Merge branch 'wip-r'

author: Ricardo Wurmus <rekado@elephly.net> 2022-05-29 11:49:03 +0200
committer: Ricardo Wurmus <rekado@elephly.net> 2022-05-29 11:49:03 +0200
commit: e640da33f3f142f24af8c63b6e1350865096bae1 (patch)
tree: 17ed9611de1e4946bace8e6d22270c6ebe36bbe9
parent: 926fcb488b756fb5d6c4c129c4348650919e5835 (diff)
parent: 89e926201234a4fe5474dc97504474323dd03f0a (diff)
download: guix-patches-e640da33f3f142f24af8c63b6e1350865096bae1.tar
guix-patches-e640da33f3f142f24af8c63b6e1350865096bae1.tar.gz
8 files changed, 1596 insertions, 1393 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1962117132..4d3f86bfd3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -358,14 +358,14 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
-    (version "1.3.99")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
-                                     version 'annotation))
-              (sha256
-               (base32
-                "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
+    (version "1.3.993")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
+                              version 'annotation))
+       (sha256
+        (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
     (build-system r-build-system)
@@ -696,14 +696,14 @@ annotations for the genome of the model mouse Mus musculus.")
 (define-public r-bsgenome-hsapiens-ucsc-hg19
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg19")
-    (version "1.4.0")
+    (version "1.4.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
                                      version 'annotation))
               (sha256
                (base32
-                "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
+                "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
     (build-system r-build-system)
@@ -720,14 +720,13 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
 (define-public r-bsgenome-hsapiens-ucsc-hg38
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg38")
-    (version "1.4.1")
+    (version "1.4.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
                                      version 'annotation))
               (sha256
-               (base32
-                "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
+               (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
     (build-system r-build-system)
@@ -892,19 +891,18 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
   (package
     (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
-    (version "3.4.6")
+    (version "3.15.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
                                      version 'annotation))
               (sha256
-               (base32
-                "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
+               (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
     (properties
      `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-genomicfeatures))
+     (list r-annotationdbi r-genomicfeatures))
     (home-page
      "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
     (synopsis "Annotation package for human genome in TxDb format")
@@ -1081,14 +1079,13 @@ data (chip hgu133plus2) assembled using data from public repositories.")
 (define-public r-pfam-db
   (package
     (name "r-pfam-db")
-    (version "3.8.2")
+    (version "3.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PFAM.db" version 'annotation))
        (sha256
-        (base32
-         "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
+        (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
     (properties `((upstream-name . "PFAM.db")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1169,13 +1166,12 @@ All datasets are restricted to protein coding genes.")
 (define-public r-adductdata
   (package
     (name "r-adductdata")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adductData" version 'experiment))
               (sha256
-               (base32
-                "0bp74p06gskwn2xl1srpnmsq27ajsrlynkzw6fcmvwwjcrzljmnj"))))
+               (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
     (properties `((upstream-name . "adductData")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationhub r-experimenthub))
@@ -1191,29 +1187,28 @@ albumin} (HSA).")
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")
-   (version "1.18.0")
+   (version "1.24.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "AneuFinderData" version 'experiment))
             (sha256
-             (base32
-              "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks"))))
+             (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
    (build-system r-build-system)
    (home-page "https://bioconductor.org/packages/AneuFinderData/")
    (synopsis "Data package for @code{AneuFinder}")
-   (description "This package contains data used by @code{AneuFinder}.")
+   (description "This package contains whole-genome single cell sequencing data for
+demonstration purposes in the @code{AneuFinder} package.")
    (license license:artistic2.0)))
 
 (define-public r-arrmdata
   (package
     (name "r-arrmdata")
-    (version "1.18.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ARRmData" version 'experiment))
               (sha256
-               (base32
-                "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
+               (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
     (properties
      `((upstream-name . "ARRmData")))
     (build-system r-build-system)
@@ -1227,14 +1222,13 @@ from Illumina 450k methylation arrays.")
 (define-public r-biscuiteerdata
   (package
     (name "r-biscuiteerdata")
-    (version "1.6.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteerData" version 'experiment))
        (sha256
-        (base32
-         "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj"))))
+        (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
     (properties
      `((upstream-name . "biscuiteerData")))
     (build-system r-build-system)
@@ -1251,13 +1245,13 @@ biscuiteer.")
 (define-public r-celldex
   (package
     (name "r-celldex")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "celldex" version 'experiment))
        (sha256
-        (base32 "04w60fx3s3wlirmr65nsz6d7ig48j9fzimdr8kbdqv1g80ivdcq1"))))
+        (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
     (properties `((upstream-name . "celldex")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1280,14 +1274,13 @@ single-cell data or deconvolution of bulk RNA-seq.")
 (define-public r-chromstardata
   (package
     (name "r-chromstardata")
-    (version "1.16.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaRData" version 'experiment))
        (sha256
-        (base32
-         "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
+        (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
     (properties `((upstream-name . "chromstaRData")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/chromstaRData/")
@@ -1300,14 +1293,13 @@ chromstaR package.")
 (define-public r-copyhelper
   (package
     (name "r-copyhelper")
-    (version "1.6.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
        (sha256
-        (base32
-         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+        (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
     (properties `((upstream-name . "CopyhelpeR")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/CopyhelpeR/")
@@ -1324,14 +1316,13 @@ GenomicRanges Bioconductor package.")
 (define-public r-genelendatabase
   (package
     (name "r-genelendatabase")
-    (version "1.18.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
        (sha256
-        (base32
-         "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
+        (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
     (properties
      `((upstream-name . "geneLenDataBase")))
     (build-system r-build-system)
@@ -1347,13 +1338,13 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "genomationData" version 'experiment))
-              (sha256
-               (base32
-                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "genomationData" version 'experiment))
+       (sha256
+        (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
     (properties
      `((upstream-name . "genomationData")))
     (build-system r-build-system)
@@ -1370,19 +1361,42 @@ genomation package.  Included are Chip Seq, Methylation and Cage data,
 downloaded from Encode.")
     (license license:gpl3+)))
 
+(define-public r-msdata
+  (package
+    (name "r-msdata")
+    (version "0.36.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "msdata" version 'experiment))
+       (sha256
+        (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
+    (properties `((upstream-name . "msdata")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/msdata")
+    (synopsis "Various Mass Spectrometry raw data example files")
+    (description
+     "This package provides Ion Trap positive ionization mode data in mzML file
+format.  It includes a subset from 500-850 m/z and 1190-1310 seconds,
+including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
+III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
+LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
+files for various search engines.")
+    (license license:gpl2+)))
+
 (define-public r-pasilla
   (package
     (name "r-pasilla")
-    (version "1.14.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "pasilla" version 'experiment))
-              (sha256
-               (base32
-                "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pasilla" version 'experiment))
+       (sha256
+        (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
     (build-system r-build-system)
-    (propagated-inputs
-     (list r-biocstyle r-dexseq r-knitr r-rmarkdown))
+    (propagated-inputs (list r-dexseq))
+    (native-inputs (list r-knitr))
     (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
@@ -1394,13 +1408,13 @@ by Brooks et al., Genome Research 2011.")
 (define-public r-hsmmsinglecell
   (package
     (name "r-hsmmsinglecell")
-    (version "1.2.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
-              (sha256
-               (base32
-                "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
+       (sha256
+        (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
     (properties
      `((upstream-name . "HSMMSingleCell")))
     (build-system r-build-system)
@@ -1423,13 +1437,13 @@ resulting in a complete gene expression profile for each cell.")
 (define-public r-all
   (package
     (name "r-all")
-    (version "1.26.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "ALL" version 'experiment))
-              (sha256
-               (base32
-                "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ALL" version 'experiment))
+       (sha256
+        (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
     (properties `((upstream-name . "ALL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1447,14 +1461,13 @@ the form of an @code{exprSet} object.")
 (define-public r-affydata
   (package
     (name "r-affydata")
-    (version "1.32.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affydata" version 'experiment))
        (sha256
-        (base32
-         "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
+        (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
     (properties `((upstream-name . "affydata")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1470,13 +1483,13 @@ package @code{affy}.")
 (define-public r-gagedata
   (package
     (name "r-gagedata")
-    (version "2.28.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gageData" version 'experiment))
        (sha256
-        (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
+        (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
     (properties `((upstream-name . "gageData")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/gageData")
@@ -1496,14 +1509,13 @@ yeast are also included.")
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")
-    (version "1.8.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
        (sha256
-        (base32
-         "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
+        (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
     (properties
      `((upstream-name . "curatedTCGAData")))
     (build-system r-build-system)
@@ -1514,6 +1526,7 @@ yeast are also included.")
            r-multiassayexperiment
            r-s4vectors
            r-summarizedexperiment))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/curatedTCGAData/")
     (synopsis "Curated data from The Cancer Genome Atlas")
     (description
@@ -1529,13 +1542,13 @@ across the entire multi-'omics experiment.")
 (define-public r-tcgabiolinksgui-data
   (package
     (name "r-tcgabiolinksgui-data")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
        (sha256
-        (base32 "08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm"))))
+        (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
     (properties `((upstream-name . "TCGAbiolinksGUI.data")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -1551,13 +1564,13 @@ TCGAbiolinksGUI package.")
 (define-public r-abarray
   (package
     (name "r-abarray")
-    (version "1.62.0")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABarray" version))
               (sha256
                (base32
-                "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k"))))
+                "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
     (properties `((upstream-name . "ABarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-multtest))
@@ -1577,13 +1590,13 @@ into folders according to the analysis settings used.")
 (define-public r-absseq
   (package
     (name "r-absseq")
-    (version "1.48.0")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABSSeq" version))
               (sha256
                (base32
-                "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650"))))
+                "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
     (properties `((upstream-name . "ABSSeq")))
     (build-system r-build-system)
     (propagated-inputs (list r-limma r-locfit))
@@ -1606,13 +1619,13 @@ ranking by fold-change and visualization.")
 (define-public r-adam
   (package
     (name "r-adam")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAM" version))
               (sha256
                (base32
-                "18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5"))))
+                "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
     (properties `((upstream-name . "ADAM")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr
@@ -1641,13 +1654,13 @@ functionally associated genes} (GFAG).")
 (define-public r-adamgui
   (package
     (name "r-adamgui")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAMgui" version))
               (sha256
                (base32
-                "0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq"))))
+                "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
     (properties `((upstream-name . "ADAMgui")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1689,13 +1702,13 @@ the @code{GFAGpathUi} function.")
 (define-public r-adimpute
   (package
     (name "r-adimpute")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADImpute" version))
               (sha256
                (base32
-                "1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2"))))
+                "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
     (properties `((upstream-name . "ADImpute")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1738,13 +1751,13 @@ results from different methods into an ensemble.")
 (define-public r-adsplit
   (package
     (name "r-adsplit")
-    (version "1.64.0")
+    (version "1.66.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adSplit" version))
               (sha256
                (base32
-                "1b4ck371h3a76m5h0brvlzsyg1g6q5fjrhra5hqv9pwxr330h9r2"))))
+                "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
     (properties `((upstream-name . "adSplit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1766,13 +1779,13 @@ the supporting gene set is determined.")
 (define-public r-affixcan
   (package
     (name "r-affixcan")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffiXcan" version))
               (sha256
                (base32
-                "06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d"))))
+                "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
     (properties `((upstream-name . "AffiXcan")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1794,13 +1807,13 @@ expression values are known.")
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffyRNADegradation" version))
               (sha256
                (base32
-                "00hzr62xn1i1w4g8krsxhivzwn8hd7hwhkdxyrpz6cs9vgr4x9kd"))))
+                "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
     (properties `((upstream-name . "AffyRNADegradation")))
     (build-system r-build-system)
     (propagated-inputs (list r-affy))
@@ -1819,13 +1832,13 @@ of samples that are affected by RNA degradation.")
 (define-public r-agdex
   (package
     (name "r-agdex")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AGDEX" version))
               (sha256
                (base32
-                "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64"))))
+                "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
     (properties `((upstream-name . "AGDEX")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-gseabase))
@@ -1846,13 +1859,13 @@ experiment.")
 (define-public r-aggregatebiovar
   (package
     (name "r-aggregatebiovar")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aggregateBioVar" version))
               (sha256
                (base32
-                "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk"))))
+                "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
     (properties `((upstream-name . "aggregateBioVar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1880,13 +1893,13 @@ bulk RNA-seq tools.")
 (define-public r-agilp
   (package
     (name "r-agilp")
-    (version "3.26.0")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "agilp" version))
               (sha256
                (base32
-                "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp"))))
+                "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
     (properties `((upstream-name . "agilp")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/agilp")
@@ -1902,13 +1915,13 @@ but which also provides utilities which may be useful for other platforms.")
 (define-public r-adductomicsr
   (package
     (name "r-adductomicsr")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adductomicsR" version))
               (sha256
                (base32
-                "0cnvxrk0h3r6jpa4g4qismg6zk5c7rf8lqixg89c24i98gffkbcl"))))
+                "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
     (properties `((upstream-name . "adductomicsR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1977,13 +1990,13 @@ objects are used so that other packages could be used as well.")
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AneuFinder" version))
               (sha256
                (base32
-                "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
+                "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -2019,14 +2032,14 @@ sequencing data.")
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.14.0")
+    (version "3.15.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik"))))
+         "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -2039,13 +2052,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.40.0")
+    (version "0.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh"))))
+                "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -2059,13 +2072,13 @@ packages.")
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as"))))
+                "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-s4vectors
@@ -2086,13 +2099,13 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.36.0")
+   (version "2.38.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql"))))
+               "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -2116,24 +2129,32 @@ used visualizations.")
 (define-public r-dearseq
   (package
     (name "r-dearseq")
-    (version "1.6.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dearseq" version))
        (sha256
         (base32
-         "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc"))))
+         "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ggplot2
+     (list r-compquadform
+           r-dplyr
+           r-ggplot2
            r-kernsmooth
+           r-magrittr
            r-matrixstats
            r-patchwork
            r-pbapply
+           r-reshape2
+           r-rlang
            r-statmod
            r-survey
-           r-kernsmooth))
+           r-tibble
+           r-viridislite))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://github.com/borishejblum/dearseq")
     (synopsis "DEA for RNA-seq data through a robust variance component test")
     (description
@@ -2146,13 +2167,13 @@ set analyses, and can deal with repeated or longitudinal data.")
 (define-public r-decipher
   (package
     (name "r-decipher")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DECIPHER" version))
               (sha256
                (base32
-                "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm"))))
+                "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
@@ -2167,16 +2188,57 @@ set analyses, and can deal with repeated or longitudinal data.")
 biological sequences.")
     (license license:gpl3)))
 
+(define-public r-decoupler
+  (package
+    (name "r-decoupler")
+    (version "2.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "decoupleR" version))
+       (sha256
+        (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
+    (properties `((upstream-name . "decoupleR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-broom
+           r-dplyr
+           r-magrittr
+           r-matrix
+           r-purrr
+           r-rlang
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-withr))
+    (native-inputs (list r-knitr))
+    (home-page "https://saezlab.github.io/decoupleR/")
+    (synopsis "Computational methods to infer biological activities from omics data")
+    (description
+     "Many methods allow us to extract biological activities from omics data using
+information from prior knowledge resources, reducing the dimensionality for
+increased statistical power and better interpretability.  decoupleR is a
+Bioconductor package containing different statistical methods to extract these
+signatures within a unified framework.  decoupleR allows the user to flexibly
+test any method with any resource.  It incorporates methods that take into
+account the sign and weight of network interactions.  decoupleR can be used
+with any omic, as long as its features can be linked to a biological process
+based on prior knowledge.  For example, in transcriptomics gene sets regulated
+by a transcription factor, or in phospho-proteomics phosphosites that are
+targeted by a kinase.")
+    (license license:gpl3)))
+
 (define-public r-deepsnv
   (package
     (name "r-deepsnv")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deepSNV" version))
               (sha256
                (base32
-                "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w"))))
+                "0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q"))))
     (properties `((upstream-name . "deepSNV")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2206,13 +2268,13 @@ bases such as COSMIC.")
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.20.0")
+    (version "0.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj"))))
+                "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -2236,13 +2298,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-derfinderhelper
   (package
     (name "r-derfinderhelper")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "derfinderHelper" version))
        (sha256
-        (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"))))
+        (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
     (properties `((upstream-name . "derfinderHelper")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2261,13 +2323,13 @@ calculation in parallel.")
 (define-public r-drimseq
   (package
     (name "r-drimseq")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DRIMSeq" version))
        (sha256
-        (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02"))))
+        (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
     (properties `((upstream-name . "DRIMSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2296,13 +2358,13 @@ results.")
 (define-public r-bluster
   (package
    (name "r-bluster")
-   (version "1.4.0")
+   (version "1.6.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "bluster" version))
             (sha256
              (base32
-              "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm"))))
+              "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
    (properties `((upstream-name . "bluster")))
    (build-system r-build-system)
    (propagated-inputs
@@ -2326,13 +2388,13 @@ and evaluate clustering results.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g"))))
+                "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -2350,13 +2412,13 @@ arbitrary genomic intervals along chromosomal ideogram.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.28.0")
+    (version "2.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg"))))
+                "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -2378,13 +2440,13 @@ possible.")
 (define-public r-isoformswitchanalyzer
   (package
     (name "r-isoformswitchanalyzer")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
        (sha256
-        (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf"))))
+        (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
     (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2580,14 +2642,14 @@ performing parallel computations on multicore machines.")
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a"))))
+         "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affyio
@@ -2608,14 +2670,14 @@ analysis.")
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21"))))
+         "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase))
@@ -2629,14 +2691,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg"))))
+         "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
@@ -2655,14 +2717,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f"))))
+         "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2678,14 +2740,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.66.0")
+    (version "1.68.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40"))))
+         "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2720,14 +2782,14 @@ to streamline the more common analyses that a Biostatistician might see.")
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm"))))
+         "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-zlibbioc))
@@ -2744,14 +2806,14 @@ CDF file formats.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.66.0")
+    (version "1.68.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal"))))
+         "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -2772,14 +2834,14 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"))))
+         "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -2799,13 +2861,13 @@ microarrays.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.56.2")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8"))))
+                "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -2829,13 +2891,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w"))))
+                "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
@@ -2854,14 +2916,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz"))))
+         "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -2886,14 +2948,14 @@ databases.  Packages produced are intended to be used with AnnotationDbi.")
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "3.2.2")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "08dk4h07gpi3rk9s80wrbx2ww2chj688qzbwlx8n4dz788lqbfz8"))))
+         "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2927,14 +2989,14 @@ by the user, helping with quick and reproducible access.")
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.24.0")
+    (version "3.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp"))))
+         "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2951,14 +3013,14 @@ classes.")
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"))))
+         "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -2981,13 +3043,13 @@ paired-end data.")
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.54.0")
+    (version "2.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"))))
+                "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -3003,13 +3065,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.50.3")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1"))))
+                "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -3041,13 +3103,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.28.3")
+    (version "1.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p"))))
+                "0rqvwhs6d8ls1rq7j5ywl5k0qgblxpzimilyw335bi1yad5s10h3"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -3094,13 +3156,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.62.0")
+    (version "2.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq"))))
+                "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -3122,14 +3184,14 @@ biological sequences or sets of sequences.")
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz"))))
+         "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3164,13 +3226,13 @@ effort and encourages consistency.")
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.62.0")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi"))))
+                "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
@@ -3195,14 +3257,14 @@ genome data packages and support for efficient SNP representation.")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427"))))
+         "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3226,13 +3288,13 @@ analysis.")
 (define-public r-chipseeker
   (package
     (name "r-chipseeker")
-    (version "1.30.3")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ChIPseeker" version))
               (sha256
                (base32
-                "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g"))))
+                "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -3272,14 +3334,14 @@ annotation, distance to TSS, and overlap of peaks or genes.")
