379b1..ec6d267c51 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2814,7 +2814,7 @@ applications. That is, compute distances and related measures for angular (base32 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881")))) (build-system r-build-system) - (inputs `(("libjpeg" ,libjpeg-turbo))) + (inputs (list libjpeg-turbo)) (home-page "https://www.rforge.net/jpeg/") (synopsis "Read and write JPEG images with R") (description "This package provides a way to read, write and display @@ -4545,8 +4545,7 @@ dimensioned arrays.") (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs - `(("mariadb-dev" ,mariadb "dev") - ("zlib" ,zlib))) + (list `(,mariadb "dev") zlib)) (propagated-inputs (list r-dbi)) (home-page "https://github.com/r-dbi/RMySQL") @@ -11389,7 +11388,7 @@ back to file after modifications.") "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi")))) (properties `((upstream-name . "gitcreds"))) (build-system r-build-system) - (inputs `(("git" ,git-minimal))) + (inputs (list git-minimal)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/gitcreds") (synopsis "Query git credentials from R") @@ -12612,9 +12611,7 @@ redundant complex conjugate when the input is real data.") "1zha6bzb1rmfl6n2xjkygs9wfi3ah9cjr7a6jzk4zqc5kvl58lak")))) (build-system r-build-system) (inputs - `(("libtiff" ,libtiff) - ("libjpeg" ,libjpeg-turbo) - ("zlib" ,zlib))) + (list libtiff libjpeg-turbo zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/tiff/") @@ -19356,8 +19353,7 @@ both R code and compiled C/C++/FORTRAN code.") (propagated-inputs (list r-cpp11)) (inputs - `(("fontconfig" ,fontconfig) - ("zlib" ,zlib))) + (list fontconfig zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/systemfonts") @@ -22075,8 +22071,7 @@ currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (properties `((upstream-name . "readbitmap"))) (build-system r-build-system) (inputs - `(("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng))) + (list libjpeg-turbo libpng)) (propagated-inputs (list r-bmp r-jpeg r-png r-tiff)) (home-page "https://github.com/jefferis/readbitmap") @@ -24795,8 +24790,7 @@ subpopulation type designs.") (properties `((upstream-name . "nbconvertR"))) (build-system r-build-system) (inputs - `(("jupyter" ,python-nbconvert) - ("pandoc" ,pandoc))) + (list python-nbconvert pandoc)) (home-page "https://cran.r-project.org/web/packages/nbconvertR/") (synopsis "Vignette engine wrapping Jupyter notebooks") (description @@ -28692,11 +28686,7 @@ the font tool-set provided by the @code{systemfonts} package.") (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("zlib" ,zlib))) + (list freetype libjpeg-turbo libpng libtiff zlib)) (propagated-inputs (list r-systemfonts r-textshaping)) (native-inputs diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 0f766e1738..00e26e4839 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -185,14 +185,14 @@ "4store-fix-buildsystem.patch")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl) - ("python" ,python-2) - ("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("libtool" ,libtool) - ("pcre" ,pcre "bin") ;for 'pcre-config' - ("pkg-config" ,pkg-config))) + (list perl + python-2 + autoconf + automake + gettext-minimal + libtool + `(,pcre "bin") ;for 'pcre-config' + pkg-config)) (inputs (list glib rasqal diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm index 66cb8e2fab..b01ef87945 100644 --- a/gnu/packages/debian.scm +++ b/gnu/packages/debian.scm @@ -281,10 +281,7 @@ unpacking them into a directory which can eventually be chrooted into.") "1sbdjcb44g2s1zxjf9kxrp9drf9mmh6b49a9z3k428gmc6zsci4r")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("po4a" ,po4a))) + (list autoconf automake gettext-minimal po4a)) (home-page "https://packages.debian.org/unstable/debianutils") (synopsis "Miscellaneous shell utilities") (description diff --git a/gnu/packages/documentation.scm b/gnu/packages/documentation.scm index c1a8c43363..6a0d8e8f2e 100644 --- a/gnu/packages/documentation.scm +++ b/gnu/packages/documentation.scm @@ -246,8 +246,7 @@ and to some extent D.") "doc++-segfault-fix.patch")))) (build-system gnu-build-system) (native-inputs - `(("flex" ,flex) - ("gettext" ,gettext-minimal))) + (list flex gettext-minimal)) (home-page "http://docpp.sourceforge.net/") (synopsis "Documentation system for C, C++, IDL, and Java") (description diff --git a/gnu/packages/easyrpg.scm b/gnu/packages/easyrpg.scm index 007e7ce5bc..e4a1e2fb42 100644 --- a/gnu/packages/easyrpg.scm +++ b/gnu/packages/easyrpg.scm @@ -54,8 +54,7 @@ (list pkg-config)) (propagated-inputs ;; Required by 'liblcf.pc'. - `(("expat" ,expat) - ("icu" ,icu4c))) + (list expat icu4c)) (home-page "https://easyrpg.org/") (synopsis "Library to handle RPG Maker 2000 and 2003 game data") (description diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 8d08355694..b0b079a1cd 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -771,8 +771,8 @@ adjust the level of difficulty.") (base32 "0dz63m9p4ggzw0yb309qmgnl664qb5q268vaa3i9v0i8qsl66d78")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) ; for msgfmt - ("pkg-config" ,pkg-config))) + (list gettext-minimal ; for msgfmt + pkg-config)) (inputs (list libxml2 gtk+)) (home-page "https://kanatest.sourceforge.io/") diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 70a72e8df3..0ba7fb8077 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -335,8 +335,7 @@ a generic Scheme interaction mode for the GNU Emacs editor.") (file-name (git-file-name name version)))) (build-system emacs-build-system) (propagated-inputs - `(("geiser" ,emacs-geiser) - ("auto-complete" ,emacs-auto-complete))) + (list emacs-geiser emacs-auto-complete)) (synopsis "Auto-complete backend for geiser") (description "This package provides an auto-complete source for Scheme projects @@ -868,10 +867,8 @@ rebasing, and other common Git operations.") (base32 "1v1y4fir1plz4kj0cvkcd29wibli4dw7vp4fmbxq4df76d8iy8yd")))) (build-system emacs-build-system) - (propagated-inputs `(("dash" ,emacs-dash) - ("with-editor" ,emacs-with-editor) - ("magit" ,emacs-magit) - ("transient" ,emacs-transient))) + (propagated-inputs (list emacs-dash emacs-with-editor emacs-magit + emacs-transient)) (home-page "https://github.com/magit/magit-svn") (synopsis "Git-SVN extension to Magit") (description @@ -927,8 +924,7 @@ process, passing on the arguments as command line arguments.") (base32 "1amr2c08mq1nnn6k66mgz4rzyni4np7gxm96g4qyla2cbfbachgk")))) (build-system emacs-build-system) (propagated-inputs - `(("magit" ,emacs-magit) - ("transient" ,emacs-transient))) + (list emacs-magit emacs-transient)) (home-page "https://github.com/magit/magit-annex/") (synopsis "Git-annex support for Magit") (description @@ -2252,7 +2248,7 @@ light user interface.") "0q80f0plch6k4lhs8c9qm3mfycfbp3kn5sjrk9zxgxwnn901y9mp")))) (build-system emacs-build-system) (propagated-inputs - `(("emms" ,emacs-emms))) + (list emacs-emms)) (home-page "https://github.com/momomo5717/emms-mode-line-cycle") (synopsis "Display the EMMS mode line as a ticker") (description @@ -3499,7 +3495,7 @@ restore the saved place.") "0sszdl4kvqbihdh8d7mybpp0d8yw2p3gyiipjcxz9xhvvmw3ww4x")))) (build-system emacs-build-system) (propagated-inputs - `(("dash" ,emacs-dash))) + (list emacs-dash)) (home-page "https://notabug.org/alezost/emacs-bui") (synopsis "Buffer interface library for Emacs") (description @@ -3583,8 +3579,7 @@ management tasks from Emacs. To begin with, run @code{M-x guix-about} or "0i0bwbav5861j2y15j9nd5m9rdqg9q97zgcbld8pivr9nyxy63lz")))) (build-system emacs-build-system) (propagated-inputs - `(("bui" ,emacs-bui) - ("magit-popup" ,emacs-magit-popup))) + (list emacs-bui emacs-magit-popup)) (home-page "https://notabug.org/alezost/emacs-build-farm") (synopsis "Emacs interface for Hydra and Cuirass build farms") (description @@ -6351,9 +6346,7 @@ with Irony mode using Clang tooling.") (base32 "0qa5a8wzvzxwqql92ibc9s43k8sj3vwn7skz9hfr8av0skkhx996")))) (build-system emacs-build-system) (inputs - `(("irony-mode" ,emacs-irony-mode) - ("flycheck-mode" ,emacs-flycheck) - ("emacs-company" ,emacs-company))) + (list emacs-irony-mode emacs-flycheck emacs-company)) (synopsis "Live syntax checking frontend for Flycheck using irony-mode") (description "This package provides a frontend for Flycheck that lets irony-mode do the syntax checking.") @@ -6375,7 +6368,7 @@ irony-mode do the syntax checking.") (base32 "1l5qpr66v1l12fb50yh73grb2rr85xxmbj19mm33b5rdrq2bqmmd")))) (build-system emacs-build-system) (inputs - `(("irony-mode" ,emacs-irony-mode))) + (list emacs-irony-mode)) (synopsis "Eldoc integration for irony-mode") (description "Irony-eldoc is an eldoc extension that shows documentation for the current function or variable in the minibuffer.") @@ -14897,7 +14890,7 @@ additions: (base32 "090dqaqyjmkzrz4szjpk1iip0bdvb0frp4l79393f8ki8w7c16c1")))) (build-system emacs-build-system) (propagated-inputs - `(("emacs-dired-subtree" ,emacs-dired-hacks))) + (list emacs-dired-hacks)) (synopsis "Sidebar for Emacs using Dired") (description "This package provides a sidebar for Emacs similar to @code{NeoTree} @@ -19350,7 +19343,7 @@ Emacs.") (base32 "07r5x256k1fjjxs1yfg41kc94nwvnjlk2vvknkra3j8v9p0j88m7")))) (propagated-inputs - `(("magit" ,emacs-magit))) + (list emacs-magit)) (build-system emacs-build-system) (home-page "https://github.com/danielma/magit-org-todos.el") (synopsis "Get todo.org into Emacs Magit status") @@ -21903,13 +21896,13 @@ buffers – other modes on the TODO list). "12ay02vk6bk77k33mhlqi41m03a77y80b15rj1dbh1n6jfrjwkfy")))) (build-system emacs-build-system) (propagated-inputs - `(("emacs-async" ,emacs-async) - ("emacs-dash" ,emacs-dash) - ("emacs-f" ,emacs-f) - ("emacs-hl-todo" ,emacs-hl-todo) - ("magit" ,emacs-magit) - ("emacs-pcre2el" ,emacs-pcre2el) - ("emacs-s" ,emacs-s))) + (list emacs-async + emacs-dash + emacs-f + emacs-hl-todo + emacs-magit + emacs-pcre2el + emacs-s)) (home-page "https://github.com/alphapapa/magit-todos") (synopsis "Show source files' TODOs (and FIXMEs, etc) in Magit status buffer") (description "This package displays keyword entries from source code @@ -22363,9 +22356,7 @@ themes comes with the package.") "1q8r95zfrh0vxna5ml2pq9b9f66clfqcl4d2qy2aizkvzyxg6skl")))) (build-system emacs-build-system) (propagated-inputs - `(("dash" ,emacs-dash) - ("powerline" ,emacs-powerline) - ("s" ,emacs-s))) + (list emacs-dash emacs-powerline emacs-s)) (home-page "https://github.com/TheBB/spaceline") (synopsis "Powerline theme from Spacemacs") (description "Spaceline provides Spacemacs' mode-line theme. @@ -22571,18 +22562,18 @@ Emacs.") "1scfv1502yg7x4bsl253cpr6plml1j4d437vci2ggs764sh3rcqq")))) (build-system emacs-build-system) (propagated-inputs - `(("a" ,emacs-a) - ("anaphora" ,emacs-anaphora) - ("dash" ,emacs-dash) - ("esxml" ,emacs-esxml) - ("f" ,emacs-f) - ("frame-purpose" ,emacs-frame-purpose) - ("ht" ,emacs-ht) - ("ov" ,emacs-ov) - ("rainbow-identifiers" ,emacs-rainbow-identifiers) - ("request" ,emacs-request) - ("s" ,emacs-s) - ("tracking" ,emacs-tracking))) + (list emacs-a + emacs-anaphora + emacs-dash + emacs-esxml + emacs-f + emacs-frame-purpose + emacs-ht + emacs-ov + emacs-rainbow-identifiers + emacs-request + emacs-s + emacs-tracking)) (home-page "https://github.com/jgkamat/matrix-client-el") (synopsis "Matrix client for Emacs") (description "@code{matrix-client} is a simple chat UI to Matrix.org @@ -22751,7 +22742,7 @@ not have any relation with variables defined by @code{defvar}, (file-name (git-file-name name version)))) (build-system emacs-build-system) (inputs - `(("dash" ,emacs-dash))) + (list emacs-dash)) (synopsis "Purpose-specific frames for Emacs") (description "@code{frame-purpose} makes it easy to open purpose-specific frames that only show certain buffers, e.g. by buffers’ major mode, their @@ -23371,11 +23362,9 @@ convenient to edit foreign files.") "0jgiawdnzjlrpx2j1y6djwbqncdpmyfd31q1qf1890049y8ppxnb")))) (build-system emacs-build-system) (native-inputs - `(("emacs-el-mock" ,emacs-el-mock) - ("ert-runner" ,emacs-ert-runner))) + (list emacs-el-mock emacs-ert-runner)) (propagated-inputs - `(("emacs-f" ,emacs-f) - ("magit" ,emacs-magit))) + (list emacs-f emacs-magit)) (home-page "https://github.com/canatella/repo-el") (synopsis "Emacs interface for the Google Repo tool") (description "This package provides integration of the Google Repo tool @@ -25432,7 +25421,7 @@ C-f} to advance by #xa4 characters. "148a5xsnbsiddhf9cl7yxdk41lrv38h0pip91kcflw9d7l0dp7pr")))) (build-system emacs-build-system) (inputs - `(("helm" ,emacs-helm))) + (list emacs-helm)) (synopsis "Search suggestions and article extracts from Wikipedia for Emacs") (description "This package provides an Emacs Helm interface for search suggestions @@ -26205,8 +26194,7 @@ Helm and Ivy.") "1sqsm5sv311xfdk4f4rsnvprdf2v2vm7l1b3vqi7pc0g8adlnw1d")))) (build-system emacs-build-system) (propagated-inputs - `(("emms" ,emacs-emms) - ("emacs-org" ,emacs-org))) + (list emacs-emms emacs-org)) (home-page "https://gitlab.com/jagrg/org-emms") (synopsis "Play multimedia files from org-mode") (description @@ -26327,7 +26315,7 @@ keybindings for skipping from host section to host section.") "1i3zmsn0w2k7p2hlzssibckm32kf05l56mkhg96x4sf06g3pwq1d")))) (build-system emacs-build-system) (propagated-inputs - `(("dash" ,emacs-dash))) + (list emacs-dash)) (home-page "https://github.com/magit/ssh-agency") (synopsis "Manage @code{ssh-agent} from Emacs") (description @@ -26755,8 +26743,7 @@ Google guidelines.") (base32 "1j2vfngq3512naaayv9kx0d1q2zg1xgs69l8afc7swg72h0l0imw")))) (build-system emacs-build-system) (propagated-inputs - `(("helm" ,emacs-helm) - ("fish-completion" ,emacs-fish-completion))) + (list emacs-helm emacs-fish-completion)) (synopsis "Helm interface for Emacs fish-completion") (description "Helm Fish Completion is a Helm interface for Emacs fish-completion. It can be used in both Eshell and M-x shell.") @@ -26778,7 +26765,7 @@ fish-completion. It can be used in both Eshell and M-x shell.") (base32 "0n8qa549c5syvgqw1h2zrakjjbygddpxzaifaq5irscgdcajrads")))) (build-system emacs-build-system) (propagated-inputs - `(("helm" ,emacs-helm))) + (list emacs-helm)) (synopsis "Helm action to switch directory in Emacs REPLs") (description "Helm \"Switch-to-REPL\" offers the @code{helm-switch-to-repl} action, a generalized and extensible version of @@ -29030,8 +29017,7 @@ included with Emacs.") (base32 "1qi092mw2n08v6yr0j6hlpx0pnlcnhxjqbsrlw9pn4yin6zk91yp")))) (build-system emacs-build-system) (propagated-inputs - `(("dash" ,emacs-dash) - ("s" ,emacs-s))) + (list emacs-dash emacs-s)) (home-page "https://github.com/plexus/html-to-hiccup") (synopsis "Turn HTML into Hiccup syntax") (description @@ -29113,8 +29099,7 @@ faithfully. See @url{https://github.com/then/promise}. (base32 "0aav9qdswnw7ynqlzn0sm34as5fj2d85syxgg8zjabzp6646ay29")))) (build-system emacs-build-system) (propagated-inputs - `(("promise" ,emacs-promise) - ("iter2" ,emacs-iter2))) + (list emacs-promise emacs-iter2)) (home-page "https://github.com/chuntaro/emacs-async-await") (synopsis "Async/Await for Emacs") (description "This is a simple implementation of Async/Await inspired by @@ -29138,8 +29123,7 @@ the TypeScript implementation.") (base32 "02a4j0yy7330kfr3rd3k2agdj01ii6989nki598anbamq6xvj5ql")))) (build-system emacs-build-system) (propagated-inputs - `(("async-await" ,emacs-async-await) - ("request" ,emacs-request))) + (list emacs-async-await emacs-request)) (home-page "https://github.com/4hiziri/rocket-chat") (synopsis "Emacs Rocket.chat client") (description "This package provides an Emacs client for the Rocket.chat @@ -29712,8 +29696,7 @@ Unlike Emacs' generic ASM mode, it understands NASM-specific syntax.") "1q30cbqq0h1gfwlcbnx9s930li7w7a0y8sx2ivbvvyyc2j5gsk4j")))) (build-system emacs-build-system) (propagated-inputs - `(("emacs-async" ,emacs-async) - ("ht" ,emacs-ht))) + (list emacs-async emacs-ht)) (synopsis "Testeable Emacs Lisp API that wraps around GNU Global") (description "This package provides a testeable Emacs Lisp API that wraps GNU Global calls and integration to editor using this API with diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm index 62d6e90ed4..4b31c3131b 100644 --- a/gnu/packages/enchant.scm +++ b/gnu/packages/enchant.scm @@ -58,12 +58,12 @@ (base32 "0wbb6dwmzlsyy224y0liis0azgzwbjdvcyzc31pw1aw6vbp36na6")))) (build-system cmake-build-system) (native-inputs - `(("catch" ,catch-framework2) - ("git" ,git-minimal) - ("perl" ,perl) - ;;FIX-ME: Building with ronn fails. - ;;("ronn" ,ronn) - ("pkg-config" ,pkg-config))) + (list catch-framework2 + git-minimal + perl + ;;FIX-ME: Building with ronn fails. + ;;("ronn" ,ronn) + pkg-config)) (inputs (list boost)) (propagated-inputs diff --git a/gnu/packages/esolangs.scm b/gnu/packages/esolangs.scm index d38d0bb75c..c37df58fe8 100644 --- a/gnu/packages/esolangs.scm +++ b/gnu/packages/esolangs.scm @@ -77,7 +77,7 @@ identified by unique ID codes).") (inputs (list readline)) (native-inputs - `(("python-2" ,python-2))) ; for the tests + (list python-2)) ; for the tests (synopsis "LOLCODE interpreter written in C") (description "@code{lci} is a LOLCODE interpreter written in C and is designed to be diff --git a/gnu/packages/fcitx5.scm b/gnu/packages/fcitx5.scm index 4bcb88dd59..d7d0c5874b 100644 --- a/gnu/packages/fcitx5.scm +++ b/gnu/packages/fcitx5.scm @@ -154,10 +154,7 @@ client.") (base32 "0f3raxzkq0nwdfpc9hxvg65vga09gznjjgy9dr6jlkamzx8zlyw9")))) (build-system cmake-build-system) (inputs - `(("fcitx5" ,fcitx5) - ("lua" ,lua) - ("gettext" ,gettext-minimal) - ("libpthread-stubs" ,libpthread-stubs))) + (list fcitx5 lua gettext-minimal libpthread-stubs)) (native-inputs (list extra-cmake-modules)) (home-page "https://github.com/fcitx/fcitx5-lua") diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 3c61e64394..696391256d 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -354,15 +354,15 @@ ones.") (native-inputs (list autoconf automake pkg-config)) (inputs - `(("bzip2" ,bzip2) - ("e2fsprogs" ,e2fsprogs) - ("libgcrypt" ,libgcrypt) - ("lz4" ,lz4) - ("lzo" ,lzo) - ("util-linux" ,util-linux "lib") - ("xz" ,xz) - ("zlib" ,zlib) - ("zstd:lib" ,zstd "lib"))) + (list bzip2 + e2fsprogs + libgcrypt + lz4 + lzo + `(,util-linux "lib") + xz + zlib + `(,zstd "lib"))) (synopsis "File system back-up, deployment, and migration tool") (description "FSArchiver saves the contents of a file system to a compressed archive diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 15bf56bd73..8d802d9511 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1835,14 +1835,10 @@ editing on the Web.") (base32 "1zd0pfiphnijh1l94swb3mjrpmjsn37z11mklamd7zw6h2d4zh4d")))) (build-system gnu-build-system) (inputs - `(("gsl" ,gsl) - ("gtk3" ,gtk+) - ("ncurses" ,ncurses))) + (list gsl gtk+ ncurses)) (native-inputs - `(("pkg-config" ,pkg-config) - ("texinfo" ,texinfo) - ("texlive" ,(texlive-updmap.cfg (list texlive-epsf - texlive-tex-texinfo))))) + (list pkg-config texinfo + (texlive-updmap.cfg (list texlive-epsf texlive-tex-texinfo)))) (home-page "https://anthonybradford.github.io/optionmatrix/") (synopsis "Financial derivative calculator") (description diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm index a01fa8d43b..764fc9b422 100644 --- a/gnu/packages/flashing-tools.scm +++ b/gnu/packages/flashing-tools.scm @@ -152,9 +152,7 @@ brick your device.") (base32 "15m1w1qad3dj7r8n5ng1qqcaiyx1gyd6hnc3p2apgjllccdp77qg")))) (build-system gnu-build-system) (inputs - `(("libelf" ,libelf) - ("libusb" ,libusb-compat) - ("libftdi" ,libftdi))) + (list libelf libusb-compat libftdi)) (native-inputs (list bison flex)) (home-page "https://www.nongnu.org/avrdude/") diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 6796bc2bad..7d95d419cb 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -849,12 +849,12 @@ maintain the Noto Fonts project.") (list check gcc-10 ;TODO: Remove when the default compiler is > GCC 7. pkg-config scdoc)) (propagated-inputs - `(;; Required by fcft.pc. - ("fontconfig" ,fontconfig) - ("freetype" ,freetype) - ("harfbuzz" ,harfbuzz) - ("pixman" ,pixman) - ("tllist" ,tllist))) + (list ;; Required by fcft.pc. + fontconfig + freetype + harfbuzz + pixman + tllist)) (synopsis "Font loading and glyph rasterization library") (description "@code{fcft} is a small font loading and glyph rasterization library @@ -995,9 +995,7 @@ Unicode Charts. It was developed for use with DejaVu Fonts project.") (base32 "1shcs5l27l7380dvacvhl8wrdq3lix0wnhzvfdh7vx2pkzjs3zk6")))) (build-system meson-build-system) (native-inputs - `(("gtk-doc" ,gtk-doc/stable) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper))) + (list gtk-doc/stable pkg-config python-wrapper)) (inputs (list freetype fribidi harfbuzz)) (home-page "https://github.com/HOST-Oman/libraqm") diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 7230b36ab7..0e403ec871 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1256,7 +1256,7 @@ formats.") (native-inputs (list pkg-config)) (inputs - `(("udev" ,eudev))) + (list eudev)) (home-page "http://0pointer.de/blog/projects/being-smart.html") (synopsis "ATA S.M.A.R.T. reading and parsing library") (description @@ -1436,9 +1436,8 @@ these interfaces, based on the useradd, usermod and userdel commands.") "16q550sy84izi5ic3sbbhjnnka2fwhj8vvdrirpn9xspbsgbc3sm")))) (build-system gnu-build-system) (native-inputs - `(("glib:bin" ,glib "bin") ; for glib-mkenums - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper))) + (list `(,glib "bin") ; for glib-mkenums + pkg-config python-wrapper)) (propagated-inputs (list glib)) ; required by mbim-glib.pc (inputs @@ -1469,9 +1468,8 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.") (inputs (list libgudev)) (native-inputs - `(("glib:bin" ,glib "bin") ; for glib-mkenums - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper))) + (list `(,glib "bin") ; for glib-mkenums + pkg-config python-wrapper)) (propagated-inputs (list glib)) ; required by qmi-glib.pc (synopsis "Library to communicate with QMI-powered modems") @@ -1577,9 +1575,7 @@ different sorts of messages in different formats.") (native-inputs (list autoconf automake libtool pkg-config)) (inputs - `(("xsltproc" ,libxslt) - ("python" ,python-2) - ("python-dbus" ,python2-dbus))) + (list libxslt python-2 python2-dbus)) (propagated-inputs (list telepathy-glib)) (home-page "https://telepathy.freedesktop.org/") @@ -1604,14 +1600,10 @@ messaging clients such as Empathy, GNOME Shell or KDE Telepathy.") (base32 "00xxv38cfdirnfvgyd56m60j0nkmsv5fz6p2ydyzsychicxl6ssc")))) (build-system gnu-build-system) (native-inputs - `(("glib:bin" ,glib "bin") ; for glib-compile-schemas, etc. - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") ; for glib-compile-schemas, etc. + pkg-config)) (inputs - `(("dconf" ,dconf) - ("gtk-doc" ,gtk-doc) - ("libgnome-keyring" ,libgnome-keyring) - ("python" ,python-2) - ("xsltproc" ,libxslt))) + (list dconf gtk-doc libgnome-keyring python-2 libxslt)) (propagated-inputs (list telepathy-glib)) (home-page "https://telepathy.freedesktop.org/wiki/Components/Mission_Control/") diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index cd172cfbfa..ee28d85602 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -161,9 +161,7 @@ FTP browser, as well as non-interactive commands such as @code{ncftpput} and "1ir761hjncr1bamaqcw9j7x57xi3s9jax3223bxwbq30a0vsw1pd")))) (build-system gnu-build-system) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf) - ("gettext" ,gettext-minimal))) + (list automake autoconf gettext-minimal)) (home-page "http://weex.sourceforge.net/") (synopsis "Non-interactive client for FTP synchronization") (description diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index dac6da3dba..19d5e71506 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -1098,10 +1098,7 @@ It offers the following features: "08ddhywdy2qg17m592ng3yr0p1ih96irg8wg729g75hsxxq9ipks")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) - (inputs `(("fontconfig" ,fontconfig) - ("freeglute" ,freeglut) - ("fribidi" ,fribidi) - ("glew" ,glew))) + (inputs (list fontconfig freeglut fribidi glew)) (home-page "http://quesoglc.sourceforge.net") (synopsis "Implementation of the OpenGL Character Renderer (GLC)") (description diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 26c93c3399..1c3cea8828 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5265,10 +5265,8 @@ in strikes against the evil corporation.") "0jk2w5b6s6nkzri585bbz16cif2fhqcnl5l1mq3rd98r9nil3hd1")))) (build-system gnu-build-system) (native-inputs (list pkg-config)) - (inputs `(("gettext" ,gettext-minimal) - ("glu" ,glu) - ("quesoglc" ,quesoglc) - ("sdl-union" ,(sdl-union (list sdl sdl-image sdl-mixer))))) + (inputs (list gettext-minimal glu quesoglc + (sdl-union (list sdl sdl-image sdl-mixer)))) (home-page "http://chromium-bsu.sourceforge.net/") (synopsis "Fast-paced, arcade-style, top-scrolling space shooter") (description @@ -7087,10 +7085,7 @@ making Yamagi Quake II one of the most solid Quake II implementations available. (base32 "12v00z3p0ymi8f3w4b4bgl4c76irawn3kmd147r0ap6s9ssx2q6m")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list autoconf automake gettext-minimal pkg-config)) (inputs (list ncurses)) (home-page "https://jubalh.github.io/nudoku/") @@ -10190,21 +10185,21 @@ can be downloaded from @url{https://zero.sjeng.org/best-network}.") (native-inputs (list extra-cmake-modules kdoctools perl)) (inputs - `(("kcompletion" ,kcompletion) - ("kconfigwidgets" ,kconfigwidgets) - ("kcoreaddons" ,kcoreaddons) - ("kcrash" ,kcrash) - ("kdbusaddons" ,kdbusaddons) - ("ki18n" ,ki18n) - ("kio" ,kio) - ("kwidgetsaddons" ,kwidgetsaddons) - ("kxmlgui" ,kxmlgui) - ("libkdegames" ,libkdegames) - ("python" ,python-wrapper) - ("qtbase" ,qtbase-5) - ("qtmultimedia" ,qtmultimedia) - ("qtdeclarative" ,qtdeclarative) - ("qtsvg" ,qtsvg))) + (list kcompletion + kconfigwidgets + kcoreaddons + kcrash + kdbusaddons + ki18n + kio + kwidgetsaddons + kxmlgui + libkdegames + python-wrapper + qtbase-5 + qtmultimedia + qtdeclarative + qtsvg)) (home-page "https://games.kde.org/") (synopsis "Stamp drawing toy") (description "KTuberling is a drawing toy intended for small children and @@ -10983,16 +10978,16 @@ This package is part of the KDE games module.") (native-inputs (list extra-cmake-modules kdoctools)) (inputs - `(("kcompletiom" ,kcompletion) - ("kconfig" ,kconfig) - ("kcoreaddons" ,kcoreaddons) - ("kcrash" ,kcrash) - ("kdbusaddons" ,kdbusaddons) - ("ki18n" ,ki18n) - ("kxmlgui" ,kxmlgui) - ("libkdegames" ,libkdegames) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative))) + (list kcompletion + kconfig + kcoreaddons + kcrash + kdbusaddons + ki18n + kxmlgui + libkdegames + qtbase-5 + qtdeclarative)) (home-page "https://games.kde.org/") (synopsis "Arcade bombing game") (description "Bomber is a single player arcade game. @@ -12005,8 +12000,7 @@ protect you.") (base32 "1y7v0jhp3apb619p7asikqr1dnwb2yxbh40wbx1ppmr5f03mq9ph")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list gettext-minimal pkg-config)) (inputs (list curl enet openal sdl2)) (home-page "https://7kfans.com/") diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index d63a3aaf4c..5fb0f633a3 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1315,11 +1315,7 @@ OpenStreetMap data files.") (native-inputs (list gnome-common gtk-doc/stable pkg-config)) (inputs - `(("cairo" ,cairo) - ("glib" ,glib) - ("gobject-introspection" ,gobject-introspection) - ("gtk+" ,gtk+) - ("libsoup" ,libsoup-minimal-2))) + (list cairo glib gobject-introspection gtk+ libsoup-minimal-2)) (home-page "https://nzjrs.github.io/osm-gps-map/") (synopsis "GTK+ widget for displaying OpenStreetMap tiles") (description diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index f6f6fef32d..a18bffac55 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -1295,16 +1295,14 @@ simple methods via GObject-Introspection.") "03sj1h0c2l08xa8phw013fnxr4fgav7l2mkjhzf9xk3dykwxcj8p")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - - ;; For