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6"))))
+         "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -3298,20 +3360,21 @@ experiments.")
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn"))))
+         "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-circlize
            r-clue
+           r-codetools
            r-colorspace
            r-digest
            r-doparallel
@@ -3337,14 +3400,14 @@ self-defined annotation graphics.")
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy"))))
+         "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3408,14 +3471,14 @@ distribution.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9"))))
+         "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3446,14 +3509,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1"))))
+         "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3491,13 +3554,13 @@ exploration of the results.")
 (define-public r-diffcyt
   (package
     (name "r-diffcyt")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "diffcyt" version))
        (sha256
-        (base32 "1yc9mlc0ifb7h6rzskq97bsdq1kwdp5qq9l9mciwyxf6yjkmv5ni"))))
+        (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
     (properties `((upstream-name . "diffcyt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3529,14 +3592,14 @@ adapted from transcriptomics.")
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6"))))
+         "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
@@ -3556,14 +3619,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7"))))
+         "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3596,13 +3659,13 @@ global-scaling and full-quantile normalization.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.36.0")
+    (version "3.38.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk"))))
+                "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3621,14 +3684,14 @@ CAGE.")
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.18.4")
+    (version "2.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1nsdcsghhh3ikv0hbn1aazdam7a6pqf1p6rz68ll2h6965kl4qzp"))))
+         "183rs74ngfvn9xz36csch495pqaash90yhhikm73m7b2bc37ziwz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -3666,14 +3729,14 @@ chromosome region or transcript models of lincRNA genes.")
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80"))))
+         "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-biocgenerics r-genomicranges r-iranges
@@ -3693,14 +3756,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar"))))
+         "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi r-go-db r-graph r-keggrest))
@@ -3721,14 +3784,14 @@ analysis using other methods.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.76.0")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2"))))
+         "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
@@ -3745,13 +3808,13 @@ high-throughput sequencing experiments.")
 (define-public r-geneoverlap
   (package
     (name "r-geneoverlap")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GeneOverlap" version))
               (sha256
                (base32
-                "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm"))))
+                "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcolorbrewer r-gplots))
@@ -3764,13 +3827,13 @@ and visualize the results.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j"))))
+                "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
@@ -3811,13 +3874,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.30.1")
+    (version "1.32.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55"))))
+                "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -3838,13 +3901,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"))))
+                "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
@@ -3871,13 +3934,13 @@ alignments.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.46.5")
+    (version "1.48.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1fhahqh87cikfrwqkm2z4nq3jyi530qvsbmf09j2hyhsm87hhrgg"))))
+                "18ain5s0ry6w0ki4c0czvwax2ncigrldyac30a6mlbzyaga6i54h"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -3915,14 +3978,14 @@ extracting the desired features in a convenient format.")
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.30.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x"))))
+         "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3949,13 +4012,13 @@ provide added flexibility for data combination and manipulation.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.46.1")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx"))))
+                "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -3976,14 +4039,14 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z"))))
+         "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4007,14 +4070,14 @@ testing and other simple calculations.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6"))))
+         "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4036,14 +4099,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"))))
+         "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -4056,14 +4119,14 @@ the Human Protein Atlas project.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4"))))
+         "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -4085,13 +4148,13 @@ of other R packages who wish to make use of HTSlib.")
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.68.0")
+    (version "1.70.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5"))))
+                "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
     (native-inputs
      (list gfortran))
     (build-system r-build-system)
@@ -4105,14 +4168,14 @@ microarray data, using nearest neighbor averaging.")
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab"))))
+         "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
@@ -4130,14 +4193,14 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279"))))
+         "0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4154,13 +4217,13 @@ Shiny-based display methods for Bioconductor objects.")
 (define-public r-lfa
   (package
     (name "r-lfa")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lfa" version))
        (sha256
-        (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr"))))
+        (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
     (properties `((upstream-name . "lfa")))
     (build-system r-build-system)
     (propagated-inputs (list r-corpcor))
@@ -4175,13 +4238,13 @@ Binomial data via estimation of latent structure in the natural parameter.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.50.3")
+    (version "3.52.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1p46sif1aygmw2p8ifiylxrrbfbgvcsa0zp40nxlxawc7h56rybp"))))
+                "193l3z2jv0kr91nl4r64p3jzb2rai9k8akx1zw7303nsnwpiiaay"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -4194,13 +4257,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx"))))
+                "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4268,14 +4331,14 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "3.4.1")
+    (version "3.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k"))))
+         "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -4314,14 +4377,14 @@ in SNV base substitution data.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.20.4")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc"))))
+         "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4359,14 +4422,14 @@ of mass spectrometry based proteomics data.")
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p"))))
+         "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (arguments
@@ -4416,14 +4479,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri"))))
+         "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4447,19 +4510,17 @@ specific parser.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1"))
+         "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
        (modules '((guix build utils)))
        (snippet
-        '(begin
-           (delete-file-recursively "src/boost")
-           #t))))
+        '(delete-file-recursively "src/boost"))))
     (properties `((upstream-name . "mzR")))
     (build-system r-build-system)
     (arguments
@@ -4473,12 +4534,9 @@ specific parser.")
                (("\\ARCH_OBJS=" line)
                 (string-append line
                                "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
-             #t)))))
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
     (inputs
-     (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
+     (list boost ; use this instead of the bundled boost sources
            zlib))
     (propagated-inputs
      (list r-biobase
@@ -4486,8 +4544,7 @@ specific parser.")
            r-ncdf4
            r-protgenerics
            r-rcpp
-           r-rhdf5lib
-           r-zlibbioc))
+           r-rhdf5lib))
     (native-inputs
      (list r-knitr))
     (home-page "https://github.com/sneumann/mzR/")
@@ -4504,14 +4561,14 @@ previously been used in XCMS.")
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83"))))
+         "1xklaiyd4mv9sf9211flq1s68fhdn53y2i4l1k2ib39a4l6y9cyr"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4536,14 +4593,14 @@ the fact that each of these packages implements a select methods.")
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.86.0")
+    (version "1.88.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg"))))
+         "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4605,14 +4662,14 @@ chromosome.  Both tumor-normal paired and tumor-only analyses are supported.")
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0"))))
+         "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
@@ -4625,14 +4682,14 @@ proteomics packages.")
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0"))))
+         "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4647,13 +4704,13 @@ the graph algorithms contained in the Boost library.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7"))))
+                "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4697,14 +4754,14 @@ library implementing most of the pipeline's features.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.26.1")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"))))
+         "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4728,14 +4785,14 @@ region sets and other genomic features.")
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7"))))
+         "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
@@ -4778,13 +4835,13 @@ browser.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.38.1")
+    (version "2.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "1mlwp7bblhbpmd90sxj02zpq1q3fyg8v7ankyjb1y284xaymp02y"))))
+                "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rhdf5filters r-rhdf5lib))
@@ -4805,14 +4862,14 @@ the available RAM.")
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rhdf5filters" version))
        (sha256
         (base32
-         "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78"))))
+         "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
     (properties `((upstream-name . "rhdf5filters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4831,13 +4888,13 @@ HDF5 datasets.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.10.0")
+    (version "2.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh"))))
+                "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -4896,13 +4953,13 @@ tab-delimited (tabix) files.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.54.0")
+    (version "1.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc"))))
+                "1d9sak1xrrkcvj0q3vnp6w2k0nx2k2ajhsbq0dyb4nhcghp5w8fd"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -4975,13 +5032,13 @@ differential expression analysis, RNAseq data and related problems.")
 (define-public r-scannotatr
   (package
     (name "r-scannotatr")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scAnnotatR" version))
        (sha256
-        (base32 "08jq04ckjw8a5y753almc5bl8vnn4j6qp2zb7bb9w3ql3ddy7b21"))))
+        (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
     (properties `((upstream-name . "scAnnotatR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5012,13 +5069,13 @@ cell types based on specific research needs.")
 (define-public r-scdblfinder
   (package
     (name "r-scdblfinder")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDblFinder" version))
        (sha256
-        (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd"))))
+        (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
     (properties `((upstream-name . "scDblFinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5028,9 +5085,14 @@ cell types based on specific research needs.")
            r-biocsingular
            r-bluster
            r-delayedarray
+           r-genomeinfodb
+           r-genomicranges
            r-igraph
+           r-iranges
            r-mass
            r-matrix
+           r-rsamtools
+           r-rtracklayer
            r-s4vectors
            r-scater
            r-scran
@@ -5094,14 +5156,14 @@ different experiment.")
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl"))))
+         "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (native-inputs
@@ -5117,13 +5179,13 @@ Stephens (1990).")
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na"))))
+                "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
@@ -5140,14 +5202,14 @@ reference point and sorted by a user defined feature.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx"))))
+         "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -5183,14 +5245,14 @@ ungapped alignment formats.")
 (define-public r-simplifyenrichment
   (package
     (name "r-simplifyenrichment")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simplifyEnrichment" version))
        (sha256
         (base32
-         "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98"))))
+         "1g3kfa17p60jkk4l34vc5hdq83w082qsxbjvpqw7r9rdd8d79z2q"))))
     (properties
      `((upstream-name . "simplifyEnrichment")))
     (build-system r-build-system)
@@ -5200,9 +5262,11 @@ ungapped alignment formats.")
            r-circlize
            r-clue
            r-cluster
+           r-colorspace
            r-complexheatmap
            r-digest
            r-getoptlong
+           r-globaloptions
            r-go-db
            r-gosemsim
            r-matrix
@@ -5222,13 +5286,13 @@ and comparing the clusterings.")
 (define-public r-transcriptr
   (package
     (name "r-transcriptr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "transcriptR" version))
        (sha256
-        (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy"))))
+        (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
     (properties `((upstream-name . "transcriptR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5272,14 +5336,14 @@ able to deal also with novel and case specific events.")
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TrajectoryUtils" version))
        (sha256
         (base32
-         "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1"))))
+         "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
     (properties
      `((upstream-name . "TrajectoryUtils")))
     (build-system r-build-system)
@@ -5299,13 +5363,13 @@ structures to hold pseudotime inference results.")
 (define-public r-slingshot
   (package
    (name "r-slingshot")
-   (version "2.2.1")
+   (version "2.4.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "slingshot" version))
             (sha256
              (base32
-              "10kjpmckhzjf41yfhzg7c8idqa9cxz33r4rza6rwihnqnw1liff3"))))
+              "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-igraph
@@ -5331,13 +5395,13 @@ graph construction.")
 (define-public r-stager
   (package
     (name "r-stager")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "stageR" version))
        (sha256
-        (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y"))))
+        (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
     (properties `((upstream-name . "stageR")))
     (build-system r-build-system)
     (propagated-inputs (list r-summarizedexperiment))
@@ -5354,13 +5418,13 @@ Biology at
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-    (version "2.6.5")
+    (version "2.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "STRINGdb" version))
        (sha256
-        (base32 "0n2r2zc2sx1a2a8wqqxz6z7i4ynaj18iwbwgif7469n13agji5mv"))))
+        (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
     (properties `((upstream-name . "STRINGdb")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5387,13 +5451,13 @@ that integrates the various evidences.")
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "StructuralVariantAnnotation" version))
        (sha256
-        (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678"))))
+        (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -5424,13 +5488,13 @@ involving two separate genomic loci encoded as GRanges objects.")
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.24.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a"))))
+                "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -5458,14 +5522,14 @@ samples.")
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.42.0")
+    (version "3.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj"))))
+         "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-edger
@@ -5489,14 +5553,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.0.8")
+    (version "2.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "0ajlw9yg6fha76rkkmsk5niq99s33k9437bkgi9whgh3pa6bkab2"))))
+         "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5532,13 +5596,13 @@ annotation infrastructure.")
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.46.0")
+    (version "2.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2"))))
+                "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
@@ -5565,13 +5629,13 @@ dependencies between GO terms can be implemented and applied.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4"))))
+                "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -5622,13 +5686,13 @@ R, enabling interactive analysis and visualization of genome-scale data.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.40.0")
+    (version "1.42.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva"))))
+                "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (propagated-inputs
@@ -5660,14 +5724,14 @@ coding changes and predict coding outcomes.")
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.62.0")
+    (version "3.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x"))))
+         "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
@@ -5729,13 +5793,13 @@ inference.")
 (define-public r-xina
   (package
     (name "r-xina")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "XINA" version))
        (sha256
-        (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp"))))
+        (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
     (properties `((upstream-name . "XINA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5765,13 +5829,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
 (define-public r-xmapbridge
   (package
     (name "r-xmapbridge")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xmapbridge" version))
        (sha256
-        (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi"))))
+        (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
     (properties `((upstream-name . "xmapbridge")))
     (build-system r-build-system)
     (home-page "https://git.bioconductor.org/packages/xmapbridge")
@@ -5792,13 +5856,13 @@ describing each of the graphs.")
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.34.0")
+    (version "0.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0"))))
+                "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -5826,13 +5890,13 @@ describing each of the graphs.")
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj"))))
+                "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
@@ -5845,13 +5909,13 @@ libraries for systems that do not have these available via other means.")
 (define-public r-zellkonverter
   (package
     (name "r-zellkonverter")
-    (version "1.4.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zellkonverter" version))
        (sha256
-        (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg"))))
+        (base32 "1w3qi35vk289cpky1pb0wgg1hr55s5kdw7np98i9c1vmwi3gvwr7"))))
     (properties `((upstream-name . "zellkonverter")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5877,14 +5941,14 @@ saving AnnData objects to disk.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8"))))
+         "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
@@ -5902,14 +5966,14 @@ saving AnnData objects to disk.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264"))))
+         "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5937,14 +6001,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6"))))
+         "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -5973,14 +6037,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138"))))
+         "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2 r-reshape2))
@@ -6027,13 +6091,13 @@ integration with @code{Rcpp}.")
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-   (version "1.16.0")
+   (version "1.18.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "apeglm" version))
             (sha256
              (base32
-              "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr"))))
+              "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
    (properties `((upstream-name . "apeglm")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6054,13 +6118,13 @@ posterior for individual coefficients.")
 (define-public r-greylistchip
   (package
    (name "r-greylistchip")
-   (version "1.26.0")
+   (version "1.28.1")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "GreyListChIP" version))
             (sha256
              (base32
-              "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv"))))
+              "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
    (properties `((upstream-name . "GreyListChIP")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6081,14 +6145,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.4.11")
+    (version "3.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1xprj3x3s3yh6fwsdcl4zgfbhn640422x1lhhrmvdr836jr8sxcj"))))
+         "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6159,13 +6223,13 @@ processing to visualization and annotation.")
 (define-public r-mbkmeans
   (package
     (name "r-mbkmeans")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "mbkmeans" version))
               (sha256
                (base32
-                "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k"))))
+                "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -6191,14 +6255,14 @@ large datasets, including support for on-disk data representation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.50.0")
+    (version "2.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"))))
+         "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-survival r-biocgenerics r-biobase r-mass))
@@ -6226,13 +6290,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0"))))
+                "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics))
@@ -6319,14 +6383,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.28.1")
+    (version "3.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw"))))
+         "1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6373,13 +6437,13 @@ enrichedGO (addGeneIDs).")
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.6.0")
+   (version "1.8.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3"))))
+              "0s7s39v9lqniirjgp8lbmffw0c8rsp6bndgzy1zlyh5vivfih0f5"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
@@ -6400,12 +6464,12 @@ incompatibilities.")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz"))))
+               (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-limma))
@@ -6419,12 +6483,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.54.0")
+   (version "1.56.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d"))))
+             (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6438,12 +6502,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.56.0")
+   (version "2.58.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr"))))
+             (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -6457,12 +6521,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj"))))
+               (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6489,14 +6553,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r"))))
+         "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6513,14 +6577,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq"))))
+         "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6547,14 +6611,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx"))))
+         "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6588,14 +6652,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd"))))
+         "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6616,14 +6680,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw"))))
+         "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -6650,14 +6714,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb"))))
+         "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -6691,14 +6755,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx"))))
+         "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
     (build-system r-build-system)
     (propagated-inputs (list r-amap))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -6711,14 +6775,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0"))))
+         "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -6737,14 +6801,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9"))))
+         "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6770,14 +6834,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki"))))
+         "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6793,14 +6857,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"))))
+         "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-mass))
@@ -6817,14 +6881,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk"))))
+         "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6863,14 +6927,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"))))
+         "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6890,14 +6954,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q"))))
+         "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6915,14 +6979,14 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr"))))
+         "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6943,14 +7007,14 @@ achieved for all methods using the BiocParallel framework.")
 (define-public r-scaledmatrix
   (package
     (name "r-scaledmatrix")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ScaledMatrix" version))
        (sha256
         (base32
-         "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc"))))
+         "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"))))
     (properties `((upstream-name . "ScaledMatrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6969,14 +7033,14 @@ multiplication.")
 (define-public r-treeio
   (package
     (name "r-treeio")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "treeio" version))
        (sha256
         (base32
-         "19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq"))))
+         "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"))))
     (properties `((upstream-name . "treeio")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7001,14 +7065,14 @@ platform for merging tree with associated data and converting file formats.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "3.2.1")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8"))))
+         "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7038,14 +7102,14 @@ data.")
 (define-public r-metapod
   (package
     (name "r-metapod")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "metapod" version))
        (sha256
         (base32
-         "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk"))))
+         "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
     (properties `((upstream-name . "metapod")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7067,14 +7131,14 @@ missing values and weighting where appropriate.")
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n"))))
+         "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7102,14 +7166,14 @@ possible, parallelization is achieved using the BiocParallel framework.")
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.8.1")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc"))))
+         "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -7146,14 +7210,14 @@ maps.")
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky"))))
+         "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7168,14 +7232,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"))))
+         "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7208,13 +7272,13 @@ sequencing data.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534"))))
+                "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
@@ -7228,14 +7292,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm"))))
+         "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -7326,14 +7390,14 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m"))))
+         "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7348,13 +7412,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.20.3")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m"))))
+                "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -7386,14 +7450,14 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs"))))
+         "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
     (build-system r-build-system)
     (inputs
      (list zlib))
@@ -7415,14 +7479,14 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx"))))
+         "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7444,14 +7508,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.22.2")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy"))))
+         "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7459,6 +7523,7 @@ independent of the p-value under the null hypothesis.")
            r-dt
            r-ggplot2
            r-limma
+           r-markdown
            r-reshape2
            r-rocr
            r-scales
@@ -7480,14 +7545,14 @@ interactive exploration of results.")
 (define-public r-residualmatrix
   (package
     (name "r-residualmatrix")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ResidualMatrix" version))
        (sha256
         (base32
-         "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg"))))
+         "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"))))
     (properties
      `((upstream-name . "ResidualMatrix")))
     (build-system r-build-system)
@@ -7552,14 +7617,14 @@ the numbers of cells across batches.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy"))))
+         "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7587,14 +7652,14 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"))))
+         "1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -7603,13 +7668,13 @@ single cell assay data.")
            r-cluster
            r-combinat
            r-ddrtree
-           r-densityclust
            r-dplyr
            r-fastica
            r-ggplot2
            r-hsmmsinglecell
            r-igraph
            r-irlba
+           r-leidenbase
            r-limma
            r-mass
            r-matrix
@@ -7642,11 +7707,11 @@ qPCR data, but could be used with other types as well.")
     (license license:artistic2.0)))
 
 (define-public r-leidenbase
-  (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce")
+  (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
         (revision "1"))
     (package
       (name "r-leidenbase")
-      (version (git-version "0.1.3" revision commit))
+      (version (git-version "0.1.9" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -7656,7 +7721,7 @@ qPCR data, but could be used with other types as well.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0"))))
+           "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
       (properties `((upstream-name . "leidenbase")))
       (build-system r-build-system)
       (inputs
@@ -7772,14 +7837,14 @@ user-defined and/or data-driven sets of hypotheses.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v"))))
+         "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7798,14 +7863,14 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5"))))
+         "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7836,14 +7901,14 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1"))))
+         "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aroma-light
@@ -7880,21 +7945,21 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.62.2")
+    (version "2.64.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw"))))
+         "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
+           r-curl
            r-data-table
            r-dplyr
-           r-httr
            r-limma
            r-magrittr
            r-r-utils
@@ -7915,14 +7980,14 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.36.0")
+    (version "0.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"))))
+         "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64))
@@ -7936,14 +8001,14 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9"))))
+         "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multtest r-scrime))
@@ -7960,14 +8025,14 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"))))
+         "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -7994,14 +8059,14 @@ studies.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx"))))
+         "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beanplot
@@ -8045,14 +8110,14 @@ methylation arrays.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.40.1")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka"))))
+         "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
@@ -8092,14 +8157,14 @@ and Infinium HD arrays are also included.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in"))))
+         "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
@@ -8131,14 +8196,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.18.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj"))))
+         "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8192,14 +8257,14 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.18.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h"))))
+         "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8283,13 +8348,13 @@ published results; and a routine for graphical display.")
 (define-public r-tradeseq
   (package
    (name "r-tradeseq")
-   (version "1.8.0")
+   (version "1.10.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "tradeSeq" version))
             (sha256
              (base32
-              "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j"))))
+              "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
@@ -8352,14 +8417,14 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl"))))
+         "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8392,14 +8457,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "3.2.0")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf"))))
+         "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8417,14 +8482,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab"))))
+         "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8444,14 +8509,14 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f"))))
+         "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-multtest r-qvalue))
@@ -8474,14 +8539,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9"))))
+            "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -8496,13 +8561,13 @@ phenotype of interest.")
 (define-public r-fcscan
   (package
     (name "r-fcscan")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fcScan" version))
        (sha256
-        (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd"))))
+        (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
     (properties `((upstream-name . "fcScan")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8529,14 +8594,14 @@ presence of additional sites within the allowed window size.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9"))))
+         "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bh
@@ -8561,14 +8626,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.20.1")
+    (version "3.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n"))))
+         "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8596,14 +8661,14 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.14.2")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2"))))
+         "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
@@ -8634,14 +8699,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.2.2")
+    (version "4.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76"))))
+         "03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -8671,13 +8736,13 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-clusterexperiment
   (package
     (name "r-clusterexperiment")
-    (version "2.14.0")
+    (version "2.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "clusterExperiment" version))
               (sha256
                (base32
-                "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"))))
+                "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -8717,14 +8782,14 @@ expression data sets.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag"))))
+         "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8759,14 +8824,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l"))))
+         "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -8791,14 +8856,14 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0"))))
+         "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8815,14 +8880,14 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb"))))
+         "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8845,14 +8910,14 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d"))))
+         "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8869,14 +8934,14 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr"))))
+         "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8893,14 +8958,14 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy"))))
+         "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8924,14 +8989,14 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m"))))
+         "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
@@ -8945,14 +9010,14 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz"))))
+         "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
@@ -8993,14 +9058,14 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"))))
+         "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel r-ellipse r-ggplot2))
@@ -9018,14 +9083,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.42.0")
+    (version "2.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v"))))
+         "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9072,12 +9137,12 @@ distributions, modules and filter motifs.")
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.36.0")
+   (version "1.38.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425"))))
+             (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
@@ -9099,12 +9164,12 @@ frequency matrices from nine public sources, for multiple organisms.")
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.8.0")
+   (version "2.10.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj"))))
+             (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -9114,7 +9179,6 @@ frequency matrices from nine public sources, for multiple organisms.")
           r-bsgenome
           r-genomeinfodb
           r-genomicranges
-          r-grimport
           r-gviz
           r-iranges
           r-matrixstats
@@ -9150,18 +9214,23 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz"))))
+         "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml))
+     (list r-ade4
+           r-biostrings
+           r-ggplot2
+           r-htmlwidgets
+           r-tfbstools
+           r-xml))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/motifStack/")
@@ -9177,14 +9246,14 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.6.1")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "17v2v7aklljy17nivwmani2jxkbffqs2yr38hlspjlvgpidpf9ln"))))
+         "0zq9k4189dlc14f9rknsc1ffhpjzb2f4fzdaszfdbnd4rr43b79i"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9214,14 +9283,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.18.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "1jmlialnhs9df1hv6l4qk2c4qjyjbz9mdj8vr52ms8vlxlxplz6c"))))
+         "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9261,14 +9330,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127"))))
+         "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9366,14 +9435,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh"))))
+         "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
@@ -9391,14 +9460,14 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq"))))
+         "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
@@ -9434,23 +9503,24 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.16.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp"))))
+         "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
            r-data-table
+           r-delayedarray
+           r-delayedmatrixstats
            r-gseabase
            r-mixtools
            r-r-utils
-           r-s4vectors
            r-shiny
            r-summarizedexperiment))
     (native-inputs
@@ -9473,14 +9543,14 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.36.0")
+    (version "4.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619"))))
+         "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9512,14 +9582,14 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab"))))
+         "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -9545,14 +9615,14 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl"))))
+         "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-circlize r-genomicranges r-getoptlong r-iranges))
@@ -9571,14 +9641,14 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql"))))
+         "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
@@ -9610,14 +9680,14 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h"))))
+         "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9659,14 +9729,14 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.66.0")
+    (version "2.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001"))))
+         "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
@@ -9741,14 +9811,14 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq"))))
+         "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -9774,14 +9844,14 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d"))))
+         "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -9811,14 +9881,14 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"))))
+         "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -9879,19 +9949,19 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.60.1")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "00irq3i5kfck7rnm8ll7rqhqfpp3bisv2h8is50a7wbd7480z7ij"))))
+         "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
-    (propagated-inputs
-     (list r-waveslim))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
     (synopsis "Mass spectrum processing by wavelet-based algorithms")
     (description
@@ -9903,14 +9973,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.16.1")
+    (version "3.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143"))))
+         "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -9944,13 +10014,13 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wppi
   (package
     (name "r-wppi")
-    (version "1.2.0")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "wppi" version))
               (sha256
                (base32
-                "1spwa8p6w3pyw21dvd1lrhcz1sphdsmsd408jv55ss9nbgvgrp23"))))
+                "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
     (properties `((upstream-name . "wppi")))
     (build-system r-build-system)
     ;; This is necessary because omnipathr attempts to write a configuration
@@ -9985,14 +10055,14 @@ scores and a path search algorithm.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n"))))
+         "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10009,14 +10079,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi"))))
+         "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -10043,14 +10113,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j"))))
+         "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -10064,14 +10134,14 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17"))))
+         "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
     (build-system r-build-system)
     (inputs
      (list netpbm perl))
@@ -10096,14 +10166,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zinbwave
   (package
     (name "r-zinbwave")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
         (base32
-         "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq"))))
+         "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel
@@ -10129,14 +10199,14 @@ the data.")
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9"))))
+         "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10154,14 +10224,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x"))))
+         "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10181,21 +10251,23 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"))))
+         "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
+           r-decoupler
            r-dplyr
            r-ggplot2
            r-ggrepel
            r-gridextra
+           r-reshape2
            r-tidyr))
     (native-inputs
      (list r-knitr))
@@ -10211,14 +10283,14 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh"))))
+         "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
@@ -10234,14 +10306,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.2.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb"))))
+         "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10267,14 +10339,14 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b"))))
+         "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -10297,14 +10369,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr"))))
+         "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (arguments
@@ -10333,14 +10405,14 @@ alignment tool.")
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja"))))
+         "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10376,14 +10448,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y"))))
+         "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
@@ -10414,14 +10486,14 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5"))))
+         "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10456,14 +10528,14 @@ quantification of genomic regions of interest.")
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071"))))
+         "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10499,14 +10571,14 @@ graphics.")
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.26.5")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "041i5d08bsc5jqx3309fixjacizs4yi992cwazxghm8mrk3kicbr"))))
+         "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10552,14 +10624,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s"))))
+         "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10589,14 +10661,14 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.26.4")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn"))))
+         "1i9g32mjknrd2lbz2nisc7nr0gk9byx9aik1i7xdwmq4ndxf8rf7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multidataset))
@@ -10626,14 +10698,14 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"))))
+         "11w28nlz0f06idbna5k9xs891w516401l1zab5gg7s0z3xxaki4f"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls))
@@ -10655,14 +10727,14 @@ datasets.")
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"))))
+         "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -10696,14 +10768,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.8.2")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "078zcchw9xl6vs2wihzzji349vq0m1a039m86jdlvb7nc3i1imfk"))))
+         "1cf80gmzz4c1pvif3350ifsmsbfplyl2na39n8g3x0zkwpl6ijdc"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -10722,14 +10794,14 @@ and to both short and long sequence reads.")
 (define-public r-flowutils
   (package
     (name "r-flowutils")
-    (version "1.58.0")
+    (version "1.59.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowUtils" version))
        (sha256
         (base32
-         "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161"))))
+         "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
     (properties `((upstream-name . "flowUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10748,14 +10820,14 @@ and to both short and long sequence reads.")
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr"))))
+         "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
@@ -10814,14 +10886,14 @@ of the analyses while minimizing technical noise.")
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.6.2")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "0ycr4wmkfi0rvzwicblkfjgppk72gwwpim0rfiz1s44lycsf4py5"))))
+         "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
@@ -10843,14 +10915,14 @@ interact with gated cytometry data.")
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp"))))
+         "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10875,14 +10947,14 @@ with flow cytometry data.")
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6"))))
+         "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10898,14 +10970,14 @@ change point detection.")
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar"))))
+         "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10929,14 +11001,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1"))))
+         "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10966,14 +11038,14 @@ statistics to the plot.")
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04"))))
+         "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10997,14 +11069,14 @@ statistics to the plot.")
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.32.0")
+    (version "3.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi"))))
+         "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
@@ -11013,13 +11085,8 @@ statistics to the plot.")
     (propagated-inputs
      (list r-biobase
            r-biocgenerics
-           r-clue
-           r-corpcor
-           r-ellipse
            r-flowcore
-           r-flowviz
-           r-graph
-           r-mnormt))
+           r-graph))
     (inputs
      (list gsl))
     (native-inputs
@@ -11036,14 +11103,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10"))))
+         "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -11052,7 +11119,7 @@ model with Box-Cox transformation.")
          (add-after 'unpack 'unpack-bundled-sources
            (lambda _
              (with-directory-excursion "src"
-               (invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
+               (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/RProtoBufLib/")
@@ -11065,14 +11132,14 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.6.0")
+    (version "4.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig"))))
+         "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11119,20 +11186,21 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.6.0")
+    (version "4.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9"))))
+         "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
            r-biocgenerics
            r-cluster
+           r-corpcor
            r-fda
            r-flowcore
            r-flowviz
@@ -11141,6 +11209,7 @@ matches the flowJo analysis.")
            r-ks
            r-lattice
            r-mass
+           r-mnormt
            r-ncdfflow
            r-rcolorbrewer
            r-rrcov))
@@ -11155,14 +11224,14 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm"))))
+         "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11199,14 +11268,14 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz"))))
+         "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
@@ -11251,14 +11320,14 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f"))))
+         "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11294,14 +11363,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.18.1")
+    (version "6.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f"))))
+         "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11340,14 +11409,14 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"))))
+         "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11386,14 +11455,14 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7"))))
+         "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11402,11 +11471,11 @@ data, to only emphasize the data that actually matters.")
            r-biocgenerics
            r-data-table
            r-dplyr
-           r-feather
            r-genomeinfodb
            r-genomicranges
            r-gseabase
            r-r-utils
+           r-s4vectors
            r-summarizedexperiment
            r-tibble))
     (native-inputs
@@ -11428,14 +11497,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-chicago
   (package
     (name "r-chicago")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Chicago" version))
        (sha256
         (base32
-         "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn"))))
+         "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
     (properties `((upstream-name . "Chicago")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11450,14 +11519,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7"))))
+         "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -11517,14 +11586,14 @@ accessibility data.")
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf"))))
+         "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
@@ -11652,14 +11721,14 @@ cisTopics and explore the nature and regulatory proteins driving them.")
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw"))))
+         "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11676,14 +11745,14 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9"))))
+         "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (native-inputs
@@ -11698,14 +11767,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3"))))
+         "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11736,14 +11805,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp"))
+         "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -11792,14 +11861,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali"))))
+         "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11823,14 +11892,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr"))))
+         "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11847,14 +11916,14 @@ genome sequence.")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1"))))
+         "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11870,14 +11939,14 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk"))))
+         "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11917,14 +11986,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"))))
+         "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
@@ -11958,14 +12027,14 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p"))))
+         "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
@@ -12064,14 +12133,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.24.1")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "14aki7d9xl4rhhzv3cl09mbj1q7xhxg69s4kzms9hfv3cqjryqd7"))))
+         "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -12112,14 +12181,14 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3"))))
+         "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12142,14 +12211,14 @@ features (e.g.  genes, microRNAs).")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk"))))
+         "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
@@ -12166,14 +12235,14 @@ data.")
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.12.4")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "01skcvzd815m3c15ka2pk7z6bggc4l8bhvaf4z9v95i36k4mn5zd"))))
+         "0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
@@ -12214,13 +12283,13 @@ motifs, and others.")
 (define-public r-ace
   (package
     (name "r-ace")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACE" version))
               (sha256
                (base32
-                "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6"))))
+                "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
     (properties `((upstream-name . "ACE")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
@@ -12243,13 +12312,13 @@ of @dfn{tumor cells} (cells with divergent segments).")
 (define-public r-acgh
   (package
     (name "r-acgh")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aCGH" version))
               (sha256
                (base32
-                "1r1q6iq3g7svfn5m4jxlxp413djb40mvf6lh595y86sgwav5k6l4"))))
+                "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
     (properties `((upstream-name . "aCGH")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
@@ -12267,13 +12336,13 @@ printing and plotting @code{aCGH} objects.")
 (define-public r-acme
   (package
     (name "r-acme")
-    (version "2.50.0")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACME" version))
               (sha256
                (base32
-                "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg"))))
+                "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
     (properties `((upstream-name . "ACME")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-biocgenerics))
@@ -12294,13 +12363,13 @@ on whole-genome tiling array experiments quite easily with enough memory.")
 (define-public r-acde
   (package
     (name "r-acde")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "acde" version))
               (sha256
                (base32
-                "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6"))))
+                "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
     (properties `((upstream-name . "acde")))
     (build-system r-build-system)
     (propagated-inputs (list r-boot))
@@ -12359,14 +12428,14 @@ using whole genome sequencing data.")
 (define-public r-activepathways
   (package
     (name "r-activepathways")
-    (version "1.0.4")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActivePathways" version))
        (sha256
         (base32
-         "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y"))))
+         "0zbrgz91mlik7j8j11wsdswqqqfsijj8jkgd5fx1ar3mc6rqsmbg"))))
     (properties
      `((upstream-name . "ActivePathways")))
     (build-system r-build-system)
@@ -12387,14 +12456,14 @@ cellular organization in health and disease.")
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn"))))
+         "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12409,14 +12478,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm"))))
+         "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12431,14 +12500,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2"))))
+         "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -12457,14 +12526,14 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6"))))
+         "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12479,14 +12548,14 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk"))))
+         "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12508,14 +12577,14 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.52.0")
+    (version "2.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2"))))
+         "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
@@ -12534,14 +12603,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf"))))
+         "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12556,14 +12625,14 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj"))))
+         "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs (list graphviz))
@@ -12578,14 +12647,14 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr"))))
+         "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12642,14 +12711,14 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q"))))
+         "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12685,14 +12754,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.46.0")
+    (version "3.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8"))))
+         "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12728,13 +12797,13 @@ structures.")
 (define-public r-fmcsr
   (package
     (name "r-fmcsr")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "fmcsR" version))
         (sha256
-          (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0"))))
+          (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
     (properties `((upstream-name . "fmcsR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12757,14 +12826,14 @@ searching and clustering.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.32.1")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i"))))
+         "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12792,14 +12861,14 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r"))))
+         "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12821,18 +12890,18 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr"))))
+         "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs))
+     (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
     (home-page "https://bioconductor.org/packages/graphite/")
     (synopsis "Networks from pathway databases")
     (description
@@ -12844,14 +12913,14 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b"))))
+         "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12876,14 +12945,14 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6"))))
+         "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12920,13 +12989,13 @@ monograph.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y"))))
+                "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -12935,7 +13004,6 @@ monograph.")
            r-graph
            r-httr
            r-knitr
-           r-optparse
            r-biocmanager
            r-biocviews
            r-stringdist))
@@ -12950,14 +13018,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq"))))
+         "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12972,13 +13040,13 @@ different graph related packages produced by Bioconductor.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd"))))
+                "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -12996,13 +13064,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.62.1")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r"))))
+                "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -13024,14 +13092,14 @@ also known as views, in a controlled vocabulary.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "2.2.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5"))))
+         "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13058,14 +13126,14 @@ access.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.28.0")
+    (version "1.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s"))))
+         "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13085,14 +13153,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9"))))
+         "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
@@ -13120,14 +13188,14 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9"))))
+         "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13165,14 +13233,14 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq"))))
+         "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13192,14 +13260,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.12.2")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny"))))
+         "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13240,14 +13308,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w"))))
+         "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13278,14 +13346,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa"))))
+         "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -13311,14 +13379,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp"))))
+         "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13333,14 +13401,14 @@ distance measures.")
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4"))))
+         "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13379,14 +13447,14 @@ dimensional mass cytometry data.")
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl"))))
+         "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13403,14 +13471,14 @@ user's input and automatically retrieving results from GREAT web server.")
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh"))))
+         "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13436,14 +13504,14 @@ hypothesis @code{K=1}.")
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs"))))
+         "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13559,14 +13627,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x"))))
+         "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -13580,13 +13648,13 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.32.4")
+    (version "0.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "17dvypxcwp8c7ih23hi2366110by6zq1mjgxkmlbiklzachg9780"))))
+                "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -13609,14 +13677,14 @@ S4Vectors package itself.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.70-3")
+    (version "1.71")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
+         "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13647,14 +13715,14 @@ data manipulation and visualization.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7"))))
+         "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
@@ -13685,13 +13753,13 @@ objects from the @code{graph} package.")
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y"))))
+                "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13709,13 +13777,13 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx"))))
+                "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13738,14 +13806,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4"))))
+         "0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -13769,22 +13837,21 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.16.0")
+    (version "1.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p"))
+         "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            ;; Delete bundled binaries
            (delete-file-recursively "src/wininclude/")
-           (delete-file-recursively "src/winlib-8.3.0/")
-           (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")
-           #t))))
+           (delete-file-recursively "src/winlib/")
+           (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
     (properties `((upstream-name . "Rhdf5lib")))
     (build-system r-build-system)
     (arguments
@@ -13793,11 +13860,8 @@ block processing.")
          (add-after 'unpack 'do-not-use-bundled-hdf5
            (lambda* (#:key inputs #:allow-other-keys)
              (for-each delete-file '("configure" "configure.ac"))
-             ;; Do not make other packages link with the proprietary libsz.
              (substitute* "R/zzz.R"
-               ((" \"%s/libsz.a\"") "")
-               (("patharch, .getDynamicLinks")
-                ".getDynamicLinks"))
+               (("return\\(links\\)") "return(\" -lz\")"))
              (with-directory-excursion "src"
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
                (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
@@ -13816,6 +13880,8 @@ block processing.")
                             "hdf5/src/libhdf5.settings")
                (rename-file "Makevars.in" "Makevars")
                (substitute* "Makevars"
+                 (("@BUILD_HDF5@") "")
+                 (("@COPY_SZIP@") "")
                  (("@ZLIB_LIB@") "-lz")
                  (("@ZLIB_INCLUDE@") "")
                  (("HDF5_CXX_LIB=.*")
@@ -13851,14 +13917,14 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb"))))
+         "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
@@ -13877,13 +13943,13 @@ matrices.")