tests. - ("dbus" ,dbus) - - ;; These are required to build the manual. - ("docbook-xml" ,docbook-xml-4.3) - ("docbook-xsl" ,docbook-xsl) - ("libxml2" ,libxml2) - ("xsltproc" ,libxslt))) + (list pkg-config + ;; For tests. + dbus + ;; These are required to build the manual. + docbook-xml-4.3 + docbook-xsl + libxml2 + libxslt)) (inputs (list glib)) (home-page "https://github.com/flatpak/xdg-dbus-proxy") diff --git a/gnu/packages/gnome-xyz.scm b/gnu/packages/gnome-xyz.scm index d7c67f183d..afe9a96b91 100644 --- a/gnu/packages/gnome-xyz.scm +++ b/gnu/packages/gnome-xyz.scm @@ -686,12 +686,12 @@ like GNOME, Unity, Budgie, Pantheon, XFCE, Mate, etc.") "154qawiga792iimkpk3a6q8f4gm4r158wmsagkbqqbhj33kxgxhg")))) (build-system meson-build-system) (native-inputs - `(("gtk+" ,gtk+) - ("glib:bin" ,glib "bin") ; for "glib-compile-resources" - ("librsvg" ,librsvg) - ("pkg-config" ,pkg-config) - ("ruby-sass" ,ruby-sass) - ("sassc" ,sassc))) + (list gtk+ + `(,glib "bin") ; for "glib-compile-resources" + librsvg + pkg-config + ruby-sass + sassc)) (home-page "https://shimmerproject.org/") (synopsis "Grey GTK+ theme based on Bluebird") (description "Greybird is a grey derivative of the Bluebird theme by the diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index e5fde29f08..5f46eb4d63 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1127,9 +1127,7 @@ tickets, and pops up a dialog when they are about to expire.") (native-inputs (list intltool pkg-config)) (inputs - `(("glib" ,glib) - ("gtk+" ,gtk+) - ("x11" ,libx11))) + (list glib gtk+ libx11)) (synopsis "Notification Daemon for GNOME Desktop") (description "Notification-Daemon is the server implementation of the freedesktop.org desktop notification specification.") @@ -1410,13 +1408,13 @@ for creating UPnP devices and control points, written in C using "0spzd2saax7w776p5laixdam6d7smyynr9qszhbmq7f14y13cghj")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("libxml" ,libxml2) - ("pkg-config" ,pkg-config) - ("vala" ,vala))) + (list gettext-minimal + `(,glib "bin") + gobject-introspection + gtk-doc/stable + libxml2 + pkg-config + vala)) (inputs (list gstreamer gupnp)) (propagated-inputs @@ -1442,13 +1440,13 @@ given profile, etc. DLNA is a subset of UPnP A/V.") "1p3grslwqm9bc8rmpn4l48d7v9s84nina4r9xbd932dbj8acz7b8")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("libxml" ,libxml2) - ("pkg-config" ,pkg-config) - ("vala" ,vala))) + (list gettext-minimal + `(,glib "bin") + gobject-introspection + gtk-doc/stable + libxml2 + pkg-config + vala)) (inputs (list gtk+ gupnp)) (synopsis "GUPnP A/V for GNOME") @@ -1471,14 +1469,10 @@ and implementation of UPnP A/V profiles.") "1mlw1qgj8nkd9ll6b6h54r1gfdy3zp8a8xqz7qfyfaj85jjgbph7")))) (build-system meson-build-system) (native-inputs - `(("glib:bin" ,glib "bin") - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") pkg-config)) (inputs - `(("gdk-pixbuf" ,gdk-pixbuf) - ("gettext" ,gettext-minimal) - ("gobject-introspection" ,gobject-introspection) - ("gtk+:doc" ,gtk+ "doc") - ("vala" ,vala))) + (list gdk-pixbuf gettext-minimal gobject-introspection + `(,gtk+ "doc") vala)) (synopsis "Media art library for the GNOME desktop") (description "The libmediaart library is the foundation for media art caching, @@ -1766,9 +1760,7 @@ project.") "07xvaf8s0fiv0035nk8zpzymn5www76w2a1vflrgqmp9plw8yd6r")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("glib" ,glib) - ("pkg-config" ,pkg-config))) + (list gettext-minimal glib pkg-config)) (synopsis "Menu support for GNOME desktop") (description "GNOME Menus contains the libgnome-menu library, the layout configuration files for the GNOME menu, as well as a simple menu editor.") @@ -1874,15 +1866,15 @@ either on a local, or remote machine via a number of methods.") (base32 "0f7l2pkyh3r1qk4hhavl7387l3bq5my3snpdppiavcpnji28dpa5")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) - ("gettext" ,gettext-minimal) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("googletest" ,googletest) - ("intltool" ,intltool) - ("itstool" ,itstool) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list desktop-file-utils + gettext-minimal + `(,glib "bin") + gobject-introspection + googletest + intltool + itstool + libtool + pkg-config)) (inputs (list gconf gnome-vfs gtk+-2 libxml2)) (home-page "https://gcmd.github.io/") @@ -1908,10 +1900,7 @@ and running smart commands.") (base32 "0p6ysdqlfc7vvzsrcanl9bhsc7666sv42xxzpbgsf5j55z3yrkpr")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config) - ("xmllint" ,libxml2))) + (list gettext-minimal itstool pkg-config libxml2)) (synopsis "User documentation for the GNOME desktop") (description "The GNOME User Documentation explains how to use the GNOME desktop and its @@ -1941,14 +1930,14 @@ and system administrators.") "04r8dspa6nmicrifhi3sh46hqvyy88hzq37xx99q3q1mwsrpmwy8")))) (build-system meson-build-system) (inputs - `(("graphene" ,graphene) - ("gtk+" ,gtk+-2) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ("poppler" ,poppler) - ;; Without Python 2, build fails: plug-ins/python/meson.build:4:0: - ;; ERROR: Unknown method "dependency" in object. - ("python-2" ,python-2))) + (list graphene + gtk+-2 + libxml2 + libxslt + poppler + ;; Without Python 2, build fails: plug-ins/python/meson.build:4:0: + ;; ERROR: Unknown method "dependency" in object. + python-2)) (native-inputs (list appstream-glib docbook-xsl `(,glib "bin") intltool pkg-config)) @@ -2020,10 +2009,7 @@ access the common Google services, and has full asynchronous support.") (native-inputs (list gobject-introspection pkg-config)) (inputs - `(("gtk+" ,gtk+) - ("libjpeg" ,libjpeg-turbo) - ("lcms" ,lcms) - ("libtiff" ,libtiff))) + (list gtk+ libjpeg-turbo lcms libtiff)) (propagated-inputs ;; In Requires of libgxps.pc. (list cairo glib libarchive)) @@ -2257,13 +2243,13 @@ The gnome-about program helps find which version of GNOME is installed.") "19n4x25ndzngaciiyd8dd6s2mf9gv6nv3wv27ggns2smm7zkj1nb")))) (build-system gnu-build-system) (native-inputs - `(("intltool" ,intltool) - ("docbook-xml" ,docbook-xml-4.4) - ("python2-libxml2" ,python2-libxml2) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ("pkg-config" ,pkg-config) - ("python-2" ,python-2))) + (list intltool + docbook-xml-4.4 + python2-libxml2 + libxml2 + libxslt + pkg-config + python-2)) (home-page "https://wiki.gnome.org/GnomeDocUtils") (synopsis "Documentation utilities for the Gnome project") @@ -3985,8 +3971,7 @@ creating interactive structured graphics.") (build-system gnu-build-system) (propagated-inputs (list libgnomecanvas)) (native-inputs - `(("gtkmm-2" ,gtkmm-2) - ("pkg-config" ,pkg-config))) + (list gtkmm-2 pkg-config)) (home-page "https://gtkmm.org") (synopsis "C++ bindings to the GNOME Canvas library") (description "C++ bindings to the GNOME Canvas library.") @@ -4009,11 +3994,7 @@ creating interactive structured graphics.") ;; Mentioned as Required in the .pc file (propagated-inputs (list libbonoboui libgnome libgnomecanvas libgnome-keyring)) - (inputs `(("libjpeg" ,libjpeg-turbo) - ("popt" ,popt) - ("libbonobo" ,libbonobo) - ("libxml2" ,libxml2) - ("libglade" ,libglade))) + (inputs (list libjpeg-turbo popt libbonobo libxml2 libglade)) (native-inputs (list `(,glib "bin") ; for glib-mkenums, etc. intltool pkg-config)) @@ -4040,8 +4021,7 @@ ported to GTK+.") (inputs (list python)) ;; needed for the optional libglade-convert program (propagated-inputs - `(("gtk+-2" ,gtk+-2) - ("libxml2" ,libxml2))) ; required by libglade-2.0.pc + (list gtk+-2 libxml2)) ; required by libglade-2.0.pc (native-inputs (list pkg-config)) (home-page "https://developer.gnome.org/libglade") @@ -4804,9 +4784,7 @@ indicators etc).") (native-inputs (list pkg-config)) (inputs - `(("python" ,python-2) - ("python2-pygtk" ,python2-pygtk) - ("librsvg" ,librsvg))) + (list python-2 python2-pygtk librsvg)) (home-page "https://www.gnome.org") (synopsis "Python bindings to librsvg") (description @@ -5745,10 +5723,9 @@ which are easy to play with the aid of a mouse.") "12v3nj1bb7507ndprjggq0hpz8k719b4bwvl8sm43p3ibmn27anm")))) (build-system meson-build-system) (native-inputs - `(("gobject-introspection" ,gobject-introspection) - ("glib:bin" ,glib "bin") ; for glib-mkenums - ("gtk-doc" ,gtk-doc/stable) - ("pkg-config" ,pkg-config))) + (list gobject-introspection + `(,glib "bin") ; for glib-mkenums + gtk-doc/stable pkg-config)) (inputs (list glib gtk+)) (home-page "https://wiki.gnome.org/Projects/Amtk") @@ -6000,9 +5977,8 @@ presentations, kiosk style applications and so on.") (base32 "17czmpl92dzi4h3rn5rishk015yi3jwiw29zv8qan94xcmnbssgy")))) (build-system gnu-build-system) (native-inputs - `(("glib:bin" ,glib "bin") ; for glib-mkenums - ("pkg-config" ,pkg-config) - ("gobject-introspection" ,gobject-introspection))) + (list `(,glib "bin") ; for glib-mkenums + pkg-config gobject-introspection)) (inputs (list clutter gstreamer gst-plugins-base)) (home-page "http://www.clutter-project.org") @@ -6030,14 +6006,14 @@ OpenGL-based interactive canvas library.") (native-inputs (list gobject-introspection pkg-config vala)) (propagated-inputs - `(("libsoup" ,libsoup-minimal-2) - ("sqlite" ,sqlite) - ("clutter" ,clutter) - ("clutter-gtk" ,clutter-gtk) - ("glib:bin" ,glib "bin") ;glib-mkenums, etc. - ("cairo" ,cairo) - ("gtk+3" ,gtk+) - ("glib" ,glib))) + (list libsoup-minimal-2 + sqlite + clutter + clutter-gtk + `(,glib "bin") ;glib-mkenums, etc. + cairo + gtk+ + glib)) (home-page "https://projects.gnome.org/libchamplain/") (synopsis "C library providing a ClutterActor to display maps") (description @@ -6165,20 +6141,20 @@ as possible!") (base32 "0ywjvh7xw4ql1q4fvl0q5n06n08pga1g1nc9l7c3x5214gr3fj6i")))) (build-system meson-build-system) (native-inputs - `(("glib:bin" ,glib "bin") ; for glib-mkenums and glib-genmarshal - ("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("vala" ,vala))) + (list `(,glib "bin") ; for glib-mkenums and glib-genmarshal + intltool + pkg-config + gobject-introspection + gtk-doc/stable + vala)) (inputs - `(("cyrus-sasl" ,cyrus-sasl) - ("glib" ,glib) - ("gtk+" ,gtk+) - ("libxml2" ,libxml2) - ("liboauth" ,liboauth) - ("libsoup" ,libsoup-minimal-2) - ("totem-pl-parser" ,totem-pl-parser))) + (list cyrus-sasl + glib + gtk+ + libxml2 + liboauth + libsoup-minimal-2 + totem-pl-parser)) (native-search-paths (list (search-path-specification (variable "GRL_PLUGIN_PATH") @@ -6525,8 +6501,7 @@ supports image conversion, rotation, and slideshows.") (home-page "https://wiki.gnome.org/Apps/EyeOfGnome/Plugins") (synopsis "Extensions for the Eye of GNOME image viewer") (native-inputs - `(("pkg-config" ,pkg-config) - ("gettext" ,gettext-minimal))) + (list pkg-config gettext-minimal)) (inputs (list eog glib @@ -7001,10 +6976,8 @@ jQuery.Syntax JavaScript libraries.") "11shrqass8ak8m10nayqssa6sbrrxa13ffpamvqi1c0yzkxdk9r5")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("glib:bin" ,glib "bin") ; for glib-genmarshal, etc. - ("intltool" ,intltool) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") ; for glib-genmarshal, etc. + intltool itstool pkg-config)) (propagated-inputs (list dconf)) (inputs @@ -7181,12 +7154,12 @@ share them with others via social networking and more.") "039w1dcpa5ypmv6sm634alk9vbcdkyvy595vkh5gn032jsiqca2a")))) (build-system meson-build-system) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database - ("intltool" ,intltool) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config) - ("gtk+" ,gtk+ "bin") ; gtk-update-icon-cache - ("glib:bin" ,glib "bin"))) + (list desktop-file-utils ; for update-desktop-database + intltool + itstool + pkg-config + `(,gtk+ "bin") ; gtk-update-icon-cache + `(,glib "bin"))) ;; TODO: Add libnautilus. (inputs (list gtk+ @@ -7428,9 +7401,7 @@ powerful general purpose text editor.") "15fdh8xfdhnwcynyh4byx3mrjxbyprqnwxzi7qn3g5wwaqryg1p7")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config))) + (list gettext-minimal itstool pkg-config)) (inputs (list libnotify webkitgtk)) (synopsis "Display graphical dialog boxes from shell scripts") @@ -8873,9 +8844,8 @@ core C library, and bindings for Python (PyGTK).") "03hmm7cjgjvyxlflghfa89s1amj16qapl2c9pv0r2bfrp87dasv4")))) (build-system meson-build-system) (native-inputs - `(("gobject-introspection" ,gobject-introspection) - ("glib:bin" ,glib "bin") - ("pkg-config" ,pkg-config))) + (list gobject-introspection + `(,glib "bin") pkg-config)) (propagated-inputs (list libarchive)) ; Required by gnome-autoar-0.pc (inputs @@ -9339,15 +9309,15 @@ associations for GNOME.") "1y0x1wyakj3ya33hgj0w1jkbcn50q21gmn2zyalxysqp55i1ij8x")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("gtk+:bin" ,gtk+ "bin") - ("pkg-config" ,pkg-config))) + (list gettext-minimal + `(,glib "bin") + gobject-introspection + gsettings-desktop-schemas + `(,gtk+ "bin") + pkg-config)) (inputs - `(("glib-networking" ,glib-networking) ; GIO plugin--for the tests - ("librest" ,rest))) + (list glib-networking ; GIO plugin--for the tests + rest)) (synopsis "GoVirt Library") (description "GoVirt is a GObject wrapper for the oVirt REST API.") (home-page "https://gitlab.gnome.org/GNOME/libgovirt") @@ -9673,9 +9643,7 @@ library.") (native-inputs (list gobject-introspection intltool pkg-config)) (inputs - `(("gnome-online-accounts:lib" ,gnome-online-accounts "lib") - ("json-glib" ,json-glib) - ("rest" ,rest))) + (list `(,gnome-online-accounts "lib") json-glib rest)) (home-page "https://wiki.gnome.org/Projects/Zapojit") (synopsis "Library for accessing SkyDrive and Hotmail") (description @@ -10171,11 +10139,8 @@ is suitable as a default application in a Desktop environment.") "0l0g5x8g6dwhf5ksnqqrjjsycy57kcvdslkmsr6bl3vrsjd7qml3")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gtk+:bin" ,gtk+ "bin") - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list autoconf automake + `(,gtk+ "bin") intltool pkg-config)) (inputs (list gtksourceview-3 libsm)) (home-page "https://wiki.gnome.org/Apps/Xpad") @@ -10305,11 +10270,7 @@ supports both X and Wayland display servers.") (native-inputs (list desktop-file-utils intltool pkg-config)) (inputs - `(("enchant" ,enchant) - ("gtk+" ,gtk+) - ("python" ,python-wrapper) - ("xmllint" ,libxml2) - ("gucharmap" ,gucharmap))) + (list enchant gtk+ python-wrapper libxml2 gucharmap)) (home-page "http://bluefish.openoffice.nl") (synopsis "Web development studio") (description @@ -10655,8 +10616,7 @@ automatically and it can stream songs from online music services and charts.") "1j6h98whgkcxrh30bwvnxvyqxrxchgpdgqhl0j71xz7x72dqxijd")))) (build-system meson-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list gettext-minimal pkg-config)) (home-page "https://wiki.gnome.org/Projects/GnomeVideoEffects") (synopsis "Video effects for Cheese and other GNOME applications") (description @@ -10812,23 +10772,19 @@ and uncluttered interface for the management of password databases.") "19qg4xv0f9rkq34lragkmhii1llxsa87llbl28i759b0ks4f6sny")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) - ("intltool" ,intltool) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config) - ("xmllint" ,libxml2))) + (list desktop-file-utils intltool itstool pkg-config libxml2)) (inputs - `(("gtk+" ,gtk+) - ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("gstreamer" ,gstreamer) - ("gst-plugins-base" ,gst-plugins-base) - ("gst-plugins-good" ,gst-plugins-good) - ("iso-codes" ,iso-codes) - ("libbrasero-media3" ,brasero) - ("libcanberra" ,libcanberra) - ("libdiscid" ,libdiscid) - ("libmusicbrainz" ,libmusicbrainz) - ("neon" ,neon))) + (list gtk+ + gsettings-desktop-schemas + gstreamer + gst-plugins-base + gst-plugins-good + iso-codes + brasero + libcanberra + libdiscid + libmusicbrainz + neon)) (home-page "https://wiki.gnome.org/Apps/SoundJuicer") (synopsis "Audio music cd ripper") (description "Sound Juicer extracts audio from compact discs and convert it @@ -11306,12 +11262,12 @@ for usage on small and big screens.") "1pmrcnsa7qdda73c3dxf47733mwprmj5ljpw3acxbj6r8k27anp0")))) (build-system meson-build-system) (native-inputs - `(("glib:bin" ,glib "bin") ;; For glib-mkenums - ("gobject-introspection" ,gobject-introspection) - ("pkg-config" ,pkg-config) - ("python-pygobject" ,python-pygobject) - ("python-wrapper" ,python-wrapper) - ("vala" ,vala))) + (list `(,glib "bin") ;; For glib-mkenums + gobject-introspection + pkg-config + python-pygobject + python-wrapper + vala)) (inputs (list glib libssh2)) (propagated-inputs @@ -11547,23 +11503,23 @@ index files needed for Adwaita to be used outside of GNOME.") (base32 "01fqdfgcl32cf40jw9q0h7f5bghl1lvf89vln1lh41ncrk0iw6vy")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("intltool" ,intltool) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config) - ("unittest-cpp" ,unittest-cpp))) ;FIXME: not found by pkg-config + (list desktop-file-utils + `(,glib "bin") + gobject-introspection + intltool + itstool + pkg-config + unittest-cpp)) ;FIXME: not found by pkg-config (inputs - `(("glibmm" ,glibmm) - ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("gspell" ,gspell) - ("gtk+" ,gtk+) - ("gtkmm" ,gtkmm-3) - ("libsecret" ,libsecret) - ("libuuid" ,util-linux "lib") - ("libxml2" ,libxml2) - ("libxslt" ,libxslt))) + (list glibmm + gsettings-desktop-schemas + gspell + gtk+ + gtkmm-3 + libsecret + `(,util-linux "lib") + libxml2 + libxslt)) (synopsis "Note-taking application for the GNOME desktop") (description "Gnote is a note-taking application written for the GNOME desktop @@ -11843,14 +11799,14 @@ card sheets that you’ll find at most office supply stores.") (base32 "0xqd49pgi82dygqnxj08i1v22b0vwwhx3zvdinhrx4jny339yam8")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("gtk-doc" ,gtk-doc/stable) - ("intltool" ,intltool) - ("itstool" ,itstool) - ("pkg-config" ,pkg-config) - ("vala" ,vala))) + (list gettext-minimal + `(,glib "bin") + gobject-introspection + gtk-doc/stable + intltool + itstool + pkg-config + vala)) (inputs (list amtk dconf @@ -12194,10 +12150,9 @@ audio files.") (inputs (list json-glib glib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("glib:bin" ,glib "bin") ; for glib-genmarshal, etc. - ("gobject-introspection" ,gobject-introspection) - ("vala" ,vala))) + (list pkg-config + `(,glib "bin") ; for glib-genmarshal, etc. + gobject-introspection vala)) (home-page "https://gitlab.gnome.org/GNOME/jsonrpc-glib") (synopsis "JSON-RPC library for GLib") (description "Jsonrpc-GLib is a library to communicate with JSON-RPC based @@ -12222,10 +12177,7 @@ host to avoid parser overhead and memory-allocator fragmentation.") "1wbkzxnqjydfgjvp7vz4ghczcz740zcb1yn90cb6gb5md4n6qx2y")))) (build-system meson-build-system) (native-inputs - `(("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("pkg-config" ,pkg-config) - ("vala" ,vala))) + (list `(,glib "bin") gobject-introspection pkg-config vala)) (inputs (list dbus gsound json-glib libgudev)) (propagated-inputs @@ -12698,10 +12650,8 @@ successor of @code{libhandy} for GTK4.") (inputs (list upower gtk+ gsettings-desktop-schemas adwaita-icon-theme)) (native-inputs - `(("desktop-file-utils" ,desktop-file-utils) - ("glib:bin" ,glib "bin") - ("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list desktop-file-utils + `(,glib "bin") gettext-minimal pkg-config)) (home-page "https://gitlab.gnome.org/GNOME/gnome-power-manager") (synopsis "Power management daemon for the GNOME desktop") (description "@code{gnome-power-manager} is a tool for viewing present and diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index bc6b1435ec..5c0dd348cc 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -168,11 +168,7 @@ tool to extract metadata from a file and print the results.") (patches (search-patches "libmicrohttpd-0.9.73-test-ssl3.patch")))) (build-system gnu-build-system) (inputs - `(("curl" ,curl) - ("gnutls" ,gnutls/dane) - ("libgcrypt" ,libgcrypt) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list curl gnutls/dane libgcrypt openssl zlib)) (synopsis "C library implementing an HTTP 1.1 server") (description "GNU libmicrohttpd is a small, embeddable HTTP server implemented as a diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index ce3e8ce9b2..48844a1683 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -138,9 +138,7 @@ (native-inputs (list luajit pkg-config)) (inputs - `(("alsa" ,alsa-lib) - ("sdl" ,sdl) - ("sdl2" ,sdl2))) + (list alsa-lib sdl sdl2)) (synopsis "Memory Mapped Machine") (description "MMM is a shared memory protocol for virtualising access to framebuffer graphics, audio output and input event.") diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index 75f86ac7a0..143e4e868e 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -151,14 +151,14 @@ and for middleware components.") (native-inputs (list doxygen perl pkg-config)) (inputs - `(("glu" ,glu) - ("libraw1394" ,libraw1394) - ("libusb" ,libusb) - ("libxv" ,libxv) - ("linux-headers" ,linux-libre-headers) - ("mesa" ,mesa) - ("sdl" ,sdl) - ("v4l" ,v4l-utils))) + (list glu + libraw1394 + libusb + libxv + linux-libre-headers + mesa + sdl + v4l-utils)) (synopsis "1394-Based Digital Camera Control Library") (description "LibDC1394 is a library that provides functionality to control any camera that conforms to the 1394-Based Digital Camera Specification written @@ -338,14 +338,14 @@ applications that want audio visualisation and audio visualisation plugins.") (base32 "141jg70fim276i8k2kyypm84gy89i1k9mm4yf68mfwnybvjw1d6n")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("gnome-common" ,gnome-common) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("tcsh" ,tcsh) ; for the tests - ("which" ,which))) + (list autoconf + automake + gettext-minimal + gnome-common + libtool + pkg-config + tcsh ; for the tests + which)) (inputs (list alsa-lib pcaudiolib tcp-wrappers)) (propagated-inputs @@ -984,10 +984,7 @@ think twice about shipping them.") (base32 "0j55jgk9sbhinfx2gsg21q609x6yzrixrn5xxlxd378fj6500bl2")))) (build-system meson-build-system) (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper) - ("ruby" ,ruby))) + (list perl pkg-config python-wrapper ruby)) (inputs (list ffmpeg)) (propagated-inputs diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index bc2dd8d592..b5df887a51 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -1344,11 +1344,7 @@ Scheme by using Guile’s foreign function interface.") "1wx5h6wa9c0na8mrnr2nv1nzjvq68zyrly8yyp11dsskhaw4y33h")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("emacs" ,emacs-minimal) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo))) + (list autoconf automake emacs-minimal pkg-config texinfo)) (inputs (list guile-3.0 gnutls guile-json-4)) (home-page "https://framagit.org/prouby/guile-mastodon") @@ -1881,13 +1877,13 @@ users and in some situations.") "037md1sg7bgsa4478hz1dbsivsxzdnl5acadlrsh4ds2yxbsb5jp")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("libtool" ,libtool) - ("texinfo" ,texinfo) - ("pkg-config" ,pkg-config) - ("which" ,which))) + (list autoconf + automake + gettext-minimal + libtool + texinfo + pkg-config + which)) (inputs (list guile-3.0 eudev)) (home-page "https://github.com/artyom-poptsov/guile-udev") @@ -2144,8 +2140,7 @@ quotes. ") (base32 "1fyjckmygkhq22lq8nqc86yl5zzbqd7a944dnz5c1f6vx92b9hiq")))) (build-system gnu-build-system) - (native-inputs `(("pkgconfig" ,pkg-config) - ("gperf" ,gperf))) + (native-inputs (list pkg-config gperf)) (inputs (list guile-3.0)) (synopsis "Framework for building readers for GNU Guile") (description @@ -2696,8 +2691,7 @@ The picture values can directly be displayed in Geiser.") (name "guile2.2-picture-language") (inputs (list guile-2.2)) (propagated-inputs - `(("guile-cairo" ,guile2.2-cairo) - ("guile-rsvg" ,guile2.2-rsvg))))) + (list guile2.2-cairo guile2.2-rsvg)))) (define-public guile-studio (let ((commit "dd0ad42e51feafebda7cc29afe7c8bc7a182a842") @@ -3823,8 +3817,7 @@ as signed sessions, multipart message support, etc.") (inputs (list guile-2.2)) (propagated-inputs - `(("guile-irregex" ,guile2.2-irregex) - ("guile-gcrypt" ,guile2.2-gcrypt))))) + (list guile2.2-irregex guile2.2-gcrypt)))) (define-public guile-lens (let ((commit "14b15d07255f9d3f55d40a3b750d13c9ee3a154f") diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm index 10f9862ff5..7f6e858ee0 100644 --- a/gnu/packages/hardware.scm +++ b/gnu/packages/hardware.scm @@ -669,8 +669,7 @@ as the Pinebook Pro.") "008vvw504kh40br5v2xkqavnp9vpmjvf768faqzv1d00fd53ingn")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("xmllint" ,libxml2))) + (list pkg-config libxml2)) (home-page "https://clusterlabs.github.io/libqb/") (synopsis "Library providing high performance logging, tracing, ipc, and poll") (description "Libqb is a library with the primary purpose of providing diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 295c42a54c..e647d65a89 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -166,14 +166,14 @@ contains the correct result for the test.") "0574hbqzxzyv6vsk5kzbf04kz58y0iy8x9ydcj4b8fpncgmgy63g")))) (build-system haskell-build-system) (inputs - `(("ghc-tagged" ,ghc-tagged) - ("ghc-regex-tdfa" ,ghc-regex-tdfa) - ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-unbounded-delays" ,ghc-unbounded-delays) - ("ghc-async" ,ghc-async) - ("ghc-ansi-terminal" ,ghc-ansi-terminal) - ("ghc-clock-bootstrap" ,ghc-clock-bootstrap) - ("ghc-wcwidth" ,ghc-wcwidth-bootstrap))) + (list ghc-tagged + ghc-regex-tdfa + ghc-optparse-applicative + ghc-unbounded-delays + ghc-async + ghc-ansi-terminal + ghc-clock-bootstrap + ghc-wcwidth-bootstrap)) (home-page "http://documentup.com/feuerbach/tasty") (synopsis "Modern and extensible testing framework") (description "Tasty is a modern testing framework for Haskell. It lets @@ -490,8 +490,7 @@ use HUnit assertions as QuickCheck properties.") "1wrnrm9sq4s0bly0q58y80g4153q45iglqa34xsi2q3bd62nqyyq")))) (build-system haskell-build-system) (inputs - `(("ghc-random" ,ghc-random) - ("ghc-splitmix" ,ghc-splitmix-bootstrap))) + (list ghc-random ghc-splitmix-bootstrap)) (home-page "https://github.com/nick8325/quickcheck") (synopsis "Automatic testing of Haskell programs") (description diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index 247110aa20..d95b87639c 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -1186,9 +1186,7 @@ Haskell data types to and from route pieces.") (base32 "1jdqdk0rz2wnvw735clnj8jh0a9rkrbqjg7vk3w6wczdql6cm0pq")))) (build-system haskell-build-system) - (inputs `(("ghc-cereal" ,ghc-cereal) - ("ghc-tagged" ,ghc-tagged) - ("ghc-crpto-api" ,ghc-crypto-api))) + (inputs (list ghc-cereal ghc-tagged ghc-crypto-api)) (native-inputs (list ghc-hspec)) (home-page "https://github.com/yesodweb/path-pieces") (synopsis "Skein family of cryptographic hash functions for Haskell") diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index e49e9d2f35..f5d15bcc2f 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -11371,10 +11371,8 @@ semigroup.") (inherit ghc-semigroups) (name "ghc-semigroups-bootstrap") (inputs - `(("ghc-nats" ,ghc-nats-bootstrap) - ("ghc-tagged" ,ghc-tagged) - ("ghc-unordered-containers" ,ghc-unordered-containers-bootstrap) - ("ghc-hashable" ,ghc-hashable-bootstrap))) + (list ghc-nats-bootstrap ghc-tagged + ghc-unordered-containers-bootstrap ghc-hashable-bootstrap)) (properties '((hidden? #t))))) (define-public ghc-serialise @@ -11824,16 +11822,16 @@ mainstream languages.") "0das5n44dhlcv5i233iakx37d17kidqvhrvp6w9nd7hc015ry026")))) (build-system haskell-build-system) (native-inputs - `(("ghc-async" ,ghc-async) - ("ghc-base-compat-batteries" ,ghc-base-compat-batteries) - ("ghc-base-compat" ,ghc-base-compat) - ("ghc-hunit" ,ghc-hunit) - ("ghc-math-functions" ,ghc-math-functions) - ("ghc-random" ,ghc-random-bootstrap) - ("ghc-test-framework" ,ghc-test-framework) - ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) - ("ghc-tf-random" ,ghc-tf-random) - ("ghc-vector" ,ghc-vector))) + (list ghc-async + ghc-base-compat-batteries + ghc-base-compat + ghc-hunit + ghc-math-functions + ghc-random-bootstrap + ghc-test-framework + ghc-test-framework-hunit + ghc-tf-random + ghc-vector)) (home-page "https://hackage.haskell.org/package/splitmix") (synopsis "Fast and splittable pseudorandom number generator") (description "This package provides a Pure Haskell implementation of the @@ -14328,9 +14326,7 @@ widths to the Char type.") (inherit ghc-wcwidth) (name "ghc-wcwidth-bootstrap") (inputs - `(("ghc-setlocale" ,ghc-setlocale) - ("ghc-utf8-string" ,ghc-utf8-string) - ("ghc-attoparsec" ,ghc-attoparsec-bootstrap))) + (list ghc-setlocale ghc-utf8-string ghc-attoparsec-bootstrap)) (properties '((hidden? #t))))) (define-public ghc-weigh diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 2248637169..93fe384aa8 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -106,13 +106,13 @@ (base32 "13j5yf3p6qj3mr17d77r3kcqchf055hgvk1w15vmdr8f54mwcnb8")))) (build-system cmake-build-system) (inputs - `(("icu4c" ,icu4c) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxml2" ,libxml2) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list icu4c + libjpeg-turbo + libpng + libtiff + libxml2 + openssl + zlib)) (native-inputs (list doxygen)) ; for HTML documentation (home-page "https://dcmtk.org") @@ -591,27 +591,27 @@ vision algorithms. It can be used to do things like: (native-inputs (list gobject-introspection pkg-config)) (inputs - `(("expat" ,expat) - ("fftw" ,fftw) - ("giflib" ,giflib) - ("glib" ,glib) - ("hdf5" ,hdf5) - ("imagemagick" ,imagemagick) - ("lcms" ,lcms) - ("libexif" ,libexif) - ("libgsf" ,libgsf) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("librsvg" ,librsvg) - ("libtiff" ,libtiff) - ("libxml2" ,libxml2) - ("libwebp" ,libwebp) - ("matio" ,matio) - ("niftilib" ,niftilib) - ("openexr" ,openexr-2) - ("orc" ,orc) - ("pango" ,pango) - ("poppler" ,poppler))) + (list expat + fftw + giflib + glib + hdf5 + imagemagick + lcms + libexif + libgsf + libjpeg-turbo + libpng + librsvg + libtiff + libxml2 + libwebp + matio + niftilib + openexr-2 + orc + pango + poppler)) (home-page "https://libvips.github.io/libvips/") (synopsis "Multithreaded image processing system with low memory needs") (description @@ -805,11 +805,7 @@ recalculates.") #t)))) (build-system cmake-build-system) (inputs - `(("libgeotiff" ,libgeotiff) - ("libtiff" ,libtiff) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("zlib" ,zlib))) + (list libgeotiff libtiff libjpeg-turbo libpng zlib)) (home-page "https://github.com/vxl/vxl/") (synopsis "Collection of C++ libraries for computer vision") (description "VXL (the Vision-something-Libraries) is a collection of C++ diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 07de231cb8..715b6fdc62 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -373,8 +373,7 @@ collection. Geeqie was initially based on GQview.") (base32 "0hi9v0rdx47nys0wvm9xasdrafa34r5kq6crb074a0ipwmc60iiq")))) (build-system gnu-build-system) - (inputs `(("gtk+" ,gtk+-2) - ("libjpeg" ,libjpeg-turbo))) + (inputs (list gtk+-2 libjpeg-turbo)) (native-inputs (list intltool pkg-config)) (synopsis "Simple and fast image viewer for X") (description "gpicview is a lightweight GTK+ 2.x based image viewer. @@ -794,10 +793,7 @@ preloading.") (native-inputs (list pkg-config)) (inputs - `(("freetype" ,freetype) - ("libjpeg" ,libjpeg-turbo) - ("glib" ,glib) - ("imagemagick" ,imagemagick))) + (list freetype libjpeg-turbo glib imagemagick)) (synopsis "Convert images to ANSI/Unicode characters") (description "Chafa is a command-line utility that converts all kinds of images, diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 64a3627bdb..b6378a3890 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1437,7 +1437,7 @@ convert, manipulate, filter and display a wide variety of image formats.") "0p3fj89gkhd2ys5ci75cwb6p7rvb2pf52jd8c9d4g76qp846njnx")))) (build-system cmake-build-system) (inputs - `(("libjpeg" ,libjpeg-turbo))) + (list libjpeg-turbo)) (synopsis "JPEG-2000 library") (description "The JasPer Project is an initiative to provide a reference implementation of the codec specified in the JPEG-2000 Part-1 standard (i.e., @@ -1947,9 +1947,7 @@ identical visual appearance.") "076frk3pa16s4r1b10zgy81vdlz0385zh3ykbnkaij25jn5aqc09")))) (build-system gnu-build-system) (inputs - `(("curl" ,curl) - ("libjpeg" ,libjpeg-turbo) - ("ncurses" ,ncurses))) + (list curl libjpeg-turbo ncurses)) (home-page "https://csl.name/jp2a/") (synopsis "Convert JPEG images to ASCII") (description diff --git a/gnu/packages/jose.scm b/gnu/packages/jose.scm index f841d1444a..9e0787bce7 100644 --- a/gnu/packages/jose.scm +++ b/gnu/packages/jose.scm @@ -42,9 +42,7 @@ "09c2kn9cjqkgx4g0rf6c2k3ng9970r468c9z7067j8kyf7ksywp2")))) (build-system meson-build-system) (native-inputs (list pkg-config)) - (inputs `(("jansson" ,jansson) - ("zlib" ,zlib) - ("libcrypto" ,openssl))) + (inputs (list jansson zlib openssl)) (home-page "https://github.com/latchset/jose") (synopsis "Object Signing and Encryption") (description "C-language implementation of Javascript Object Signing and diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 0f2a6b7514..2ad1c4cd5d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -565,9 +565,7 @@ sensitivities for functions without the need to depend on ChainRules itself.") (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9")))) (build-system julia-build-system) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-compat" ,julia-compat) - ("julia-finitedifference" ,julia-finitedifferences))) + (list julia-chainrulescore julia-compat julia-finitedifferences)) (home-page "https://github.com/JuliaDiff/ChainRulesTestUtils.jl") (synopsis "Common utilities used by downstream automatic differentiation tools") (description "This package is designed to help in testing @@ -1252,7 +1250,7 @@ valuable enough at this time.") (inputs ;; We don't want to propagate the bootstrap version. ;; Cycle with Documenter.jl in later versions. - `(("julia-documenter" ,julia-documenter-bootstrap))) + (list julia-documenter-bootstrap)) (home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl") (synopsis "Documenter's Markdown") (description "This package enables the Markdown / MkDocs backend of diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 71bcfdb939..65937f8970 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -3604,29 +3604,29 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") (native-inputs (list extra-cmake-modules perl)) (inputs - `(("giflib" ,giflib) - ("gperf" ,gperf) - ("karchive" ,karchive) - ("kcodecs" ,kcodecs) - ("kglobalaccel" ,kglobalaccel) - ("ki18n" ,ki18n) - ("kiconthemes" ,kiconthemes) - ("kio" ,kio) - ("kjs" ,kjs) - ("knotifications" ,knotifications) - ("kparts" ,kparts) - ("ktextwidgets" ,ktextwidgets) - ("kwallet" ,kwallet) - ("kwidgetsaddons" ,kwidgetsaddons) - ("kwindowsystem" ,kwindowsystem) - ("kxmlgui" ,kxmlgui) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("openssl" ,openssl) - ("phonon" ,phonon) - ("qtbase" ,qtbase-5) - ("qtx11extras" ,qtx11extras) - ("sonnet" ,sonnet))) + (list giflib + gperf + karchive + kcodecs + kglobalaccel + ki18n + kiconthemes + kio + kjs + knotifications + kparts + ktextwidgets + kwallet + kwidgetsaddons + kwindowsystem + kxmlgui + libjpeg-turbo + libpng + openssl + phonon + qtbase-5 + qtx11extras + sonnet)) (home-page "https://community.kde.org/Frameworks") (synopsis "KDE Frameworks 5 HTML widget and component") (description "KHTML is a web rendering engine, based on the KParts diff --git a/gnu/packages/kde-internet.scm b/gnu/packages/kde-internet.scm index 7697920365..4e08bd5337 100644 --- a/gnu/packages/kde-internet.scm +++ b/gnu/packages/kde-internet.scm @@ -256,50 +256,50 @@ Features are: (native-inputs (list extra-cmake-modules kdoctools pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("boost" ,boost) - ("expat" ,expat) - ("glib" ,glib) - ("gpgme" ,gpgme) - ("jsoncpp" ,jsoncpp) - ("kcmutils" ,kcmutils) - ("kconfig" ,kconfig) - ("kcontacts" ,kcontacts) - ("kcoreaddons" ,kcoreaddons) - ("kcrash" ,kcrash) - ("kdbusaddons" ,kdbusaddons) - ("kdelibs4support" ,kdelibs4support) - ("kdnssd" ,kdnssd) - ("kemoticons" ,kemoticons) - ("khtml" ,khtml) - ("ki18n" ,ki18n) - ("kidentitymanagement" ,kidentitymanagement) - ("kjs" ,kjs) - ;; TODO? kleopatra (additionally to libkleo) - ("knotifyconfig" ,knotifyconfig) - ("kparts" ,kparts) - ("kpimtextedit" ,kpimtextedit) - ("ktexteditor" ,ktexteditor) - ("kwallet" ,kwallet) - ;; TODO: Libgadu - ("libidn" ,libidn) - ("libkleo" ,libkleo) - ;; TODO: LibMeanwhile - ("libotr" ,libotr) - ("libsrtp" ,libsrtp) - ("libxml2" ,libxml2) - ("libxstl" ,libxslt) - ;; TODO: Mediastreamer - ("openssl" ,openssl) - ("ortp" ,ortp) - ("phonon" ,phonon) - ("qca" ,qca) - ("qgpgme" ,qgpgme) - ("qtbase" ,qtbase-5) - ("speex" ,speex) - ("v4l-utils" ,v4l-utils) - ;; TODO: Xmms - ("zlib" ,zlib))) + (list alsa-lib + boost + expat + glib + gpgme + jsoncpp + kcmutils + kconfig + kcontacts + kcoreaddons + kcrash + kdbusaddons + kdelibs4support + kdnssd + kemoticons + khtml + ki18n + kidentitymanagement + kjs + ;; TODO? kleopatra (additionally to libkleo) + knotifyconfig + kparts + kpimtextedit + ktexteditor + kwallet + ;; TODO: Libgadu + libidn + libkleo + ;; TODO: LibMeanwhile + libotr + libsrtp + libxml2 + libxslt + ;; TODO: Mediastreamer + openssl + ortp + phonon + qca + qgpgme + qtbase-5 + speex + v4l-utils + ;; TODO: Xmms + zlib)) ;; TODO: enable video support (home-page "https://kde.org/applications/internet/org.kde.kopete") (synopsis "Instant messaging and chat application") @@ -332,25 +332,25 @@ This package is part of the KDE networking module.") (native-inputs (list extra-cmake-modules kdoctools)) (inputs - `(("kbookmarks" ,kbookmarks) - ("freerdp" ,freerdp) - ("kcmutils" ,kcmutils) - ("kcompletion" ,kcompletion) - ("kconfig" ,kconfig) - ("kdnssd" ,kdnssd) - ("ki18n" ,ki18n) - ("kiconthemes" ,kiconthemes) - ("knotifications" ,knotifications) - ("knotifyconfig" ,knotifyconfig) - ("knotifyconfig" ,knotifyconfig) - ("kwallet" ,kwallet) - ("kwidgetsaddons" ,kwidgetsaddons) - ("kwindowsystem" ,kwindowsystem) - ("kxmlgui" ,kxmlgui) - ("libssh2" ,libssh) - ;; TODO: libvnc{server,client} - is not tigervnc-{server,client} - ("oxygen-icons" ,oxygen-icons) ; default icon set - ("qtbase" ,qtbase-5))) + (list kbookmarks + freerdp + kcmutils + kcompletion + kconfig + kdnssd + ki18n + kiconthemes + knotifications + knotifyconfig + knotifyconfig + kwallet + kwidgetsaddons + kwindowsystem + kxmlgui + libssh + ;; TODO: libvnc{server,client} - is not tigervnc-{server,client} + oxygen-icons ; default icon set + qtbase-5)) (home-page "https://kde.org/applications/internet/org.kde.krdc") (synopsis "Remote desktop client") (description "KRDC is a client application that allows you to view or even diff --git a/gnu/packages/kde-multimedia.scm b/gnu/packages/kde-multimedia.scm index bc88c72407..7537ac1ddd 100644 --- a/gnu/packages/kde-multimedia.scm +++ b/gnu/packages/kde-multimedia.scm @@ -599,33 +599,33 @@ Some features: (native-inputs (list extra-cmake-modules librsvg pkg-config kdoctools)) (inputs - `(("also-lib" ,alsa-lib) - ("audiofile" ,audiofile) - ("flac" ,flac) - ("id3lib" ,id3lib) - ("karchive" ,karchive) - ("kcompletion" ,kcompletion) - ("kconfig" ,kconfig) - ("kconfigwidgets" ,kconfigwidgets) - ("kcoreaddons" ,kcoreaddons) - ("kcrash" ,kcrash) - ("kdbusaddons" ,kdbusaddons) - ("ki18n" ,ki18n) - ("kiconthemes" ,kiconthemes) - ("kio" ,kio) - ("kservice" ,kservice) - ("ktextwidgets" ,ktextwidgets) - ("kwidgetsaddons" ,kwidgetsaddons) - ("kxmlgui" ,kxmlgui) - ("libmad" ,libmad) - ("libsamplerate" ,libsamplerate) - ("libvorbis" ,libvorbis) - ("opus" ,opus) - ("oxygen-icons" ,oxygen-icons) ; default icon set - ("pulseaudio" ,pulseaudio) - ("qtbase" ,qtbase-5) - ("qtmultimedia" ,qtmultimedia) - ("zlib" ,zlib))) + (list alsa-lib + audiofile + flac + id3lib + karchive + kcompletion + kconfig + kconfigwidgets + kcoreaddons + kcrash + kdbusaddons + ki18n + kiconthemes + kio + kservice + ktextwidgets + kwidgetsaddons + kxmlgui + libmad + libsamplerate + libvorbis + opus + oxygen-icons ; default icon set + pulseaudio + qtbase-5 + qtmultimedia + zlib)) (home-page "https://kde.org/applications/multimedia/org.kde.kwave") (synopsis "Sound editor for KDE") (description "Kwave is a sound editor designed for the KDE Desktop diff --git a/gnu/packages/kde-pim.scm b/gnu/packages/kde-pim.scm index a2edb13ea6..dd18a95062 100644 --- a/gnu/packages/kde-pim.scm +++ b/gnu/packages/kde-pim.scm @@ -358,33 +358,33 @@ Akonadi PIM data server. It uses Xapian for indexing and querying.") (native-inputs (list extra-cmake-modules)) (inputs - `(("akonadi" ,akonadi) - ("akonadi-calendar" ,akonadi-calendar) - ("akonadi-contacts" ,akonadi-contacts) - ("akonadi-mime" ,akonadi-mime) - ("boost" ,boost) - ("kcalendarcore" ,kcalendarcore) - ("kcalendarsupport" ,kcalendarsupport) - ("kcalutils" ,kcalutils) - ("kcodecs" ,kcodecs) - ("kcontacts" ,kcontacts) - ("kdbusaddons" ,kdbusaddons) - ("kdepim-apps-libs" ,kdepim-apps-libs) - ("kdiagram" ,kdiagram) - ("keventviews" ,keventviews) - ("ki18n" ,ki18n) - ("kiconthemes" ,kiconthemes) - ("kidentitymanagement" ,kidentitymanagement) - ("kio" ,kio) - ("kitemmodels" ,kitemmodels) - ("kldap" ,kldap) - ("kmailtransport" ,kmailtransport) - ("kmime" ,kmime) - ("kpimtextedit" ,kpimtextedit) - ("ktextwidgets" ,ktextwidgets) - ("kwallat" ,kwallet) - ("libkdepim" ,libkdepim) - ("qtbase" ,qtbase-5))) + (list akonadi + akonadi-calendar + akonadi-contacts + akonadi-mime + boost + kcalendarcore + kcalendarsupport + kcalutils + kcodecs + kcontacts + kdbusaddons + kdepim-apps-libs + kdiagram + keventviews + ki18n + kiconthemes + kidentitymanagement + kio + kitemmodels + kldap + kmailtransport + kmime + kpimtextedit + ktextwidgets + kwallet + libkdepim + qtbase-5)) (home-page "https://invent.kde.org/pim/incidenceeditor") (synopsis "KDE PIM library for editing incidences") (description "This library provides an incidence editor for KDE PIM.") diff --git a/gnu/packages/kde-utils.scm b/gnu/packages/kde-utils.scm index 6a65b7b1f3..2b3a0dd15e 100644 --- a/gnu/packages/kde-utils.scm +++ b/gnu/packages/kde-utils.scm @@ -508,30 +508,30 @@ remind you to take a break now and then.") (native-inputs (list extra-cmake-modules kdoctools)) (inputs - `(("kauth" ,kauth) - ("kconfig" ,kconfig) - ("kconfigwidgets" ,kconfigwidgets) - ("kcompletion" ,kcompletion) - ("kcoreaddons" ,kcoreaddons) - ("kcrash" ,kcrash) - ("kdbusaddons" ,kdbusaddons) - ("ki18n" ,ki18n) - ("kiconthemes" ,kiconthemes) - ("kio" ,kio) - ("kjobwidgets" ,kjobwidgets) - ("knotifications" ,knotifications) - ("knotifyconfig" ,knotifyconfig) - ("ktextwidgets" ,ktextwidgets) - ("kwallet" ,kwallet) - ("kwidgetsaddons" ,kwidgetsaddons) - ("kwindowsystem" ,kwindowsystem) - ("kxmlgui" ,kxmlgui) - ("libsmbclient" ,samba) - ("oxygen-icons" ,oxygen-icons) ;; default icon set - ("plasma-framework" ,plasma-framework) - ("qtbase" ,qtbase-5) - ("qtdeclarative" ,qtdeclarative) - ("solid" ,solid))) + (list kauth + kconfig + kconfigwidgets + kcompletion + kcoreaddons + kcrash + kdbusaddons + ki18n + kiconthemes + kio + kjobwidgets + knotifications + knotifyconfig + ktextwidgets + kwallet + kwidgetsaddons + kwindowsystem + kxmlgui + samba + oxygen-icons ;; default icon set + plasma-framework + qtbase-5 + qtdeclarative + solid)) (home-page "https://kde.org/applications/utilities/org.kde.smb4k") (synopsis "Samba (SMB) share advanced browser") (description "Smb4K is an network neighborhood browser for the KDE diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm index 0ea6a73c92..851a3495b7 100644 --- a/gnu/packages/kde.scm +++ b/gnu/packages/kde.scm @@ -1099,8 +1099,7 @@ a variety of formats, including PDF, PostScript, DejaVu, and EPub.") (native-inputs (list extra-cmake-modules kdoctools)) (inputs - `(("gettext" ,gettext-minimal) - ("qtbase" ,qtbase-5))) + (list gettext-minimal qtbase-5)) (home-page "https://kde.org/applications/development") (synopsis "Tools for translating DocBook XML files with Gettext") (description "This is a collection of tools that facilitate translating diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm index a3f74a62d7..db7ae86cc7 100644 --- a/gnu/packages/libusb.scm +++ b/gnu/packages/libusb.scm @@ -557,8 +557,7 @@ devices.") (base32 "1nr4z4b10vpbh3ss525r7spz4i43zim2ba5qzfl15dgdxshxxivb")))) (build-system gnu-build-system) (inputs - `(("libusb" ,libusb) - ("udev" ,eudev))) + (list libusb eudev)) (native-inputs (list autoconf automake libtool pkg-config)) (home-page "https://github.com/libusb/hidapi") diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ed76159bff..2e659836e2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -8670,8 +8670,8 @@ kernel side implementation.") (base32 "1ygaw69pfz2hfzw9cqzg9rfnjzrdbfkwsiinz6qs2h56dssjz0y9")))) (build-system gnu-build-system) (inputs - `(("lz4" ,lz4) - ("libuuid" ,util-linux "lib"))) + (list lz4 + `(,util-linux "lib"))) (native-inputs (list autoconf automake libtool pkg-config)) (home-page "https://git.kernel.org/pub/scm/linux/kernel/git/xiang/erofs-utils.git/") diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index 9a37bdcfbf..1cdd7d8300 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -78,9 +78,7 @@ (base32 "1kbjwpniffdpv003igmlz5r0vy65m7wpfnhg54fhwirp1227hgg7")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("closer-mop" ,sbcl-closer-mop) - ("optima" ,sbcl-optima))) + (list sbcl-alexandria sbcl-closer-mop sbcl-optima)) (native-inputs (list sbcl-stefil)) (home-page "https://github.com/arclanguage/Clamp") @@ -156,9 +154,7 @@ against the last run.") (base32 "0f40wikcf783jx26ip0nnhwjjfjvjiw7njqsqrb6kaphc8bgw0i1")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("closer-mop" ,sbcl-closer-mop) - ("trivia" ,sbcl-trivia))) + (list sbcl-alexandria sbcl-closer-mop sbcl-trivia)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/Ferada/cl-mock") @@ -315,8 +311,7 @@ that of Eos has not. Thus, Eos is now deprecated in favor of FiveAM.") "1k8i2kq57201bvy3zfpsxld530hd104dgbglxigqb6i408c1a7aw")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-alexandria sbcl-trivial-gray-streams)) (synopsis "Simple and powerful test framework for Common Lisp") (description "A Common Lisp test framework that treasures your failures, logical continuation of Stefil. It focuses on interactive debugging.") @@ -347,9 +342,8 @@ logical continuation of Stefil. It focuses on interactive debugging.") (sha256 (base32 "04mh5plmlb15jbq3dkd8b9jl1dmbbg4hnd3k7859vpf6s12k5p4j")))) (inputs - `(("alexandria" ,sbcl-alexandria) - ("net.didierverna.asdf-flv" ,sbcl-net.didierverna.asdf-flv) - ("trivial-backtrace" ,sbcl-trivial-backtrace))) + (list sbcl-alexandria sbcl-net.didierverna.asdf-flv + sbcl-trivial-backtrace)) (build-system asdf-build-system/sbcl) (synopsis "Common Lisp testing framework") (description "FiveAM is a simple (as far as writing and running tests @@ -413,7 +407,7 @@ with a focus on interactive development.") (base32 "10a78032vnf12kjjpfmq9ign38cad237ycyq37dwnx922nxjjaj4")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (home-page "https://github.com/foretspaisibles/cl-kaputt") (synopsis "Simple interactive test framework for Common Lisp") (description @@ -527,10 +521,8 @@ testing. It is an extension of the library written by Chris Riesbeck.") "1rsqy8y0jqll6xn9a593848f5wvd5ribv4csry1ly0hmdhfnqzlp")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-interpol" ,sbcl-cl-interpol) - ("iterate" ,sbcl-iterate) - ("symbol-munger" ,sbcl-symbol-munger))) + (list sbcl-alexandria sbcl-cl-interpol sbcl-iterate + sbcl-symbol-munger)) (synopsis "Test Framework for Common Lisp") (description "LISP-UNIT2 is a Common Lisp library that supports unit testing in the @@ -562,8 +554,7 @@ by Chris Riesbeck.") (base32 "1hf3r6pqbnd9vsd1i24qmz928kia72hdgmiafiwb6jw1hmj3r6ga")))) (build-system asdf-build-system/sbcl) (inputs - `(("closer-mop" ,sbcl-closer-mop) - ("org-sampler" ,sbcl-org-sampler))) + (list sbcl-closer-mop sbcl-org-sampler)) (home-page "https://github.com/jphmrst/cl-nst") (synopsis "Unit testing for Common Lisp") (description @@ -595,8 +586,7 @@ by Chris Riesbeck.") "1mvsm3r0r6a2bg75nw0q7n9vlby3ch45qjl7hnb5k1z2n5x5lh60")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils) - ("form-fiddle" ,sbcl-form-fiddle))) + (list sbcl-documentation-utils sbcl-form-fiddle)) (synopsis "Extensible and cross-compatible testing framework for Common Lisp") (description "Parachute is a simple-to-use and extensible testing framework. @@ -628,10 +618,8 @@ Each test can contain a bunch of test forms that make up its body.") (file-name (git-file-name "prove" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-colors" ,sbcl-cl-colors) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("cl-ansi-text" ,sbcl-cl-ansi-text))) + (list sbcl-alexandria sbcl-cl-colors sbcl-cl-ppcre + sbcl-cl-ansi-text)) (synopsis "Yet another unit testing framework for Common Lisp") (description "This project was originally called @command{cl-test-more}. @@ -699,9 +687,7 @@ tester module.") "07ala4l2fncxf540fzxj3h5mhi9i4wqllhj0rqk8m2ljl5zbz89q")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("dissect" ,sbcl-dissect) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-bordeaux-threads sbcl-dissect sbcl-trivial-gray-streams)) (home-page "https://github.com/fukamachi/rove") (synopsis "Yet another common lisp testing library") @@ -761,10 +747,7 @@ This is intended to be a successor of Prove.") (base32 "1fqqa7lhf28qg60ji9libkylkcy747x576qpjn1y7c945j2fxmnm")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("local-time" ,sbcl-local-time) - ("osicat" ,sbcl-osicat) - ("rutils" ,sbcl-rutils))) + (list sbcl-cl-ppcre sbcl-local-time sbcl-osicat sbcl-rutils)) (home-page "https://github.com/vseloved/should-test") (synopsis "Minimal yet feature-rich Common Lisp test framework") (description diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index b15ca5e9ce..760ac80000 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -154,15 +154,15 @@ portable between implementations.") (base32 "1z1blj05q71vzh323qwyn9p3xs7v0mq2yhwfyzza5libp37wqm3c")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("claw" ,sbcl-claw) - ("dissect" ,sbcl-dissect) - ("local-time" ,sbcl-local-time) - ("log4cl" ,sbcl-log4cl) - ("split-sequence" ,sbcl-split-sequence) - ("static-vectors" ,sbcl-static-vectors) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-alexandria + sbcl-cffi + sbcl-claw + sbcl-dissect + sbcl-local-time + sbcl-log4cl + sbcl-split-sequence + sbcl-static-vectors + sbcl-trivial-gray-streams)) (home-page "https://github.com/borodust/bodge-utilities") (synopsis "Common Lisp utilities library for CL-BODGE") (description @@ -224,7 +224,7 @@ implementation with no external dependencies.") (base32 "1ljc8yj32lmd1d60446rzl9m0r1ar15gdzacsf6blw1kny8xlrsr")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (synopsis "Common Lisp utility library") (description "This is a Common Lisp library providing various utilities.") @@ -438,7 +438,7 @@ timeouts.") (base32 "19i443fz3488v1pbbr9x24y8h8vlyhny9vj6c9jk5prm702awrp6")) (file-name (git-file-name "bordeaux-threads" version)))) - (inputs `(("alexandria" ,sbcl-alexandria))) + (inputs (list sbcl-alexandria)) (native-inputs (list sbcl-fiveam)) (build-system asdf-build-system/sbcl) (synopsis "Portable shared-state concurrency library for Common Lisp") @@ -646,7 +646,7 @@ compatible with ANSI-compliant Common Lisp implementations.") (base32 "1y2gq2sckspnq8118bix55p2j43dk9qn3p8a2rplp1ip2qxqbb1i")))) (build-system asdf-build-system/sbcl) (inputs - `(("parse" ,sbcl-parse))) + (list sbcl-parse)) (home-page "https://github.com/massung/re") (synopsis "Lua-style Pattern Matching for Common Lisp") (description @@ -748,7 +748,7 @@ RFC7564.") (native-inputs (list sbcl-flexi-streams)) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (home-page "http://weitz.de/cl-unicode/") (synopsis "Portable Unicode library for Common Lisp") (description "CL-UNICODE is a portable Unicode library Common Lisp, which @@ -930,8 +930,7 @@ a sequence (or chain) of such elements.") (base32 "0w6igiav35a65h6r4p1g6dw2i7mw0s06mviw31768r6z62l1ny1v")))) (build-system asdf-build-system/sbcl) (inputs - `(("iterate" ,sbcl-iterate) - ("zpb-ttf" ,sbcl-zpb-ttf))) + (list sbcl-iterate sbcl-zpb-ttf)) (home-page "https://github.com/mbattyani/cl-pdf") (synopsis "Common Lisp library for generating PDF files") (description @@ -1001,12 +1000,12 @@ from other CLXes around the net.") #t)))) (build-system asdf-build-system/sbcl) (inputs - `(("clx" ,sbcl-clx) - ("zpb-ttf" ,sbcl-zpb-ttf) - ("cl-vectors" ,sbcl-cl-vectors) - ("cl-fad" ,sbcl-cl-fad) - ("cl-store" ,sbcl-cl-store) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-clx + sbcl-zpb-ttf + sbcl-cl-vectors + sbcl-cl-fad + sbcl-cl-store + sbcl-trivial-features)) (home-page "https://github.com/l04m33/clx-truetype") (synopsis "Antialiased TrueType font rendering using CLX and XRender") (description "CLX-TrueType is pure common lisp solution for @@ -1443,8 +1442,7 @@ to DeRemer and Pennello, which is used by Bison and lalr.scm (not lalr.cl).") "1qs1bv3m0ki8l5czhsflxcryh22r9d9g9a3a3b0cr0pl954q5rld")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("trivial-garbage" ,sbcl-trivial-garbage))) + (list sbcl-bordeaux-threads sbcl-trivial-garbage)) (synopsis "Futures promises synchronization mechanism for Common Lisp") (description "Eager Future2 is a Common Lisp library that provides composable @@ -1567,9 +1565,7 @@ pure Common Lisp.") (base32 "1ldpsbp3qrfzvknclsxj3sdyms1jf9ad20dvh4w0kw3zgahn2nr5")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-pcg" ,sbcl-cl-pcg) - ("golden-utils" ,sbcl-golden-utils) - ("ironclad" ,sbcl-ironclad))) + (list sbcl-cl-pcg sbcl-golden-utils sbcl-ironclad)) (home-page "https://git.mfiano.net/mfiano/seedable-rng") (synopsis "Common Lisp random number generator") (description @@ -1648,8 +1644,7 @@ several blockable channels.)") "08bmf3pi7n5hadpmqqkg65cxcj6kbvm997wcs1f53ml1nb79d9z8")))) (build-system asdf-build-system/sbcl) (inputs - `(("jpl-queues" ,sbcl-jpl-queues) - ("bordeaux-threads" ,sbcl-bordeaux-threads))) + (list sbcl-jpl-queues sbcl-bordeaux-threads)) (native-inputs (list sbcl-eager-future2)) (synopsis "Thread-safe message-passing channels in Common Lisp") @@ -1704,9 +1699,7 @@ libraries such as Bordeaux-Threads and Eager Future.") (native-inputs (list sbcl-fiveam)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("trivial-with-current-source-form" - ,sbcl-trivial-with-current-source-form))) + (list sbcl-alexandria sbcl-trivial-with-current-source-form)) (synopsis "Common Lisp packrat parser") (description "This is a packrat parser for Common Lisp. @@ -1803,9 +1796,7 @@ satisfying the test.") (file-name (git-file-name "colorize" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("split-sequence" ,sbcl-split-sequence) - ("html-encode" ,sbcl-html-encode))) + (list sbcl-alexandria sbcl-split-sequence sbcl-html-encode)) (synopsis "Common Lisp for syntax highlighting") (description "@command{colorize} is a Lisp library for syntax highlighting @@ -1880,7 +1871,7 @@ for parsing, and grammar based on @command{peg-markdown}.") (file-name (string-append "cl-fad" version "-checkout")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads))) + (list sbcl-bordeaux-threads)) (synopsis "Portable pathname library for Common Lisp") (description "CL-FAD (for \"Files and Directories\") is a thin layer atop Common @@ -1914,7 +1905,7 @@ Common Lisp.") (base32 "0yyp9z6iwx476whz0n1rpjznjyqqhlylhzwpgg5xx92lxmskl752")))) (build-system asdf-build-system/sbcl) (inputs - `(("named-readtables" ,sbcl-named-readtables))) + (list sbcl-named-readtables)) (home-page "https://github.com/cbaggers/fn") (synopsis "Macros for lambda brevity") (description @@ -1993,8 +1984,7 @@ also be supported.") ;; Tests only. (list sbcl-rt)) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("flexi-streams" ,sbcl-flexi-streams))) + (list sbcl-bordeaux-threads sbcl-flexi-streams)) (synopsis "Cryptographic toolkit written in Common Lisp") (description "Ironclad