 (define-public r-cner
   (package
     (name "r-cner")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CNEr" version))
        (sha256
-        (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2"))))
+        (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
     (properties `((upstream-name . "CNEr")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -13925,14 +13991,14 @@ advanced visualization of sets of conserved noncoding elements.")
 (define-public r-tfbstools
   (package
     (name "r-tfbstools")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TFBSTools" version))
        (sha256
         (base32
-         "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g"))))
+         "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
     (properties `((upstream-name . "TFBSTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13971,17 +14037,22 @@ provides a wrapper of de novo motif discovery software.")
 (define-public r-maftools
   (package
     (name "r-maftools")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "maftools" version))
        (sha256
-        (base32 "1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd"))))
+        (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
     (properties `((upstream-name . "maftools")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-data-table r-rcolorbrewer r-rhtslib r-survival r-zlibbioc))
+     (list r-data-table
+           r-dnacopy
+           r-rcolorbrewer
+           r-rhtslib
+           r-survival
+           r-zlibbioc))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/PoisonAlien/maftools")
     (synopsis "Summarize, analyze and visualize MAF files")
@@ -13995,14 +14066,14 @@ customizable visualzations with minimal effort.")
 (define-public r-motifmatchr
   (package
     (name "r-motifmatchr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifmatchr" version))
        (sha256
         (base32
-         "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z"))))
+         "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
     (properties `((upstream-name . "motifmatchr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14029,13 +14100,13 @@ This package wraps C++ code from the MOODS motif calling library.")
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk"))))
+        (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14076,14 +14147,14 @@ sequence (@code{DNAse-seq}) experiments.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39"))))
+         "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
@@ -14104,13 +14175,13 @@ libraries.")
 (define-public r-singler
   (package
     (name "r-singler")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleR" version))
        (sha256
-        (base32 "0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi"))))
+        (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
     (properties `((upstream-name . "SingleR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14136,14 +14207,14 @@ cell types to infer the cell of origin of each single cell independently.")
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.4.0")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467"))))
+         "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14171,13 +14242,13 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg"))))
+                "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -14193,6 +14264,7 @@ of other packages.")
            r-gridextra
            r-matrix
            r-rcolorbrewer
+           r-rcppml
            r-rlang
            r-rtsne
            r-s4vectors
@@ -14212,14 +14284,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic"))))
+         "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -14255,14 +14327,14 @@ variable and significantly correlated genes.")
 (define-public r-sparsematrixstats
   (package
     (name "r-sparsematrixstats")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sparseMatrixStats" version))
        (sha256
         (base32
-         "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1"))))
+         "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
     (properties
      `((upstream-name . "sparseMatrixStats")))
     (build-system r-build-system)
@@ -14280,14 +14352,14 @@ data in the column sparse format.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk"))))
+         "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
@@ -14316,14 +14388,14 @@ memory usage and processing time is minimized.")
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.6.2")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "0614a830gf676ck8j5lkm04158pfvhjb61p3xfdd69gg3d44mk1d"))))
+         "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14345,13 +14417,13 @@ within the R for Mass Spectrometry packages.")
 (define-public r-msfeatures
   (package
     (name "r-msfeatures")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsFeatures" version))
        (sha256
-        (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq"))))
+        (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
     (properties `((upstream-name . "MsFeatures")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14375,14 +14447,14 @@ the respective packages (such as e.g. @code{xcms}).")
 (define-public r-biocio
   (package
     (name "r-biocio")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "BiocIO" version))
         (sha256
           (base32
-            "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr"))))
+            "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
     (properties `((upstream-name . "BiocIO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14408,14 +14480,14 @@ as well as local access.  Developers can register a file extension, e.g.,
 (define-public r-msmseda
   (package
     (name "r-msmseda")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsEDA" version))
        (sha256
         (base32
-         "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9"))))
+         "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
     (properties `((upstream-name . "msmsEDA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14431,14 +14503,14 @@ experiments, and visualize de influence of the involved factors.")
 (define-public r-msmstests
   (package
     (name "r-msmstests")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsTests" version))
        (sha256
         (base32
-         "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb"))))
+         "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
     (properties `((upstream-name . "msmsTests")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14460,14 +14532,14 @@ relevant, and the minimum expression of the most abundant condition.")
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.18.1")
+    (version "1.20.1")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0"))))
+            "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14523,14 +14595,14 @@ preprocessing of cytometry data, including:
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z"))))
+         "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -14563,14 +14635,14 @@ by Ernst and Kellis.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7"))))
+         "1lvms07ba99nzf10gpn50wjca84nj5jrb6902z069p2bfi4xyd27"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -14731,14 +14803,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.38.4")
+    (version "1.40.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "14qybi5b3h9z5b0m127jf7z695amf612rh5wq2g2n1yirfhzbdja"))))
+         "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14780,14 +14852,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.26.0")
+    (version "2.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx"))))
+         "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -14814,13 +14886,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4"))))
+        (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14838,14 +14910,14 @@ functionalities including parsing, graph operation, visualization and etc.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg"))))
+         "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
@@ -14874,14 +14946,14 @@ defining LD blocks.")
 (define-public r-ldheatmap
   (package
     (name "r-ldheatmap")
-    (version "1.0-4")
+    (version "1.0-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "LDheatmap" version))
        (sha256
         (base32
-         "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
+         "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
     (properties `((upstream-name . "LDheatmap")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14900,14 +14972,14 @@ on the plot.")
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "2.7-0")
+    (version "2.7-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "13i2f4lw1rzj89bp31sn03prq1bqj7bsxwdr8z2ql02yqks9phg0"))))
+         "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
     (build-system r-build-system)
     (inputs
      (list gsl))
@@ -14962,13 +15034,13 @@ other functional sequencing data.")
 (define-public r-pathview
   (package
     (name "r-pathview")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pathview" version))
        (sha256
-        (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr"))))
+        (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
     (properties `((upstream-name . "pathview")))
     (build-system r-build-system)
     (propagated-inputs
@@ -14996,14 +15068,14 @@ large-scale and fully automated analysis.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq"))))
+         "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs (list zlib))
@@ -15020,14 +15092,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
 (define-public r-chromstar
   (package
     (name "r-chromstar")
-    (version "1.20.2")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaR" version))
        (sha256
         (base32
-         "1akcmxzn4j9ph4n3lsgfh8fh8hrb28jjamz037w59bsdkcv6wyjq"))))
+         "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
     (properties `((upstream-name . "chromstaR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15058,14 +15130,14 @@ analyses.")
 (define-public r-guitar
   (package
     (name "r-guitar")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Guitar" version))
        (sha256
         (base32
-         "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9"))))
+         "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
     (properties `((upstream-name . "Guitar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15090,13 +15162,13 @@ starting site, start codon, stop codon and transcription ending site.")
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4"))))
+                "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15111,14 +15183,14 @@ visualizations for publication-quality multi-panel figures.")
 (define-public r-ballgown
   (package
     (name "r-ballgown")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ballgown" version))
        (sha256
         (base32
-         "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"))))
+         "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15145,14 +15217,14 @@ to annotation.")
 (define-public r-megadepth
   (package
     (name "r-megadepth")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "megadepth" version))
        (sha256
         (base32
-         "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"))))
+         "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
     (properties `((upstream-name . "megadepth")))
     (build-system r-build-system)
     (inputs (list megadepth))
@@ -15178,23 +15250,23 @@ regions or annotations of your choice from BigWig files.")
 (define-public r-beclear
   (package
     (name "r-beclear")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BEclear" version))
        (sha256
         (base32
-         "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29"))))
+         "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
     (properties `((upstream-name . "BEclear")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-abind
            r-biocparallel
            r-data-table
+           r-dixontest
            r-futile-logger
            r-matrix
-           r-outliers
            r-rcpp
            r-rdpack))
     (native-inputs
@@ -15211,14 +15283,14 @@ real numbers.")
 (define-public r-bgeecall
   (package
     (name "r-bgeecall")
-    (version "1.10.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeCall" version))
        (sha256
         (base32
-         "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16"))))
+         "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
     (properties `((upstream-name . "BgeeCall")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15247,14 +15319,14 @@ all RNA-Seq libraries of each species integrated in Bgee.")
 (define-public r-bgeedb
   (package
     (name "r-bgeedb")
-    (version "2.20.1")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeDB" version))
        (sha256
         (base32
-         "0mrw7fwjx8k0a5c3iw2j94h1yn5pkvqil7fbzih9xiafnpbn374m"))))
+         "093zk43x8i9ajaqsdhndkyal3dizllr3g85ziavb3k73dzvarzsc"))))
     (properties `((upstream-name . "BgeeDB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15281,14 +15353,14 @@ anatomical terms, mapped to genes by expression patterns.")
 (define-public r-biobtreer
   (package
     (name "r-biobtreer")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobtreeR" version))
        (sha256
         (base32
-         "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s"))))
+         "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
     (properties `((upstream-name . "biobtreeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15305,14 +15377,14 @@ mappings functionalities.")
 (define-public r-minet
   (package
     (name "r-minet")
-    (version "3.52.0")
+    (version "3.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minet" version))
        (sha256
         (base32
-         "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd"))))
+         "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
     (properties `((upstream-name . "minet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15327,14 +15399,14 @@ information networks from data.")
 (define-public r-genetclassifier
   (package
     (name "r-genetclassifier")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geNetClassifier" version))
        (sha256
         (base32
-         "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km"))))
+         "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
     (properties
      `((upstream-name . "geNetClassifier")))
     (build-system r-build-system)
@@ -15352,14 +15424,14 @@ interface to query the classifier.")
 (define-public r-dir-expiry
   (package
     (name "r-dir-expiry")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dir.expiry" version))
        (sha256
         (base32
-         "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00"))))
+         "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
     (properties `((upstream-name . "dir.expiry")))
     (build-system r-build-system)
     (propagated-inputs (list r-filelock))
@@ -15376,14 +15448,14 @@ eliminating obsolete caches generated by old versions of packages.")
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk.utils" version))
        (sha256
         (base32
-         "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99"))))
+         "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
     (properties
      `((upstream-name . "basilisk.utils")))
     (build-system r-build-system)
@@ -15400,14 +15472,14 @@ package, primarily for creation of the underlying Conda instance.")
 (define-public r-basilisk
   (package
     (name "r-basilisk")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk" version))
        (sha256
         (base32
-         "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a"))))
+         "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
     (properties `((upstream-name . "basilisk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15426,14 +15498,14 @@ Python environments in a single R session.")
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocthis" version))
        (sha256
         (base32
-         "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39"))))
+         "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
     (properties `((upstream-name . "biocthis")))
     (build-system r-build-system)
     (arguments
@@ -15460,14 +15532,14 @@ Bioconductor-friendly.")
 (define-public r-biocdockermanager
   (package
     (name "r-biocdockermanager")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocDockerManager" version))
        (sha256
         (base32
-         "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w"))))
+         "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
     (properties
      `((upstream-name . "BiocDockerManager")))
     (build-system r-build-system)
@@ -15490,14 +15562,14 @@ the Bioconductor project.")
 (define-public r-biodb
   (package
     (name "r-biodb")
-    (version "1.2.2")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biodb" version))
        (sha256
         (base32
-         "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638"))))
+         "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
     (properties `((upstream-name . "biodb")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15535,14 +15607,14 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"))))
+         "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15564,14 +15636,14 @@ as extensions of common core functions/methods.")
 (define-public r-mvcclass
   (package
     (name "r-mvcclass")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MVCClass" version))
        (sha256
         (base32
-         "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z"))))
+         "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
     (properties `((upstream-name . "MVCClass")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/MVCClass")
@@ -15584,14 +15656,14 @@ design.")
 (define-public r-biomvcclass
   (package
     (name "r-biomvcclass")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioMVCClass" version))
        (sha256
         (base32
-         "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j"))))
+         "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
     (properties `((upstream-name . "BioMVCClass")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15606,14 +15678,14 @@ design.")
 (define-public r-biomvrcns
   (package
     (name "r-biomvrcns")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomvRCNS" version))
        (sha256
         (base32
-         "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"))))
+         "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
     (properties `((upstream-name . "biomvRCNS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15631,14 +15703,14 @@ using aCGH or sequencing.")
 (define-public r-bionero
   (package
     (name "r-bionero")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNERO" version))
        (sha256
         (base32
-         "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p"))))
+         "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
     (properties `((upstream-name . "BioNERO")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15687,14 +15759,14 @@ networks.")
 (define-public r-bionet
   (package
     (name "r-bionet")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNet" version))
        (sha256
         (base32
-         "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg"))))
+         "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
     (properties `((upstream-name . "BioNet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15716,14 +15788,14 @@ scoring subnetwork.")
 (define-public r-bionetstat
   (package
     (name "r-bionetstat")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNetStat" version))
        (sha256
         (base32
-         "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8"))))
+         "0f387j35lj32ryiw48jz8gc08al2lmmv9zvbbgyjq9wmqlca3dfb"))))
     (properties `((upstream-name . "BioNetStat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15758,14 +15830,14 @@ network and metabolic pathways view.")
 (define-public r-bioqc
   (package
     (name "r-bioqc")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioQC" version))
        (sha256
         (base32
-         "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407"))))
+         "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
     (properties `((upstream-name . "BioQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15784,23 +15856,23 @@ optimised for high performance.")
 (define-public r-biotip
   (package
     (name "r-biotip")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioTIP" version))
        (sha256
         (base32
-         "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys"))))
+         "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
     (properties `((upstream-name . "BioTIP")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cluster
            r-genomicranges
-           r-hmisc
            r-igraph
            r-mass
            r-psych
+           r-scran
            r-stringr))
     (native-inputs
      (list r-knitr))
@@ -15814,14 +15886,14 @@ help unravel disease regulatory trajectory.")
 (define-public r-biotmle
   (package
     (name "r-biotmle")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biotmle" version))
        (sha256
         (base32
-         "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g"))))
+         "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
     (properties `((upstream-name . "biotmle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15856,14 +15928,14 @@ ensemble machine learning for the estimation of nuisance functions.")
 (define-public r-bsseq
   (package
     (name "r-bsseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bsseq" version))
        (sha256
         (base32
-         "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"))))
+         "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
     (properties `((upstream-name . "bsseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15902,14 +15974,14 @@ visualizing bisulfite sequencing data.")
 (define-public r-dmrseq
   (package
     (name "r-dmrseq")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dmrseq" version))
        (sha256
         (base32
-         "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd"))))
+         "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
     (properties `((upstream-name . "dmrseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15948,13 +16020,13 @@ interest on transformed methylation proportions.")
 (define-public r-omnipathr
   (package
     (name "r-omnipathr")
-    (version "3.2.8")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OmnipathR" version))
        (sha256
-        (base32 "0vr16ar3rbjsfw4qz2g86lbhvmqwgq0vcahc6vrc4d9rdjxwg6sb"))))
+        (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
     (properties `((upstream-name . "OmnipathR")))
     (build-system r-build-system)
     (arguments
@@ -15984,6 +16056,7 @@ interest on transformed methylation proportions.")
            r-tibble
            r-tidyr
            r-tidyselect
+           r-withr
            r-xml2
            r-yaml))
     (native-inputs (list r-knitr))
@@ -16000,14 +16073,14 @@ for ligand activity prediction from transcriptomics data.")
 (define-public r-biscuiteer
   (package
     (name "r-biscuiteer")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteer" version))
        (sha256
         (base32
-         "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj"))))
+         "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
     (properties `((upstream-name . "biscuiteer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16025,6 +16098,7 @@ for ligand activity prediction from transcriptomics data.")
            r-hdf5array
            r-homo-sapiens
            r-impute
+           r-iranges
            r-matrix
            r-matrixstats
            r-mus-musculus
@@ -16051,13 +16125,13 @@ estimates, etc.")
 (define-public r-tcgabiolinks
   (package
     (name "r-tcgabiolinks")
-    (version "2.22.4")
+    (version "2.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinks" version))
        (sha256
-        (base32 "071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332"))))
+        (base32 "0kw4lrg8xm0ipj7f7h1rwfj7a8mknkril1pn05x08mx13f7p5p14"))))
     (properties `((upstream-name . "TCGAbiolinks")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16106,27 +16180,29 @@ starburst plots) in order to easily develop complete analysis pipelines.")
 (define-public r-tricycle
   (package
     (name "r-tricycle")
-    (version "1.2.1")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tricycle" version))
               (sha256
                (base32
-                "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"))))
+                "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
     (properties `((upstream-name . "tricycle")))
     (build-system r-build-system)
-    (propagated-inputs (list r-annotationdbi
-                             r-circular
-                             r-dplyr
-                             r-genomicranges
-                             r-ggplot2
-                             r-iranges
-                             r-rcolorbrewer
-                             r-s4vectors
-                             r-scater
-                             r-scattermore
-                             r-singlecellexperiment
-                             r-summarizedexperiment))
+    (propagated-inputs
+     (list r-annotationdbi
+           r-circular
+           r-dplyr
+           r-genomicranges
+           r-ggnewscale
+           r-ggplot2
+           r-iranges
+           r-rcolorbrewer
+           r-s4vectors
+           r-scater
+           r-scattermore
+           r-singlecellexperiment
+           r-summarizedexperiment))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/hansenlab/tricycle")
     (synopsis "Transferable representation and inference of cell cycle")
@@ -16143,14 +16219,14 @@ embeddings and functions to build new reference.")
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-    (version "1.12.4")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "tximeta" version))
        (sha256
         (base32
-         "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g"))))
+         "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
     (properties `((upstream-name . "tximeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16184,13 +16260,13 @@ reproducibility.")
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s"))))
+        (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
     (properties `((upstream-name . "phyloseq")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 239a8c13df..1d8397c1aa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11094,6 +11094,15 @@ expression report comparing samples in an easily configurable manner.")
        (modify-phases %standard-phases
          (add-before 'bootstrap 'autoreconf
            (lambda _
+             ;; This was fixed in commit
+             ;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no
+             ;; release with this fix.
+             (call-with-output-file "VERSION"
+               (lambda (port) (display ,version port)))
+             ;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176
+             (substitute* "m4/ax_r_package.m4"
+               (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
+                "if(system.file(package=\"PKG\") == \"\")"))
              (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-PYTHONPATH
            (lambda _
@@ -11182,6 +11191,15 @@ in an easily configurable manner.")
        (modify-phases %standard-phases
          (add-before 'bootstrap 'autoreconf
            (lambda _
+             ;; This was fixed in commit
+             ;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no
+             ;; release with this fix.
+             (call-with-output-file "VERSION"
+               (lambda (port) (display ,version port)))
+             ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181
+             (substitute* "m4/ax_r_package.m4"
+               (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
+                "if(system.file(package=\"PKG\") == \"\")"))
              (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-PYTHONPATH
            (lambda _
@@ -11249,8 +11267,20 @@ methylation and segmentation.")
                 "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:phases
+     `(#:phases
        (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             ;; This was fixed in commit
+             ;; c4ac067438ae9312b5786a72e2bfb3d795e3ec8a, but there is no
+             ;; release with this fix.
+             (call-with-output-file "VERSION"
+               (lambda (port) (display ,version port)))
+             ;; https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/59
+             (substitute* "m4/ax_r_package.m4"
+               (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
+                "if(system.file(package=\"PKG\") == \"\")"))
+             (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-additional-environment-variables
            (lambda _
              ;; Needed because of loompy
@@ -11299,6 +11329,8 @@ methylation and segmentation.")
            r-singlecellexperiment
            r-stringr
            r-yaml))
+    (native-inputs
+     (list autoconf automake))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
     (description
@@ -11327,6 +11359,13 @@ based methods.")
      `(#:tests? #f ;requires huge kraken database
        #:phases
        (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             ;; https://github.com/BIMSBbioinfo/pigx_sars-cov-2/issues/123
+             (substitute* "m4/ax_r_package.m4"
+               (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
+                "if(system.file(package=\"PKG\") == \"\")"))
+             (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-PYTHONPATH
            (lambda _
              (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 95de77e3a7..5a8285b342 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -255,14 +255,14 @@ etc.")
 (define-public r-datawizard
   (package
     (name "r-datawizard")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "datawizard" version))
        (sha256
         (base32
-         "1j26xv1zm7qwp80gy6vlysq3zxdj9r8ivi54b1d6s0ckqkww6gja"))))
+         "09lyh1awm2rplfzgwbdw4iy76mbaqwjd4hwlrsgvxj9pwdnjs4cx"))))
     (properties `((upstream-name . "datawizard")))
     (build-system r-build-system)
     (propagated-inputs
@@ -347,6 +347,29 @@ visualization of their differences.")
     (description "This package implements Dirichlet regression models.")
     (license license:gpl2+)))
 
+(define-public r-dixontest
+  (package
+    (name "r-dixontest")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dixonTest" version))
+       (sha256
+        (base32 "1a3yc30g5rbb0jhm2b0iir5i1dy4jyl67spkhx4yysg4snz131wv"))))
+    (properties `((upstream-name . "dixonTest")))
+    (build-system r-build-system)
+    (native-inputs (list gfortran))
+    (home-page "https://cran.r-project.org/package=dixonTest")
+    (synopsis "Dixon's ratio test for outlier detection")
+    (description
+     "For outlier detection in small and normally distributed samples the ratio
+test of Dixon (Q-test) can be used.  Density, distribution function, quantile
+function and random generation for Dixon's ratio statistics are provided as
+wrapper functions.  The core applies McBane's Fortran functions that use
+Gaussian quadrature for a numerical solution.")
+    (license license:gpl3)))
+
 (define-public r-emdist
   (package
     (name "r-emdist")
@@ -682,14 +705,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser
 (define-public r-v8
   (package
     (name "r-v8")
-    (version "4.1.0")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "V8" version))
        (sha256
         (base32
-         "15ylzcxlhkba99cccw5rvhwhg9i4zcax2fhmr03w8g4fdhbd3n89"))))
+         "0hs7ajjw6y3q7mp7z00a9712y4cn6wgcnk5dbjbzlc6cfk4zsqkc"))))
     (properties `((upstream-name . "V8")))
     (build-system r-build-system)
     (arguments
@@ -814,13 +837,13 @@ known as Dynamic Linear Models.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-9")
+    (version "1.8-10")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
+                "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice))
@@ -1202,13 +1225,13 @@ available as companion packages.")
 (define-public r-scales
   (package
     (name "r-scales")
-    (version "1.1.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scales" version))
        (sha256
-        (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
+        (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-farver
@@ -1216,6 +1239,7 @@ available as companion packages.")
            r-lifecycle
            r-munsell
            r-rcolorbrewer
+           r-rlang
            r-r6
            r-viridislite))
     (home-page "https://github.com/hadley/scales")
@@ -1345,13 +1369,13 @@ with default R plot functions.")
 (define-public r-polychrome
   (package
     (name "r-polychrome")
-    (version "1.3.1")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Polychrome" version))
        (sha256
-        (base32 "044vbylgbqf0ccv4r15nmbw1vz0j95g67i6blw73hvbvbm6w5x4d"))))
+        (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
     (properties `((upstream-name . "Polychrome")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1497,13 +1521,13 @@ objects.")
 (define-public r-mboost
   (package
    (name "r-mboost")
-   (version "2.9-6")
+   (version "2.9-7")
    (source (origin
             (method url-fetch)
             (uri (cran-uri "mboost" version))
             (sha256
              (base32
-              "1gvcq1y9prpgxw5kxa20l31p384gksfx0pn7gf29jbl3cknqiyix"))))
+              "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-lattice
@@ -1526,13 +1550,13 @@ high-dimensional data.")
 (define-public r-shadowtext
   (package
    (name "r-shadowtext")
-   (version "0.1.1")
+   (version "0.1.2")
    (source (origin
             (method url-fetch)
             (uri (cran-uri "shadowtext" version))
             (sha256
              (base32
-              "01h0w3b02r8snjkx5sxkf2x8xm4gd0r8jm27xqz9cv6hgqfmh1pb"))))
+              "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
    (properties `((upstream-name . "shadowtext")))
    (build-system r-build-system)
    (propagated-inputs
@@ -1623,13 +1647,13 @@ read a protected key.")
 (define-public r-astsa
   (package
     (name "r-astsa")
-    (version "1.14")
+    (version "1.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "astsa" version))
        (sha256
-        (base32 "09zx2q419p0b1c336ybh4i62v5dvn3sp39dxn5kwlrqchjj7f5z6"))))
+        (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp"))))
     (properties `((upstream-name . "astsa")))
     (build-system r-build-system)
     (home-page "https://github.com/nickpoison/astsa/")
@@ -1646,14 +1670,14 @@ Analysis Approach Using R.  Chapman-Hall, 2019,
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.5-7")
+    (version "2.6-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
+         "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr ; needed for vignettes
@@ -2299,14 +2323,14 @@ data structures in C++.")
 (define-public r-fastghquad
   (package
     (name "r-fastghquad")
-    (version "1.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fastGHQuad" version))
        (sha256
         (base32
-         "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
+         "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
     (properties `((upstream-name . "fastGHQuad")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2321,14 +2345,14 @@ rules and utility functions for adaptive GH quadrature.")
 (define-public r-rstpm2
   (package
     (name "r-rstpm2")
-    (version "1.5.2")
+    (version "1.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rstpm2" version))
        (sha256
         (base32
-         "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
+         "17mhzfxh761vl64ar6pynpj3k2jkhjgbacxsjhkrfkbmy3aiv0d1"))))
     (properties `((upstream-name . "rstpm2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2814,13 +2838,13 @@ application framework for R, making it easy to create attractive dashboards.")
 (define-public r-shinyfiles
   (package
     (name "r-shinyfiles")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyFiles" version))
        (sha256
-        (base32 "0f8dfdiar376lx0979ccyghgx5rhr08v5z3z60asrrjsxlq4cs85"))))
+        (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg"))))
     (properties `((upstream-name . "shinyFiles")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3451,14 +3475,14 @@ including functions for geolocation and routing.")
 (define-public r-haven
   (package
     (name "r-haven")
-    (version "2.4.3")
+    (version "2.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "haven" version))
        (sha256
         (base32
-         "0pr9jcdk1r9pi9iz0xm1g5yy5qyjk5r7hh9467abx4kpwx3hzdwm"))
+         "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m"))
        (modules '((guix build utils)))
        (snippet
         ;; unvendor readstat
@@ -3477,9 +3501,11 @@ including functions for geolocation and routing.")
     (native-inputs
      (list r-knitr))
     (propagated-inputs
-     (list r-cpp11
+     (list r-cli
+           r-cpp11
            r-forcats
            r-hms
+           r-lifecycle
            r-rlang
            r-readr
            r-tibble
@@ -3740,13 +3766,13 @@ print, summary, plot, update, etc.
 (define-public r-ps
   (package
     (name "r-ps")
-    (version "1.6.0")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ps" version))
        (sha256
-        (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
+        (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842"))))
     (build-system r-build-system)
     (home-page "https://ps.r-lib.org")
     (synopsis "List, query, and manipulate system processes")
@@ -3855,6 +3881,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
 @code{citation(\"Rcpp\")} for details on these last two.")
     (license license:gpl2+)))
 
+(define-public r-rcppml
+  (package
+    (name "r-rcppml")
+    (version "0.3.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppML" version))
+       (sha256
+        (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
+    (properties `((upstream-name . "RcppML")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/zdebruine/RcppML")
+    (synopsis "Rcpp machine learning library")
+    (description
+     "This package provides fast machine learning algorithms including matrix
+factorization and divisive clustering for large sparse and dense matrices.")
+    (license license:gpl2+)))
+
 (define-public r-rcppthread
   (package
     (name "r-rcppthread")
@@ -3899,13 +3946,13 @@ with @code{Rcpp}.")
 (define-public r-rcppxptrutils
   (package
     (name "r-rcppxptrutils")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppXPtrUtils" version))
        (sha256
-        (base32 "0jh64c46gp99d2nsih14vx34pamc8i7gkmiy2nj94rx3sxq62yh5"))))
+        (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
     (properties `((upstream-name . "RcppXPtrUtils")))
     (build-system r-build-system)
     (propagated-inputs (list r-rcpp))
@@ -4044,14 +4091,14 @@ validation and filtering on the values, making options invisible or private.")
 (define-public r-circlize
   (package
     (name "r-circlize")
-    (version "0.4.14")
+    (version "0.4.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "circlize" version))
        (sha256
         (base32
-         "0b0yqjmbj1s1jg7y6cgyawadlfv0i6xrls8a4qy9qs7hz8zrpvb1"))))
+         "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-colorspace r-globaloptions r-shape))
@@ -4196,14 +4243,14 @@ any subsequent lookup as it keeps the hash table in memory.")
 (define-public r-ff
   (package
     (name "r-ff")
-    (version "4.0.5")
+    (version "4.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ff" version))
        (sha256
         (base32
-         "0dsh6llfdz04w94xr3yl2b4vkk9g3rwhvfnxcd025v2424krxfls"))))
+         "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
     (build-system r-build-system)
     (propagated-inputs (list r-bit))
     (home-page "http://ff.r-forge.r-project.org/")
@@ -4278,17 +4325,17 @@ curve to a data matrix in arbitrary dimensions.")
 (define-public r-reshape
   (package
     (name "r-reshape")
-    (version "0.8.8")
+    (version "0.8.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reshape" version))
        (sha256
         (base32
-         "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
+         "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-plyr r-rcpp))
+     (list r-plyr))
     (home-page "http://had.co.nz/reshape")
     (synopsis "Flexibly reshape data")
     (description
@@ -4299,16 +4346,17 @@ curve to a data matrix in arbitrary dimensions.")
 (define-public r-restrserve
   (package
     (name "r-restrserve")
-    (version "1.0.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RestRserve" version))
        (sha256
-        (base32 "0qb1x13n2sm0lg52x3289jsln3gw9rawfs1z2372pvr9ydpjsfqb"))))
+        (base32 "1ydsdgy6mxl0zqk7xqf4v6if5nf2qv7k48q340fhaqyjk2gd60p7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-checkmate
+           r-digest
            r-jsonlite
            r-mime
            r-r6
@@ -4411,13 +4459,13 @@ most popular ones.")
 (define-public r-sp
   (package
     (name "r-sp")
-    (version "1.4-6")
+    (version "1.4-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sp" version))
        (sha256
-        (base32 "09m2ddbrbs2aqnq5si42ipa0g1vbd0pxg4zbcx59is2047pv7sws"))))
+        (base32 "1bdi06n5zkjnnyh0rallf04s0vlcx9rg9p5q7s6vfqvkf19nk501"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice))
@@ -4455,14 +4503,14 @@ a variety of different samplers.")
 (define-public r-rmtstat
   (package
     (name "r-rmtstat")
-    (version "0.3")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RMTstat" version))
        (sha256
         (base32
-         "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
+         "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
     (properties `((upstream-name . "RMTstat")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/RMTstat")
@@ -4616,14 +4664,14 @@ spreadsheet software.")
 (define-public r-extremes
   (package
     (name "r-extremes")
-    (version "2.1-1")
+    (version "2.1-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extRemes" version))
        (sha256
         (base32
-         "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as"))))
+         "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
     (properties `((upstream-name . "extRemes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4763,14 +4811,14 @@ matrices, a special case of sparse matrices.")
 (define-public r-bbmle
   (package
     (name "r-bbmle")
-    (version "1.0.24")
+    (version "1.0.25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bbmle" version))
        (sha256
         (base32
-         "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81"))))
+         "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bdsmatrix
@@ -4899,14 +4947,14 @@ data).  Weighted versions of MLE, MME and QME are available.")
 (define-public r-energy
   (package
     (name "r-energy")
-    (version "1.7-9")
+    (version "1.7-10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "energy" version))
        (sha256
         (base32
-         "1ndssfi0hbnsm5jwrns7m63ppxm221hd6gk0b0wa1a7mk7ny1l38"))))
+         "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-boot r-gsl r-rcpp))
@@ -5265,14 +5313,14 @@ Optimization problems by using the simplex algorithm.")
 (define-public r-geometry
   (package
     (name "r-geometry")
-    (version "0.4.5")
+    (version "0.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "geometry" version))
        (sha256
         (base32
-         "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
+         "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
@@ -5401,14 +5449,14 @@ problems as well as resampling based estimators of prediction error.")
 (define-public r-psych
   (package
     (name "r-psych")
-    (version "2.2.3")
+    (version "2.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "psych" version))
        (sha256
         (base32
-         "0fi7gcaxcb1mdyfpgjm03sxz3qgp1s0hnrgx8pyswni5skb903pn"))))
+         "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice r-mnormt r-nlme))
@@ -5454,14 +5502,14 @@ by base R methods related to model fitting.")
 (define-public r-broom
   (package
     (name "r-broom")
-    (version "0.7.12")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "broom" version))
        (sha256
         (base32
-         "1nbv4a4s8548h2q226xmhyp42higayh95yvllh1rcs264lmw3yh4"))))
+         "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports
@@ -5538,14 +5586,14 @@ models.")
 (define-public r-pdist
   (package
     (name "r-pdist")
-    (version "1.2")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pdist" version))
        (sha256
         (base32
-         "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
+         "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
     (build-system r-build-system)
     (home-page "https://github.com/jeffwong/pdist")
     (synopsis "Partitioned distance function")
@@ -5907,14 +5955,14 @@ programming} (SQP) based solver).")
 (define-public r-hardyweinberg
   (package
     (name "r-hardyweinberg")
-    (version "1.7.4")
+    (version "1.7.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "HardyWeinberg" version))
        (sha256
         (base32
-         "11y3zg8aqxk5xdzsv7i3bgqkky6a0wgf2n8saa3a4adq75k328ib"))))
+         "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
     (properties `((upstream-name . "HardyWeinberg")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5959,13 +6007,13 @@ and density estimation")
 (define-public r-venndiagram
   (package
     (name "r-venndiagram")
-    (version "1.7.1")
+    (version "1.7.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "VennDiagram" version))
               (sha256
                (base32
-                "0yw54j9as0vf8ypnq4a3sl2w0lajri6s979f4y11hjzpgmr1m16b"))))
+                "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
     (properties `((upstream-name . "VennDiagram")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6293,14 +6341,14 @@ plots in @code{ggplot2}.")
 (define-public r-cli
   (package
     (name "r-cli")
-    (version "3.2.0")
+    (version "3.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cli" version))
        (sha256
         (base32
-         "0qp8k1afrn6ppwi6d9n05fjgj02196qcsppji3q37ph99msinnnd"))))
+         "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-glue))
@@ -6442,14 +6490,14 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and
 (define-public r-webshot
   (package
     (name "r-webshot")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "webshot" version))
        (sha256
         (base32
-         "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
+         "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-callr r-jsonlite r-magrittr))
@@ -6497,13 +6545,13 @@ iVAT).")
 (define-public r-xfun
   (package
     (name "r-xfun")
-    (version "0.30")
+    (version "0.31")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xfun" version))
        (sha256
-        (base32 "1vn0cbskyrk8ww9yx75jni9s684yv4cvbj643lvg0lg00briry7b"))))
+        (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi"))))
     (build-system r-build-system)
     ;; knitr itself depends on xfun
     #;
@@ -6584,14 +6632,14 @@ estimated from a given sample.")
 (define-public r-vctrs
   (package
     (name "r-vctrs")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vctrs" version))
        (sha256
         (base32
-         "0bslr22jnnwxx45s1a19az6saqf2svi8vkjf64pnpc6rma4ygpl9"))))
+         "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli r-glue r-rlang))
@@ -6671,14 +6719,14 @@ packages that work with genomic data.")
 (define-public r-uuid
   (package
     (name "r-uuid")
-    (version "1.0-4")
+    (version "1.1-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "uuid" version))
        (sha256
         (base32
-         "08j3ylf49l9qslhlcxvix3mqw6hh8kxainnklv0qmwmwj6q6i5i8"))))
+         "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
     (build-system r-build-system)
     (home-page "https://www.rforge.net/uuid")
     (synopsis "Tools for generating and handling of UUIDs")
@@ -6690,14 +6738,14 @@ packages that work with genomic data.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.38")
+    (version "0.39")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "11hww4x4q44xg559gplmjc6hmzmap0w249nnzyw5dy2ys30bbhga"))))
+         "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-xfun))
@@ -6749,14 +6797,14 @@ features:
 (define-public r-network
   (package
     (name "r-network")
-    (version "1.17.1")
+    (version "1.17.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "network" version))
        (sha256
         (base32
-         "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w"))))
+         "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-magrittr r-statnet-common r-tibble))
@@ -6818,14 +6866,14 @@ vectors.")
 (define-public r-statnet-common
   (package
     (name "r-statnet-common")
-    (version "4.5.0")
+    (version "4.6.0")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "statnet.common" version))
         (sha256
           (base32
-            "0bw8dwnv568i60xrj6d7gv0hnna1x7rvqaayy5i0827khvdj7nrw"))))
+            "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx"))))
     (properties
       `((upstream-name . "statnet.common")))
     (build-system r-build-system)
@@ -7235,14 +7283,14 @@ Fisher's method), and Sidak correction.")
 (define-public r-quantmod
   (package
     (name "r-quantmod")
-    (version "0.4.18")
+    (version "0.4.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantmod" version))
        (sha256
         (base32
-         "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
+         "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-curl r-ttr r-xts r-zoo))
@@ -7256,14 +7304,14 @@ financial trading strategies.")
 (define-public r-tseries
   (package
     (name "r-tseries")
-    (version "0.10-50")
+    (version "0.10-51")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tseries" version))
        (sha256
         (base32
-         "16654v691jqpgiisz442h9znlxgj96c9gvhk3pgmm48bfsxs6iqw"))))
+         "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-quadprog r-quantmod r-zoo))
@@ -7702,14 +7750,14 @@ Memorial-Sloan-Kettering Cancer Center (MSKCC).")
 (define-public r-import
   (package
     (name "r-import")
-    (version "1.2.0")
+    (version "1.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "import" version))
        (sha256
         (base32
-         "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
+         "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -7728,14 +7776,14 @@ files.")
 (define-public r-shinyace
   (package
     (name "r-shinyace")
-    (version "0.4.1")
+    (version "0.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyAce" version))
        (sha256
         (base32
-         "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
+         "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
     (properties `((upstream-name . "shinyAce")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7819,14 +7867,14 @@ systems.")
 (define-public r-radiant-data
   (package
     (name "r-radiant-data")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "radiant.data" version))
        (sha256
         (base32
-         "12x4nz5n6yz1a67ji79pwvznp9flmn50hpp9y9sfhixir7dvwy27"))
+         "0c5c99q13pwv6k0b07x3r2bxmh0h2w15h02xb1pincgs61qwi15k"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -7880,13 +7928,13 @@ the application.")
 (define-public r-algdesign
   (package
     (name "r-algdesign")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "AlgDesign" version))
        (sha256
-        (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
+        (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
     (properties `((upstream-name . "AlgDesign")))
     (build-system r-build-system)
     (home-page "https://github.com/jvbraun/AlgDesign")
@@ -8086,14 +8134,14 @@ multivariate plot methods.")
 (define-public r-fnn
   (package
     (name "r-fnn")
-    (version "1.1.3")
+    (version "1.1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "FNN" version))
        (sha256
         (base32
-         "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
+         "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
     (properties `((upstream-name . "FNN")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/FNN")
@@ -8310,14 +8358,14 @@ goodness-of-fit.")