is a cryptography library written entirely in Common Lisp. @@ -2056,7 +2046,7 @@ readtables, which is akin to package namespacing in Common Lisp.") (base32 "0i4rqz5cv7d7c2w81x5lwy05s6fbi3zikf4k5kpi3bkx3cabwdxj")))) (build-system asdf-build-system/sbcl) (inputs - `(("parse-number" ,sbcl-parse-number))) + (list sbcl-parse-number)) (home-page "http://common-lisp.net/project/py-configparser/") (synopsis "ConfigParser Python module functionality for Common Lisp") (description "The py-configparser package implements the ConfigParser @@ -2089,7 +2079,7 @@ values in other options.") (file-name (git-file-name "pythonic-string-reader" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("named-readtables" ,sbcl-named-readtables))) + (list sbcl-named-readtables)) (home-page "https://github.com/smithzvk/pythonic-string-reader") (synopsis "Read table modification inspired by Python's three quote strings") (description "This piece of code sets up some reader macros that make it @@ -2282,8 +2272,7 @@ new fiends in addition to old friends like @command{aif} and (file-name (git-file-name "let-plus" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora))) + (list sbcl-alexandria sbcl-anaphora)) (native-inputs (list sbcl-lift)) (synopsis "Destructuring extension of let*") @@ -2324,8 +2313,7 @@ not counting tests) (file-name (git-file-name "cl-colors" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("let-plus" ,sbcl-let-plus))) + (list sbcl-alexandria sbcl-let-plus)) (synopsis "Simple color library for Common Lisp") (description "This is a very simple color library for Common Lisp, providing @@ -2365,8 +2353,7 @@ This library is no longer supported by its author.") (file-name (git-file-name "cl-ansi-text" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-colors2" ,sbcl-cl-colors2))) + (list sbcl-alexandria sbcl-cl-colors2)) (native-inputs (list sbcl-fiveam)) (synopsis "ANSI terminal color implementation for Common Lisp") @@ -2562,15 +2549,15 @@ Lisp programs. It parses URI according to the RFC 2396 specification.") "06gw5wxcpdclb6a5i5k9lbmdlyqsp182czrm9bm1cpklzbj0ihrl")))) (build-system asdf-build-system/sbcl) (inputs - `(("asdf-finalizers" ,sbcl-asdf-finalizers) - ("babel" ,sbcl-babel) - ("chipz" ,sbcl-chipz) - ("cl+ssl" ,sbcl-cl+ssl) - ("flexi-streams" ,sbcl-flexi-streams) - ("ironclad" ,sbcl-ironclad) - ("salza2" ,sbcl-salza2) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams) - ("usocket" ,sbcl-usocket))) + (list sbcl-asdf-finalizers + sbcl-babel + sbcl-chipz + sbcl-cl+ssl + sbcl-flexi-streams + sbcl-ironclad + sbcl-salza2 + sbcl-trivial-gray-streams + sbcl-usocket)) (home-page "https://github.com/qitab/qmynd") (synopsis "QITAB MySQL Native Driver for Common Lisp") (description "QMyND, the QITAB MySQL Native Driver, is a MySQL client @@ -2639,7 +2626,7 @@ non-consing thread safe queues and fibonacci priority queues.") (base32 "0k2f1771wd9kdrcasldy1r00k5bdgi9fd07in52zmjggc0i7dd80")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "https://github.com/3b/glsl-packing/") (synopsis "Common Lisp utilities to calculate OpenGL layouts") (description @@ -2701,9 +2688,7 @@ from GLSL as data.") (base32 "0bhxxnv7ldkkb18zdxyz2rj2a3iawzq2kcp7cn5i91iby7n0082x")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("documentation-utils" ,sbcl-documentation-utils) - ("glsl-symbols" ,sbcl-glsl-spec))) + (list sbcl-alexandria sbcl-documentation-utils sbcl-glsl-spec)) (home-page "https://github.com/cbaggers/rtg-math") (synopsis "Common Lisp library of game-related math functions") (description @@ -2736,14 +2721,14 @@ for making realtime graphics in Lisp.") (native-inputs (list sbcl-fiveam)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("documentation-utils" ,sbcl-documentation-utils) - ("fn" ,sbcl-fn) - ("glsl-spec" ,sbcl-glsl-spec) - ("named-readtables" ,sbcl-named-readtables) - ("parse-float" ,sbcl-parse-float) - ("vas-string-metrics" ,sbcl-vas-string-metrics))) + (list sbcl-alexandria + sbcl-cl-ppcre + sbcl-documentation-utils + sbcl-fn + sbcl-glsl-spec + sbcl-named-readtables + sbcl-parse-float + sbcl-vas-string-metrics)) (home-page "https://github.com/cbaggers/varjo") (synopsis "Lisp to GLSL Language Translator") (description @@ -2844,8 +2829,7 @@ package.") (file-name (git-file-name "cffi-c-ref" version)))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi))) + (list sbcl-alexandria sbcl-cffi)) (synopsis "Streamlined access to foreign memory") (description "This Common Lisp library provides macros to access foreign memory.") @@ -2973,9 +2957,7 @@ Redis data structure store.") "0c22lqarrpbq82dg1sb3y6mp6w2faczp34ymzhnmff88yfq1xzsf")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("anaphora" ,sbcl-anaphora) - ("named-readtables" ,sbcl-named-readtables))) + (list sbcl-cl-ppcre sbcl-anaphora sbcl-named-readtables)) (home-page "https://common-lisp.net/project/parenscript/") (synopsis "Translator from a subset of Common Lisp to JavaScript") (description @@ -3609,7 +3591,7 @@ This XML parser implementation has the following limitations: "02z7k163d51v0pzk8mn1xb6h5s6x64gjqkslhwm3a5x26k2gfs11")))) (build-system asdf-build-system/sbcl) (inputs - `(("s-xml" ,sbcl-s-xml))) + (list sbcl-s-xml)) (home-page "https://common-lisp.net/project/s-xml-rpc/") (synopsis "Implementation of XML-RPC in Common Lisp for both client and server") (description @@ -3798,7 +3780,7 @@ RFC 1321 by R. Rivest, published April 1992.") (package (inherit (sbcl-package->ecl-package sbcl-md5)) (inputs - `(("flexi-streams" ,ecl-flexi-streams))))) + (list ecl-flexi-streams)))) (define-public sbcl-cl+ssl (let ((commit "701e645081e6533a3f0f0b3ac86389d6f506c4b5") @@ -4761,9 +4743,7 @@ Long Painful History of Time\".") (native-inputs (list sbcl-lisp-unit)) (inputs - `(("cl-interpol" ,sbcl-cl-interpol) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("local-time" ,sbcl-local-time))) + (list sbcl-cl-interpol sbcl-cl-ppcre sbcl-local-time)) (home-page "https://github.com/chaitanyagupta/chronicity") (synopsis "Natural language date and time parser for Common Lisp") (description @@ -5010,7 +4990,7 @@ theory accurate to internal-time-units-per-second.") (native-inputs (list sbcl-stefil)) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads))) + (list sbcl-bordeaux-threads)) (home-page "https://github.com/7max/log4cl") (synopsis "Common Lisp logging framework, modeled after Log4J") (description @@ -5100,11 +5080,8 @@ by either a symbol or a keyword.") (base32 "0r51ydj5v7afi2jrlscbhxprv13d9vzg5316g1yzwaxc1kzsdsw6")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("dissect" ,sbcl-dissect) - ("documentation-utils" ,sbcl-documentation-utils) - ("local-time" ,sbcl-local-time) - ("piping" ,sbcl-piping))) + (list sbcl-bordeaux-threads sbcl-dissect sbcl-documentation-utils + sbcl-local-time sbcl-piping)) (home-page "https://shinmera.github.io/verbose/") (synopsis "Logging framework using the piping library") (description @@ -5228,7 +5205,7 @@ the CFFI approach used by burgled-batteries, but has the same goal.") (base32 "0q9b07spmhg1b576cnnacvkf7zr3mab2rdydfylbn92y9mms9vyj")))) (build-system asdf-build-system/sbcl) (inputs - `(("trivial-arguments" ,sbcl-trivial-arguments))) + (list sbcl-trivial-arguments)) (synopsis "Scheme style syntax/macros/functions for Common Lisp") (description "Schemeish implements several useful Scheme constructs for Common Lisp. @@ -5437,8 +5414,7 @@ basic everyday functions and macros.") "0maxs8392953fhnaa6zwnm2mdbhxjxipp4g4rvypm06ixr6pyv1c")))) (build-system asdf-build-system/sbcl) (inputs - `(("close-mop" ,sbcl-closer-mop) - ("fare-utils" ,sbcl-fare-utils))) + (list sbcl-closer-mop sbcl-fare-utils)) (home-page "https://github.com/fare/fare-mop") (synopsis "General purpose Common Lisp utilities using the MOP") (description @@ -5474,11 +5450,8 @@ great for REPL interaction and debugging.") (native-inputs (list sbcl-hu.dwim.stefil)) (inputs - `(("alexandira" ,sbcl-alexandria) - ("fare-mop" ,sbcl-fare-mop) - ("fare-quasiquote" ,sbcl-fare-quasiquote) - ("fare-utils" ,sbcl-fare-utils) - ("trivia" ,sbcl-trivia))) + (list sbcl-alexandria sbcl-fare-mop sbcl-fare-quasiquote + sbcl-fare-utils sbcl-trivia)) (home-page "https://github.com/fare/inferior-shell") (synopsis "Spawn local or remote processes and shell pipes") (description @@ -5547,7 +5520,7 @@ UTF-8 has is that it doesn't depend on any other libraries.") (base32 "00nbr3mffxhlq14gg9d16pa6691s4qh35inyw76v906s77khm5a2")))) (inputs - `(("split-sequence" ,sbcl-split-sequence))) + (list sbcl-split-sequence)) (synopsis "IDNA string encoding and decoding routines for Common Lisp") (description "This Common Lisp library provides string encoding and decoding routines for IDNA, the International Domain Names in Applications.") @@ -5576,7 +5549,7 @@ decoding routines for IDNA, the International Domain Names in Applications.") (base32 "1hw1v1lw26rifyznpnj1csphha9jgzwpiic16ni3pvs6hcsni9rz")))) (inputs - `(("trivial-features" ,sbcl-trivial-features))) + (list sbcl-trivial-features)) (native-inputs (list sbcl-fiveam)) (synopsis "Efficient endianness conversion for Common Lisp") @@ -5732,9 +5705,7 @@ Closure is a reference to the web browser it was originally written for.") "13kif7rf3gqdycsk9zq0d7y0g9y81krkl0z87k0p2fkbjfgrph37")))) (build-system asdf-build-system/sbcl) (inputs - `(("closure-common" ,sbcl-closure-common) - ("puri" ,sbcl-puri) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-closure-common sbcl-puri sbcl-trivial-gray-streams)) (synopsis "Common Lisp XML parser") (description "CXML implements a namespace-aware, validating XML 1.0 parser as well as the DOM Level 2 Core interfaces. Two parser interfaces are @@ -5766,11 +5737,8 @@ offered, one SAX-like, the other similar to StAX.") "1rld038hmvm0whaffkszd5ks7mg44z1vfbgddal434df8sgspzql")))) (build-system asdf-build-system/sbcl) (inputs - `(("cxml" ,sbcl-cxml) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("yacc" ,sbcl-cl-yacc) - ("parse-number" ,sbcl-parse-number) - ("cl-base64" ,sbcl-cl-base64))) + (list sbcl-cxml sbcl-cl-ppcre sbcl-cl-yacc sbcl-parse-number + sbcl-cl-base64)) (synopsis "Relax NG for Closure XML (CXML)") (description "An implementation of Relax NG schema validation written in Common Lisp, including support for compact syntax, DTD Compatibility, and the @@ -6365,8 +6333,7 @@ arrows.") (base32 "0w4rqvrgdgk3fwfq3kx4r7wwdr2bv3b6n3bdqwsiriw9psqzpz2s")))) (inputs - `(("cxml" ,sbcl-cxml) - ("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cxml sbcl-cl-ppcre)) (synopsis "Concise, regexp-like pattern matching on streaming XML for Common Lisp") (description "CXML does an excellent job at parsing XML elements, but what do you do when you have a XML file that's larger than you want to fit in @@ -6404,14 +6371,14 @@ power of CXML is available when necessary.") "0fw2q866yddbf23nk9pxphm9gsasx35vjyss82xzvndnjmzlqfl5")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("trivial-garbage" ,sbcl-trivial-garbage) - ("babel" ,sbcl-babel) - ("iolib" ,sbcl-iolib) - ("ieee-floats" ,sbcl-ieee-floats) - ("flexi-streams" ,sbcl-flexi-streams) - ("cl-xmlspam" ,sbcl-cl-xmlspam) - ("ironclad" ,sbcl-ironclad))) + (list sbcl-alexandria + sbcl-trivial-garbage + sbcl-babel + sbcl-iolib + sbcl-ieee-floats + sbcl-flexi-streams + sbcl-cl-xmlspam + sbcl-ironclad)) (synopsis "D-Bus client library for Common Lisp") (description "This is a Common Lisp library that publishes D-Bus objects as well as send and notify other objects connected to a bus.") @@ -6442,10 +6409,8 @@ objects as well as send and notify other objects connected to a bus.") (base32 "0bg3l0a28lw5gqqjp6p6b5nhwqk46sgkb7184w5qbfngw1hk8x9y")))) (inputs - `(("alexandria" ,sbcl-alexandria) - ("let-plus" ,sbcl-let-plus) - ("trivial-garbage" ,sbcl-trivial-garbage) - ("closer-mop" ,sbcl-closer-mop))) + (list sbcl-alexandria sbcl-let-plus sbcl-trivial-garbage + sbcl-closer-mop)) (native-inputs (list sbcl-fiveam)) (synopsis "Hooks extension point mechanism (as in Emacs) for Common Lisp") @@ -6543,8 +6508,7 @@ extension-points via the concept of hooks.") (base32 "1fh8r7kf8s3hvqdg6b71b8p7w3v2kkga9bw8j3qqdxhzr6anpm0b")))) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("usocket" ,sbcl-usocket))) + (list sbcl-bordeaux-threads sbcl-usocket)) (synopsis "Common Lisp abstraction layer over platform dependent functionality") (description "@code{s-sysdeps} is an abstraction layer over platform dependent functionality. This simple package is used as a building block in a @@ -6585,8 +6549,7 @@ number of other open source projects. (base32 "050h6hwv8f16b5v6fzba8zmih92hgaaq27i2x9wv1iib41gbia3r")))) (inputs - `(("s-sysdeps" ,sbcl-s-sysdeps) - ("s-xml" ,sbcl-s-xml))) + (list sbcl-s-sysdeps sbcl-s-xml)) (native-inputs (list sbcl-fiveam)) (synopsis "Implementation of object prevalence for Common Lisp") @@ -6864,8 +6827,7 @@ system.") (base32 "18ig7rvxcra69437g0i8sxyv7c5dg26jqnx1rc2f9pxmihdprgk8")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("alexandria" ,sbcl-alexandria) - ("fiveam" ,sbcl-fiveam))) + (list sbcl-alexandria sbcl-fiveam)) (synopsis "Binary search tree for Common Lisp") (description "BST is a Common Lisp library for working with binary search trees that @@ -6896,7 +6858,7 @@ can contain any kind of values.") (native-inputs (list sbcl-fiveam)) (inputs - `(("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-trivial-gray-streams)) (synopsis "In-memory octet streams for Common Lisp") (description "CL-octet-streams is a library implementing in-memory octet @@ -6976,7 +6938,7 @@ compression/decompression using bindings to the lzlib C library.") (native-inputs (list sbcl-fiveam)) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads))) + (list sbcl-bordeaux-threads)) (synopsis "Portable channel-based concurrency for Common Lisp") (description "Common Lisp library for channel-based concurrency. In a nutshell, you create various threads sequentially executing tasks you need @@ -7042,8 +7004,7 @@ ability to store all Common Lisp data types into streams.") (native-inputs (list sbcl-fiveam)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("introspect-environment" ,sbcl-introspect-environment))) + (list sbcl-alexandria sbcl-introspect-environment)) (home-page "https://github.com/markcox80/specialization-store") (synopsis "Different type of generic function for Common Lisp") (description @@ -7463,7 +7424,7 @@ Clojure, as well as several expansions on the idea.") (native-inputs (list sbcl-fiveam)) (inputs - `(("chanl" ,sbcl-chanl))) + (list sbcl-chanl)) (synopsis "Common Lisp library to evaluate some forms in parallel") (description "This is a simple Common Lisp library to evaluate some forms in parallel.") @@ -7525,8 +7486,7 @@ binary heap and a Fibonacci heap) as well as an efficient priority queue.") "0rv9bl8xrad5wfcg5zs1dazvnpmvqz6297lbn8bywsrcfnlf7h98")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("named-readtables" ,sbcl-named-readtables))) + (list sbcl-alexandria sbcl-named-readtables)) (synopsis "Reader macros for partial application and composition") (description "This Common Lisp library provides reader macros for concise expression @@ -7556,8 +7516,7 @@ of function partial application and composition.") "0479rbjgbj80jpk5bby18inlv1kfp771a82rlcq5psrz65qqa9bj")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-alexandria sbcl-trivial-gray-streams)) (synopsis "Common Lisp JSON parser/encoder") (description "YASON is a Common Lisp library for encoding and decoding data in the @@ -7668,7 +7627,7 @@ results.") "098qhkqskmmrh4wix34mawf7p5c87yql28r51r75yjxj577k5idq")))) (build-system asdf-build-system/sbcl) (inputs - `(("trivial-indent" ,sbcl-trivial-indent))) + (list sbcl-trivial-indent)) (synopsis "Few simple tools to document Common Lisp libraries") (description "This is a small library to help you with managing the Common Lisp @@ -7700,7 +7659,7 @@ docstrings for your library.") "0pn45c9rbxlnhn5nvhqz6kyv0nlirwxpg4j27niwdq80yxzsn51f")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (home-page "https://github.com/sirherrbatka/documentation-utils-extensions") (synopsis "Set of extensions for documentation-utils") (description @@ -7740,7 +7699,7 @@ for more information.") "041iznc9mpfyrl0sv5893ys9pbb2pvbn9g3clarqi7gsfj483jln")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (synopsis "Utilities to destructure Common Lisp lambda forms") (description "Often times we need to destructure a form definition in a Common Lisp @@ -7775,7 +7734,7 @@ macro. This library provides a set of simple utilities to help with that.") (native-inputs (list sbcl-parachute)) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (synopsis "Tiny collection of array and vector utilities for Common Lisp") (description "A miniature toolkit that contains some useful shifting/popping/pushing @@ -7808,8 +7767,7 @@ functions for arrays and vectors. Originally from Plump.") "1w4wz7f6dc2ckdq9wq9r5014bg2nxjifj9yz1zzn41r8h1h5xfcd")))) (build-system asdf-build-system/sbcl) (inputs - `(("array-utils" ,sbcl-array-utils) - ("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-array-utils sbcl-documentation-utils)) (synopsis "Lenient XML / XHTML / HTML parser for Common Lisp") (description "Plump is a parser for HTML/XML-like documents, focusing on being @@ -8007,8 +7965,7 @@ intending to program in Lisp.") "1kr00zf62m7la7rxa2m5w49r9cyzamc106hvjcc8ffmi7a4jw490")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-unicode" ,sbcl-cl-unicode) - ("named-readtables" ,sbcl-named-readtables))) + (list sbcl-cl-unicode sbcl-named-readtables)) (native-inputs (list sbcl-flexi-streams)) (synopsis "String interpolation for Common Lisp") @@ -8126,7 +8083,7 @@ from/to strings, streams and files.") "0vww1x3yilb3bjwg6k184vaj4vxyxw4vralhnlm6lk4xac67kc9z")))) (build-system asdf-build-system/sbcl) (inputs - `(("trivial-features" ,sbcl-trivial-features))) + (list sbcl-trivial-features)) (native-inputs (list sbcl-fiveam)) (synopsis "Common Lisp library for running external programs") @@ -8217,8 +8174,7 @@ visualization.") "0pvsc9fmybx7rxd0kmzq4shi6hszdpwdc1sfy7jwyfxf8n3hnv4p")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-fad" ,sbcl-cl-fad) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-cl-fad sbcl-trivial-gray-streams)) (synopsis "Common Lisp library for tar and cpio archives") (description "This is a Common Lisp library to read and write disk-based file @@ -8316,9 +8272,7 @@ for Common Lisp.") #t)))) (build-system asdf-build-system/sbcl) (inputs - `(("misc-extensions" ,sbcl-misc-extensions) - ("mt19937" ,sbcl-mt19937) - ("named-readtables" ,sbcl-named-readtables))) + (list sbcl-misc-extensions sbcl-mt19937 sbcl-named-readtables)) (synopsis "Functional set-theoretic collections library") (description "FSet is a functional set-theoretic collections library for Common Lisp. @@ -8357,8 +8311,7 @@ may contain sets, maps may be keyed by sets, etc.") "1zf8zvb0i6jm3hhfks4w74hibm6avgc6f9s1qwgjrn2bcik8lrvz")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("closer-mop" ,sbcl-closer-mop))) + (list sbcl-alexandria sbcl-closer-mop)) (native-inputs (list sbcl-rt)) (synopsis "Delimited continuations for Common Lisp") @@ -8604,10 +8557,9 @@ Common Lisp. It uses the libuv library as backend.") "0xfds5yaya64arzr7w1x38karyz11swzbhxx1afldpradj9dh19c")))) (build-system asdf-build-system/sbcl) (inputs - `(("vom" ,sbcl-vom))) + (list sbcl-vom)) (native-inputs - `(("cl-async" ,sbcl-cl-async) - ("fiveam" ,sbcl-fiveam))) + (list sbcl-cl-async sbcl-fiveam)) (synopsis "Promise implementation for Common Lisp") (description "This is a standalone promise implementation for Common Lisp. It is @@ -8639,10 +8591,9 @@ the successor to the now-deprecated cl-async-future project.") "0z0sc7qlzzxk99f4l26zp6rai9kv0kj0f599sxai5s44p17zbbvh")))) (build-system asdf-build-system/sbcl) (inputs - `(("blackbird" ,sbcl-blackbird))) + (list sbcl-blackbird)) (native-inputs - `(("cl-async" ,sbcl-cl-async) - ("eos" ,sbcl-eos))) + (list sbcl-cl-async sbcl-eos)) (synopsis "Futures implementation for Common Lisp") (description "This is futures implementation for Common Lisp. It plugs in nicely @@ -8752,8 +8703,7 @@ defined in RFC4648.") (base32 "0r27pidjaxbm7k1rr90nnajwl5xm2kp65g1fv0fva17lzy45z1mp")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("cl-octet-streams" ,sbcl-cl-octet-streams) - ("fiveam" ,sbcl-fiveam))) + (list sbcl-cl-octet-streams sbcl-fiveam)) (synopsis "Common Lisp library for Z85 encoding and decoding") (description "This package provides functions to encode or decode byte vectors or @@ -8839,7 +8789,7 @@ in pure Common Lisp and does not require any Tk knowledge for its usage.") (base32 "1kg50f76bfpfxcv4dfivq1n9a0xlsra2ajb0vd68lxwgbidgyc2y")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (synopsis "Common Lisp macros for generating lexical analyzers") (description "This is a Common Lisp library providing a set of macros for generating @@ -8873,8 +8823,7 @@ be used with @code{cl-yacc}.") (native-inputs (list sbcl-clunit2)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-alexandria sbcl-cl-ppcre)) (synopsis "Color library for Common Lisp") (description "This is a very simple color library for Common Lisp, providing: @@ -9065,11 +9014,9 @@ ones.") (base32 "1p48lxdibnps5rpyh5cmnk0vc77bmmxb32qdzfz93zadr8wwas10")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("chipz" ,sbcl-chipz) - ("flexi-streams" ,sbcl-flexi-streams) - ("parachute" ,sbcl-parachute))) + (list sbcl-chipz sbcl-flexi-streams sbcl-parachute)) (inputs - `(("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-trivial-gray-streams)) (synopsis "Common Lisp library for zlib, deflate and gzip compression") (description "Salza2 is a Common Lisp library for creating compressed data in the zlib, @@ -9103,8 +9050,7 @@ respectively.") (native-inputs (list sbcl-parachute)) (inputs - `(("golden-utils" ,sbcl-golden-utils) - ("specialization-store" ,sbcl-specialization-store))) + (list sbcl-golden-utils sbcl-specialization-store)) (home-page "https://git.mfiano.net/mfiano/origin") (synopsis "Common Lisp graphics math library") (description @@ -9135,9 +9081,7 @@ performance and correctness.") (base32 "0vyczbcwskrygrf1hgrsnk0jil8skmvf1kiaalw5jps4fjrfdkw0")))) (build-system asdf-build-system/sbcl) (inputs - `(("babel" ,sbcl-babel) - ("chipz" ,sbcl-chipz) - ("iterate" ,sbcl-iterate))) + (list sbcl-babel sbcl-chipz sbcl-iterate)) (synopsis "PNG decoder for Common Lisp") (description "This is a Common Lisp library for reading PNG images.") (home-page "https://github.com/Ramarren/png-read") @@ -9206,7 +9150,7 @@ read/write Bit Map Font (BMF) into text, JSON and XML.") (base32 "0b3ag3jhl3z7kdls3ahdsdxsfhhw5qrizk769984f4wkxhb69rcm")))) (build-system asdf-build-system/sbcl) (inputs - `(("salza2" ,sbcl-salza2))) + (list sbcl-salza2)) (synopsis "PNG encoder for Common Lisp") (description "This is a Common Lisp library for creating PNG images.") (home-page "https://www.xach.com/lisp/zpng/") @@ -9235,7 +9179,7 @@ read/write Bit Map Font (BMF) into text, JSON and XML.") (native-inputs (list sbcl-lisp-unit)) (inputs - `(("zpng" ,sbcl-zpng))) + (list sbcl-zpng)) (synopsis "QR code encoder for Common Lisp") (description "This Common Lisp library provides function to make QR codes and to save @@ -9537,7 +9481,7 @@ correctly.") (native-inputs (list sbcl-ptester)) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (home-page "https://common-lisp.net/project/cl-unification/") (synopsis "Unification framework for Common Lisp") (description @@ -9800,8 +9744,7 @@ lightweight messaging kernel.") (base32 "0la4dbcda78x29szanylccrsljqrn9d1mhh569sqkyp44ni5fv91")) (file-name (git-file-name name version)))) (inputs - `(("array-utils" ,sbcl-array-utils) - ("plump" ,sbcl-plump))) + (list sbcl-array-utils sbcl-plump)) (build-system asdf-build-system/sbcl) (synopsis "DOM tree searching engine based on CSS selectors") (description "CLSS is a DOM traversal engine based on CSS @@ -9834,10 +9777,7 @@ selectors. It makes use of the Plump-DOM and is used by lQuery.") (native-inputs (list sbcl-fiveam)) (inputs - `(("array-utils" ,sbcl-array-utils) - ("form-fiddle" ,sbcl-form-fiddle) - ("plump" ,sbcl-plump) - ("clss" ,sbcl-clss))) + (list sbcl-array-utils sbcl-form-fiddle sbcl-plump sbcl-clss)) (build-system asdf-build-system/sbcl) (synopsis "Library to allow jQuery-like HTML/DOM manipulation") (description "@code{lQuery} is a DOM manipulation library written in @@ -10281,8 +10221,7 @@ interfaces as well as a functional and an object oriented interface.") (base32 "00bv1aj89q5vldmq92zp2364jq312zjq2mbd3iyz1s2b4widzhl7")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-alexandria sbcl-cl-ppcre)) (synopsis "Purely functional data structure library in Common Lisp") (description "Sycamore is a fast, purely functional data structure library in Common Lisp. @@ -10423,8 +10362,7 @@ multiple checkers, including Aspell and Hunspell.") (base32 "0qmk341zzcsbf8sq0w9ix3r080zg4ri6vzxym63lhdjfzwz3y8if")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("cl-ppcre-unicode" ,sbcl-cl-ppcre-unicode))) + (list sbcl-cl-ppcre sbcl-cl-ppcre-unicode)) (native-inputs (list sbcl-fiveam)) (synopsis @@ -10497,10 +10435,8 @@ tie modules together in functionality, hook into each other and so on.") (base32 "12kjvin8hxidwkzfb7inqv5b6g5qzcssnj9wc497v2ixc56fqdz7")))) (build-system asdf-build-system/sbcl) (inputs - `(("closer-mop" ,sbcl-closer-mop) - ("lambda-fiddle" ,sbcl-lambda-fiddle) - ("modularize" ,sbcl-modularize) - ("trivial-arguments" ,sbcl-trivial-arguments))) + (list sbcl-closer-mop sbcl-lambda-fiddle sbcl-modularize + sbcl-trivial-arguments)) (home-page "https://shinmera.github.io/modularize-hooks/") (synopsis "Generic hooks and triggers extension for Modularize") (description @@ -10531,10 +10467,8 @@ define and trigger hooks, which other modules can hook on to.") (base32 "0bjf4wy39cwf75m7vh0r7mmcchs09yz2lrbyap98hnq8blq70fhc")))) (build-system asdf-build-system/sbcl) (inputs - `(("lambda-fiddle" ,sbcl-lambda-fiddle) - ("modularize" ,sbcl-modularize) - ("trivial-arguments" ,sbcl-trivial-arguments) - ("trivial-indent" ,sbcl-trivial-indent))) + (list sbcl-lambda-fiddle sbcl-modularize sbcl-trivial-arguments + sbcl-trivial-indent)) (home-page "https://shinmera.github.io/modularize-interfaces/") (synopsis "Programmatical interfaces extension for Modularize") (description @@ -10604,9 +10538,7 @@ MOP easier to use.") (base32 "18g137iqf86i247c9cg7d86b8k9cfq3yv272l73fsv734qpnv0g9")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-alexandria sbcl-cffi sbcl-trivial-features)) (native-inputs (list sbcl-rt)) (synopsis "Operating system interface for Common Lisp") @@ -10757,8 +10689,7 @@ Streams in ICDE’05.") "0jnyp2kibcf5cwi60l6grjrj8wws9chasjvsw7xzwyym2lyid46f")))) (build-system asdf-build-system/sbcl) (inputs - `(("ironclad" ,sbcl-ironclad) - ("trivial-utf-8" ,sbcl-trivial-utf-8))) + (list sbcl-ironclad sbcl-trivial-utf-8)) (home-page "https://github.com/dardoria/uuid") (synopsis "Common Lisp implementation of UUIDs according to RFC4122") @@ -10789,7 +10720,7 @@ Streams in ICDE’05.") "0rmsjkgjl90gl6ssvgd60hb0d5diyhsiyypvw9hbc0ripvbmk5r5")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (home-page "https://shinmera.github.io/dissect/") (synopsis "Introspection library for the call stack and restarts") @@ -10850,13 +10781,13 @@ learn about each of the parameters.") (base32 "1i1crdsf2nbyxxpvjgrwmwpjxn6a4drbcmqs4q4shfi8zyap7vng")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-package-locks" ,sbcl-cl-package-locks) - ("cl-syntax" ,sbcl-cl-syntax) - ("iterate" ,sbcl-iterate) - ("optima" ,sbcl-optima) - ("split-sequence" ,sbcl-split-sequence) - ("trivial-types" ,sbcl-trivial-types))) + (list sbcl-alexandria + sbcl-cl-package-locks + sbcl-cl-syntax + sbcl-iterate + sbcl-optima + sbcl-split-sequence + sbcl-trivial-types)) (native-inputs (list sbcl-prove)) (home-page "https://github.com/fukamachi/sxql") @@ -10990,7 +10921,7 @@ weight, temperature, names of physical quantitites, etc.") (base32 "1639msyagsswj85gc0wd90jgh8588j3qg5q70by9s2brf2q6w4lh")))) (inputs - `(("acclimation" ,sbcl-acclimation))) + (list sbcl-acclimation)) (build-system asdf-build-system/sbcl) (home-page "https://github.com/robert-strandh/Clump") (synopsis "Collection of tree implementations for Common Lisp") @@ -11030,8 +10961,7 @@ sequences of objects.") "1bcg13g7qb3dr8z50aihdjqa6miz5ivlc9wsj2csgv1km1mak2kj")))) (build-system asdf-build-system/sbcl) (inputs - `(("acclimation" ,sbcl-acclimation) - ("clump" ,sbcl-clump))) + (list sbcl-acclimation sbcl-clump)) (home-page "https://github.com/robert-strandh/cluffer") (synopsis "Common Lisp library providing a protocol for text-editor buffers") (description "Cluffer is a library for representing the buffer of a text @@ -11066,7 +10996,7 @@ implementations of those protocols for different purposes.") (native-inputs (list sbcl-prove)) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (synopsis "LibSVM data format reader for Common Lisp") (description "This Common Lisp library provides a fast reader for data in LibSVM @@ -11379,7 +11309,7 @@ non-RLE encoded forms of the files.") (base32 "072v417vmcnvmyh8ddq9vmwwrizm7zwz9dpzi14qy9nsw8q649zw")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "https://github.com/gigamonkey/monkeylib-binary-data") (synopsis "Common Lisp library for reading and writing binary data") (description @@ -11518,7 +11448,7 @@ with other libraries which may also use Freetype.") (base32 "0458bllabcdjghfrqx6aki49c9qmvfmkk8jl75cfpi7q0i12kh95")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "https://github.com/slyrus/opticl-core") (synopsis "Core classes and pixel access macros for Opticl") (description @@ -11551,12 +11481,12 @@ macros for the Opticl image processing library.") (native-inputs (list sbcl-fiveam)) (inputs - `(("cl-jpeg" ,sbcl-cl-jpeg) - ("com.gigamonkeys.binary-data" ,sbcl-com.gigamonkeys.binary-data) - ("deflate" ,sbcl-deflate) - ("flexi-streams" ,sbcl-flexi-streams) - ("ieee-floats" ,sbcl-ieee-floats) - ("opticl-core" ,sbcl-opticl-core))) + (list sbcl-cl-jpeg + sbcl-com.gigamonkeys.binary-data + sbcl-deflate + sbcl-flexi-streams + sbcl-ieee-floats + sbcl-opticl-core)) (home-page "https://github.com/slyrus/retrospectiff") (synopsis "Common Lisp library for TIFF images") (description @@ -11587,13 +11517,10 @@ in the TIFF (Tagged Image File Format) format.") (base32 "0qd0xp20i1pcfn12kkapv9pirb6hd4ns7kz4zf1mmjwykpsln96q")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("parachute" ,sbcl-parachute) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-alexandria sbcl-cffi sbcl-parachute + sbcl-trivial-features)) (inputs - `(("cffi" ,sbcl-cffi) - ("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-cffi sbcl-documentation-utils)) (home-page "https://shinmera.github.io/mmap/") (synopsis "File memory mapping for Common Lisp") (description @@ -11627,12 +11554,12 @@ than a few Kb.") (base32 "0kvvlvf50jhhw1s510f3clpr1a68632bq6d698yxcrx722igcrg4")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("babel" ,sbcl-babel) - ("cffi" ,sbcl-cffi) - ("mmap" ,sbcl-mmap) - ("nibbles" ,sbcl-nibbles) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-alexandria + sbcl-babel + sbcl-cffi + sbcl-mmap + sbcl-nibbles + sbcl-trivial-features)) (home-page "https://github.com/3b/3bz") (synopsis "Deflate decompression for Common Lisp") (description @@ -11864,8 +11791,7 @@ specification}, a toolkit for writing GUIs in Common Lisp.") (native-inputs (list sbcl-lisp-unit2)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-alexandria sbcl-cl-ppcre)) (home-page "https://github.com/AccelerationNet/cl-inflector") (synopsis "Library to pluralize/singularize English and Portuguese words") (description @@ -11897,13 +11823,13 @@ Inflector module.") (base32 "1wjdnf4vr9z7lcfc49kl43g6l2i23q9n81siy494k17d766cdvqa")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("babel" ,sbcl-babel) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("ieee-floats" ,sbcl-ieee-floats) - ("local-time" ,sbcl-local-time) - ("md5" ,sbcl-md5) - ("split-sequence" ,sbcl-split-sequence))) + (list sbcl-alexandria + sbcl-babel + sbcl-cl-ppcre + sbcl-ieee-floats + sbcl-local-time + sbcl-md5 + sbcl-split-sequence)) (home-page "https://github.com/dimitri/cl-ixf") (synopsis "Parse IBM IXF file format") (description @@ -11932,8 +11858,7 @@ Inflector module.") (base32 "1dir0s70ca3hagxv9x15zq4p4ajgl7jrcgqsza2n2y7iqbxh0dwi")))) (build-system asdf-build-system/sbcl) (inputs - `(("metabang-bind" ,sbcl-metabang-bind) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-metabang-bind sbcl-trivial-gray-streams)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/chaitanyagupta/qbase64") @@ -11993,8 +11918,7 @@ LispWorks library that are used in software such as ContextL.") (base32 "0gk1izx6l6g48nypmnm9r6mzjx0jixqjj2kc6klf8a88rr5xd226")))) (build-system asdf-build-system/sbcl) (inputs - `(("closer-mop" ,sbcl-closer-mop) - ("lw-compat" ,sbcl-lw-compat))) + (list sbcl-closer-mop sbcl-lw-compat)) (home-page "https://github.com/pcostanza/contextl") (synopsis "Context-oriented programming for Common Lisp") (description "ContextL is a CLOS extension for Context-Oriented @@ -12059,12 +11983,12 @@ package that includes a number of renames and shadows. ") (native-inputs (list sbcl-hu.dwim.asdf)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("closer-mop" ,sbcl-closer-mop) - ("hu.dwim.common-lisp" ,sbcl-hu.dwim.common-lisp) - ("iterate" ,sbcl-iterate) - ("metabang-bind" ,sbcl-metabang-bind))) + (list sbcl-alexandria + sbcl-anaphora + sbcl-closer-mop + sbcl-hu.dwim.common-lisp + sbcl-iterate + sbcl-metabang-bind)) (home-page "http://dwim.hu/") (synopsis "Common Lisp library shared by other hu.dwim systems") (description "This package contains a support library for other @@ -12386,8 +12310,7 @@ camelCase, snake_case, kebab-case (lisp-case).") (base32 "0k2i3d4k9cpci235mwfm0c5a4yqfkijr716bjv7cdlpzx88lazm9")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("babel" ,sbcl-babel))) + (list sbcl-alexandria sbcl-babel)) (synopsis "Percent Encoding (aka URL Encoding) Common Lisp library") (description "This library provides trivial percent encoding and decoding functions for URLs.") @@ -12417,7 +12340,7 @@ decoding functions for URLs.") (base32 "1xcm31n7afh5316lwz8iqbjx7kn5lw0l11arg8mhdmkx42aj4gkk")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (synopsis "Templating system for Common Lisp") (description "A mixture of features from eRuby and HTML::Template. You could name it \"Yet Another LSP\" (LispServer Pages) but it's a bit more than @@ -12648,7 +12571,7 @@ Common Lisp.") (base32 "1b2yl6lf6vis17y4n5s505p7ica96bdafcl6vydy1hg50fy33nfr")))) (build-system asdf-build-system/sbcl) (inputs - `(("ppcre" ,sbcl-cl-ppcre))) + (list sbcl-cl-ppcre)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/BnMcGn/html-entities/") @@ -12679,16 +12602,16 @@ encode and decode entities in HTML.") (base32 "16k19zjkhh7r64vjq371k5jwjs7cdfjz83flh561n4h4v1z89fps")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("iterate" ,sbcl-iterate) - ("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("ppcre" ,sbcl-cl-ppcre) - ("drakma" ,sbcl-drakma) - ("html-entities" ,sbcl-html-entities) - ("yason" ,sbcl-yason) - ("flexi-streams" ,sbcl-flexi-streams) - ("do-urlencode" ,sbcl-do-urlencode))) + (list sbcl-bordeaux-threads + sbcl-iterate + sbcl-alexandria + sbcl-anaphora + sbcl-cl-ppcre + sbcl-drakma + sbcl-html-entities + sbcl-yason + sbcl-flexi-streams + sbcl-do-urlencode)) (home-page "https://github.com/tkych/quicksearch/") (synopsis "Search Engine Interface for Common Lisp packages") (description "Quicksearch is a search-engine-interface for Common Lisp. @@ -12723,8 +12646,7 @@ function @code{?} is abbreviation wrapper for @code{quicksearch}.") (base32 "1xpnyzksk2xld64b6lw6rw0gn5zxlb77jwna59sd4yl7kxhxlfpf")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("trivia" ,sbcl-trivia))) + (list sbcl-alexandria sbcl-trivia)) (home-page "https://github.com/alex-gutev/agutil/") (synopsis "Collection of Common Lisp utilities") (description "A collection of Common Lisp utility functions and macros @@ -12786,9 +12708,7 @@ directly.") (base32 "1si68n1j6rpns8jw6ksqjpb937pdl30v7xza8rld7j5vh0jhy2yi")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("closer-mop" ,sbcl-closer-mop) - ("symbol-munger" ,sbcl-symbol-munger))) + (list sbcl-alexandria sbcl-closer-mop sbcl-symbol-munger)) (native-inputs (list sbcl-lisp-unit2)) (home-page "https://github.com/AccelerationNet/collectors/") @@ -12818,10 +12738,7 @@ collecting values easier.") (base32 "10jxj043d2dw5vc0i0lz0lsa4qszn8him5is8jdhl4nsyfcazmky")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("collectors" ,sbcl-collectors) - ("optima" ,sbcl-optima))) + (list sbcl-alexandria sbcl-anaphora sbcl-collectors sbcl-optima)) (native-inputs (list sbcl-prove)) (home-page "https://github.com/alex-gutev/cl-environments") @@ -12857,14 +12774,14 @@ environment access API.") (native-inputs (list sbcl-fiveam)) (inputs - `(("agutil" ,sbcl-agutil) - ("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("arrows" ,sbcl-arrows) - ("cl-environments" ,sbcl-cl-environments) - ("closer-mop" ,sbcl-closer-mop) - ("iterate" ,sbcl-iterate) - ("optima" ,sbcl-optima))) + (list sbcl-agutil + sbcl-alexandria + sbcl-anaphora + sbcl-arrows + sbcl-cl-environments + sbcl-closer-mop + sbcl-iterate + sbcl-optima)) (home-page "https://github.com/alex-gutev/static-dispatch") (synopsis "Static generic function dispatch for Common Lisp") (description "Static dispatch is a Common Lisp library, inspired by @@ -12903,12 +12820,12 @@ and comparison operations when used heavily in numeric code.") "17kdjqmm2ib347b8lqm3k4kca2j53kr0azb6h7m0v5i157ibndsw")))) (build-system asdf-build-system/sbcl) (inputs - `(("agutil" ,sbcl-agutil) - ("anaphora" ,sbcl-anaphora) - ("arrows" ,sbcl-arrows) - ("cl-environments" ,sbcl-cl-environments) - ("introspect-environment" ,sbcl-introspect-environment) - ("optima" ,sbcl-optima))) + (list sbcl-agutil + sbcl-anaphora + sbcl-arrows + sbcl-cl-environments + sbcl-introspect-environment + sbcl-optima)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/alex-gutev/cl-form-types") @@ -12992,7 +12909,7 @@ objects, which is extensible to user-defined types.") (base32 "0lzljvf343xb6mlh6lni2i27hpm5qd376522mk6hr2pa20vd6rdq")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "https://github.com/rpav/defpackage-plus") (synopsis "Extensible @code{DEFPACKAGE} variant with version support") (description @@ -13065,10 +12982,8 @@ applications with foreign library dependencies that run some kind of GUI.") (base32 "062cnb2dwli6pw3zvv46jfxyxdzcbzwsck5pa6nw03qf1j1hyg3k")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("closer-mop" ,sbcl-closer-mop) - ("form-fiddle" ,sbcl-form-fiddle) - ("lambda-fiddle" ,sbcl-lambda-fiddle))) + (list sbcl-bordeaux-threads sbcl-closer-mop sbcl-form-fiddle + sbcl-lambda-fiddle)) (home-page "https://github.com/Shinmera/deeds") (synopsis "Extensible Event Delivery System") (description @@ -13156,13 +13071,13 @@ package.") (base32 "146yv0hc4hmk72562ssj2d41143pp84dcbd1h7f4nx1c7hf2bb0d")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("cl-json" ,sbcl-cl-json) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("claw-support" ,sbcl-claw-support) - ("local-time" ,sbcl-local-time) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-alexandria + sbcl-cffi + sbcl-cl-json + sbcl-cl-ppcre + sbcl-claw-support + sbcl-local-time + sbcl-trivial-features)) (home-page "https://github.com/borodust/claw") (synopsis "Autowrapper for Common Lisp") (description @@ -13194,9 +13109,7 @@ and lean bindings to C libraries.") (base32 "01df3kyf2qs3czi332dnz2s35x2j0fq46vgmsw7wjrrvnqc22mk5")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("claw" ,sbcl-claw))) + (list sbcl-alexandria sbcl-cffi sbcl-claw)) (home-page "https://github.com/borodust/claw-utils") (synopsis "Utilities for easier autowrapping") (description @@ -13227,10 +13140,9 @@ autowrapping with @code{claw}.") (base32 "0ip49hhq32w80qsc7jmspyda5r2rsszvw0mk2r3341cld78sz9ya")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("alexandria" ,sbcl-alexandria) - ("clunit2" ,sbcl-clunit2))) + (list sbcl-alexandria sbcl-clunit2)) (inputs - `(("let-plus" ,sbcl-let-plus))) + (list sbcl-let-plus)) (synopsis "Simple array operations library for Common Lisp") (description "This library is a collection of functions and macros for manipulating @@ -13263,17 +13175,17 @@ Common Lisp arrays and performing numerical calculations with them.") (patches (search-patches "sbcl-clml-fix-types.patch")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandia" ,sbcl-alexandria) - ("array-operations" ,sbcl-array-operations) - ("cl-fad" ,sbcl-cl-fad) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("drakma" ,sbcl-drakma) - ("introspect-environment" ,sbcl-introspect-environment) - ("iterate" ,sbcl-iterate) - ("lparallel" ,sbcl-lparallel) - ("parse-number" ,sbcl-parse-number) - ("split-sequence" ,sbcl-split-sequence) - ("trivial-garbage" ,sbcl-trivial-garbage))) + (list sbcl-alexandria + sbcl-array-operations + sbcl-cl-fad + sbcl-cl-ppcre + sbcl-drakma + sbcl-introspect-environment + sbcl-iterate + sbcl-lparallel + sbcl-parse-number + sbcl-split-sequence + sbcl-trivial-garbage)) (synopsis "Common Lisp machine learning library") (description "CLML (Common Lisp Machine Learning) is a high performance and large @@ -13336,7 +13248,7 @@ Polar Stereographic).") (native-inputs (list sbcl-fiveam)) (inputs - `(("utm-ups" ,sbcl-utm-ups))) + (list sbcl-utm-ups)) (synopsis "Convert coordinates between latitude/longitude and MGRS") (description @@ -13565,8 +13477,7 @@ It's independent of the implementation and operating system.") (base32 "012ry02djnqyvvs61wbbqj3saz621w2l9gczrywdxhi5p4ycx318")))) (build-system asdf-build-system/sbcl) (inputs - `(("trivial-shell" ,sbcl-trivial-shell) - ("named-readtables" ,sbcl-named-readtables))) + (list sbcl-trivial-shell sbcl-named-readtables)) (home-page "https://github.com/Neronus/Clesh") (synopsis "Embed shell code in Common Lisp") (description @@ -13598,8 +13509,7 @@ backtick. It has been forked from SHELISP.") (base32 "04wnxcgk40x8p0gxnz9arv1a5wasdqrdxa8c4p5v7r2mycfps6jj")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("trivial-timeout" ,sbcl-trivial-timeout))) + (list sbcl-bordeaux-threads sbcl-trivial-timeout)) (home-page "https://github.com/rpav/trivial-channels") (synopsis "Common Lisp simple thread-safe channels with timeout") (description @@ -13628,7 +13538,7 @@ backtick. It has been forked from SHELISP.") (base32 "06f46zr3gp3wlm2kgxna24qd2gpr1v89x9fynh1x5vrw6c6hqjcv")))) (build-system asdf-build-system/sbcl) (inputs - `(("drakma" ,sbcl-drakma))) + (list sbcl-drakma)) (home-page "https://github.com/eudoxia0/trivial-download/") (synopsis "Download files from Common Lisp") (description @@ -13657,8 +13567,7 @@ from Common Lisp. It provides a progress bar.") (base32 "0lkraw0dwh4is4x5sp5rjrw6f93m0gr9849abrbi12s25ws7jbw4")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("osicat" ,sbcl-osicat) - ("prove" ,sbcl-prove))) + (list sbcl-osicat sbcl-prove)) (home-page "https://github.com/cbeo/gtwiwtg/") (synopsis "Naive generators for Common Lisp") (description @@ -13689,8 +13598,7 @@ and understandable.") (base32 "1ldb4qhmx431n3lsq71ynwb9ybazbfqd55icjbhi06mj52ngndir")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("documentation-utils-extensions" ,sbcl-documentation-utils-extensions))) + (list sbcl-bordeaux-threads sbcl-documentation-utils-extensions)) (home-page "https://github.com/sirherrbatka/cl-progress-bar/") (synopsis "Progress bars in Common Lisp") (description @@ -13751,12 +13659,9 @@ whichever package you switch to.") (base32 "0n369n6b7y1m49biccnnr7svymjdsk8sksrkqrn3mj21vgv7s7bg")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("cffi-grovel" ,sbcl-cffi) - ("rove" ,sbcl-rove) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("bordeaux-threads" ,sbcl-bordeaux-threads))) + (list sbcl-cffi sbcl-rove sbcl-cl-ppcre sbcl-bordeaux-threads)) (inputs - `(("cffi" ,sbcl-cffi))) + (list sbcl-cffi)) (home-page "https://github.com/fukamachi/supertrace") (synopsis "Improved Common Lisp tracing for debugging and profiling") (description @@ -13786,7 +13691,7 @@ for debugging and profiling real world applications.") (base32 "0fbzqbpm2ixz85555krl36kbbbjyn699vdj6k383khi3g9y629fa")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "http://shinmera.github.io/trivial-benchmark/") (synopsis "Easy to use benchmarking system for Common Lisp") (description @@ -13819,9 +13724,7 @@ even by adding additional statistical @code{compute}ations. ") (base32 "17kai1anbkk5dj5sbrsin2fc019cmcbglb900db60v38myj0y0wf")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("parenscript" ,sbcl-parenscript) - ("named-readtables" ,sbcl-named-readtables))) + (list sbcl-cl-ppcre sbcl-parenscript sbcl-named-readtables)) (home-page "https://github.com/ahungry/glyphs/") (synopsis "Reduce Common Lisp verbosity") (description @@ -13851,12 +13754,12 @@ Lisp, inspired by BODOL (@url{https://github.com/bodil/BODOL}).") (base32 "186v95wgsj2hkxdw2jl9x1w4fddjclp7arp0rrd9vf5ly8h8sbf3")))) (build-system asdf-build-system/sbcl) (inputs - `(("drakma" ,sbcl-drakma) - ("alexandria" ,sbcl-alexandria) - ("cxml" ,sbcl-cxml) - ("ironclad" ,sbcl-ironclad) - ("puri" ,sbcl-puri) - ("cl-base64" ,sbcl-cl-base64))) + (list sbcl-drakma + sbcl-alexandria + sbcl-cxml + sbcl-ironclad + sbcl-puri + sbcl-cl-base64)) (synopsis "Work with Amazon S3 and Amazon CloudFront from Common Lisp") (description "This is ZS3, a library for working with Amazon's Simple Storage Service (S3) and CloudFront service from Common Lisp.") @@ -14122,10 +14025,7 @@ determination library using @emph{magic} numbers.") (base32 "16ag48sswgimr1fzr582vhym4s03idpd4lkydw5s58lv80ibpim8")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("serapeum" ,sbcl-serapeum) - ("ppcre" ,sbcl-cl-ppcre) - ("unicode" ,sbcl-cl-unicode))) + (list sbcl-alexandria sbcl-serapeum sbcl-cl-ppcre sbcl-cl-unicode)) (home-page "https://github.com/ruricolist/cl-shlex") (synopsis "Common Lisp lexical analyzer for shell-like syntaxes") (description @@ -14212,15 +14112,14 @@ be usable from multi-threaded programs.") (base32 "1c46q9lmzqv14z80d3fwdawgn3pn4922x31fyqvsvbcjm4hd16fb")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("osicat" ,sbcl-osicat) - ("ppcre" ,sbcl-cl-ppcre) - ("split-sequence" ,sbcl-split-sequence) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-alexandria + sbcl-cffi + sbcl-osicat + sbcl-cl-ppcre + sbcl-split-sequence + sbcl-trivial-features)) (native-inputs - `(("cl-fad" ,sbcl-cl-fad) - ("prove" ,sbcl-prove))) + (list sbcl-cl-fad sbcl-prove)) (home-page "https://github.com/fourier/ppath") (synopsis "Common Lisp's implementation of the Python's os.path module") (description @@ -14255,7 +14154,7 @@ corresponding OS system functions are called.") (base32 "0v6h8lk17iqv1qkxgqjyzn8gi6v0hvq2vmfbb01md3zjvjqxn6lr")))) (build-system asdf-build-system/sbcl) (inputs - `(("named-readtables" ,sbcl-named-readtables))) + (list sbcl-named-readtables)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/williamyaoh/trivial-escapes") @@ -14289,12 +14188,10 @@ It provides four readtables. The default one lets you write strings like this: (base32 "0ha36bhg474vr76vfhr13szc8cfdj1ickg92k1icz791bqaqg67p")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("command-line-arguments" ,sbcl-command-line-arguments) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-alexandria sbcl-command-line-arguments + sbcl-trivial-gray-streams)) (native-inputs - `(("trivial-escapes" ,sbcl-trivial-escapes) - ("rove" ,sbcl-rove))) + (list sbcl-trivial-escapes sbcl-rove)) (home-page "https://github.com/yitzchak/cl-indentify") (synopsis "Code beautifier for Common Lisp") (description @@ -14324,7 +14221,7 @@ source files.") (base32 "1lyrglc3h1if44gxd9cwv90wa90nrdjvb7fry39b1xn8ywdfa7di")))) (build-system asdf-build-system/sbcl) (inputs - `(("acclimation" ,sbcl-acclimation))) + (list sbcl-acclimation)) (home-page "https://github.com/s-expressionists/Concrete-Syntax-Tree") (synopsis "Parse Common Lisp code into a concrete syntax tree") (description @@ -14445,7 +14342,7 @@ objects themselves.") (base32 "00p5c053kmgq4ks6l9mxsqz6g3bjcybvkvj0bh3r90qgpkaawm1p")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (home-page "https://shinmera.github.io/system-locale/") (synopsis "Get the system's locale and language settings in Common Lisp") (description @@ -14476,7 +14373,7 @@ display messages in the user's native language.") (base32 "0py176ibmsc01n5r0q1bs1ykqf5jwdbh8kx0j1a814l9y51241v0")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (home-page "https://shinmera.github.io/language-codes/") (synopsis "Map ISO language codes to language names in Common Lisp") (description @@ -14506,9 +14403,8 @@ language name mapping.") (base32 "13y5jskx8n2b7kimpfarr8v777w3b7zj5swg1b99nj3hk0843ixw")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils) - ("language-codes" ,sbcl-language-codes) - ("system-locale" ,sbcl-system-locale))) + (list sbcl-documentation-utils sbcl-language-codes + sbcl-system-locale)) (home-page "https://shinmera.github.io/multilang-documentation/") (synopsis "Add multiple languages support to Common Lisp documentation") (description @@ -14569,25 +14465,25 @@ and @code{doseq*}.") (base32 "0si69xfzi769dprwfy7gp1x3bl7lxz6d4n98sa26w9r41wvay5ja")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("babel" ,sbcl-babel) - ("bordeaux-threads" ,sbcl-bordeaux-threads) - ("cl-base64" ,sbcl-cl-base64) - ("cl-indentify" ,sbcl-cl-indentify) - ("closer-mop" ,sbcl-closer-mop) - ("dissect" ,sbcl-dissect) - ("eclector" ,sbcl-eclector) - ("ironclad" ,sbcl-ironclad) - ("iterate" ,sbcl-iterate) - ("multilang-documentation" ,sbcl-multilang-documentation) - ("puri" ,sbcl-puri) - ("pzmq" ,sbcl-pzmq) - ("shasht" ,sbcl-shasht) - ("static-vectors" ,sbcl-static-vectors) - ("trivial-do" ,sbcl-trivial-do) - ("trivial-garbage" ,sbcl-trivial-garbage) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams) - ("trivial-mimes" ,sbcl-trivial-mimes))) + (list sbcl-alexandria + sbcl-babel + sbcl-bordeaux-threads + sbcl-cl-base64 + sbcl-cl-indentify + sbcl-closer-mop + sbcl-dissect + sbcl-eclector + sbcl-ironclad + sbcl-iterate + sbcl-multilang-documentation + sbcl-puri + sbcl-pzmq + sbcl-shasht + sbcl-static-vectors + sbcl-trivial-do + sbcl-trivial-garbage + sbcl-trivial-gray-streams + sbcl-trivial-mimes)) (home-page "https://yitzchak.github.io/common-lisp-jupyter/") (synopsis "Common Lisp kernel for Jupyter") (description @@ -14686,7 +14582,7 @@ adaptations.") (base32 "1kdxfnhh9fz34j8qs7pn7mwjz3v33q4v9nh0hqkyzraq5xs2j3f4")))) (build-system asdf-build-system/sbcl) (inputs - `(("trivial-features" ,sbcl-trivial-features))) + (list sbcl-trivial-features)) (home-page "https://github.com/snmsts/daemon") (synopsis "Daemonize Common Lisp processes") (description @@ -14716,9 +14612,7 @@ on UNIX like platforms.") (base32 "0n8q818ry2shggjfhp8gjby8v5mla9pg97c5g19pcglpnwim7a74")))) (build-system asdf-build-system/sbcl) (inputs - `(("cffi" ,sbcl-cffi) - ("documentation-utils" ,sbcl-documentation-utils) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-cffi sbcl-documentation-utils sbcl-trivial-features)) (home-page "https://shinmera.github.io/file-attributes/") (synopsis "Access to common file attributes in Common Lisp") (description @@ -14785,7 +14679,7 @@ sequences based on the Python difflib module.") (base32 "1varnijivzd4jpimn1cz8p5ks713zzha5cgl4vmb0xr8ahravwzb")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-difflib" ,sbcl-cl-difflib))) + (list sbcl-cl-difflib)) (home-page "https://github.com/wiseman/cl-html-diff") (synopsis "Generate a human-readable diff of two HTML documents") (description @@ -14923,11 +14817,8 @@ UTF-8 block characters.") (native-inputs (list sbcl-lisp-unit2)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("closer-mop" ,sbcl-closer-mop) - ("interpol" ,sbcl-cl-interpol) - ("iterate" ,sbcl-iterate))) + (list sbcl-alexandria sbcl-anaphora sbcl-closer-mop + sbcl-cl-interpol sbcl-iterate)) (synopsis "Common lisp library to unify access to dictionary-like structures") (description @@ -14959,7 +14850,7 @@ dictionary-like data structures.") (base32 "1agkrj3ymskzc3c7pxbrj123d1kygjqcls145m0ap3i07q96hh1r")))) (build-system asdf-build-system/sbcl) (inputs - `(("sxql" ,sbcl-sxql))) + (list sbcl-sxql)) (synopsis "Build and compose SXQL queries dynamically") (description "This is a Common Lisp library to build and compose SXQL queries @@ -14990,9 +14881,7 @@ dynamically.") (base32 "1mdhfkk61djj39vgnns5y1cssd12h0m1cfwd21m8xpa2l3rqvmgf")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("babel" ,sbcl-babel) - ("cl-ppcre-unicode" ,sbcl-cl-ppcre-unicode))) + (list sbcl-alexandria sbcl-babel sbcl-cl-ppcre-unicode)) (synopsis "Internationalisation framework for Common Lisp") (description "This is a Gettext-style internationalisation framework for Common @@ -15023,9 +14912,7 @@ Lisp.") (base32 "0c0m0ar04jn7qf2v8c4sivamlzki03r13rnxy8b3n27rh9r6hgin")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-base64" ,sbcl-cl-base64) - ("flexi-stream" ,sbcl-flexi-streams) - ("ironclad" ,sbcl-ironclad))) + (list sbcl-cl-base64 sbcl-flexi-streams sbcl-ironclad)) (synopsis "Collection of common cryptography functions") (description "This is a collection of common cryptography functions for Common @@ -15056,13 +14943,9 @@ Lisp.") (base32 "04if61wigylsmn996rbfl8ylsd0d9hzdmg7p2wiglncibjzcl5k9")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("json-streams" ,sbcl-json-streams) - ("split-sequence" ,sbcl-split-sequence) - ("stefil" ,sbcl-stefil))) + (list sbcl-json-streams sbcl-split-sequence sbcl-stefil)) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("flexi-stream" ,sbcl-flexi-streams) - ("string-case" ,sbcl-string-case))) + (list sbcl-cl-ppcre sbcl-flexi-streams sbcl-string-case)) (synopsis "HTML5 parser for Common Lisp") (description "This a Common Lisp library to parse HTML5 documents.") (home-page "https://github.com/rotatef/cl-html5-parser") @@ -15093,8 +14976,7 @@ Lisp.") (native-inputs (list sbcl-fiveam)) (inputs - `(("anaphora" ,sbcl-anaphora) - ("babel" ,sbcl-babel))) + (list sbcl-anaphora sbcl-babel)) (synopsis "RFC 3986 percent-encoding library") (description "This is a Common Lisp library providing RFC 3986 percent-encoding.") @@ -15124,9 +15006,7 @@ Lisp.") (base32 "0vza9gj9q42nzb5v8aj22lmn4aqx9vrddsb5a343nbwfz89hbh9x")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("cl-ppcre" ,sbcl-cl-ppcre))) + (list sbcl-alexandria sbcl-cffi sbcl-cl-ppcre)) (home-page "https://notabug.org/cage/cl-mount-info.git") (synopsis "Library to get information about mounted filesystems") (description @@ -15200,7 +15080,7 @@ line tool @code{df} and get disk space information using @code{statvfs}.") (base32 "0sdaff9hpsx7bpkkkqavmxmrrlc2d61gmqjjgn8xchncng4a0rf8")))) (build-system asdf-build-system/sbcl) (inputs - `(("cffi" ,sbcl-cffi))) + (list sbcl-cffi)) (home-page "https://github.com/muyinliu/cl-cpus") (synopsis "Common Lisp feature to get number of CPUs") (description @@ -15382,8 +15262,7 @@ immediately loaded.") (base32 "0r3vnl9lywn4ksy34apcv6j825qp7l1naddawr14v4lwacndb80v")))) (build-system asdf-build-system/sbcl) (inputs - `(("bodge-utilities" ,sbcl-bodge-utilities) - ("rtg-math" ,sbcl-rtg-math))) + (list sbcl-bodge-utilities sbcl-rtg-math)) (home-page "https://github.com/borodust/bodge-math") (synopsis "Common Lisp core math utilities of BODGE library collection") (description @@ -15416,8 +15295,7 @@ immediately loaded.") (native-inputs (list sbcl-trivial-features)) (inputs - `(("cffi" ,sbcl-cffi) - ("sbcl-alexandria" ,sbcl-alexandria))) + (list sbcl-cffi sbcl-alexandria)) (home-page "https://github.com/borodust/bodge-blobs-support") (synopsis "Common Lisp utilities for blob packages") (description @@ -15547,12 +15425,12 @@ OpenGL (Mesa), GLU and GLUT (FreeGLUT) APIs using CFFI.") (base32 "0w1i734gkdkziin74ql2nhx7jdjxx02ylssaa6qdrvnj4br1124a")))) (build-system asdf-build-system/sbcl) (inputs - `(("cffi" ,sbcl-cffi) - ("cl-opengl" ,sbcl-cl-opengl) - ("glsl-packing" ,sbcl-glsl-packing) - ("golden-utils" ,sbcl-golden-utils) - ("static-vectors" ,sbcl-static-vectors) - ("varjo" ,sbcl-varjo))) + (list sbcl-cffi + sbcl-cl-opengl + sbcl-glsl-packing + sbcl-golden-utils + sbcl-static-vectors + sbcl-varjo)) (home-page "https://git.mfiano.net/mfiano/shadow") (synopsis "Management system for OpenGL shader programs") (description @@ -15586,9 +15464,7 @@ buffer object types (UBO, SSBO currently).") (base32 "04vyh2j00zdpb8ryxr8g81wjcmqlz9wrn55r3cypcj4qg970r5wi")))) (build-system asdf-build-system/sbcl) (inputs - `(("golden-utils" ,sbcl-golden-utils) - ("shadow" ,sbcl-shadow) - ("varjo" ,sbcl-varjo))) + (list sbcl-golden-utils sbcl-shadow sbcl-varjo)) (home-page "https://git.mfiano.net/mfiano/umbra") (synopsis "Common Lisp library of reusable GPU shader functions") (description @@ -15654,13 +15530,13 @@ abstract, final and singleton classes.") (native-inputs (list sbcl-fiasco)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("float-features" ,sbcl-float-features) - ("fset" ,sbcl-fset) - ("global-vars" ,sbcl-global-vars) - ("json-streams" ,sbcl-json-streams) - ("serapeum" ,sbcl-serapeum) - ("trivia" ,sbcl-trivia))) + (list sbcl-alexandria + sbcl-float-features + sbcl-fset + sbcl-global-vars + sbcl-json-streams + sbcl-serapeum + sbcl-trivia)) (home-page "https://coalton-lang.github.io") (synopsis "Dialect of ML in Common Lisp") (description @@ -15692,8 +15568,7 @@ allows one to gradually make their programs safer.") (base32 "13kkajkva2shm19fvn4yashsw18l6imv2rmy3hmpcky7g5ay7bv3")))) (build-system asdf-build-system/sbcl) (inputs - `(("array-utils" ,sbcl-array-utils) - ("lquery" ,sbcl-lquery))) + (list sbcl-array-utils sbcl-lquery)) (home-page "https://shinmera.github.io/clip/") (synopsis "Common Lisp HTML templating engine") (description @@ -15759,11 +15634,8 @@ handling the accessing of files on the underlying system however.") (base32 "0pnqflgz410zydc1ivwnd8hcl24bgr7x12yjzr7g4lq3ibc8y97b")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils) - ("fast-io" ,sbcl-fast-io) - ("ieee-floats" ,sbcl-ieee-floats) - ("static-vectors" ,sbcl-static-vectors) - ("trivial-garbage" ,sbcl-trivial-garbage))) + (list sbcl-documentation-utils sbcl-fast-io sbcl-ieee-floats + sbcl-static-vectors sbcl-trivial-garbage)) (home-page "https://shirakumo.github.io/terrable/") (synopsis "Parser library for Terragen TER terrain files") (description @@ -15825,7 +15697,7 @@ color palette for a GUI or web page.") (base32 "099h0rrdzxnlmn8avi72mg2dl0kccp7w01b2p9nwyy4b8yr32cir")))) (build-system asdf-build-system/sbcl) (inputs - `(("flexi-streams" ,sbcl-flexi-streams))) + (list sbcl-flexi-streams)) (home-page "https://github.com/eugeneia/cl-qprint/") (synopsis "Implementation of the quoted-printable encoding") (description @@ -15858,9 +15730,7 @@ described in RFC 2045 (see @url{http://tools.ietf.org/html/rfc2045}).") (base32 "0qn8if0fj6vzc897pqqqs0m1y107gmzqngpqhqmwrcsp1ckj5k0v")))) (build-system asdf-build-system/sbcl) (inputs - `(("ppcre" ,sbcl-cl-ppcre) - ("cl-base64" ,sbcl-cl-base64) - ("cl-qprint" ,sbcl-cl-qprint))) + (list sbcl-cl-ppcre sbcl-cl-base64 sbcl-cl-qprint)) (native-inputs (list sbcl-rove)) (home-page "https://github.com/eugeneia/cl-qprint/") @@ -15938,14 +15808,10 @@ in Common Lisp.") (base32 "15vrp1kayhjb5c1vc9x8wlm8rimk73vpa7yc101cf0gsg1fjazl6")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("ppcre" ,sbcl-cl-ppcre))) + (list sbcl-alexandria sbcl-cl-ppcre)) (native-inputs - `(("fiveam" ,sbcl-fiveam) - ("cl-csv" ,sbcl-cl-csv) - ("parse-float" ,sbcl-parse-float) - ("lispbuilder-sdl" ,sbcl-lispbuilder-sdl) - ("lparallel" ,sbcl-lparallel))) + (list sbcl-fiveam sbcl-cl-csv sbcl-parse-float sbcl-lispbuilder-sdl + sbcl-lparallel)) (home-page "https://github.com/privet-kitty/dufy") (synopsis "Color library for Common Lisp") (description @@ -16038,8 +15904,7 @@ for Common Lisp.") (native-inputs (list sbcl-fiveam)) (inputs - `(("clsql" ,sbcl-clsql) - ("ironclad" ,sbcl-ironclad))) + (list sbcl-clsql sbcl-ironclad)) (home-page "https://github.com/charje/cl-authentic") (synopsis "User/password management for Common Lisp applications") (description "Authentic provides a light-weight and extendible @@ -16073,7 +15938,7 @@ confirmation tokens, and user authentication.") (native-inputs (list sbcl-parachute)) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (home-page "https://shinmera.github.io/3d-vectors/") (synopsis "Utility library implementing 2D, 3D, and 4D vectors") (description @@ -16107,8 +15972,7 @@ offers them both in non-modifying and modifying versions where applicable.") (native-inputs (list sbcl-parachute)) (inputs - `(("3d-vectors" ,sbcl-3d-vectors) - ("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-3d-vectors sbcl-documentation-utils)) (home-page "https://shinmera.github.io/3d-matrices/") (synopsis "Utility library implementing 2x2, 3x3, 4x4 and NxM matrices") (description @@ -16183,10 +16047,8 @@ application fail and be unable to do so using its standard UI.") (base32 "0as5796yazchq1qkna3srxlz5v7cf7ffny9cbqi41wsa2s20vbh9")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("documentation-utils" ,sbcl-documentation-utils) - ("parse-float" ,sbcl-parse-float) - ("trivial-indent" ,sbcl-trivial-indent))) + (list sbcl-cl-ppcre sbcl-documentation-utils sbcl-parse-float + sbcl-trivial-indent)) (home-page "https://shirakumo.github.io/glsl-toolkit/") (synopsis "Parser for OpenGL Shader Language source files") (description @@ -16217,9 +16079,7 @@ allow to wrangle OpenGL Shader Language (GLSL) source files.") (base32 "1ls1pij7dvb65g4nam7nvik1218jvfk5iplr48vy290fw3lq7v98")))) (build-system asdf-build-system/sbcl) (inputs - `(("array-utils" ,sbcl-array-utils) - ("bordeaux-threads" ,sbcl-bordeaux-threads) - ("dissect" ,sbcl-dissect))) + (list sbcl-array-utils sbcl-bordeaux-threads sbcl-dissect)) (home-page "https://shinmera.github.io/simple-tasks/") (synopsis "Simple task scheduling framework") (description "This is a task scheduling framework for Common Lisp.") @@ -16248,9 +16108,7 @@ allow to wrangle OpenGL Shader Language (GLSL) source files.") (base32 "0bw1887i7396lqg75qvmgjfzz4xbiq9w5dp8wxdgrcsm0qwlraw7")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("simple-tasks" ,sbcl-simple-tasks) - ("trivial-features" ,sbcl-trivial-features))) + (list sbcl-bordeaux-threads sbcl-simple-tasks sbcl-trivial-features)) (home-page "https://shinmera.github.io/trivial-main-thread/") (synopsis "Compatibility library to run things in the main thread") (description @@ -16347,10 +16205,9 @@ all kind of typesetting applications.") (base32 "01mh20s5gj0lajq45anxji77ykq1wcg72mn1y9a1k8i7q1ainjlr")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("alexandria" ,sbcl-alexandria) - ("parachute" ,sbcl-parachute))) + (list sbcl-alexandria sbcl-parachute)) (inputs - `(("trivial-do" ,sbcl-trivial-do))) + (list sbcl-trivial-do)) (home-page "https://yitzchak.github.io/shasht/") (synopsis "Common Lisp JSON reading and writing library") (description @@ -16510,8 +16367,7 @@ is built on top of the @code{libev} event library.") (base32 "0cia3721im04q73dfkd688d8splgpz03qa4h8s3r39kar4w3xll2")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("cl-quickcheck" ,sbcl-cl-quickcheck) - ("flexi-streams" ,sbcl-flexi-streams))) + (list sbcl-cl-quickcheck sbcl-flexi-streams)) (home-page "https://github.com/rotatef/json-streams") (synopsis "Common Lisp library for reading and writing JSON") (description @@ -16596,9 +16452,7 @@ or GOLDEN-UTILS.") (native-inputs (list sbcl-stefil)) (inputs - `(("flexi-streams" ,sbcl-flexi-streams) - ("split-sequence" ,sbcl-split-sequence) - ("yacc" ,sbcl-cl-yacc))) + (list sbcl-flexi-streams sbcl-split-sequence sbcl-cl-yacc)) (home-page "https://github.com/rotatef/gettext") (synopsis "Common Lisp implementation of Gettext") (description @@ -16722,9 +16576,7 @@ CL-I18N and CL-L10N.") (native-inputs (list sbcl-clunit)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("let-plus" ,sbcl-let-plus))) + (list sbcl-alexandria sbcl-anaphora sbcl-let-plus)) (home-page "https://github.com/tpapp/cl-slice") (synopsis "Array slices for Common Lisp") (description @@ -16756,20 +16608,20 @@ CL-I18N and CL-L10N.") (native-inputs (list sbcl-fiveam)) (inputs - `(("access" ,sbcl-access) - ("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("babel" ,sbcl-babel) - ("cl-locale" ,sbcl-cl-locale) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("cl-slice" ,sbcl-cl-slice) - ("closer-mop" ,sbcl-closer-mop) - ("gettext" ,sbcl-gettext) - ("iterate" ,sbcl-iterate) - ("local-time" ,sbcl-local-time) - ("parser-combinators" ,sbcl-parser-combinators) - ("split-sequence" ,sbcl-split-sequence) - ("trivial-backtrace" ,sbcl-trivial-backtrace))) + (list sbcl-access + sbcl-alexandria + sbcl-anaphora + sbcl-babel + sbcl-cl-locale + sbcl-cl-ppcre + sbcl-cl-slice + sbcl-closer-mop + sbcl-gettext + sbcl-iterate + sbcl-local-time + sbcl-parser-combinators + sbcl-split-sequence + sbcl-trivial-backtrace)) (home-page "https://mmontone.github.io/djula/") (synopsis "Common Lisp port of the Django templating language") (description @@ -16800,9 +16652,7 @@ Django with a syntax similar to Python Jinja2.") (base32 "1akz9ggh33x2cq3h0f1cd0p632v1mbagv3dzsb0r10bwg9lh3nmv")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils) - ("form-fiddle" ,sbcl-form-fiddle) - ("lambda-fiddle" ,sbcl-lambda-fiddle))) + (list sbcl-documentation-utils sbcl-form-fiddle sbcl-lambda-fiddle)) (home-page "https://shinmera.github.io/for/") (synopsis "Extensible iteration macro library") (description @@ -16835,12 +16685,12 @@ require code-walking and is easier to extend.") (base32 "00nm3sjngbflj2gd5q0xs2m136w4kix6krww23nk64pkkyq2fs86")))) (build-system asdf-build-system/sbcl) (inputs - `(("3d-vectors" ,sbcl-3d-vectors) - ("array-utils" ,sbcl-array-utils) - ("documentation-utils" ,sbcl-documentation-utils) - ("for" ,sbcl-for) - ("lambda-fiddle" ,sbcl-lambda-fiddle) - ("trivial-garbage" ,sbcl-trivial-garbage))) + (list sbcl-3d-vectors + sbcl-array-utils + sbcl-documentation-utils + sbcl-for + sbcl-lambda-fiddle + sbcl-trivial-garbage)) (home-page "https://shinmera.github.io/flare/") (synopsis "Easy particle systems with fine grained control") (description @@ -16872,8 +16722,7 @@ any existing or future application.") (base32 "08vsvqv3768bwb2y8mwxbw5wyqzzwqr7rd004r6gafdgf9p9mcx3")))) (build-system asdf-build-system/sbcl) (inputs - `(("bordeaux-threads" ,sbcl-bordeaux-threads) - ("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-bordeaux-threads sbcl-documentation-utils)) (home-page "https://shinmera.github.io/simple-inferiors/") (synopsis "Common Lisp library to use inferior processes") (description @@ -16906,10 +16755,8 @@ running into parallelism problems when having to change directory.") (base32 "181aqpj4zkfk1aavj5jw8rym6gw4ma3gd64z2h5fpryabgmwk236")))) (build-system asdf-build-system/sbcl) (inputs - `(("simple-inferiors" ,sbcl-simple-inferiors) - ("lambda-fiddle" ,sbcl-lambda-fiddle) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-simple-inferiors sbcl-lambda-fiddle sbcl-cl-ppcre + sbcl-documentation-utils)) (home-page "https://shinmera.github.io/legit/") (synopsis "Interface to the git binary") (description @@ -17088,7 +16935,7 @@ coverage.") ("split-sequence" ,sbcl-split-sequence) ("varjo" ,sbcl-varjo))) (propagated-inputs - `(("quickproject" ,sbcl-quickproject))) + (list sbcl-quickproject)) (home-page "https://github.com/cbaggers/cepl") (synopsis "Development playground to work with OpenGL") (description @@ -17128,11 +16975,8 @@ window it creates as just another output for your graphics, analogous to how (base32 "1hfmh4vj271jdilir97qs6nqbi5nmn5alyls0w3d3xxqwi6ffqjs")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("bordeaux-threads" ,sbcl-bordeaux-threads) - ("log4cl" ,sbcl-log4cl) - ("closer-mop" ,sbcl-closer-mop) - ("trivial-garbage" ,sbcl-trivial-garbage))) + (list sbcl-alexandria sbcl-bordeaux-threads sbcl-log4cl + sbcl-closer-mop sbcl-trivial-garbage)) (home-page "https://stmx.org/") (synopsis "High performance Transactional Memory for Common Lisp") (description @@ -17217,7 +17061,7 @@ impossible to merge back upstream.") (base32 "0mp5jdqq0aamdhgnvw149cqqi3zg7dkkibp25qi4rafw1fnpd40z")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-documentation-utils)) (native-inputs (list sbcl-parachute)) (home-page "https://shinmera.github.io/atomics/") @@ -17254,7 +17098,7 @@ implementations offer.") "0251r0mpjm0y3qsm4lm7ncvrkxvgwc53spdm1p2mpayhvkkqqsws")))) (build-system asdf-build-system/sbcl) (inputs - `(("babel" ,sbcl-babel))) + (list sbcl-babel)) (native-inputs (list sbcl-fiveam)) (synopsis "32-bit version of Murmurhash3 for Common Lisp") @@ -17287,7 +17131,7 @@ non-crytographic hashing algorithm.") (base32 "1ycbd73ykfj5j9sdhlzamyv18qbjj6xqf7fhm4fa0nsyr6sr3rf5")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-murmurhash" ,sbcl-cl-murmurhash))) + (list sbcl-cl-murmurhash)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/danshapero/cl-hamt") @@ -17322,19 +17166,18 @@ Common Lisp based on the hash array-mapped trie data structure.") (base32 "1bfz7z8v417dvsp1jz76ir3ihcs8g7zis2d56xx1dpzqzjd95g7z")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("bordeaux-threads" ,sbcl-bordeaux-threads) - ("lparallel" ,sbcl-lparallel) - ("cl-speedy-queue" ,sbcl-cl-speedy-queue) - ("log4cl" ,sbcl-log4cl) - ("str" ,sbcl-cl-str) - ("blackbird" ,sbcl-blackbird) - ("cl-hamt" ,sbcl-cl-hamt) - ("binding-arrows" ,sbcl-binding-arrows) - ("atomics" ,sbcl-atomics))) + (list sbcl-alexandria + sbcl-bordeaux-threads + sbcl-lparallel + sbcl-cl-speedy-queue + sbcl-log4cl + sbcl-cl-str + sbcl-blackbird + sbcl-cl-hamt + sbcl-binding-arrows + sbcl-atomics)) (native-inputs - `(("fiveam" ,sbcl-fiveam) - ("mock" ,sbcl-cl-mock))) + (list sbcl-fiveam sbcl-cl-mock)) (home-page "https://mdbergmann.github.io/cl-gserver/index.html") (synopsis "Actor framework for easy access to state and async operations") (description @@ -17452,8 +17295,7 @@ from the Let Over Lambda book, including community updates.") (base32 "0q8jhp040cvpppyn820mm6a550yfxyr1lar298x13c42mm807f4f")))) (build-system asdf-build-system/sbcl) (inputs - `(("assoc-utils" ,sbcl-assoc-utils) - ("let-over-lambda" ,sbcl-let-over-lambda))) + (list sbcl-assoc-utils sbcl-let-over-lambda)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/ailisp/flute") @@ -17652,39 +17494,39 @@ joysticks, and other such HID devices.") (native-inputs (list sbcl-trivial-features)) (inputs - `(("alexandria" ,sbcl-alexandria) - ("3d-matrices" ,sbcl-3d-matrices) - ("3d-vectors" ,sbcl-3d-vectors) - ("bordeaux-threads" ,sbcl-bordeaux-threads) - ("cl-gamepad" ,sbcl-cl-gamepad) - ("cl-jpeg" ,sbcl-cl-jpeg) - ("cl-opengl" ,sbcl-cl-opengl) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("cl-tga" ,sbcl-cl-tga) - ("closer-mop" ,sbcl-closer-mop) - ("deploy" ,sbcl-deploy) - ("fast-io" ,sbcl-fast-io) - ("flare" ,sbcl-flare) - ("float-features" ,sbcl-float-features) - ("flow" ,sbcl-flow) - ("for" ,sbcl-for) - ("form-fiddle" ,sbcl-form-fiddle) - ("glsl-toolkit" ,sbcl-glsl-toolkit) - ("ieee-floats" ,sbcl-ieee-floats) - ("jsown" ,sbcl-jsown) - ("lambda-fiddle" ,sbcl-lambda-fiddle) - ("lquery" ,sbcl-lquery) - ("messagebox" ,sbcl-messagebox) - ("mmap" ,sbcl-mmap) - ("pathname-utils" ,sbcl-pathname-utils) - ("pngload" ,sbcl-pngload) - ("retrospectiff" ,sbcl-retrospectiff) - ("static-vectors" ,sbcl-static-vectors) - ("terrable" ,sbcl-terrable) - ("trivial-garbage" ,sbcl-trivial-garbage) - ("trivial-indent" ,sbcl-trivial-indent) - ("verbose" ,sbcl-verbose) - ("zpng" ,sbcl-zpng))) + (list sbcl-alexandria + sbcl-3d-matrices + sbcl-3d-vectors + sbcl-bordeaux-threads + sbcl-cl-gamepad + sbcl-cl-jpeg + sbcl-cl-opengl + sbcl-cl-ppcre + sbcl-cl-tga + sbcl-closer-mop + sbcl-deploy + sbcl-fast-io + sbcl-flare + sbcl-float-features + sbcl-flow + sbcl-for + sbcl-form-fiddle + sbcl-glsl-toolkit + sbcl-ieee-floats + sbcl-jsown + sbcl-lambda-fiddle + sbcl-lquery + sbcl-messagebox + sbcl-mmap + sbcl-pathname-utils + sbcl-pngload + sbcl-retrospectiff + sbcl-static-vectors + sbcl-terrable + sbcl-trivial-garbage + sbcl-trivial-indent + sbcl-verbose + sbcl-zpng)) (home-page "https://github.com/Shirakumo/trial") (synopsis "Common Lisp game engine") (description @@ -17761,12 +17603,9 @@ developing library for Common Lisp.") (base32 "1jsqjr6sf86hcdvnjp4gd10qv0r7kfkr9hmda85irb5lha4q9n7w")))) (build-system asdf-build-system/sbcl) (native-inputs - `(("alexandria" ,sbcl-alexandria) - ("parachute" ,sbcl-parachute))) + (list sbcl-alexandria sbcl-parachute)) (inputs - `(("array-utils" ,sbcl-array-utils) - ("closer-mop" ,sbcl-closer-mop) - ("documentation-utils" ,sbcl-documentation-utils))) + (list sbcl-array-utils sbcl-closer-mop sbcl-documentation-utils)) (home-page "https://shirakumo.github.io/alloy/") (synopsis "Common Lisp user interface protocol and toolkit implementation") @@ -17799,7 +17638,7 @@ integrate Alloy into a target backend.") (base32 "1dg029in14928qfxvfshyxmdwhzskzhxx3na0zy98ybx69b21qla")))) (build-system asdf-build-system/sbcl) (inputs - `(("iterate" ,sbcl-iterate))) + (list sbcl-iterate)) (home-page "https://github.com/jphmrst/cl-org-sampler") (synopsis "Extracting Common Lisp docstrings as Emacs Org-mode documents") (description @@ -17930,16 +17769,16 @@ functions allow Lisp programs to explore the web.") (base32 "0ll1s9w29yhhgqssgiw58fcapw4n040gkvpz4sxwv3q2v60rbidj")))) (build-system asdf-build-system/sbcl) (inputs - `(("chipz" ,sbcl-chipz) - ("chunga" ,sbcl-chunga) - ("cl+ssl" ,sbcl-cl+ssl) - ("cl-binding-arrows" ,sbcl-binding-arrows) - ("cl-str" ,sbcl-cl-str) - ("cl-usocket" ,sbcl-usocket) - ("flexi-streams" ,sbcl-flexi-streams) - ("rutils" ,sbcl-rutils) - ("salza2" ,sbcl-salza2) - ("trivial-garbage" ,sbcl-trivial-garbage))) + (list sbcl-chipz + sbcl-chunga + sbcl-cl+ssl + sbcl-binding-arrows + sbcl-cl-str + sbcl-usocket + sbcl-flexi-streams + sbcl-rutils + sbcl-salza2 + sbcl-trivial-garbage)) (home-page "https://github.com/charje/cl-yxorp") (synopsis "Reverse proxy server written in and configurable in Common Lisp") @@ -18007,9 +17846,7 @@ language).") (base32 "0wv3j13fj73gigriw5r9vi920hz05ld7zllsvbxdxvmyfy9k1kly")))) (build-system asdf-build-system/sbcl) (inputs - `(("aserve" ,sbcl-aserve) - ("kmrcl" ,sbcl-kmrcl) - ("xmls" ,sbcl-xmls))) + (list sbcl-aserve sbcl-kmrcl sbcl-xmls)) (home-page "https://github.com/nsrahmad/cl-rss") (synopsis "Common Lisp RSS processor") (description @@ -18039,7 +17876,7 @@ RSS feeds data via HTTP. Currently, it supports RSS versions 0.90, (base32 "15zs7mc422ycp1cvcxmirif1dq15mlmv8vzd6l6nzn4qgmph9wz0")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "https://github.com/scymtym/trivial-with-current-source-form") (synopsis "Help producing better errors for macro users") (description @@ -18074,10 +17911,8 @@ concept of a source-form to report where the error or warning is located.") (base32 "1h8m2npdzd2cpnl75pvv4yvvfwxa7kl6qvalc9s0y4yws0kaih3i")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandia" ,sbcl-alexandria) - ("trivial-macroexpand-all" ,sbcl-trivial-macroexpand-all) - ("trivial-with-current-source-form" - ,sbcl-trivial-with-current-source-form))) + (list sbcl-alexandria sbcl-trivial-macroexpand-all + sbcl-trivial-with-current-source-form)) (home-page "https://github.com/charje/tailrec") (synopsis "Macro to optimize a Common Lisp function for tail recursion") (description "Just wrap your Common Lisp function in this macro call and @@ -18108,10 +17943,7 @@ is not tail recursive.") (base32 "1bajb09crzadkirdpd6jrpcc55irjd4sxzavygr25l85pafyhniw")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-str" ,sbcl-cl-str) - ("global-vars" ,sbcl-global-vars) - ("plump" ,sbcl-plump) - ("tailrec" ,sbcl-tailrec))) + (list sbcl-cl-str sbcl-global-vars sbcl-plump sbcl-tailrec)) (home-page "https://github.com/interactive-ssr/client/blob/master/main.org") (synopsis "The core functionality for ISSR server modules") @@ -18145,15 +17977,15 @@ and DOM cleaning, to ensure that all remote DOMs are the same.") (base32 "1012jc068qdd8df6mmbn8vmmqlniqm5j2jbyrraw3yz8c13c8280")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("arrows" ,sbcl-arrows) - ("cl-base64" ,sbcl-cl-base64) - ("cl-str" ,sbcl-cl-str) - ("flexi-streams" ,sbcl-flexi-streams) - ("global-vars" ,sbcl-global-vars) - ("ironclad" ,sbcl-ironclad) - ("parse-float" ,sbcl-parse-float) - ("usocket" ,sbcl-usocket))) + (list sbcl-alexandria + sbcl-arrows + sbcl-cl-base64 + sbcl-cl-str + sbcl-flexi-streams + sbcl-global-vars + sbcl-ironclad + sbcl-parse-float + sbcl-usocket)) (home-page "https://github.com/charJe/portal") (synopsis "Portable Websocket Server for Common Lisp") (description @@ -18187,13 +18019,13 @@ customizable errors.") (base32 "0826qrvk64pjspdklns29dv3zhzfhd6k42fq030xajv8a7hkcxda")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-base64" ,sbcl-cl-base64) - ("cl-str" ,sbcl-cl-str) - ("hunchentoot" ,sbcl-hunchentoot) - ("issr-core" ,sbcl-issr-core) - ("jonathan" ,sbcl-jonathan) - ("plump" ,sbcl-plump) - ("portal" ,sbcl-portal))) + (list sbcl-cl-base64 + sbcl-cl-str + sbcl-hunchentoot + sbcl-issr-core + sbcl-jonathan + sbcl-plump + sbcl-portal)) (home-page "https://github.com/interactive-ssr/hunchenissr") (synopsis "Interactive Server Side Rendering backend for Hunchentoot") (description @@ -18226,10 +18058,8 @@ Javascript.") (base32 "1xyqacihxwk4vnffqlg93czmalscglp6sh3bwy3qwb7hdxv6yxz6")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("cl-unification" ,sbcl-cl-unification) - ("hunchenissr" ,sbcl-hunchenissr))) + (list sbcl-alexandria sbcl-cl-ppcre sbcl-cl-unification + sbcl-hunchenissr)) (home-page "https://github.com/interactive-ssr/hunchenissr-routes") (synopsis "Enable path variables when using Hunchenissr") (description @@ -18290,13 +18120,13 @@ bound to whatever value was in the same place in the URL (as a string).") (base32 "0jllnsi2ibw0gax9szpdrjxvw9qqibydpdbnkf683yfb1d5jlci1")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("global-vars" ,sbcl-global-vars) - ("parenscript" ,sbcl-parenscript) - ("cl-markdown" ,sbcl-cl-markdown) - ("ppcre" ,sbcl-cl-ppcre) - ("serapeum" ,sbcl-serapeum) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-alexandria + sbcl-global-vars + sbcl-parenscript + sbcl-cl-markdown + sbcl-cl-ppcre + sbcl-serapeum + sbcl-trivial-gray-streams)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/ruricolist/spinneret") @@ -18351,7 +18181,7 @@ semantics in Lisp and Parenscript. (base32 "10mxm6q62cfpv3hw2w8k968ba8a1xglqdkwlkqs4l4nby3b11aaq")))) (build-system asdf-build-system/sbcl) (inputs - `(("split-sequence" ,sbcl-split-sequence))) + (list sbcl-split-sequence)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/eudoxia0/path-parse") @@ -18471,8 +18301,7 @@ child nodes enumeration, etc. (base32 "01gvshpxil0ggjgfmgcymbgmpsfaxy6aggm0bywkn40rck3038vb")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("bordeaux-threads" ,sbcl-bordeaux-threads))) + (list sbcl-alexandria sbcl-bordeaux-threads)) (native-inputs (list sbcl-hu.dwim.stefil)) (home-page "https://github.com/nikodemus/pileup") @@ -18506,9 +18335,7 @@ for Common Lisp.") (base32 "1dpbzhycg50snl3j01c8dh8gdvhfhz0hnfl54xy55a3wbr3m6rp7")))) (build-system asdf-build-system/sbcl) (inputs - `(("documentation-utils" ,sbcl-documentation-utils) - ("local-time" ,sbcl-local-time) - ("plump" ,sbcl-plump))) + (list sbcl-documentation-utils sbcl-local-time sbcl-plump)) (home-page "https://shinmera.github.io/feeder/") (synopsis "RSS, Atom and general feed parsing and generating") (description @@ -18616,7 +18443,7 @@ provides a method for determining which capabilities a terminal (base32 "0y31za8xr8734p2pf8mrw1jd1fksh2d4y1p12wwjyn8hxxsvsx1w")))) (build-system asdf-build-system/sbcl) (inputs - `(("closer-mop" ,sbcl-closer-mop))) + (list sbcl-closer-mop)) (home-page "https://github.com/sharplispers/conium") (synopsis "Portability library for debugger- and compiler-related tasks") (description @@ -18647,8 +18474,7 @@ tasks in Common Lisp. It is fork of SWANK-BACKEND.") (base32 "1212wbadms9jzrqgarpj3d9xh9w4dab8jhx4k2aryqgf116zs42h")))) (build-system asdf-build-system/sbcl) (inputs - `(("cffi" ,sbcl-cffi) - ("osicat" ,sbcl-osicat))) + (list sbcl-cffi sbcl-osicat)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/eudoxia0/terminal-size") @@ -18727,7 +18553,7 @@ previous commands.") (base32 "01ma0cwirxarwwmdwflnh8kmysmr2smh5kyvzhb2074ljxg8yq2p")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/pnathan/generic-comparability") @@ -18808,16 +18634,11 @@ For a YAML parser and emitter using this, check out cl-yaml.") (base32 "1izjg0v6rf7dh069bbnnr67l30lsqj86wdk7y9ggbgiwh6v9j185")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cl-libyaml" ,sbcl-cl-libyaml) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("parse-number" ,sbcl-parse-number))) + (list sbcl-alexandria sbcl-cl-libyaml sbcl-cl-ppcre + sbcl-parse-number)) (native-inputs - `(("cl-fad" ,sbcl-cl-fad) - ("fiveam" ,sbcl-fiveam) - ("generic-comparability" ,sbcl-generic-comparability) - ("trivial-benchmark" ,sbcl-trivial-benchmark) - ("yason" ,sbcl-yason))) + (list sbcl-cl-fad sbcl-fiveam sbcl-generic-comparability + sbcl-trivial-benchmark sbcl-yason)) (home-page "https://github.com/eudoxia0/cl-yaml") (synopsis "YAML parser for Common Lisp") (description @@ -18848,10 +18669,7 @@ libyaml.") (base32 "0hhh7xn6q12rviayfihg1ym6x6csa0pdjgb88ykqbrz2rs3pgpz5")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("osicat" ,sbcl-osicat) - ("terminfo" ,sbcl-terminfo))) + (list sbcl-alexandria sbcl-cffi sbcl-osicat sbcl-terminfo)) (home-page "https://github.com/sharplispers/linedit") (synopsis "Readline-style line-editor for Common Lisp") (description @@ -18882,8 +18700,7 @@ provides customizable line-editing for Common Lisp programs.") (base32 "1giafck8qfvb688kx5bn9g32rfc12jjywg8vdav36aqbd6lxf5z5")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-ppcre" ,sbcl-cl-ppcre) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-cl-ppcre sbcl-trivial-gray-streams)) (home-page "https://github.com/froydnj/diff") (synopsis "Common Lisp library for computing differences between files") (description @@ -19048,9 +18865,7 @@ higher-level lispier interface.") (base32 "0ydlirfk4dbpqqjwwph99v5swcrhd8v9g8q24fvs35wn2vm08lh1")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("cffi" ,sbcl-cffi) - ("split-sequence" ,sbcl-split-sequence))) + (list sbcl-alexandria sbcl-cffi sbcl-split-sequence)) (home-page "https://github.com/jasom/clinenoise") (synopsis "Port of linenoise to Common Lisp") (description @@ -19113,8 +18928,7 @@ Lisp.") (base32 "11c4krpq5x55qkchx6ykcnb455ssb4r3jjywx3c3irfrkj733ybp")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("trivial-raw-io" ,sbcl-trivial-raw-io))) + (list sbcl-alexandria sbcl-trivial-raw-io)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/eudoxia0/terminal-keypress") @@ -19273,9 +19087,7 @@ This package provides the text-based interface for Chemboy.") (base32 "05qx4jrkxqbqi72cxgswbpnifbdvp9mh7apc7566v522899bh0hb")))) (build-system asdf-build-system/sbcl) (inputs - `(("ironclad" ,sbcl-ironclad) - ("trivial-utf-8" ,sbcl-trivial-utf-8) - ("split-sequence" ,sbcl-split-sequence))) + (list sbcl-ironclad sbcl-trivial-utf-8 sbcl-split-sequence)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/eudoxia0/cl-pass") @@ -19307,8 +19119,7 @@ This package provides the text-based interface for Chemboy.") (base32 "127pm9h4rm4w9aadw5yvamnfzhk2rr69kchx10rf9k7sk7izqqfk")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-fad" ,sbcl-cl-fad) - ("path-parse" ,sbcl-path-parse))) + (list sbcl-cl-fad sbcl-path-parse)) (native-inputs (list sbcl-fiveam)) (home-page "https://github.com/eudoxia0/which") @@ -19341,11 +19152,8 @@ command in Common Lisp.") (base32 "15ihsxxs76xnldmqfsbxybckqjwrxwcpphgghiwzr2mnbqjpdqkh")))) (build-system asdf-build-system/sbcl) (inputs - `(("anaphora" ,sbcl-anaphora) - ("alexandria" ,sbcl-alexandria) - ("array-operations" ,sbcl-array-operations) - ("cl-slice" ,sbcl-cl-slice) - ("let-plus" ,sbcl-let-plus))) + (list sbcl-anaphora sbcl-alexandria sbcl-array-operations + sbcl-cl-slice sbcl-let-plus)) (native-inputs (list sbcl-clunit)) (home-page "https://github.com/tpapp/cl-num-utils") @@ -19485,15 +19293,15 @@ to serve as a building block for such an interface.") (base32 "0jn80xphyvyp2v72acr6b8a2f6dw06myr5vrjfl14brsvks7wr89")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("anaphora" ,sbcl-anaphora) - ("array-operations" ,sbcl-array-operations) - ("cl-num-utils" ,sbcl-cl-num-utils) - ("cl-rmath" ,sbcl-cl-rmath) - ("cl-slice" ,sbcl-cl-slice) - ("gsll" ,sbcl-gsll) - ("let-plus" ,sbcl-let-plus) - ("lla" ,sbcl-lla))) + (list sbcl-alexandria + sbcl-anaphora + sbcl-array-operations + sbcl-cl-num-utils + sbcl-cl-rmath + sbcl-cl-slice + sbcl-gsll + sbcl-let-plus + sbcl-lla)) (native-inputs (list sbcl-clunit)) (home-page "https://github.com/tpapp/cl-random") @@ -19527,8 +19335,7 @@ density, distribution and quantiles for these distributions.") (base32 "0w51dqixh277k6sl8bqvvp1400y6kd1l5h3d9q2f40l9bpxy8gjx")))) (build-system asdf-build-system/sbcl) (inputs - `(("cl-random" ,sbcl-cl-random) - ("mgl-pax" ,sbcl-mgl-pax))) + (list sbcl-cl-random sbcl-mgl-pax)) (home-page "https://melisgl.github.io/mgl-gpr/") (synopsis "Common Lisp library of evolutionary algorithms") (description @@ -19589,13 +19396,9 @@ information is taken from @url{https://publicsuffix.org}.") (base32 "00c8hq7vzgb89ab3q7mrp60x743kiqmsk1g51ynhxlqhph2bnslf")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria) - ("local-time" ,sbcl-local-time) - ("ppcre" ,sbcl-cl-ppcre) - ("serapeum" ,sbcl-serapeum))) + (list sbcl-alexandria sbcl-local-time sbcl-cl-ppcre sbcl-serapeum)) (native-inputs - `(("fiveam" ,sbcl-fiveam) - ("cffi" ,sbcl-cffi))) + (list sbcl-fiveam sbcl-cffi)) (home-page "https://github.com/ruricolist/cl-strftime") (synopsis "Common Lisp compiler for the strftime language") (description @@ -19814,10 +19617,7 @@ is available in a separate repository. See (base32 "1fb03fgnzrvh22lw1jdg04pmyja5fib5n42rzwp5mhr829yvxkvp")))) (build-system asdf-build-system/sbcl) (inputs - `(("cxml" ,sbcl-cxml) - ("parse-number" ,sbcl-parse-number) - ("cl-ppcre" ,sbcl-cl-ppcre) - ("yacc" ,sbcl-cl-yacc))) + (list sbcl-cxml sbcl-parse-number sbcl-cl-ppcre sbcl-cl-yacc)) (home-page "https://github.com/sharplispers/xpath/") (synopsis "Implementation of the XML Path Language (XPath) Version 1.0") (description @@ -19848,19 +19648,16 @@ Version 1.0.") (base32 "1vxdb1cjjqi986f72bggnw1s4yzv12g4li7vn4y49b6lphshr8lm")))) (build-system asdf-build-system/sbcl) (inputs - `(("babel" ,sbcl-babel) - ("named-readtables" ,sbcl-named-readtables) - ("serapeum" ,sbcl-serapeum) - ("quri" ,sbcl-quri) - ("flexi-streams" ,sbcl-flexi-streams) - ("split-sequence" ,sbcl-split-sequence) - ("alexandria" ,sbcl-alexandria) - ("trivial-gray-streams" ,sbcl-trivial-gray-streams))) + (list sbcl-babel + sbcl-named-readtables + sbcl-serapeum + sbcl-quri + sbcl-flexi-streams + sbcl-split-sequence + sbcl-alexandria + sbcl-trivial-gray-streams)) (native-inputs - `(("fiveam" ,sbcl-fiveam) - ("cxml" ,sbcl-cxml) - ("cxml-rng" ,sbcl-cxml-rng) - ("xpath" ,sbcl-xpath))) + (list sbcl-fiveam sbcl-cxml sbcl-cxml-rng sbcl-xpath)) (home-page "https://github.com/ruricolist/fxml") (synopsis "XML parser and serializer in Common Lisp") (description @@ -20095,7 +19892,7 @@ library inspired by @code{cl-data-format-validation} and WTForms validators.") (base32 "1vyklyh99712zsll4qi0m4mm8yb1nz04403vl8i57bjv5p5max49")))) (build-system asdf-build-system/sbcl) (inputs - `(("alexandria" ,sbcl-alexandria))) + (list sbcl-alexandria)) (home-page "https://github.com/jorgetavares/zsort") (synopsis "Collection of portable sorting algorithms in Common Lisp") (description diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm index 6000ca881a..e3cdd6a1c6 100644 --- a/gnu/packages/lxde.scm +++ b/gnu/packages/lxde.scm @@ -501,7 +501,7 @@ menu spec-compliant desktop menus for LXDE.") "123f3yn4rp1w5b3n5aj3ad9snkxab29qkrs7bcvf5bx4cn57g3sf")))) (build-system gnu-build-system) (inputs - `(("gtk+-2" ,gtk+-2))) + (list gtk+-2)) (native-inputs (list pkg-config intltool)) (synopsis "Tool for mouse and keyboard configuration in LXDE") diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 2f8f2ece3e..3bcc6d3df4 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -2422,12 +2422,9 @@ in a fast and accurate way.") "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l")))) (build-system python-build-system) (propagated-inputs - `(("ipython" ,python-ipython) - ("numpy" ,python-numpy) - ("pandas" ,python-pandas) - ("scipy" ,python-scipy))) + (list python-ipython python-numpy python-pandas python-scipy)) (native-inputs - `(("nose" ,python-nose))) + (list python-nose)) (home-page "https://github.com/interpretable-ml/iml") (synopsis "Interpretable Machine Learning (iML) package") (description "Interpretable ML (iML) is a set of data type objects, diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 83e62d46b1..c069e9e928 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -239,10 +239,7 @@ mail client.") "0dvm6acl32dv8bixx9z50gzwfp6kj4kxnn1j3dcwjlp7sasjp41s")))) (build-system gnu-build-system) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf) - ("gettext" ,gettext-minimal) - ("m4" ,m4))) ;for the test suite + (list automake autoconf gettext-minimal m4)) ;for the test suite (inputs (list gdbm gnutls @@ -1524,10 +1521,7 @@ and search library.") (native-inputs (list pandoc pkg-config)) (inputs - `(("libcrypto" ,openssl) - ("notmuch" ,notmuch) - ("sqlite" ,sqlite) - ("xapian" ,xapian))) + (list openssl notmuch sqlite xapian)) (home-page "http://www.muchsync.org/") (synopsis "Synchronize notmuch mail across machines") (description @@ -4136,15 +4130,15 @@ IMAP, Atom feeds or HTML archives.") (native-inputs (list pkg-config)) (inputs - `(("bogofilter" ,bogofilter) - ("compface" ,compface) - ("gnupg" ,gnupg-1) - ("gpgme" ,gpgme) - ("gtk+-2.0" ,gtk+-2) - ("gtkspell" ,gtkspell3) - ("libnsl" ,libnsl) - ("openldap" ,openldap) - ("openssl" ,openssl))) + (list bogofilter + compface + gnupg-1 + gpgme + gtk+-2 + gtkspell3 + libnsl + openldap + openssl)) (home-page "https://sylpheed.sraoss.jp/en/") (synopsis "Lightweight GTK+ email client") (description diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm index 494046c6d7..dd6baa42b6 100644 --- a/gnu/packages/mate.scm +++ b/gnu/packages/mate.scm @@ -107,11 +107,11 @@ MATE applications.") (base32 "0fni41p3kraxwjnx9l5mdspng0zib1gfdxwlaiyq31mh4g79yjyj")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("yelp-tools" ,yelp-tools) - ("gettext" ,gettext-minimal) - ("glib" ,glib "bin") ; glib-gettextize - ("polkit" ,polkit))) ; for ITS rules + (list pkg-config + yelp-tools + gettext-minimal + `(,glib "bin") ; glib-gettextize + polkit)) ; for ITS rules (inputs (list gtk+ glib @@ -206,10 +206,8 @@ from Mint-X-F and Faenza-Fresh icon packs.") (base32 "051g2vq817g84yrqzf7hjcqr4xrghnw1rprjd6jf5mhhzmwcas6n")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("gdk-pixbuf" ,gdk-pixbuf) ; gdk-pixbuf+svg isn't needed - ("gtk" ,gtk+-2))) + (list pkg-config intltool gdk-pixbuf ; gdk-pixbuf+svg isn't needed + gtk+-2)) (home-page "https://mate-desktop.org/") (synopsis "Official themes for the MATE desktop") @@ -233,12 +231,12 @@ themes for both gtk+-2 and gtk+-3.") (base32 "1nd1dn8mm1z6x4r68a25q4vzys1a6fmbzc94ss1z1n1872pczs6i")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("yelp-tools" ,yelp-tools) - ("gtk-doc" ,gtk-doc))) + (list pkg-config + intltool + `(,glib "bin") + gobject-introspection + yelp-tools + gtk-doc)) (inputs (list gtk+ libxrandr iso-codes startup-notification)) (propagated-inputs @@ -387,24 +385,24 @@ configuration program to choose applications starting on login.") (native-inputs (list pkg-config intltool gobject-introspection)) (inputs - `(("cairo" ,cairo) - ("dbus" ,dbus) - ("dbus-glib" ,dbus-glib) - ("dconf" ,dconf) - ("fontconfig" ,fontconfig) - ("gtk+" ,gtk+) - ("libcanberra" ,libcanberra) - ("libmatekbd" ,libmatekbd) - ("libmatemixer" ,libmatemixer) - ("libnotify" ,libnotify) - ("libx11" ,libx11) - ("libxext" ,libxext) - ("libxi" ,libxi) - ("libxklavier" ,libxklavier) - ("mate-desktop" ,mate-desktop) - ("nss" ,nss) - ("polkit" ,polkit) - ("startup-notification" ,startup-notification))) + (list cairo + dbus + dbus-glib + dconf + fontconfig + gtk+ + libcanberra + libmatekbd + libmatemixer + libnotify + libx11 + libxext + libxi + libxklavier + mate-desktop + nss + polkit + startup-notification)) (home-page "https://mate-desktop.org/") (synopsis "Settings Daemon for MATE") (description @@ -514,34 +512,34 @@ assorted menu related utility programs.") (base32 "0h70i4x3bk017pgv4zn280682wm58vwdjm7kni91ni8rmblnnvyp")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("libxslt" ,libxslt) - ("yelp-tools" ,yelp-tools) - ("scrollkeeper" ,scrollkeeper) - ("gettext" ,gettext-minimal) - ("docbook-xml" ,docbook-xml) - ("gobject-introspection" ,gobject-introspection))) + (list pkg-config + intltool + libxslt + yelp-tools + scrollkeeper + gettext-minimal + docbook-xml + gobject-introspection)) (inputs - `(("atk" ,atk) - ("dbus" ,dbus) - ("dbus-glib" ,dbus-glib) - ("glib" ,glib) - ("gucharmap" ,gucharmap) - ("gtk+" ,gtk+) - ("gtksourceview" ,gtksourceview-3) - ("libgtop" ,libgtop) - ("libmateweather" ,libmateweather) - ("libnotify" ,libnotify) - ("libx11" ,libx11) - ("libxml2" ,libxml2) - ("libwnck" ,libwnck) - ("mate-panel" ,mate-panel) - ("pango" ,pango) - ("polkit" ,polkit) ; either polkit or setuid - ("python" ,python-2) - ("upower" ,upower) - ("wireless-tools" ,wireless-tools))) + (list atk + dbus + dbus-glib + glib + gucharmap + gtk+ + gtksourceview-3 + libgtop + libmateweather + libnotify + libx11 + libxml2 + libwnck + mate-panel + pango + polkit ; either polkit or setuid + python-2 + upower + wireless-tools)) (propagated-inputs (list python-pygobject)) (home-page "https://mate-desktop.org/") @@ -586,10 +584,7 @@ Interactive Weather Information Network (IWIN). (base32 "118i4w2i2g3hfgbfn3hjzjkfq8vjj6049r7my3vna9js23b7ab92")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("gettext" ,gettext-minimal) - ("gobject-introspection" ,gobject-introspection))) + (list pkg-config intltool gettext-minimal gobject-introspection)) (inputs (list cairo gtk+ @@ -1064,10 +1059,7 @@ sessions, panels, menus, file management, and preferences.") (base32 "0imdimq5d5rjq8mkjcrsd683a2bn9acmhc0lmvyw71y0040inbaw")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("yelp-tools" ,yelp-tools))) + (list gettext-minimal intltool pkg-config yelp-tools)) (inputs (list atk glib @@ -1117,9 +1109,7 @@ can be used as backgrounds in the MATE Desktop environment.") "1bmk9gq5gcqkvfppa7i1hqfph8sajc3xs189s4ha97g0ifwd98a8")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list gettext-minimal intltool pkg-config)) (inputs (list cairo glib @@ -1228,15 +1218,15 @@ can be used as backgrounds in the MATE Desktop environment.") "1b16n1628gcsym5mph6lr9x5xm4rgkxsa8xwr2wlx8g2gw2775i1")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("gtk-doc" ,gtk-doc) - ("intltool" ,intltool) - ("libice" ,libice) - ("libsm" ,libsm) - ("pkg-config" ,pkg-config) - ("scrollkeeper" ,scrollkeeper) - ("xorgproto" ,xorgproto) - ("yelp-tools" ,yelp-tools))) + (list gettext-minimal + gtk-doc + intltool + libice + libsm + pkg-config + scrollkeeper + xorgproto + yelp-tools)) (inputs (list atk cairo @@ -1280,35 +1270,35 @@ can be used as backgrounds in the MATE Desktop environment.") (base32 "0dralsc0dvs0l38cysdhx6kiaiqlb8qi6g9xz2cm6mjqyq3d3f9f")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("gtk-doc" ,gtk-doc) - ("gobject-introspection" ,gobject-introspection) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("yelp-tools" ,yelp-tools))) + (list gettext-minimal + gtk-doc + gobject-introspection + intltool + pkg-config + yelp-tools)) (inputs - `(("atk" ,atk) - ("cairo" ,cairo) - ("dconf" ,dconf) - ("dbus" ,dbus) - ("dbus-glib" ,dbus-glib) - ("exempi" ,exempi) - ("glib" ,glib) - ("gtk+" ,gtk+) - ("libcanberra" ,libcanberra) - ("libx11" ,libx11) - ("libxext" ,libxext) - ("libpeas" ,libpeas) - ("libxml2" ,libxml2) - ("libexif" ,libexif) - ("libjpeg" ,libjpeg-turbo) - ("librsvg" ,(librsvg-for-system)) - ("lcms" ,lcms) - ("mate-desktop" ,mate-desktop) - ("pango" ,pango) - ("shared-mime-info" ,shared-mime-info) - ("startup-notification" ,startup-notification) - ("zlib" ,zlib))) + (list atk + cairo + dconf + dbus + dbus-glib + exempi + glib + gtk+ + libcanberra + libx11 + libxext + libpeas + libxml2 + libexif + libjpeg-turbo + (librsvg-for-system) + lcms + mate-desktop + pango + shared-mime-info + startup-notification + zlib)) (home-page "https://mate-desktop.org/") (synopsis "Eye of MATE") (description @@ -1429,11 +1419,7 @@ can be used as backgrounds in the MATE Desktop environment.") (base32 "1i2r4lw6xsk972yp15g5hm8p8xx9pp6jmcvvzbdq80xyx3x898qz")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("gettext" ,gettext-minimal) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("yelp-tools" ,yelp-tools))) + (list autoconf gettext-minimal intltool pkg-config yelp-tools)) (inputs (list cairo glib @@ -1469,11 +1455,7 @@ MATE Desktop to monitor your system resources and usage.") "1450bqzlnvwy3xa98lj102j2cf7piqbxcd1cy2zp41rdl8ri3gvn")))) (build-system glib-or-gtk-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("gtk-doc" ,gtk-doc) - ("intltool" ,intltool) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list gettext-minimal gtk-doc intltool libtool pkg-config)) (inputs (list accountsservice glib diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b447af305b..3bac086666 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -225,7 +225,7 @@ Some of the features include: "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id")))) (build-system gnu-build-system) (inputs - `(("fortran" ,gfortran))) + (list gfortran)) (synopsis "Visualizing and demonstrating convolution") (description "GNU C-Graph is a tool for demonstrating the theory of convolution. @@ -847,9 +847,7 @@ halfspaces) or by their double description with both representations.") (native-inputs (list autoconf automake libtool pkg-config)) (inputs - `(("eigen" ,eigen) - ("lapack" ,lapack) - ("fortran" ,gfortran))) + (list eigen lapack gfortran)) (synopsis "Fortran subroutines for solving eigenvalue problems") (description "ARPACK-NG is a collection of Fortran77 subroutines designed to solve @@ -1060,7 +1058,7 @@ plotting engine by third-party applications like Octave.") (sha256 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd")))) (native-inputs - `(("fortran" ,gfortran))) + (list gfortran)) (build-system gnu-build-system) (synopsis "General Cartographic Transformation Package (GCTP)") (description diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 11a8f62f3b..ea7a74263b 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -1049,9 +1049,7 @@ many popular chat protocols.") (base32 "1i5s9rrgbyss9rszq6c6y53hwqyw1k86s40cpsfx5ccl9bprxdgl")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list gettext-minimal intltool pkg-config)) (inputs (list glib gtk+-2 @@ -1135,7 +1133,7 @@ simultaneously and therefore appear under the same nickname on IRC.") (base32 "1s2phiipq7ks8vrd93p96dzd5wgmgg8q9h2rxsnh2gg7iy06gj9c")))) (build-system python-build-system) (native-inputs - `(("glib:bin" ,glib "bin"))) + (list `(,glib "bin"))) (inputs (list glib glib-networking diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index a11e2beb6f..b3e20760e2 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -556,10 +556,7 @@ devices.") "1yz65jsbgdx4cmy16x24wz5di352lvyi7fp6jm90bhgl1vpzxlsx")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("libtool" ,libtool))) + (list autoconf automake gettext-minimal libtool)) (synopsis "File system monitor") (description "This package provides a file system monitor.") (home-page "https://github.com/emcrisostomo/fswatch") diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 1e10b0fa93..1882f7ae8d 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1335,12 +1335,12 @@ interface. It is implemented as a frontend to @code{klick}.") libtool pkg-config)) (inputs - `(("alsa-lib" ,alsa-lib) - ("fftw" ,fftw) - ("gtk+" ,gtk+) - ("jack" ,jack-2) - ("json-c" ,json-c) - ("pulseaudio" ,pulseaudio))) + (list alsa-lib + fftw + gtk+ + jack-2 + json-c + pulseaudio)) (home-page "http://lingot.nongnu.org/") (synopsis "Accurate & configurable musical instrument tuner") (description @@ -1852,8 +1852,7 @@ complete studio.") (inputs (list liblo gtkmm-3 alsa-lib libxml++-2)) (native-inputs - `(("glib:bin" ,glib "bin") - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") pkg-config)) (home-page "https://github.com/onkelDead/tascam-gtk") (synopsis "GTK+ based application to control Tascam US-16x08 DSP mixer") (description "This is a mixer application to control the Tascam US-16x08 @@ -3136,8 +3135,7 @@ improves on support for JACK features, such as JACK MIDI.") "1zs5yy124bymfyapsnljr6rv2lnn5inwchm0xnwiw44b2d39l8hn")))) (build-system gnu-build-system) (inputs - `(("libuuid" ,util-linux "lib") - ("libsndfile" ,libsndfile))) + (list `(,util-linux "lib") libsndfile)) (native-inputs (list pkg-config)) (home-page "https://linuxsampler.org/libgig/") @@ -3283,8 +3281,7 @@ you to switch between different audio setups with just two mouse clicks.") (native-inputs (list pkg-config)) ;; TODO: See https://github.com/iyoko/cursynth/issues/4 which currently ;; prevents us from using pulseaudio - (inputs `(("ncurses" ,ncurses) - ("alsa" ,alsa-lib))) + (inputs (list ncurses alsa-lib)) (home-page "https://www.gnu.org/software/cursynth/") (synopsis "Polyphonic and MIDI subtractive music synthesizer using curses") (description "GNU cursynth is a polyphonic synthesizer that runs @@ -4057,26 +4054,26 @@ available memory.") "026v977kwb0wbmlmf6mnik328plxg8wykfx9ryvqhirac0aq39pk")))) (build-system gnu-build-system) (inputs - `(("alsa-lib" ,alsa-lib) - ("curl" ,curl) - ("faad2" ,faad2) - ("ffmpeg" ,ffmpeg-3.4) - ("file" ,file) - ("jack" ,jack-1) - ("libid3tag" ,libid3tag) - ("libltdl" ,libltdl) - ("libmodplug" ,libmodplug) - ("libmpcdec" ,libmpcdec) - ("libmad" ,libmad) - ("libogg" ,libogg) - ("libvorbis" ,libvorbis) - ("ncurses" ,ncurses) - ("openssl" ,openssl) - ("sasl" ,cyrus-sasl) - ("speex" ,speex) - ("taglib" ,taglib) - ("wavpack" ,wavpack) - ("zlib" ,zlib))) + (list alsa-lib + curl + faad2 + ffmpeg-3.4 + file + jack-1 + libid3tag + libltdl + libmodplug + libmpcdec + libmad + libogg + libvorbis + ncurses + openssl + cyrus-sasl + speex + taglib + wavpack + zlib)) (native-inputs (list pkg-config)) (synopsis "Console audio player designed to be powerful and easy to use") diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index 3710d4ff11..cd694f53f0 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -39,8 +39,7 @@ (base32 "0ds9qas1zxvvx8qbpjmh4yk4gdg3cgs3ly27krcp6a5vlk6vhzbm")))) (build-system gnu-build-system) (inputs - `(("gettext" ,gettext-minimal) - ("ncurses" ,ncurses))) + (list gettext-minimal ncurses)) (home-page "https://www.nano-editor.org/") (synopsis "Small, user-friendly console text editor") (description diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 214255ccb5..1ec1586fb3 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -163,12 +163,12 @@ (base32 "10ndzkip8blgkw572n3dicl6mgjaa7kygwn3vls80liq92vf1sa9")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper) - ("which" ,which))) + (list autoconf + automake + libtool + pkg-config + python-wrapper + which)) (home-page "https://github.com/sctplab/usrsctp/") (synopsis "SCTP user-land implementation") (description "UsrSCTP is a portable SCTP userland stack. SCTP is a message @@ -190,8 +190,7 @@ runs on top of IP or UDP, and supports both v4 and v6 versions.") (base32 "0kmlqk04sgkshsll4r9w3k0rvrgz0gpk987618r50khwl484zss6")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list gettext-minimal pkg-config)) (inputs (list libressl)) (home-page "https://github.com/axel-download-accelerator/axel") @@ -496,7 +495,7 @@ performance across unpredictable networks, such as the Internet.") (native-inputs (list autoconf automake libtool pkg-config)) (inputs - `(("linux-headers" ,linux-libre-headers))) + (list linux-libre-headers)) (synopsis "@acronym{SCTP, Stream Control Transmission Protocol} helpers for Linux") (description @@ -3488,10 +3487,7 @@ A very simple IM client working over the DHT. (inputs (list c-ares json-c libcap libyang readline)) (native-inputs - `(("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-wrapper) - ("python-pytest" ,python-pytest))) + (list perl pkg-config python-wrapper python-pytest)) (home-page "https://frrouting.org/") (synopsis "IP routing protocol suite") (description "FRRouting (FRR) is an IP routing protocol suite which includes diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index da378febf2..624637dd8a 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1328,8 +1328,7 @@ compilers that can directly deal with packages.") "0gxjw1bhmjcjzri6x6psqrkbbyq678b69bqfl9i1zswp7cj2lryg")))) (build-system dune-build-system) (propagated-inputs - `(("lwt" ,ocaml-lwt) - ("ocaml-stdlib-shims" ,ocaml-stdlib-shims))) + (list ocaml-lwt ocaml-stdlib-shims)) (home-page "https://github.com/gildor478/ounit") (synopsis "Unit testing framework for OCaml") (description "OUnit2 is a unit testing framework for OCaml. It is similar @@ -4397,8 +4396,7 @@ Dedukti files.") (file-name (git-file-name name version)))) (build-system emacs-build-system) (inputs - `(("dedukti-mode" ,emacs-dedukti-mode) - ("flycheck-mode" ,emacs-flycheck))) + (list emacs-dedukti-mode emacs-flycheck)) (synopsis "Flycheck integration for the dedukti language") (description "This package provides a frontend for Flycheck to perform syntax checking on dedukti files.") diff --git a/gnu/packages/openbox.scm b/gnu/packages/openbox.scm index fb590ce97f..873592c19e 100644 --- a/gnu/packages/openbox.scm +++ b/gnu/packages/openbox.scm @@ -50,17 +50,17 @@ (build-system gnu-build-system) (native-inputs (list pkg-config)) (propagated-inputs (list python2-pyxdg)) - (inputs `(("imlib2" ,imlib2) - ("libxml2" ,libxml2) - ("librsvg" ,(librsvg-for-system)) - ("libsm" ,libsm) - ("libxcursor" ,libxcursor) - ("libxinerama" ,libxinerama) - ("libxml2" ,libxml2) - ("libxrandr" ,libxrandr) - ("libxft" ,libxft) - ("pango" ,pango) - ("python-2" ,python-2))) + (inputs (list imlib2 + libxml2 + (librsvg-for-system) + libsm + libxcursor + libxinerama + libxml2 + libxrandr + libxft + pango + python-2)) (synopsis "Box style window manager") (description "Openbox is a highly configurable, next generation window manager with diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index f7dcacfde1..081ff92ec5 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1489,11 +1489,8 @@ Microsoft cabinet (.@dfn{CAB}) files.") (native-inputs (list bison pkg-config)) (inputs - `(("gcab" ,gcab) - ("glib" ,glib) - ("libgsf" ,libgsf) - ("libxml2" ,libxml2) - ("uuid" ,util-linux "lib"))) + (list gcab glib libgsf libxml2 + `(,util-linux "lib"))) (home-page "https://wiki.gnome.org/msitools") (synopsis "Windows Installer file manipulation tool") (description diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 5e44e1e677..d241b65b79 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -873,11 +873,7 @@ SyncTeX support, and rudimentary support for annotations and forms.") "09i88v3wacmx7f96dmq0l3afpyv95lh6jrx16xzm0jd1szdrhn5j")))) (build-system gnu-build-system) (inputs - `(("gtk" ,gtk+-2) - ("pango" ,pango) - ("poppler" ,poppler) - ("glib" ,glib) - ("libgnomecanvas" ,libgnomecanvas))) + (list gtk+-2 pango poppler glib libgnomecanvas)) (native-inputs (list pkg-config)) (home-page "http://xournal.sourceforge.net/") @@ -1092,9 +1088,8 @@ the PDF pages.") (base32 "17z0bn8kihiyqjd1m5jr80m7ry06l1qn0l8v918xg5gs7q2calcf")))) (build-system python-build-system) (propagated-inputs - `(("python-pikepdf" ,python-pikepdf) - ("python-pillow" ,python-pillow) - ("python-tkinter" ,python "tk"))) + (list python-pikepdf python-pillow + `(,python "tk"))) (home-page "https://gitlab.mister-muffin.de/josch/img2pdf") (synopsis "Convert images to PDF via direct JPEG inclusion") (description diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 815c59ecd4..c6d63ce041 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1875,9 +1875,7 @@ of the style used by the Git version control system.") "0clphq6a17chvb663fvjnxqvyvh26g03x0fl4bg9vy4ibdnzg2v2")))) (build-system perl-build-system) (inputs - `(("perl-mixin-linewise" ,perl-mixin-linewise) - ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) - ("perl-sub-exporter" ,perl-sub-exporter))) + (list perl-mixin-linewise perl-perlio-utf8_strict perl-sub-exporter)) (home-page "https://metacpan.org/release/Config-INI") (synopsis "Simple .ini-file format reader and writer") (description "@code{Config::INI} is a module that facilates the reading @@ -4789,7 +4787,7 @@ file names in a directory.") (native-inputs (list perl-test-warnings)) (propagated-inputs - `(("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict))) + (list perl-perlio-utf8_strict)) (home-page "https://metacpan.org/release/File-Slurper") (synopsis "Simple, sane and efficient module to slurp a file") (description "This module provides functions for fast and correct file @@ -6374,8 +6372,7 @@ knowledge of Apache.") "1wmfr19w9y8qys7b32mnj1vmps7qwdahqas71a9p62ac8xw0dwkx")))) (build-system perl-build-system) (inputs - `(("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) - ("perl-sub-exporter" ,perl-sub-exporter))) + (list perl-perlio-utf8_strict perl-sub-exporter)) (home-page "https://metacpan.org/release/Mixin-Linewise") (synopsis "Write your linewise code for handles; this does the rest") (description "It's boring to deal with opening files for IO, converting @@ -10998,10 +10995,8 @@ attribute names.") (base32 "0pyqr12jsqagna75fm2gijfzw06wy1hrh5chn9hwnmcfddda66g8")))) (build-system perl-build-system) (native-inputs - `(("perl-test-distribution" ,perl-test-distribution) - ("perl-text-pod" ,perl-test-pod) - ("perl-test-pod-coverage" ,perl-test-pod-coverage) - ("perl-test-portability-files" ,perl-test-portability-files))) + (list perl-test-distribution perl-test-pod perl-test-pod-coverage + perl-test-portability-files)) (home-page "https://metacpan.org/dist/XSLoader") (synopsis "Dynamically load C libraries into Perl code") (description "XSLoader module defines a standard simplified interface to the @@ -11305,14 +11300,18 @@ such that being individual extensions would be wasteful.") perl-test-most perl-tie-simple)) (inputs - `(("freeglut" ,freeglut) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libsmpeg" ,libsmpeg) - ("libtiff" ,libtiff) - ("mesa" ,mesa) - ("sdl" ,(sdl-union - (list sdl sdl-gfx sdl-image sdl-mixer sdl-pango sdl-ttf))))) + (list freeglut + libjpeg-turbo + libpng + libsmpeg + libtiff + mesa + (sdl-union (list sdl + sdl-gfx + sdl-image + sdl-mixer + sdl-pango + sdl-ttf)))) (propagated-inputs (list perl-file-sharedir perl-tie-simple)) (home-page "https://metacpan.org/release/SDL") diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 454a5dd19b..fa603a60be 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -188,7 +188,7 @@ cards and generate meaningful file and folder names.") (native-inputs (list pkg-config)) (inputs - `(("libjpeg" ,libjpeg-turbo))) ;for lossy DNGs and old Kodak cameras + (list libjpeg-turbo)) ;for lossy DNGs and old Kodak cameras (propagated-inputs (list lcms)) ;for color profiles (home-page "https://www.libraw.org") @@ -360,10 +360,7 @@ and a wide variety of other metadata.") "12cv4886l1czfjwy7k6ipgf3zjksgwhdjzr2s9fdg33vqcv2hlrv")))) (build-system cmake-build-system) (inputs - `(("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("zlib" ,zlib))) + (list libjpeg-turbo libpng libtiff zlib)) (home-page "http://panotools.sourceforge.net/") (synopsis "Library for panoramic images") (description diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm index 72c60cd60e..415d7ad2a5 100644 --- a/gnu/packages/plotutils.scm +++ b/gnu/packages/plotutils.scm @@ -151,7 +151,7 @@ using the Cairo drawing library.") (inherit guile-charting) (name "guile2.2-charting") (inputs (list guile-2.2)) - (propagated-inputs `(("guile-cairo" ,guile2.2-cairo))))) + (propagated-inputs (list guile2.2-cairo)))) (define-public ploticus (package diff --git a/gnu/packages/pulseaudio.scm b/gnu/packages/pulseaudio.scm index 57499920c1..5cda29789f 100644 --- a/gnu/packages/pulseaudio.scm +++ b/gnu/packages/pulseaudio.scm @@ -507,8 +507,7 @@ README.md for a detailed list of features.") "189z5p20hk0xv9vwvym293503j4pwl03xqk9hl7cl6dwgv0l7wkf")))) (build-system meson-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list gettext-minimal pkg-config)) (inputs (list gtkmm-3 pulseaudio)) (home-page "https://freedesktop.org/software/pulseaudio/paprefs/") diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 4d2a956532..e94e2d0011 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -322,8 +322,7 @@ of tests run in a specific order.") (base32 "1y87agr324p6x5gvhziymxjlw54pyn4gqnd49papbl941djpkp5g")))) (build-system python-build-system) (native-inputs - `(("pytest" ,python-pytest) - ("setuptools-scm" ,python-setuptools-scm))) + (list python-pytest python-setuptools-scm)) (home-page "https://www.astropy.org/") (synopsis "Pytest plugin adding diagnostic data to the header of the test output") diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index e8e03b48a0..c966710512 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2131,8 +2131,7 @@ Markup Language.") "14h7nyfbl5vpfk0rbviy4ygdfx0yx5kncvg6jpbdb0dhwna0ssm6")))) (build-system python-build-system) (native-inputs - `(("python-zope-security" ,python-zope-security-bootstrap) - ("python-zope-testrunner" ,python-zope-testrunner))) + (list python-zope-security-bootstrap python-zope-testrunner)) (propagated-inputs (list python-zope-interface)) (home-page "https://pypi.org/project/zope.proxy/") @@ -2224,12 +2223,12 @@ Zope3, which are are special objects that have a structural location.") python-zope-proxy python-zope-schema)) (native-inputs - `(("python-btrees" ,python-btrees) - ("python-zope-component" ,python-zope-component-bootstrap) - ("python-zope-configuration" ,python-zope-configuration-bootstrap) - ("python-zope-location" ,python-zope-location-bootstrap) - ("python-zope-testing" ,python-zope-testing) - ("python-zope-testrunner" ,python-zope-testrunner))) + (list python-btrees + python-zope-component-bootstrap + python-zope-configuration-bootstrap + python-zope-location-bootstrap + python-zope-testing + python-zope-testrunner)) (home-page "https://pypi.org/project/zope.security/") (synopsis "Zope security framework") (description "Zope.security provides a generic mechanism to implement @@ -3015,9 +3014,7 @@ library.") (propagated-inputs (list python-gevent python-requests)) (native-inputs - `(("python-nose" ,python-nose) - ("python-zope.interface" ,python-zope-interface) - ("python-zope.event" ,python-zope-event))) + (list python-nose python-zope-interface python-zope-event)) (home-page "https://github.com/kennethreitz/grequests") (synopsis "Python library for asynchronous HTTP requests") (description "GRequests is a Python library that allows you to use diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a76138c1c6..e13c47f959 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -877,7 +877,7 @@ interacting with the low-level LibRaw C APIs.") "1zmvmwgxyzvm83818skhn8b4wrci4kmnixaax8q3ia5cn7xrmj6v")))) (build-system python-build-system) (propagated-inputs - `(("python-tkinter" ,python "tk"))) + (list `(,python "tk"))) (home-page "https://github.com/robertlugg/easygui") (synopsis "GUI programming module for Python") (description "EasyGUI is a module for very simple, very easy GUI @@ -2978,10 +2978,8 @@ software.") (base32 "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc")))) (build-system python-build-system) (native-inputs - `(("coverage" ,python-coverage) - ("pytest" ,python-pytest-astropy) - ("pytest-cov" ,python-pytest-cov) - ("setuptools-scm" ,python-setuptools-scm))) + (list python-coverage python-pytest-astropy python-pytest-cov + python-setuptools-scm)) (home-page "https://github.com/astropy/astropy-helpers") (synopsis "Utilities for building and installing packages in the Astropy ecosystem") @@ -9865,9 +9863,7 @@ plugin for flake8 to check PEP-8 naming conventions.") "07w3p1qm44hgxf3vvwz84kswpsx6s7kvaibzrsx5dzm0hli1i3fx")))) (build-system python-build-system) (native-inputs - `(("python-toml", python-toml) - ("python-pytest" ,python-pytest-bootstrap) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-toml python-pytest-bootstrap python-pytest-runner)) (home-page "https://github.com/PyCQA/mccabe") (synopsis "McCabe checker, plugin for flake8") (description "This package provides a Flake8 plug-in to compute the McCabe @@ -17104,13 +17100,13 @@ multitouch applications.") (patches (search-patches "python-argcomplete-1.11.1-fish31.patch")))) (build-system python-build-system) (native-inputs - `(("python-coverage" ,python-coverage) - ("python-flake8" ,python-flake8) - ("python-pexpect" ,python-pexpect) - ("python-wheel" ,python-wheel) - ("tcsh" ,tcsh) - ("fish" ,fish) - ("bash-full" ,bash))) ;full Bash for 'test_file_completion' + (list python-coverage + python-flake8 + python-pexpect + python-wheel + tcsh + fish + bash)) ;full Bash for 'test_file_completion' (home-page "https://github.com/kislyuk/argcomplete") (synopsis "Shell tab completion for Python argparse") (description "argcomplete provides extensible command line tab completion @@ -18139,7 +18135,7 @@ multitouch applications.") (base32 "1priacxym85yjcf68hh38w55nqswaxp71ryjyfdk222kg9l85ln7")))) (native-inputs - `(("python-setuptools_scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (build-system python-build-system) (home-page "https://github.com/jaraco/configparser/") (synopsis "Backport of configparser from python 3.5") @@ -18333,7 +18329,7 @@ multitouch applications.") "1gm82jddm1lkazdi8lfsl1b3vi1z0252ng60mzjym8irnv94qfhy")))) (build-system python-build-system) (propagated-inputs - `(("six" ,python-six))) + (list python-six)) (home-page "https://github.com/tkhyn/dirsync") (synopsis "Advanced directory tree synchronisation tool") (description "Advanced directory tree synchronisation tool.") @@ -25072,18 +25068,18 @@ cryptographically signed ones).") "1lk3qmy1hkaphk4n7ayfk0wl6m2yvd6r7qkam6yncqfzgkbc1phs")))) (build-system python-build-system) (native-inputs - `(("python-check-manifest" ,python-check-manifest) - ("python-coverage" ,python-coverage) - ("python-isort" ,python-isort) - ("python-mock" ,python-mock) - ("python-pydoctstyle" ,python-pydocstyle) - ("python-pytest-cache" ,python-pytest-cache) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-pep8" ,python-pytest-pep8) - ("python-pytest-runner" ,python-pytest-runner) - ("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm) - ("python-tox" ,python-tox))) + (list python-check-manifest + python-coverage + python-isort + python-mock + python-pydocstyle + python-pytest-cache + python-pytest-cov + python-pytest-pep8 + python-pytest-runner + python-pytest + python-setuptools-scm + python-tox)) (home-page "https://github.com/inveniosoftware/dictdiffer") (synopsis "Diff and patch Python dictionary objects") (description diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 9d6c01187a..01bf961bbf 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1977,7 +1977,7 @@ instances.") "1idaivamp1jvbbai9yzv471c62xbqxhaawccvskaizihkd0lq0jx")))) (build-system python-build-system) (native-inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (propagated-inputs (list python-toml python-packaging)) (home-page "https://www.riverbankcomputing.com/software/sip/intro") diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index d16e321bb6..6e2cacfb4d 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -874,10 +874,7 @@ using GNU Radio and the Qt GUI toolkit.") (base32 "0y43241s3p8qzn7x6x28v5v2bf934riznj14bb7m6k6vgd849qzl")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (list autoconf automake gettext-minimal pkg-config)) (inputs (list alsa-lib fltk diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index e07ab70ea1..55af2beb8b 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -5232,7 +5232,7 @@ across multiple CPU cores.") (build-system ruby-build-system) (native-inputs ;; TODO: Add ruby-minitest-proveit once available. - `(("hoe" ,ruby-hoe))) + (list ruby-hoe)) (synopsis "ParseTree fork which includes generic S-exp processing tools") (description "The sexp_processor package is derived from ParseTree, but contrary to ParseTree, it includes all the generic S-exp processing tools. @@ -5254,9 +5254,7 @@ Amongst the included tools are @code{Sexp}, @code{SexpProcessor} and "09qcdyjjw3p7g6cjm5m9swkms1xnv35ndiy7yw24cas16qrhha6c")))) (build-system ruby-build-system) (native-inputs - `(("hoe" ,ruby-hoe) - ("racc" ,ruby-racc) - ("unifdef" ,unifdef))) + (list ruby-hoe ruby-racc unifdef)) (propagated-inputs (list ruby-sexp-processor)) (home-page "https://github.com/seattlerb/ruby_parser/") diff --git a/gnu/packages/sawfish.scm b/gnu/packages/sawfish.scm index 1a09f8ca32..ab715b4a7d 100644 --- a/gnu/packages/sawfish.scm +++ b/gnu/packages/sawfish.scm @@ -50,12 +50,7 @@ "1bmcjl1x1rdh514q9z3hzyjmjmwwwkziipjpjsl301bwmiwrd8a8")))) (build-system gnu-build-system) (native-inputs - `(("makeinfo" ,texinfo) - ("pkg-config" ,pkg-config) - - ("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list texinfo pkg-config autoconf automake libtool)) (inputs (list gdbm gmp libffi readline)) (native-search-paths diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index 97ac36c5fe..1eb92d8f96 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -89,9 +89,7 @@ different (virtual) machine than the one to which the USB device is attached.") "06kf0q4l52gzx5p63l8850hff8pmhp7xv1hk8zgx2apbw18y6jd5")))) (build-system gnu-build-system) (inputs - `(("libepoxy" ,libepoxy) - ("mesa" ,mesa) - ("udev" ,eudev))) + (list libepoxy mesa eudev)) (native-inputs (list pkg-config)) (synopsis "Virtual 3D GPU library") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7435866ec6..c2578c35a9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -109,23 +109,23 @@ "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan")))) (build-system gnu-build-system) (inputs - `(("cairo" ,cairo) - ("gettext" ,gettext-minimal) - ("gsl" ,gsl) - ("libxml2" ,libxml2) - ("pango" ,pango) - ("readline" ,readline) - ("gtk" ,gtk+) - ("gtksourceview" ,gtksourceview-3) - ("spread-sheet-widget" ,spread-sheet-widget) - ("zlib" ,zlib))) + (list cairo + gettext-minimal + gsl + libxml2 + pango + readline + gtk+ + gtksourceview-3 + spread-sheet-widget + zlib)) (native-inputs - `(("autoconf" ,autoconf) ;for tests - ("glib" ,glib "bin") ;for glib-genmarshal - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-2) ;for tests - ("texinfo" ,texinfo))) + (list autoconf ;for tests + `(,glib "bin") ;for glib-genmarshal + perl + pkg-config + python-2 ;for tests + texinfo)) (home-page "https://www.gnu.org/software/pspp/") (synopsis "Statistical analysis") (description @@ -1226,9 +1226,7 @@ agnes cluster diagrams.") (native-inputs (list pkg-config)) (inputs - `(("cairo" ,cairo) - ("freetype2" ,freetype) - ("zlib" ,zlib))) + (list cairo freetype zlib)) (propagated-inputs (list r-rcpp r-systemfonts)) (home-page "https://cran.r-project.org/web/packages/gdtools") diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 7ad5782226..2ab0b05d9b 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -417,7 +417,7 @@ input bits thoroughly but are not suitable for cryptography.") (base32 "0dc9fxcdmppbs9s06jvq61zbk552laxps0xyk098gj41697ihd96")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal))) + (list gettext-minimal)) (home-page "https://billposer.org/Software/a2b.html") (synopsis "Convert between ASCII, hexadecimal and binary representations") (description "The two programs are useful for generating test data, for diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 915cc3cd35..0b5f0eade1 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -2147,8 +2147,8 @@ masters from remote CVS hosts.") (build-system gnu-build-system) (inputs (list perl)) (native-inputs - `(("emacs" ,emacs-minimal) ; for `ctags' - ("inetutils" ,inetutils))) ; for `hostname', used in the tests + (list emacs-minimal ; for `ctags' + inetutils)) ; for `hostname', used in the tests (home-page "https://www.gnu.org/software/vc-dwim/") (synopsis "Version-control-agnostic ChangeLog diff and commit tool") (description diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 710c723e85..9b57d3cbb8 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -433,24 +433,22 @@ as a joint effort between the BBC and Fluendo.") (search-patches "libquicktime-ffmpeg.patch")))) (build-system gnu-build-system) (native-inputs - `(("gettext" ,gettext-minimal) - ("doxygen" ,doxygen) - ("pkg-config" ,pkg-config))) + (list gettext-minimal doxygen pkg-config)) (inputs - `(("alsa" ,alsa-lib) - ("ffmpeg" ,ffmpeg) - ("gtk+-2" ,gtk+-2) - ("lame" ,lame) - ("libdv" ,libdv) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libvorbis" ,libvorbis) - ("opengl" ,mesa) - ("schroedinger" ,schroedinger) - ("x11" ,libx11) - ("x264" ,libx264) - ("xaw" ,libxaw) - ("xv" ,libxv))) + (list alsa-lib + ffmpeg + gtk+-2 + lame + libdv + libjpeg-turbo + libpng + libvorbis + mesa + schroedinger + libx11 + libx264 + libxaw + libxv)) (synopsis "Quick Time Library") (description "The goal of this project is to enhance the quicktime4linux library.") @@ -516,11 +514,7 @@ receiving MJPG streams.") (base32 "0kvhxr5hkabj9v7ah2rzkbirndfqdijd9hp8v52c1z6bxddf019w")))) (build-system gnu-build-system) (inputs - `(("gtk+-2" ,gtk+-2) - ("libdv" ,libdv) - ("libpng" ,libpng) - ("libquicktime" ,libquicktime) - ("sdl" ,sdl))) + (list gtk+-2 libdv libpng libquicktime sdl)) (synopsis "Tools for handling MPEG") (description "Mjpeg tools is a suite of programs which support video capture, editing, playback, and compression to MPEG of MJPEG video. Edit, play and diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 9dabb7f76a..0031037920 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -2195,20 +2195,16 @@ which is a hypervisor.") "1h23a8nzdxjyvw44dwh903563n3b1z5skx8g0b1p1v5cif3iqpr5")))) (build-system meson-build-system) (inputs - `(("libsoup" ,libsoup-minimal-2) - ("libxml2" ,libxml2) - ("libxslt" ,libxslt) - ("json-glib" ,json-glib) - ("libarchive" ,libarchive))) + (list libsoup-minimal-2 libxml2 libxslt json-glib libarchive)) (native-inputs - `(("perl" ,perl) - ("gobject-introspection" ,gobject-introspection) - ("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config) - ;; Tests - ("python" ,python) - ("pytest" ,python-pytest) - ("requests" ,python-requests))) + (list perl + gobject-introspection + gettext-minimal + pkg-config + ;; Tests + python + python-pytest + python-requests)) (home-page "https://gitlab.com/libosinfo/osinfo-db-tools") (synopsis "Tools for managing the osinfo database") (description "This package contains a set of tools to assist diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 1eeb560717..358913d5db 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -690,9 +690,7 @@ and probably others.") "1qsfgpxg553s8rc9cyrc4k96z0pislxsdxb9wyhp8fdprkak2mw2")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("autotools" ,automake) - ("pkg-config" ,pkg-config))) + (list autoconf automake pkg-config)) (inputs (list openssl ppp)) (home-page "https://github.com/adrienverge/openfortivpn") diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 2285f23994..fff7e48ba3 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -5927,15 +5927,13 @@ configuration language.") "0qq5g6bbd1a1ml1wk8jj9z39a899jzqbf7aizr3pvyz0f4kz8mis")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - - ;; For bootstrapping. - ("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - - ;; For generating manuals. - ("rst2man" ,python-docutils))) + (list pkg-config + ;; For bootstrapping. + autoconf + automake + libtool + ;; For generating manuals. + python-docutils)) (inputs (list python varnish)) (synopsis "Collection of Varnish modules") @@ -7981,9 +7979,7 @@ tools: (base32 "1ffzia679axcsccx2fxjpxhb0i5xc42zxn446x6c1170w6v69qf6")))) (build-system cmake-build-system) - (native-inputs `(("gtest" ,googletest) - ("doxygen" ,doxygen) - ("graphviz" ,graphviz))) + (native-inputs (list googletest doxygen graphviz)) (synopsis "Strictly RFC 3986 compliant URI parsing and handling library") (description "uriparser is a strictly RFC 3986 compliant URI parsing and handling library written in C89 (\"ANSI C\"). uriparser is fast and supports diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 65c040cd92..20f9abec67 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -1216,8 +1216,7 @@ all of them. Currently supported window managers include: "0h52hj3ay8mfhwvmfxbxlfyq74hifdk8wxgxp7fr4iy6189hg7w7")))) (build-system gnu-build-system) (inputs - `(("python-2" ,python-2) - ("gtk+-2" ,gtk+-2))) + (list python-2 gtk+-2)) (native-inputs (list python2-pygtk gtk-doc pkg-config)) (synopsis "Library for registering global keyboard shortcuts") @@ -1699,24 +1698,21 @@ display a clock or apply image manipulation techniques to the background image." (sha256 (base32 "109a49f064ma5js2d7maribmfalswbmmhq2fraa7hfz5pf2jxs2w")))) (build-system meson-build-system) - (inputs `(("date" ,date) - ("fmt" ,fmt) - ("gtk-layer-shell" ,gtk-layer-shell) - ("gtkmm" ,gtkmm-3) - ("jsoncpp" ,jsoncpp) - ("libdbusmenu" ,libdbusmenu) - ("libinput" ,libinput) - ("libmpdclent" ,libmpdclient) - ("libnl" ,libnl) - ("libxml2" ,libxml2) - ("pulseaudio" ,pulseaudio) - ("spdlog" ,spdlog) - ("wayland" ,wayland))) + (inputs (list date + fmt + gtk-layer-shell + gtkmm-3 + jsoncpp + libdbusmenu + libinput + libmpdclient + libnl + libxml2 + pulseaudio + spdlog + wayland)) (native-inputs - `(("glib:bin" ,glib "bin") - ("pkg-config" ,pkg-config) - ("scdoc" ,scdoc) - ("wayland-protocols" ,wayland-protocols))) + (list `(,glib "bin") pkg-config scdoc wayland-protocols)) (home-page "https://github.com/Alexays/Waybar") (synopsis "Wayland bar for Sway and Wlroots based compositors") (description "Waybar is a highly customisable Wayland bar for Sway and diff --git a/gnu/packages/wv.scm b/gnu/packages/wv.scm index 43ec1106f1..1fdcf0ac2b 100644 --- a/gnu/packages/wv.scm +++ b/gnu/packages/wv.scm @@ -43,11 +43,7 @@ (base32 "17f16lkdv1c3amaz2hagiicih59ynpp4786k1m2qa1sw68xhswsc")))) (build-system gnu-build-system) (inputs - `(("glib" ,glib) - ("libgsf" ,libgsf) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("zlib" ,zlib))) + (list glib libgsf libjpeg-turbo libpng zlib)) (native-inputs (list `(,glib "bin") pkg-config)) (synopsis "Microsoft Word conversion library and utilities") diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 34ce54e554..f345d9f5a3 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -763,13 +763,13 @@ move windows, switch between desktops, etc.).") (native-inputs (list autoconf autoconf-archive automake pkg-config)) (inputs - `(("giblib" ,giblib) - ("imlib2" ,imlib2) - ("libbsd" ,libbsd) - ("libx11" ,libx11) - ("libxcomposite" ,libxcomposite) - ("libxext" ,libxext) - ("libXfixes" ,libxfixes))) + (list giblib + imlib2 + libbsd + libx11 + libxcomposite + libxext + libxfixes)) (home-page "https://github.com/resurrecting-open-source-projects/scrot") (synopsis "Command-line screen capture utility for X Window System") (description diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index d542348e7b..689c1fcd6d 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -315,8 +315,7 @@ upstream occasionally.") (list pkg-config intltool)) (propagated-inputs ;; exo-2.pc refers to all these. - `(("gtk+-3" ,gtk+) - ("libxfce4util" ,libxfce4util))) + (list gtk+ libxfce4util)) (inputs (list libxfce4ui)) (home-page "https://www.xfce.org/") @@ -342,13 +341,10 @@ development.") "07fjsgdjqxbcm84ga3cl495782k381k6mwksyrks3zf1l8klk4c4")))) (build-system gnu-build-system) (native-inputs - `(("glib:bin" ,glib "bin") - ("gobject-introspection" ,gobject-introspection) - ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") gobject-introspection intltool pkg-config)) (propagated-inputs - `(("gtk+-3" ,gtk+) ; required by garcon-gtk3-1.pc - ("libxfce4ui" ,libxfce4ui))) ; required by garcon-gtk3-1.pc + (list gtk+ ; required by garcon-gtk3-1.pc + libxfce4ui)) ; required by garcon-gtk3-1.pc (home-page "https://www.xfce.org/") (synopsis "Implementation of the freedesktop.org menu specification") (description @@ -372,23 +368,22 @@ merging features essential for loading menus modified with menu editors.") "0rmga1l7da0pjrs6jlyq1nfn513r543v7cchshrif1341knpy2wv")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("glib:bin" ,glib "bin") ; need glib-genmarshal - ("dbus-glib" ,dbus-glib))) ; need dbus-binding-tool + (list pkg-config intltool + `(,glib "bin") ; need glib-genmarshal + dbus-glib)) ; need dbus-binding-tool (propagated-inputs (list glib)) ; required by tumbler-1.pc (inputs - `(("dbus" ,dbus) - ("gdk-pixbuf" ,gdk-pixbuf) - ("cairo" ,cairo) ;; Needed for pdf thumbnails (poppler-glibc.pc) - ("freetype" ,freetype) - ("libjpeg" ,libjpeg-turbo) - ("libgsf" ,libgsf) - ("poppler" ,poppler) - ;; FIXME Provide gstreamer and gstreamer-tag to get video thumbnails - ;; ("gstreamer" ,gstreamer) - )) + (list dbus + gdk-pixbuf + cairo ;; Needed for pdf thumbnails (poppler-glibc.pc) + freetype + libjpeg-turbo + libgsf + poppler + ;; FIXME Provide gstreamer and gstreamer-tag to get video thumbnails + ;; ("gstreamer" ,gstreamer) + )) (home-page "https://www.xfce.org/") (synopsis "D-Bus service for applications to request thumbnails") (description @@ -1224,14 +1219,10 @@ of data to either CD/DVD/BD.") "196swmc4amab8xcwv4q9p8b43fzzi9xagg20gnyjvf5x7yssxj1k")))) (build-system gnu-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("intltool" ,intltool) - ("glib:bin" ,glib "bin"))) ; glib-genmarshal + (list pkg-config intltool + `(,glib "bin"))) ; glib-genmarshal (inputs - `(("exo" ,exo) - ("libsoup" ,libsoup-minimal-2) - ("libxfce4ui" ,libxfce4ui) - ("xfce4-panel" ,xfce4-panel))) + (list exo libsoup-minimal-2 libxfce4ui xfce4-panel)) (home-page "https://goodies.xfce.org/projects/applications/xfce4-screenshooter") (synopsis "Xfce's application to take screenshots") (description @@ -1385,9 +1376,7 @@ watch your every step.") (native-inputs (list intltool pkg-config)) (inputs - `(("gtk+-2" ,gtk+-2) - ("libxfce4ui" ,libxfce4ui) - ("xfce4-panel" ,xfce4-panel))) + (list gtk+-2 libxfce4ui xfce4-panel)) (home-page "https://goodies.xfce.org/projects/panel-plugins/xfce4-equake-plugin") (synopsis "Earthquake monitor for the Xfce panel") @@ -1514,9 +1503,7 @@ performance (bytes transferred per second).") (native-inputs (list intltool pkg-config)) (inputs - `(("libxfce4ui" ,libxfce4ui) - ("xfce4-panel" ,xfce4-panel) - ("gtk+-2" ,gtk+-2))) + (list libxfce4ui xfce4-panel gtk+-2)) (home-page "https://goodies.xfce.org/projects/panel-plugins/xfce4-embed-plugin") (synopsis "Embed arbitrary applications inside the Xfce panel") @@ -1605,10 +1592,7 @@ button and a personalized tooltip.") (native-inputs (list intltool pkg-config)) (inputs - `(("gtk+-2" ,gtk+-2) - ("libxfce4ui" ,libxfce4ui) - ("exo" ,exo) - ("xfce4-panel" ,xfce4-panel))) + (list gtk+-2 libxfce4ui exo xfce4-panel)) (home-page "https://goodies.xfce.org/projects/panel-plugins/xfce4-mailwatch-plugin") (synopsis "Mail watch plugin for the Xfce panel") @@ -1735,10 +1719,7 @@ interfaces of your choice in the panel.") (native-inputs (list intltool desktop-file-utils pkg-config)) (inputs - `(("gtk+-2" ,gtk+-2) - ("exo" ,exo) - ("libxfce4ui" ,libxfce4ui) - ("xfce4-panel" ,xfce4-panel))) + (list gtk+-2 exo libxfce4ui xfce4-panel)) (home-page "https://goodies.xfce.org/projects/panel-plugins/xfce4-places-plugin") (synopsis "Gnome-like Places menu for the Xfce panel") @@ -1799,9 +1780,8 @@ favorite search engine or bug tracker right from the Xfce panel.") "1d2n56g12dhnjznrq7xvr6d3brpp0lmm080xmgjb7ybc1yygpxrc")))) (build-system gnu-build-system) (native-inputs - `(("intltool" ,intltool) - ("pkg-config" ,pkg-config) - ("glib:bin" ,glib "bin"))) + (list intltool pkg-config + `(,glib "bin"))) (inputs (list libxfce4ui libdbusmenu xfce4-panel)) (home-page @@ -1991,11 +1971,7 @@ lan interface (signal state, signal quality, network name (SSID)).") (native-inputs (list intltool pkg-config)) (inputs - `(("gtk+" ,gtk+) - ("libsoup" ,libsoup-minimal-2) - ("libxfce4ui" ,libxfce4ui) - ("libxml2" ,libxml2) - ("xfce4-panel" ,xfce4-panel))) + (list gtk+ libsoup-minimal-2 libxfce4ui libxml2 xfce4-panel)) (home-page "https://goodies.xfce.org/projects/panel-plugins/xfce4-weather-plugin") (synopsis "Show information about local weather in the Xfce panel") diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm index fca1ddc123..ccd99de7c6 100644 --- a/gnu/packages/xiph.scm +++ b/gnu/packages/xiph.scm @@ -273,10 +273,7 @@ meaning that audio is compressed in FLAC without any loss in quality.") (build-system gnu-build-system) (native-inputs (list doxygen bison pkg-config)) ;; FIXME: Add optional input liboggz - (inputs `(("libogg" ,libogg) - ("libpng" ,libpng) - ("python" ,python-wrapper) - ("zlib" ,zlib))) + (inputs (list libogg libpng python-wrapper zlib)) (synopsis "Karaoke and text codec for embedding in ogg") (description "Kate is an overlay codec, originally designed for karaoke and text, diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 8f4c9706bd..bc76a95c59 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -1001,21 +1001,21 @@ server, collect the answer, and finally decoding the XML to Perl.") (native-inputs (list perl-module-build perl-uri perl-class-data-inheritable)) (propagated-inputs - `(("perl-class-errorhandler" ,perl-class-errorhandler) - ("perl-datetime" ,perl-datetime) - ("perl-datetime-format-flexible" ,perl-datetime-format-flexible) - ("perl-datetime-format-iso8601" ,perl-datetime-format-iso8601) - ("perl-datetime-format-mail" ,perl-datetime-format-mail) - ("perl-datetime-format-natural" ,perl-datetime-format-natural) - ("perl-datetime-format-w3cdtf" ,perl-datetime-format-w3cdtf) - ("perl-feed-find" ,perl-feed-find) - ("perl-html-parser" ,perl-html-parser) - ("perl-libwww-perl" ,perl-libwww) - ("perl-module-pluggable" ,perl-module-pluggable) - ("perl-uri-fetch" ,perl-uri-fetch) - ("perl-xml-atom" ,perl-xml-atom) - ("perl-xml-libxml" ,perl-xml-libxml) - ("perl-xml-rss" ,perl-xml-rss))) + (list perl-class-errorhandler + perl-datetime + perl-datetime-format-flexible + perl-datetime-format-iso8601 + perl-datetime-format-mail + perl-datetime-format-natural + perl-datetime-format-w3cdtf + perl-feed-find + perl-html-parser + perl-libwww + perl-module-pluggable + perl-uri-fetch + perl-xml-atom + perl-xml-libxml + perl-xml-rss)) (home-page "https://metacpan.org/release/XML-Feed") (synopsis "XML Syndication Feed Support") (description "@code{XML::Feed} is a syndication feed parser for both RSS and diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index b396c0bba5..85a93dee30 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -6253,12 +6253,12 @@ Conventions Manual) and some of the @dfn{EWMH} (native-inputs (list pkg-config autoconf automake)) (inputs - `(("libX11" ,libx11) - ("libXext" ,libxext) - ("libXcomposite" ,libxcomposite) - ("libXfixes" ,libxfixes) - ("libXdamage" ,libxdamage) - ("libXrender" ,libxrender))) + (list libx11 + libxext + libxcomposite + libxfixes + libxdamage + libxrender)) (synopsis "X Compositing manager using RENDER") (description "xcompmgr is a sample compositing manager for X servers supporting the XFIXES, DAMAGE, RENDER, and COMPOSITE extensions. It enables -- cgit v1.2.3