 (define-public r-abc
   (package
     (name "r-abc")
-    (version "2.1")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abc" version))
        (sha256
         (base32
-         "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
+         "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
@@ -8416,14 +8464,14 @@ simple method for converting between file types.")
 (define-public r-maptools
   (package
     (name "r-maptools")
-    (version "1.1-3")
+    (version "1.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "maptools" version))
        (sha256
         (base32
-         "0ixvh4qbdjjl19ghgbb2r26yksya977q1yzs4yn5wshwm0763xph"))))
+         "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-foreign r-lattice r-sp))
@@ -8858,14 +8906,14 @@ those searches and pull data into their R sessions.")
 (define-public r-renv
   (package
     (name "r-renv")
-    (version "0.15.4")
+    (version "0.15.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "renv" version))
        (sha256
         (base32
-         "0byfs4cydhyqzdrxjv7sa6i30xc7qhnx0qw9d8wwwlzdkv235flf"))))
+         "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl"))))
     (properties `((upstream-name . "renv")))
     (build-system r-build-system)
     (native-inputs
@@ -8975,14 +9023,14 @@ always locate the files relative to your project root.")
 (define-public r-reticulate
   (package
     (name "r-reticulate")
-    (version "1.24")
+    (version "1.25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reticulate" version))
        (sha256
         (base32
-         "1k0nv43fa9lx44pamxpprnvvmsp15adn5z6hg9siyq0n94hca65r"))))
+         "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991"))))
     (build-system r-build-system)
     (inputs (list python))
     (propagated-inputs
@@ -9375,14 +9423,14 @@ that account for the effects of ANSI text formatting control sequences.")
 (define-public r-nbclust
   (package
     (name "r-nbclust")
-    (version "3.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NbClust" version))
        (sha256
         (base32
-         "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
+         "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
     (properties `((upstream-name . "NbClust")))
     (build-system r-build-system)
     (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
@@ -9549,14 +9597,14 @@ functions.")
 (define-public r-rjags
   (package
     (name "r-rjags")
-    (version "4-12")
+    (version "4-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rjags" version))
        (sha256
         (base32
-         "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr"))))
+         "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-coda))
@@ -9839,14 +9887,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.17.0")
+    (version "0.17.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1rxcy8nyg3y50czm3y1x2pibivywcb1bjmvpyqlzg4yy2j84v69p"))))
+         "0dffrsimgijdqsgvr9cad4g4w97d5ssjl3l0fm5ssly9l115ag35"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
@@ -10124,14 +10172,14 @@ matches version and feature constraints.")
 (define-public r-argparse
   (package
     (name "r-argparse")
-    (version "2.1.3")
+    (version "2.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "argparse" version))
        (sha256
         (base32
-         "0vm6nrzl6rsq2qw3km3i4s92kq9phs3cbxzv3i8hlyld9ajk3nmf"))))
+         "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3"))))
     (build-system r-build-system)
     (inputs (list python))
     (propagated-inputs
@@ -10218,14 +10266,14 @@ the work.")
 (define-public r-doby
   (package
     (name "r-doby")
-    (version "4.6.12")
+    (version "4.6.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doBy" version))
        (sha256
         (base32
-         "1m60ya4cdickqsj0dc90bv4n47df6qg6n82fikxrkl4yhg7yyn1i"))))
+         "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz"))))
     (properties `((upstream-name . "doBy")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10529,14 +10577,14 @@ from the @code{stats} package (plus some extra parameters).")
 (define-public r-cmplot
   (package
     (name "r-cmplot")
-    (version "4.0.0")
+    (version "4.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CMplot" version))
        (sha256
         (base32
-         "0xyh75y0c84nnkrv6c8xrvla54w51phgdwn8a69799f2r87z7c81"))))
+         "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg"))))
     (properties `((upstream-name . "CMplot")))
     (build-system r-build-system)
     (home-page "https://github.com/YinLiLin/CMplot")
@@ -10859,14 +10907,14 @@ a library of prediction algorithms to be used in the super learner.")
 (define-public r-drtmle
   (package
     (name "r-drtmle")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "drtmle" version))
        (sha256
         (base32
-         "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa"))))
+         "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
     (properties `((upstream-name . "drtmle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10884,14 +10932,14 @@ both to consistency and asymptotic normality.")
 (define-public r-dofuture
   (package
     (name "r-dofuture")
-    (version "0.12.1")
+    (version "0.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doFuture" version))
        (sha256
         (base32
-         "0fhk32ih9cbwxw3mvkddqjv0dsaw9xk8qjdslfcabvmixhnh3s6m"))))
+         "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
     (properties `((upstream-name . "doFuture")))
     (build-system r-build-system)
     (arguments
@@ -10995,14 +11043,14 @@ subsequence} (LCS) using a dynamic programming algorithm.")
 (define-public r-labelled
   (package
     (name "r-labelled")
-    (version "2.9.0")
+    (version "2.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "labelled" version))
        (sha256
         (base32
-         "0ffnhlr239nqcwb35m4hll21abnnhpmyy5wlxnyahrg0kqb0xb1n"))))
+         "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy"))))
     (properties `((upstream-name . "labelled")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11189,13 +11237,13 @@ calls to the particular toolkits in use in function of the context.")
 (define-public r-svdialogs
   (package
     (name "r-svdialogs")
-    (version "1.0.3")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "svDialogs" version))
        (sha256
-        (base32 "0j00xjvkwv992ir48czhvyj29rb9vpd243vbyyj2binn0q0qa431"))))
+        (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
     (properties `((upstream-name . "svDialogs")))
     (build-system r-build-system)
     (inputs
@@ -11282,18 +11330,17 @@ genotypes as \"graphical genotypes\".")
 (define-public r-furrr
   (package
     (name "r-furrr")
-    (version "0.2.3")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "furrr" version))
        (sha256
         (base32
-         "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a"))))
+         "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ellipsis
-           r-future
+     (list r-future
            r-globals
            r-lifecycle
            r-purrr
@@ -12052,14 +12099,14 @@ cross-sectional, time series, clustered, panel, and longitudinal data.")
 (define-public r-th-data
   (package
     (name "r-th-data")
-    (version "1.1-0")
+    (version "1.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TH.data" version))
        (sha256
         (base32
-         "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1"))))
+         "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
     (properties `((upstream-name . "TH.data")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12076,14 +12123,14 @@ packages maintained by Torsten Hothorn.")
 (define-public r-multcomp
   (package
     (name "r-multcomp")
-    (version "1.4-18")
+    (version "1.4-19")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "multcomp" version))
        (sha256
         (base32
-         "01i8gjppyxl3xph1dw0kags8qbb7r06j91kk3lkqn5gzrxjmwyhh"))))
+         "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
@@ -12121,14 +12168,14 @@ the differences were not significantly different.")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.7.3")
+    (version "1.7.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "0kbbin3zfxqkm5awq4331fv7y2kfpdhkwrqh91prl7qpf8kscin6"))))
+         "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-estimability r-mvtnorm r-numderiv r-xtable))
@@ -12250,14 +12297,14 @@ Bayesian modeling.")
 (define-public r-tmb
   (package
     (name "r-tmb")
-    (version "1.8.1")
+    (version "1.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TMB" version))
        (sha256
         (base32
-         "1hzvvx1g5nkmiqwzihj8nir48k7idbw1jvb14ldjk9rsikgpywdl"))))
+         "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c"))))
     (properties `((upstream-name . "TMB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12353,14 +12400,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.11.5")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "0lz8mzacxgmll576p88654mrvlk4pzvhwwghvn5pm7zxisgx0kq0"))))
+         "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12434,14 +12481,14 @@ results using @code{ggplot2}.")
 (define-public r-effectsize
   (package
     (name "r-effectsize")
-    (version "0.6.0.1")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "effectsize" version))
        (sha256
         (base32
-         "1rhpbhyrv0avinm6dz6v2qw4xxdl9m1wknq1dv2flfxgcz0k9qiz"))))
+         "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz"))))
     (properties `((upstream-name . "effectsize")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12723,14 +12770,14 @@ User credentials are shared with command line git through the
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "2.1.5")
+    (version "2.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "0lph2rxv7nq3h022gp8d50wbq5lwicnx85d2l5dx876wxhb9wlvx"))))
+         "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cli
@@ -12911,14 +12958,14 @@ ways.")
 (define-public r-summarytools
   (package
     (name "r-summarytools")
-    (version "1.0.0")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "summarytools" version))
        (sha256
         (base32
-         "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn"))))
+         "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64enc
@@ -13082,14 +13129,14 @@ analysing multivariate abundance data in community ecology.")
 (define-public r-afex
   (package
     (name "r-afex")
-    (version "1.1-0")
+    (version "1.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "afex" version))
        (sha256
         (base32
-         "0h8zqv82dqll19l3p89a2csvgnx8ayb2bajq7b35a8svhj427zax"))))
+         "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6"))))
     (build-system r-build-system)
     ;; This is needed for the vignette builder
     (arguments
@@ -13373,13 +13420,13 @@ netCDF files.")
 (define-public r-biocmanager
   (package
     (name "r-biocmanager")
-    (version "1.30.16")
+    (version "1.30.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BiocManager" version))
        (sha256
-        (base32 "0m9qxwqajg8lp0z06blbpgk3zw0z73aly1cvmjk6mvwja6jm99vm"))))
+        (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp"))))
     (properties `((upstream-name . "BiocManager")))
     (build-system r-build-system)
     (native-inputs
@@ -13394,14 +13441,14 @@ Bioconductor packages.")
 (define-public r-rgl
   (package
     (name "r-rgl")
-    (version "0.108.3")
+    (version "0.108.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgl" version))
        (sha256
         (base32
-         "0fqkx079z9y5b1gdg6qfz2wpw2j8q3ddflfkd9wwrkyacas6xyc9"))))
+         "0r9wzhjzl346i37ngs6hqzmizhi53kzqz582lv822v6yxang6fh3"))))
     (build-system r-build-system)
     (native-inputs
      (list pkg-config r-knitr))
@@ -13475,13 +13522,13 @@ isosurfaces.")
 (define-public r-ks
   (package
     (name "r-ks")
-    (version "1.13.4")
+    (version "1.13.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ks" version))
        (sha256
-        (base32 "15sm1ys7sk0gn7hr1vik4xrn4jdf837knwk7j8h32lr29w9mh917"))))
+        (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-fnn
@@ -13560,14 +13607,14 @@ University Press, 2007.")
 (define-public r-circular
   (package
     (name "r-circular")
-    (version "0.4-94")
+    (version "0.4-95")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "circular" version))
        (sha256
         (base32
-         "0wanbd6n7g1avvyc7pm0lnkwg868dix2byiz4wm6vmxzm0y47fmr"))))
+         "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-boot r-mvtnorm))
@@ -13584,17 +13631,17 @@ Scientific.")
 (define-public r-activity
   (package
     (name "r-activity")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "activity" version))
        (sha256
         (base32
-         "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
+         "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-circular r-insol r-pbapply))
+     (list r-insol r-pbapply))
     (home-page "https://cran.r-project.org/web/packages/activity/")
     (synopsis "Animal activity statistics")
     (description
@@ -13608,14 +13655,14 @@ circular variables).")
 (define-public r-ouch
   (package
     (name "r-ouch")
-    (version "2.17")
+    (version "2.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ouch" version))
        (sha256
         (base32
-         "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf"))))
+         "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
     (build-system r-build-system)
     (propagated-inputs (list r-subplex))
     (home-page "https://kingaa.github.io/ouch/")
@@ -13712,13 +13759,13 @@ Anderson-Darling Distribution\".")
 (define-public r-admisc
   (package
     (name "r-admisc")
-    (version "0.26")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "admisc" version))
        (sha256
-        (base32 "19zkwyp8gvq8f74midmwld4azx44sbqxqx9mgs726i6dhnls6821"))))
+        (base32 "07hfrhv3pcldsffnyfzpa1q3x32gxr1386r8fik1nhql2w46mm13"))))
     (properties `((upstream-name . "admisc")))
     (build-system r-build-system)
     (home-page "https://github.com/dusadrian/admisc")
@@ -13933,14 +13980,14 @@ over-plotting in scatter plots with text.")
 (define-public r-colorramps
   (package
     (name "r-colorramps")
-    (version "2.3")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "colorRamps" version))
        (sha256
         (base32
-         "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
+         "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
     (properties `((upstream-name . "colorRamps")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/colorRamps")
@@ -14191,18 +14238,20 @@ definiteness of a matrix.")
 (define-public r-rspectra
   (package
     (name "r-rspectra")
-    (version "0.16-0")
+    (version "0.16-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RSpectra" version))
        (sha256
         (base32
-         "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
+         "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
     (properties `((upstream-name . "RSpectra")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-matrix r-rcpp r-rcppeigen))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://github.com/yixuan/RSpectra")
     (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
     (description
@@ -14238,14 +14287,14 @@ diagnostics for controlling type-1 errors are also provided.")
 (define-public r-flare
   (package
     (name "r-flare")
-    (version "1.7.0")
+    (version "1.7.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flare" version))
        (sha256
         (base32
-         "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
+         "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-igraph r-lattice r-mass r-matrix))
@@ -14379,13 +14428,13 @@ methods, incorporating one or more trees and trait data.")
 (define-public r-rnexml
   (package
     (name "r-rnexml")
-    (version "2.4.6")
+    (version "2.4.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RNeXML" version))
               (sha256
                (base32
-                "0k56brcg80mvx35hgc5gj8arwba4k7q0075g38qp0qgq9d1b87cs"))))
+                "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ape
@@ -14929,14 +14978,14 @@ want to include run-time testing features in their own packages.")
 (define-public r-assertive-properties
   (package
     (name "r-assertive-properties")
-    (version "0.0-4")
+    (version "0.0-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "assertive.properties" version))
        (sha256
         (base32
-         "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
+         "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
     (properties
      `((upstream-name . "assertive.properties")))
     (build-system r-build-system)
@@ -15390,14 +15439,14 @@ covariance functions for large data sets.")
 (define-public r-spatialextremes
   (package
     (name "r-spatialextremes")
-    (version "2.0-9")
+    (version "2.1-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SpatialExtremes" version))
        (sha256
         (base32
-         "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
+         "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
     (properties
      `((upstream-name . "SpatialExtremes")))
     (build-system r-build-system)
@@ -15666,14 +15715,14 @@ model with finite state space using the Aalen-Johansen estimator.")
 (define-public r-epi
   (package
     (name "r-epi")
-    (version "2.44")
+    (version "2.46")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Epi" version))
        (sha256
         (base32
-         "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
+         "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0"))))
     (properties `((upstream-name . "Epi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15681,12 +15730,12 @@ model with finite state space using the Aalen-Johansen estimator.")
            r-data-table
            r-dplyr
            r-etm
+           r-magrittr
            r-mass
            r-matrix
            r-mgcv
            r-numderiv
            r-plyr
-           r-purrr
            r-survival
            r-zoo))
     (home-page "https://BendixCarstensen.com/Epi/")
@@ -15823,14 +15872,14 @@ subsetting.")
 (define-public r-globals
   (package
     (name "r-globals")
-    (version "0.14.0")
+    (version "0.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "globals" version))
        (sha256
         (base32
-         "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
+         "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-codetools))
@@ -15847,14 +15896,14 @@ them in distributed compute environments.")
 (define-public r-parallelly
   (package
     (name "r-parallelly")
-    (version "1.31.0")
+    (version "1.31.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parallelly" version))
        (sha256
         (base32
-         "0kjwxgxnlpjbxpr1dyzk3nyx9fwa6vwqr22bvsxz56xwxnirzdxx"))))
+         "1nhp66psk3m79is5qm4ppxkj7bdy46jr2h2pir22ia9ghhyzris0"))))
     (properties `((upstream-name . "parallelly")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/parallelly")
@@ -15875,14 +15924,14 @@ port-forwarding to your local computer.")
 (define-public r-future
   (package
     (name "r-future")
-    (version "1.24.0")
+    (version "1.26.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future" version))
        (sha256
         (base32
-         "0xmj17fq9paww796490bmakv6pcvrzk15i8mzhxk1mp9l0mj32vv"))))
+         "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -15910,14 +15959,14 @@ the local machine to, say, distributed processing on a remote compute cluster.")
 (define-public r-future-apply
   (package
     (name "r-future-apply")
-    (version "1.8.1")
+    (version "1.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "future.apply" version))
        (sha256
         (base32
-         "1ix61bfbk43pwnjb0wk8lkfgdsy5zi8svk74gar5nrl90b5w6nqd"))))
+         "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1"))))
     (properties `((upstream-name . "future.apply")))
     (build-system r-build-system)
     (arguments
@@ -16093,14 +16142,14 @@ several common set, element and attribute related tasks.")
 (define-public r-shinybs
   (package
     (name "r-shinybs")
-    (version "0.61")
+    (version "0.61.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyBS" version))
        (sha256
         (base32
-         "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
+         "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
     (properties `((upstream-name . "shinyBS")))
     (build-system r-build-system)
     ;; The tests spawn Shiny browser apps.  They cannot be run
@@ -16531,14 +16580,14 @@ marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
 (define-public r-minpack-lm
   (package
     (name "r-minpack-lm")
-    (version "1.2-1")
+    (version "1.2-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "minpack.lm" version))
        (sha256
         (base32
-         "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
+         "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
     (properties `((upstream-name . "minpack.lm")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -16555,14 +16604,14 @@ for lower and upper parameter bounds.  The implementation can be used via
 (define-public r-moments
   (package
     (name "r-moments")
-    (version "0.14")
+    (version "0.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "moments" version))
        (sha256
         (base32
-         "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
+         "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/moments")
     (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
@@ -16666,14 +16715,14 @@ obtain confidence intervals associated with AIC and BIC.")
 (define-public r-penalized
   (package
     (name "r-penalized")
-    (version "0.9-51")
+    (version "0.9-52")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "penalized" version))
        (sha256
         (base32
-         "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
+         "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcpp r-rcpparmadillo r-survival))
@@ -16884,14 +16933,14 @@ network.")
 (define-public r-gmodels
   (package
     (name "r-gmodels")
-    (version "2.18.1")
+    (version "2.18.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gmodels" version))
        (sha256
         (base32
-         "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
+         "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-gdata r-mass))
@@ -17239,14 +17288,14 @@ barplots or heatmaps.")
 (define-public r-seqinr
   (package
     (name "r-seqinr")
-    (version "4.2-8")
+    (version "4.2-16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqinr" version))
        (sha256
         (base32
-         "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq"))))
+         "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ade4 r-segmented))
@@ -17499,13 +17548,13 @@ datum transformations.")
 (define-public r-spdep
   (package
     (name "r-spdep")
-    (version "1.2-3")
+    (version "1.2-4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "spdep" version))
               (sha256
                (base32
-                "0qd7qjblx49gp07pcf4qb2f93ab3p126pa77g6mq4z3jaa510hak"))
+                "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59"))
               (snippet
                '(for-each delete-file '("inst/doc/CO69.html"
                                         "inst/doc/CO69.R"
@@ -17541,14 +17590,14 @@ spanning tree.")
 (define-public r-adegenet
   (package
     (name "r-adegenet")
-    (version "2.1.5")
+    (version "2.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "adegenet" version))
        (sha256
         (base32
-         "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4"))))
+         "0sx25p7bgz0h9mc3jsdnnjhvmb7sy8nb3r0z923vhk336d4xw8vq"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ade4
@@ -17678,13 +17727,13 @@ either PDF/EPS files.")
 (define-public r-polspline
   (package
     (name "r-polspline")
-    (version "1.1.19")
+    (version "1.1.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "polspline" version))
        (sha256
-        (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
+        (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
     (build-system r-build-system)
     (native-inputs (list gfortran))
     (home-page "https://cran.r-project.org/web/packages/polspline/")
@@ -17698,13 +17747,13 @@ lspec, polyclass, and polymars.")
 (define-public r-rms
   (package
     (name "r-rms")
-    (version "6.2-0")
+    (version "6.3-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rms" version))
        (sha256
-        (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h"))))
+        (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cluster
@@ -17944,13 +17993,13 @@ SELECT or UPDATE queries to an end-point.")
 (define-public r-bookdown
   (package
     (name "r-bookdown")
-    (version "0.25")
+    (version "0.26")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "bookdown" version))
               (sha256
                (base32
-                "0v5nlm3lbm0h5cvd9j2211yqk68rkm416aq8qp6r8klj69xm1bri"))))
+                "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-htmltools
@@ -17965,7 +18014,7 @@ SELECT or UPDATE queries to an end-point.")
     ;; input to knitr.
     #;
     (native-inputs
-     `(("r-knitr" ,r-knitr)))
+     (list r-knitr))
     (home-page "https://github.com/rstudio/bookdown")
     (synopsis "Authoring books and technical documents with R markdown")
     (description "This package provides output formats and utilities for
@@ -18020,14 +18069,14 @@ and a QP solver.")
 (define-public r-hierfstat
   (package
     (name "r-hierfstat")
-    (version "0.5-10")
+    (version "0.5-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hierfstat" version))
        (sha256
         (base32
-         "1p4vlna185sa3b5xjbysiqxcj9aa5s7dmxy41hg79vlqdivf874r"))))
+         "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ade4 r-adegenet r-gaston r-gtools))
@@ -18046,14 +18095,14 @@ variance components, using the likelihood-ratio statistics G.")
 (define-public r-hapassoc
   (package
     (name "r-hapassoc")
-    (version "1.2-8")
+    (version "1.2-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hapassoc" version))
        (sha256
         (base32
-         "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
+         "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
     (build-system r-build-system)
     (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
     (synopsis "Inference of trait associations with SNP haplotypes")
@@ -18088,14 +18137,14 @@ handle missing genotypes at some SNPs.")
 (define-public r-r2html
   (package
     (name "r-r2html")
-    (version "2.3.2")
+    (version "2.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "R2HTML" version))
        (sha256
         (base32
-         "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
+         "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
     (properties `((upstream-name . "R2HTML")))
     (build-system r-build-system)
     (home-page "https://github.com/nalimilan/R2HTML")
@@ -18251,14 +18300,14 @@ interaction search in high-dimensional data.")
 (define-public r-extrafont
   (package
     (name "r-extrafont")
-    (version "0.17")
+    (version "0.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extrafont" version))
        (sha256
         (base32
-         "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
+         "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-extrafontdb r-rttf2pt1))
@@ -19265,14 +19314,14 @@ external dependencies.  This package has is implemented purely in R.")
 (define-public r-aplot
   (package
     (name "r-aplot")
-    (version "0.1.3")
+    (version "0.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "aplot" version))
        (sha256
         (base32
-         "10cqa35bh4lhpnybaalp3d69k392b25ba16dgbngqz0vikzp4czk"))))
+         "1b4jjj05a602dgn6yr1bsmbzlzkj6wf6af3k3w63g3mkqv0xzsfd"))))
     (properties `((upstream-name . "aplot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19280,8 +19329,7 @@ external dependencies.  This package has is implemented purely in R.")
            r-ggplot2
            r-ggplotify
            r-magrittr
-           r-patchwork
-           r-yulab-utils))
+           r-patchwork))
     (home-page "https://github.com/YuLab-SMU/aplot")
     (synopsis "Decorate a ggplot with associated information")
     (description
@@ -19341,14 +19389,14 @@ colored by the number of neighboring points.  This is useful to visualize the
 (define-public r-arrow
   (package
     (name "r-arrow")
-    (version "7.0.0")
+    (version "8.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arrow" version))
        (sha256
         (base32
-         "1s9h2aw6iig45nz2rfk13qbp0qydx6cc4r6qs58f9cm9vgwsg76l"))))
+         "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc"))))
     (properties `((upstream-name . "arrow")))
     (build-system r-build-system)
     (inputs
@@ -19402,14 +19450,14 @@ regular expressions from human readable expressions")
 (define-public r-mlapi
   (package
     (name "r-mlapi")
-    (version "0.1.0")
+    (version "0.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mlapi" version))
        (sha256
         (base32
-         "023vk5bp8cjcq88sapkl87kdxr92bay1dyxl6xirnyj699pyj51k"))))
+         "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
     (properties `((upstream-name . "mlapi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19488,14 +19536,14 @@ Row} (CSR) format.")
 (define-public r-text2vec
   (package
     (name "r-text2vec")
-    (version "0.6")
+    (version "0.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "text2vec" version))
        (sha256
         (base32
-         "0r75cv77x2zm1z66s95hic71dpbqmybz39n48q6mz7gfd3m7312y"))))
+         "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi"))))
     (properties `((upstream-name . "text2vec")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19524,14 +19572,14 @@ multicore machines.")
 (define-public r-mcmcpack
   (package
     (name "r-mcmcpack")
-    (version "1.6-2")
+    (version "1.6-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MCMCpack" version))
        (sha256
         (base32
-         "18nyncvgb75q8flndni99ldr7ynqhillphkj7ydsmfv5w8b0zvqp"))))
+         "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
     (properties `((upstream-name . "MCMCpack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19724,14 +19772,14 @@ the functions can also be applied to other types of categorical data.")
 (define-public r-pbmcapply
   (package
     (name "r-pbmcapply")
-    (version "1.5.0")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbmcapply" version))
        (sha256
         (base32
-         "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
+         "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
     (build-system r-build-system)
     (home-page "https://github.com/kvnkuang/pbmcapply")
     (synopsis "Track the progress of apply procedures with a progress bar")
@@ -19984,14 +20032,14 @@ been used in the call to @code{aov}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "2.4.0")
+    (version "2.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "1s7r7k5ihdbj69r27vbcs3ghra9s4yqw7cyh2rkm2ry901zq3114"))))
+         "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20155,14 +20203,14 @@ the current document.")
 (define-public r-xgboost
   (package
     (name "r-xgboost")
-    (version "1.5.2.1")
+    (version "1.6.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xgboost" version))
        (sha256
         (base32
-         "13mi3rmpxhgm4qbm4xcqml9n5d1xyai2k1mi52i8x60jd5m8s319"))))
+         "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-data-table r-jsonlite r-matrix))
@@ -20368,14 +20416,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
 (define-public r-leiden
   (package
     (name "r-leiden")
-    (version "0.3.9")
+    (version "0.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leiden" version))
        (sha256
         (base32
-         "03gaxpcab3a1av5lk8r5ll1s858gvyx5ndknci1sia96w1v44xc1"))))
+         "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna"))))
     (properties `((upstream-name . "leiden")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20745,14 +20793,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.17.0")
+    (version "0.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "0wrhs3rhr62441cghg4nsrlp6r41nf7x5nclzz71v5c0rfn8jh79"))))
+         "0r6bj29frhqyv75cviw0p8kns6h8z10n7g7khyk0hzq2fqjsjrwh"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -20773,13 +20821,13 @@ effect size.")
 (define-public r-rgdal
   (package
     (name "r-rgdal")
-    (version "1.5-30")
+    (version "1.5-32")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgdal" version))
        (sha256
-        (base32 "1f4zshgkaifbfcgq61vqb7jw5w2cc128d98rq2465r8696q2p0s9"))))
+        (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5"))))
     (properties `((upstream-name . "rgdal")))
     (build-system r-build-system)
     (inputs
@@ -20904,13 +20952,13 @@ programming problems.")
 (define-public r-desolve
   (package
     (name "r-desolve")
-    (version "1.31")
+    (version "1.32")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "deSolve" version))
        (sha256
-        (base32 "06gsh514msqdmri78969snhgh22d2bzmnkqfgh0s74aprfd93m8r"))))
+        (base32 "1bfr4w760nr7mjhpmf32z39swr6isnn1665cld2d1pdgx8b0yrvl"))))
     (properties `((upstream-name . "deSolve")))
     (build-system r-build-system)
     (native-inputs
@@ -20980,14 +21028,14 @@ porting.")
 (define-public r-subplex
   (package
     (name "r-subplex")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "subplex" version))
        (sha256
         (base32
-         "11zqzydbj6ivgvlw1gv1r2yxra7misbc622g575p2vckhjjg9v6m"))))
+         "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran))
@@ -21588,18 +21636,18 @@ elicitation options based on Kass and Vaidyanathan (1992)
 (define-public r-reldist
   (package
     (name "r-reldist")
-    (version "1.7-0")
+    (version "1.7-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reldist" version))
        (sha256
         (base32
-         "0i04d6w3r6fzm4bykz6lnnh6dngmd61v5wlpli70r3fzdzhi7fji"))))
+         "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6"))))
     (properties `((upstream-name . "reldist")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-densestbayes r-hmisc r-mgcv))
+     (list r-densestbayes r-mgcv))
     (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
     (synopsis "Relative distribution methods")
     (description
@@ -21760,14 +21808,14 @@ data.")
 (define-public r-mda
   (package
     (name "r-mda")
-    (version "0.5-2")
+    (version "0.5-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mda" version))
        (sha256
         (base32
-         "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
+         "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx"))))
     (properties `((upstream-name . "mda")))
     (build-system r-build-system)
     (propagated-inputs (list r-class))
@@ -21929,20 +21977,18 @@ and prints vectorized images.")
 (define-public r-randtoolbox
   (package
     (name "r-randtoolbox")
-    (version "1.31.1")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "randtoolbox" version))
        (sha256
         (base32
-         "1b9vjzqg014hxp1vfb62m01d7xim5vmpbyxzlbll49bqas0jx69h"))))
+         "005x2igljc6vm0nsmkld9aqjqz1ccwapc8z3aw5c3ivh4n2bghf9"))))
     (properties `((upstream-name . "randtoolbox")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rngwell))
-    (native-inputs
-     (list gfortran))
     (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
     (synopsis "Toolbox for pseudo and quasi random number generation")
     (description
@@ -22089,14 +22135,14 @@ models.")
 (define-public r-gamlss
   (package
     (name "r-gamlss")
-    (version "5.4-1")
+    (version "5.4-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gamlss" version))
        (sha256
         (base32
-         "0fp9bmgykpqd950bk58dk423iy5r1fm3dy2gw0cwwmgivpq2lx0q"))))
+         "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6"))))
     (properties `((upstream-name . "gamlss")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22801,14 +22847,14 @@ R\" (ISBN 978-1-119-15272-9.)")
 (define-public r-alabama
   (package
     (name "r-alabama")
-    (version "2015.3-1")
+    (version "2022.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "alabama" version))
        (sha256
         (base32
-         "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
+         "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8"))))
     (properties `((upstream-name . "alabama")))
     (build-system r-build-system)
     (propagated-inputs (list r-numderiv))
@@ -23039,18 +23085,20 @@ variable observed over time.")
 (define-public r-fda
   (package
     (name "r-fda")
-    (version "5.5.1")
+    (version "6.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fda" version))
        (sha256
         (base32
-         "0fm2vswc8fdi2p1axby0hjwh8m6lc1zrdikrpiamilr6w9m2zanw"))))
+         "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10"))))
     (properties `((upstream-name . "fda")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-desolve r-fds r-matrix))
+     (list r-desolve r-fds))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://www.functionaldata.org")
     (synopsis "Functional data analysis")
     (description
@@ -23402,14 +23450,14 @@ it may be seen by an animal with less acute vision.")
 (define-public r-caret
   (package
     (name "r-caret")
-    (version "6.0-91")
+    (version "6.0-92")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "caret" version))
        (sha256
         (base32
-         "1kbx51cf71z2x19a0jflwnhx5jd9wk9q9203kzdxlqw5izdjvmdz"))))
+         "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-e1071
@@ -24033,14 +24081,14 @@ Francesca Mazzia (2012).")
 (define-public r-lim
   (package
     (name "r-lim")
-    (version "1.4.6")
+    (version "1.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "LIM" version))
        (sha256
         (base32
-         "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
+         "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
     (properties `((upstream-name . "LIM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24080,14 +24128,14 @@ automatically show a loader when the output is (re)calculating.")
 (define-public r-rsvg
   (package
     (name "r-rsvg")
-    (version "2.2.0")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rsvg" version))
        (sha256
         (base32
-         "05mvi1ijnxayyj1f4p8nb56pncmm7x0sbq0d87asv7c7kw765n1a"))))
+         "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj"))))
     (properties `((upstream-name . "rsvg")))
     (build-system r-build-system)
     (inputs
@@ -24811,13 +24859,13 @@ actuarial models such as pension mathematics.")
 (define-public r-matrixextra
   (package
     (name "r-matrixextra")
-    (version "0.1.9-1")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MatrixExtra" version))
        (sha256
-        (base32 "098apgqlncgxspa8mi4bx2nk5fbk3880whqiwkvydsfsqrbv1sj0"))))
+        (base32 "00f6sgw6p2709gs3df68yr59nvsr429pk9xql71id3kachjzh618"))))
     (properties `((upstream-name . "MatrixExtra")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24879,14 +24927,14 @@ least squares.")
 (define-public r-semtools
   (package
     (name "r-semtools")
-    (version "0.5-5")
+    (version "0.5-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "semTools" version))
        (sha256
         (base32
-         "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x"))))
+         "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
     (properties `((upstream-name . "semTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25053,14 +25101,14 @@ importation and recoding.")
 (define-public r-rockchalk
   (package
     (name "r-rockchalk")
-    (version "1.8.151")
+    (version "1.8.152")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rockchalk" version))
        (sha256
         (base32
-         "17mfaxn3gj0vac5wdmsjj2z2668cszbpvan7hnxp7ic9bvsm1w2y"))))
+         "1d15jlgcy35pvaicaddd4zrhwm5ajb9yc3jk6dyxm99gc5wcn6h3"))))
     (properties `((upstream-name . "rockchalk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25080,14 +25128,14 @@ fairly comprehensive overview.")
 (define-public r-lisreltor
   (package
     (name "r-lisreltor")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lisrelToR" version))
        (sha256
         (base32
-         "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
+         "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
     (properties `((upstream-name . "lisrelToR")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/package=lisrelToR")
@@ -25100,18 +25148,20 @@ output in R.")
 (define-public r-bdgraph
   (package
     (name "r-bdgraph")
-    (version "2.65")
+    (version "2.67")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BDgraph" version))
        (sha256
         (base32
-         "0rg3wi9xwsbj90gb60p3vzkfrf76hwh47nc6fwv6c21yzd3s7vm4"))))
+         "0s2j4462zlgyjnqvvvxg4lynhmwwnjaw1cr1chzmagfvaj94qhhz"))))
     (properties `((upstream-name . "BDgraph")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-igraph))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://www.uva.nl/profile/a.mohammadi")
     (synopsis "Bayesian structure learning in graphical models")
     (description
@@ -25226,14 +25276,14 @@ translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
 (define-public r-cdm
   (package
     (name "r-cdm")
-    (version "7.6-11")
+    (version "8.1-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CDM" version))
        (sha256
         (base32
-         "0k3arkzz7nzswjcsr7fdmpfs94ilg8l265dyn49555fw3673cgqj"))))
+         "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i"))))
     (properties `((upstream-name . "CDM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25257,14 +25307,14 @@ well as Ravand and Robitzsch (2015).")
 (define-public r-tam
   (package
     (name "r-tam")
-    (version "3.7-16")
+    (version "4.0-16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TAM" version))
        (sha256
         (base32
-         "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd"))))
+         "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw"))))
     (properties `((upstream-name . "TAM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25314,18 +25364,20 @@ elimination, and a simulation module for various binary data matrices.")
 (define-public r-irtoys
   (package
     (name "r-irtoys")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "irtoys" version))
        (sha256
         (base32
-         "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
+         "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
     (properties `((upstream-name . "irtoys")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ltm r-sm))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://cran.r-project.org/package=irtoys")
     (synopsis "Collection of functions related to Item Response Theory (IRT)")
     (description
@@ -25381,14 +25433,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.")
 (define-public r-packrat
   (package
     (name "r-packrat")
-    (version "0.7.0")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "packrat" version))
        (sha256
         (base32
-         "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78"))))
+         "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h"))))
     (properties `((upstream-name . "packrat")))
     (build-system r-build-system)
     (home-page "https://github.com/rstudio/packrat/")
@@ -26539,14 +26591,14 @@ estimation.")
 (define-public r-optimx
   (package
     (name "r-optimx")
-    (version "2021-10.12")
+    (version "2022-4.30")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "optimx" version))
        (sha256
         (base32
-         "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r"))))
+         "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
     (properties `((upstream-name . "optimx")))
     (build-system r-build-system)
     (propagated-inputs (list r-numderiv))
@@ -26567,14 +26619,14 @@ here.")
 (define-public r-projpred
   (package
     (name "r-projpred")
-    (version "2.1.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "projpred" version))
        (sha256
         (base32
-         "170pskvcsyk22xl4q8mklx8nw29miqzb42wajcab7bki8ap1ix46"))))
+         "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8"))))
     (properties `((upstream-name . "projpred")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26688,14 +26740,14 @@ inference diagnostics.
 (define-public r-brms
   (package
     (name "r-brms")
-    (version "2.16.3")
+    (version "2.17.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "brms" version))
        (sha256
         (base32
-         "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38"))))
+         "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94"))))
     (properties `((upstream-name . "brms")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26797,14 +26849,14 @@ pies on a map.")
 (define-public r-scrypt
   (package
     (name "r-scrypt")
-    (version "0.1.3")
+    (version "0.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "scrypt" version))
        (sha256
         (base32
-         "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
+         "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
     (properties `((upstream-name . "scrypt")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27280,14 +27332,14 @@ simple interface for all functions.")
 (define-public r-iml
   (package
     (name "r-iml")
-    (version "0.10.1")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iml" version))
        (sha256
         (base32
-         "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r"))))
+         "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5"))))
     (properties `((upstream-name . "iml")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27297,7 +27349,6 @@ simple interface for all functions.")
            r-future
            r-future-apply
            r-ggplot2
-           r-keras
            r-metrics
            r-prediction
            r-r6))
@@ -27368,14 +27419,14 @@ diagonals.  This package allows you to compute the tensor product of arrays.")
 (define-public r-spatstat-utils
   (package
     (name "r-spatstat-utils")
-    (version "2.3-0")
+    (version "2.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.utils" version))
        (sha256
         (base32
-         "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az"))))
+         "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av"))))
     (properties
      `((upstream-name . "spatstat.utils")))
     (build-system r-build-system)
@@ -27389,14 +27440,14 @@ which may also be useful for other purposes.")
 (define-public r-spatstat-sparse
   (package
     (name "r-spatstat-sparse")
-    (version "2.1-0")
+    (version "2.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.sparse" version))
        (sha256
         (base32
-         "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680"))))
+         "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs"))))
     (properties
      `((upstream-name . "spatstat.sparse")))
     (build-system r-build-system)
@@ -27413,14 +27464,14 @@ matrix calculations that are common in statistics, such as quadratic forms.")
 (define-public r-spatstat-data
   (package
     (name "r-spatstat-data")
-    (version "2.1-4")
+    (version "2.2-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.data" version))
        (sha256
         (base32
-         "0bq9randa3lgkh2q932iss5cxazq743q6p8asiqqf0yi32b003jq"))))
+         "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k"))))
     (properties `((upstream-name . "spatstat.data")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27458,14 +27509,14 @@ for the geometry of linear networks.")
 (define-public r-spatstat-core
   (package
     (name "r-spatstat-core")
-    (version "2.4-2")
+    (version "2.4-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.core" version))
        (sha256
         (base32
-         "0bhdxyw212yf9y9nsvbz4yy08ka3wr3hkjqpag0ys2s1p22c51b9"))))
+         "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
     (properties `((upstream-name . "spatstat.core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28045,14 +28096,14 @@ the @code{survival} package.")
 (define-public r-exactranktests
   (package
     (name "r-exactranktests")
-    (version "0.8-34")
+    (version "0.8-35")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "exactRankTests" version))
        (sha256
         (base32
-         "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9"))))
+         "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
     (properties
      `((upstream-name . "exactRankTests")))
     (build-system r-build-system)
@@ -28255,14 +28306,14 @@ model.")
 (define-public r-igraph
   (package
     (name "r-igraph")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "igraph" version))
        (sha256
         (base32
-         "09dzc8lslljvhj2q46075vxcmlgkvq2qs500zdqyy9g8scq6iqbi"))))
+         "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran))
@@ -28713,14 +28764,14 @@ models without involving a test set.")
 (define-public r-tidypredict
   (package
     (name "r-tidypredict")
-    (version "0.4.8")
+    (version "0.4.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidypredict" version))
        (sha256
         (base32
-         "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
+         "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
     (properties `((upstream-name . "tidypredict")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28834,14 +28885,14 @@ vignettes in all common formats.")
 (define-public r-tidytext
   (package
     (name "r-tidytext")
-    (version "0.3.2")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytext" version))
        (sha256
         (base32
-         "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g"))))
+         "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm"))))
     (properties `((upstream-name . "tidytext")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29034,14 +29085,14 @@ data structures of the tidyverse.")
 (define-public r-lsa
   (package
     (name "r-lsa")
-    (version "0.73.2")
+    (version "0.73.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lsa" version))
        (sha256
         (base32
-         "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
+         "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
     (properties `((upstream-name . "lsa")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29123,14 +29174,14 @@ phylogenetic relatedness) can also be conducted.")
 (define-public r-altmeta
   (package
     (name "r-altmeta")
-    (version "3.3")
+    (version "4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "altmeta" version))
        (sha256
         (base32
-         "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm"))))
+         "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5"))))
     (properties `((upstream-name . "altmeta")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29302,18 +29353,26 @@ data to rasters.  It speeds up plotting of data with millions of points.")
 (define-public r-seuratobject
   (package
     (name "r-seuratobject")
-    (version "4.0.4")
+    (version "4.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "SeuratObject" version))
        (sha256
         (base32
-         "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq"))))
+         "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w"))))
     (properties `((upstream-name . "SeuratObject")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-matrix r-rcpp r-rcppeigen r-rlang))
+     (list r-future
+           r-future-apply
+           r-matrix
+           r-progressr
+           r-rcpp
+           r-rcppeigen
+           r-rgeos
+           r-rlang
+           r-sp))
     (home-page "https://satijalab.org/seurat")
     (synopsis "Data structures for single cell data")
     (description
@@ -29327,13 +29386,13 @@ other R users.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "4.1.0")
+    (version "4.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195"))))
+                "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29652,14 +29711,14 @@ kernel estimators.")
 (define-public r-lpme
   (package
     (name "r-lpme")
-    (version "1.1.2")
+    (version "1.1.3")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "lpme" version))
         (sha256
           (base32
-            "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw"))))
+            "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
     (properties `((upstream-name . "lpme")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29816,13 +29875,13 @@ package also supersedes the package @code{BBmisc}.")
 (define-public r-mlr3pipelines
   (package
     (name "r-mlr3pipelines")
-    (version "0.4.0")
+    (version "0.4.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3pipelines" version))
               (sha256
                (base32
-                "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p"))))
+                "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports
@@ -29879,13 +29938,13 @@ performing ordinal regression.")
 (define-public r-paradox
   (package
     (name "r-paradox")
-    (version "0.8.0")
+    (version "0.9.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "paradox" version))
               (sha256
                (base32
-                "1jfzbpqi1rp3r8hnk37dqwggp48ha5bnilmdz7dwzfdaskssycxa"))))
+                "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
@@ -29937,13 +29996,13 @@ computational operations, add-on packages provide additional functionality.")
 (define-public r-mlr3learners
   (package
     (name "r-mlr3learners")
-    (version "0.5.2")
+    (version "0.5.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3learners" version))
               (sha256
                (base32
-                "1d9hcrnj622ynrzg0ii0fkhz2n66ip46yln21jq1pwpwkqwqzv35"))))
+                "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-checkmate
@@ -29964,14 +30023,14 @@ vector machines, and gradient boosting.")
 (define-public r-bbotk
   (package
     (name "r-bbotk")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bbotk" version))
        (sha256
         (base32
-         "0k1vlh14mfbcgdw2yfhab7shkrqm4d2h6af12mybr9gks26xmw82"))))
+         "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734"))))
     (properties `((upstream-name . "bbotk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -29994,13 +30053,13 @@ annealing.")
 (define-public r-mlr3tuning
   (package
     (name "r-mlr3tuning")
-    (version "0.13.0")
+    (version "0.13.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3tuning" version))
               (sha256
                (base32
-                "0czlpi8bshn8cjq7pa1cyy7lpv35g4hv2nbyhc59zrcykzfv8afm"))))
+                "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bbotk
@@ -30347,14 +30406,14 @@ in output to the equivalent HTML.")
 (define-public r-pkgdown
   (package
     (name "r-pkgdown")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgdown" version))
        (sha256
         (base32
-         "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h"))))
+         "0wqga9bcl7wmvkwpkkmf5hx1cl7rjq5ddvqmxhl4p1dczys3adnr"))))
     (properties `((upstream-name . "pkgdown")))
     (build-system r-build-system)
     (inputs (list pandoc))
@@ -30456,14 +30515,14 @@ visualized at any level of the experiment's design.")
 (define-public r-qdapregex
   (package
     (name "r-qdapregex")
-    (version "0.7.2")
+    (version "0.7.5")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "qdapRegex" version))
         (sha256
           (base32
-            "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
+            "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
     (properties `((upstream-name . "qdapRegex")))
     (build-system r-build-system)
     (propagated-inputs (list r-stringi))
@@ -30802,14 +30861,14 @@ data you need the @code{pdftools} package.")
 (define-public r-pdftools
   (package
     (name "r-pdftools")
-    (version "3.1.1")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pdftools" version))
        (sha256
         (base32
-         "1lflqf2ypdm4w033vyjykmsy8cl34sp42fzkfgfdhvl2d0xjhl96"))))
+         "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi"))))
     (properties `((upstream-name . "pdftools")))
     (build-system r-build-system)
     (inputs (list zlib poppler))
@@ -31503,16 +31562,16 @@ asynchronously from formatting.")
 (define-public r-rmisc
   (package
     (name "r-rmisc")
-    (version "1.5")
+    (version "1.5.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Rmisc" version))
               (sha256
                (base32
-                "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8"))))
+                "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-plyr r-rcpp r-lattice))
+     (list r-plyr r-lattice))
     (home-page "https://cran.r-project.org/web/packages/Rmisc/")
     (synopsis "Ryan Miscellaneous")
     (description "The Rmisc library contains functions for data analysis and
@@ -31576,13 +31635,13 @@ reading and writing arbitrary protocol-buffer data in R.")
 (define-public r-opencpu
   (package
     (name "r-opencpu")
-    (version "2.2.7")
+    (version "2.2.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "opencpu" version))
        (sha256
-        (base32 "06jpmk95hm39ib5c75xw0mdrdv9x9zz1qil3m8ysb6pp1xx47jz0"))))
+        (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
     (properties `((upstream-name . "opencpu")))
     (build-system r-build-system)
     (inputs
@@ -31619,14 +31678,14 @@ Apache2.")
 (define-public r-exactextractr
   (package
     (name "r-exactextractr")
-    (version "0.8.1")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "exactextractr" version))
        (sha256
         (base32
-         "11s58vc63r9kah815a18ihb0x2nmnjnpngybw3yr2d6715sz89nc"))))
+         "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc"))))
     (properties `((upstream-name . "exactextractr")))
     (build-system r-build-system)
     (inputs (list geos))
@@ -31645,14 +31704,14 @@ the @code{raster} package that is suitable for extracting raster values using
 (define-public r-stringfish
   (package
     (name "r-stringfish")
-    (version "0.15.5")
+    (version "0.15.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringfish" version))
        (sha256
         (base32
-         "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx"))))
+         "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
     (properties `((upstream-name . "stringfish")))
     (build-system r-build-system)
     (propagated-inputs
@@ -31799,14 +31858,14 @@ Tensorflow graphs.")
 (define-public r-tensorflow
   (package
     (name "r-tensorflow")
-    (version "2.8.0")
+    (version "2.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tensorflow" version))
        (sha256
         (base32
-         "19ayjvlxmgjais0kx6fj9an1h1i8mh4c9dhah7dj6390p53pgz93"))))
+         "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
     (properties `((upstream-name . "tensorflow")))
     (build-system r-build-system)
     (inputs (list tensorflow))
@@ -31830,14 +31889,14 @@ between them.")
 (define-public r-keras
   (package
     (name "r-keras")
-    (version "2.8.0")
+    (version "2.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "keras" version))
        (sha256
         (base32
-         "10zvy4lmhb2sbn0gsm12pf95pxj9bmi8241ap1n6170xsld9phcf"))))
+         "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
     (properties `((upstream-name . "keras")))
     (build-system r-build-system)
     (propagated-inputs
@@ -32016,24 +32075,25 @@ with the dynamic plots from @code{dygraphs}.")
 (define-public r-rfigshare
   (package
     (name "r-rfigshare")
-    (version "0.3.7")
+    (version "0.3.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rfigshare" version))
        (sha256
         (base32
-         "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq"))))
+         "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
     (properties `((upstream-name . "rfigshare")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2
            r-httpuv
            r-httr
-           r-plyr
            r-rjsonio
            r-xml
            r-yaml))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://github.com/ropensci/rfigshare")
     (synopsis "R Interface to figshare")
     (description
@@ -32523,14 +32583,14 @@ zoom/navigate any plot when called with any active plot.")
 (define-public r-zoolog
   (package
     (name "r-zoolog")
-    (version "0.4.1")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zoolog" version))
        (sha256
         (base32
-         "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks"))))
+         "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p"))))
     (properties `((upstream-name . "zoolog")))
     (build-system r-build-system)
     (propagated-inputs
@@ -32577,14 +32637,14 @@ large datasets.")
 (define-public r-mlearning
   (package
     (name "r-mlearning")
-    (version "1.0-0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mlearning" version))
        (sha256
         (base32
-         "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r"))))
+         "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
     (properties `((upstream-name . "mlearning")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 2161340ef9..2d72c78233 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4207,7 +4207,7 @@ the SQL language using a syntax that reflects the resulting query.")
 (define-public apache-arrow
   (package
     (name "apache-arrow")
-    (version "7.0.0")
+    (version "8.0.0")
     (source
      (origin
        (method git-fetch)
@@ -4217,7 +4217,7 @@ the SQL language using a syntax that reflects the resulting query.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "19xx6mlddca79q6d3wga574m4y32ixmxx2rmk6j3f22i5c37mjzw"))))
+         "1gwiflk72pq1krc0sjzabypmh7slfyf7ak71fiypy3xgzw8a777c"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 98e239d5bd..16faf1ec18 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2014-2022 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015–2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015–2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
@@ -152,6 +152,7 @@
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tex)
@@ -1915,34 +1916,34 @@ with the provided training tools.")
 (define-public nlopt
   (package
     (name "nlopt")
-    (version "2.4.2")
+    (version "2.7.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
-                                  version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/stevengj/nlopt/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
-               (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
-    (build-system gnu-build-system)
+               (base32 "1xpdza28i8w441fwv6a5f3qk4zi7ys6ws9fx6kr5ny27dfdz6rr1"))))
+    (build-system cmake-build-system)
     (arguments
-     `(;; Shared libraries are not built by default.  They are required to
-       ;; build the Guile, Octave, and Python bindings.
-       #:configure-flags '("--enable-shared")
-
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'configure 'set-libnlopt-file-name
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Make sure the Scheme module refers to the library by its
-             ;; absolute file name (we cannot do that from a snippet
-             ;; because the expansion of @libdir@ contains
-             ;; ${exec_prefix}.)
+             ;; absolute file name.
              (let ((out (assoc-ref outputs "out")))
-               (substitute* "swig/nlopt.scm.in"
-                 (("libnlopt")
-                  (string-append out "/lib/libnlopt")))
-               #t))))))
-    (inputs (list guile-2.0))
-    (native-inputs (list pkg-config))
+               (substitute* "src/swig/nlopt-guile.i"
+                 (("\"nlopt_guile\"")
+                  (format #f "~s"
+                          `(format #f "~anlopt_guile"
+                                   (if (getenv "NLOPT_UNINSTALLED")
+                                       ""
+                                       ,(format #f "~a/lib/guile/3.0/extensions/" out))))))
+               (setenv "NLOPT_UNINSTALLED" "1")))))))
+    (inputs (list guile-3.0 octave python))
+    (native-inputs (list pkg-config swig))
     (home-page "http://ab-initio.mit.edu/wiki/")
     (synopsis "Library for nonlinear optimization")
     (description "NLopt is a library for nonlinear optimization, providing a
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index aad329400f..43b9c1b804 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -68,6 +68,7 @@
   #:use-module (gnu packages java)
   #:use-module (gnu packages javascript)
   #:use-module (gnu packages libffi)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
@@ -203,7 +204,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "4.1.3")
+    (version "4.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -211,7 +212,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1mpy4sar1amx5ai9rqr9s0nw8p65iqfrqbm5n9h402b17hrmpzqm"))))
+                "123l17sv3smh5cz0vrjxjj8jf81bb860kah6iww9bl3skdqvgsiq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -237,6 +238,16 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                  (("uname") uname-bin))
                (substitute* "src/unix/sys-std.c"
                  (("rm -Rf ") (string-append rm-bin " -Rf "))))))
+         (add-after 'unpack 'patch-tests
+           (lambda _
+             ;; This is needed because R is run during the check phase and
+             ;; /bin/sh doesn't exist in the build container.
+             (substitute* "src/unix/sys-unix.c"
+               (("\"/bin/sh\"")
+                (string-append "\"" (which "sh") "\"")))
+             ;; This test fails because line numbers are off by two.
+             (substitute* "tests/reg-packages.R"
+               (("8 <= print" m) (string-append "## " m)))))
          (add-after 'unpack 'build-reproducibly
            (lambda _
              ;; The documentation contains time stamps to demonstrate
@@ -315,6 +326,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
              (setenv "TZDIR"
                      (search-input-directory inputs
                                              "share/zoneinfo"))))
+         (add-before 'check 'set-home
+           ;; Some tests require that HOME be set.
+           (lambda _ (setenv "HOME" "/tmp")))
          (add-after 'build 'make-info
           (lambda _ (invoke "make" "info")))
          (add-after 'build 'install-info
@@ -493,14 +507,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-56")
+    (version "7.3-57")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "11gv5965ba6xr4qsp1945vd39rp0sggzpa103rwj1c5hw0abvnlv"))))
+         "13asg609szqq8d1a4ybr508qcanr9gvqd439vfras6mw0l0qi2xx"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -912,13 +926,13 @@ additions (tooltips, bipartite diagram type).")
 (define-public r-dichromat
   (package
     (name "r-dichromat")
-    (version "2.0-0")
+    (version "2.0-0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dichromat" version))
        (sha256
-        (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
+        (base32 "10b0avdar3d1y8x2ya3x5kqxqg0z0mq872hdzvc1nn4amplph1d1"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/dichromat")
     (synopsis "Color schemes for dichromats")
@@ -1215,13 +1229,13 @@ using just two functions: melt and dcast (or acast).")
 (define-public r-ggplot2
   (package
     (name "r-ggplot2")
-    (version "3.3.5")
+    (version "3.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggplot2" version))
        (sha256
-        (base32 "1si46bf9p09qzs208hqffwcb40305p361whmwhc1pwrsmx7jjxdh"))))
+        (base32 "1aa377jdfajj8ld2fh159y8havlibsr4pjisf6mkzk8g5awlxjxz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-digest
@@ -1537,13 +1551,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.38")
+    (version "1.39")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "1bg7nmd2bvfd2gscp4nly4a2c05bpgzq536bmmf93vaf860yhf6i"))))
+                "0wmcj6xv0bcqzmp5vm8s574rfx366rkgm03lgyppk9ywxgnna6n9"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-evaluate r-highr r-stringr r-xfun r-yaml))
@@ -1680,13 +1694,13 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "3.1.3")
+    (version "3.1.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "0c7whxl6zwapqzdplwplvhs73w9blb419h2mdl21pwmqjhzjaq68"))))
+                "02cwdix7v8zsvcmcl3h5hfi66w1ln9qi60risf5nl62f3c1yqzm4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-brio
@@ -1760,14 +1774,14 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "3.1.6")
+    (version "3.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "14l2i6ri3v5y0h8g0ahc4kz0pdqsp5yabxk2w8wavss6y44xjcsv"))))
+         "0wn8j7slfqrdl126g536sg1xkrvjd9rlsk0bjqk3b03nyj8hi9g1"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ellipsis
@@ -1790,13 +1804,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "1.0.8")
+    (version "1.0.9")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "0xb04ckp29pva1h2rfahqhmk9gcwp2dbbx3av8ip40v7dnha6siv"))))
+                "0sxl9yzccsdhlrrwj26lmh9frsijxyfaf7csv8mf7d0q4qqzgqg2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-generics
@@ -2113,14 +2127,14 @@ chain.")
 (define-public r-ade4
   (package
     (name "r-ade4")
-    (version "1.7-18")
+    (version "1.7-19")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "ade4" version))
         (sha256
           (base32
-            "09f5kh2mwygqpnvf53k0r54k0cvaafxm9x4nm819gwv05k2g9dpc"))))
+            "1vv5y6badksnpjb3bcphhjdzzh6i2grmwnsalcf2cfpr3y412lf8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-mass r-pixmap r-sp))
@@ -2245,17 +2259,19 @@ R version.")
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "2.0.0")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
+         "1ii11lypfz8qwswaiagaxnfq6wqkg3cq4j7k9q40sdd0cd8xv15p"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-backports))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://github.com/mllg/checkmate")
     (synopsis "Fast and versatile argument checks")
     (description
@@ -2406,16 +2422,17 @@ tables, autolinks and strikethrough text.")
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "7.1.2")
+    (version "7.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "1zf55wywlpy7mk7zfyi3s9fhhg1m9kvafzj46iqw5cbvnlg3ssdk"))))
+                "12s436jn7aagjpc2lnlrhzwqgsdl8lbbwhkddih6rnxrczawzgrf"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-brew
+           r-cli
            r-commonmark
            r-cpp11
            r-desc
@@ -2427,6 +2444,7 @@ tables, autolinks and strikethrough text.")
            r-rlang
            r-stringi
            r-stringr
+           r-withr
            r-xml2))
     (native-inputs
      (list r-knitr))
@@ -2440,14 +2458,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "2.0.0")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "0jsnzxa72bfxsdai25xyklmmrraaf9yv2nmqmf0bgzrkbzkgsa7b"))))
+         "1i7il5kkr1yp2xk8zw7max4llga4hfz0cx9sx0v2xnb9pg4ksbc6"))))
     (build-system r-build-system)
     (arguments
      (list
@@ -2482,13 +2500,13 @@ integers.")
 (define-public r-httr
   (package
     (name "r-httr")
-    (version "1.4.2")
+    (version "1.4.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httr" version))
               (sha256
                (base32
-                "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6"))))
+                "0skwi501rzndywn81704d68n1l6lrvqilf91q08cjfhpjvx171ls"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-curl r-jsonlite r-openssl r-mime r-r6))
@@ -2721,13 +2739,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.11.0.0.0")
+    (version "0.11.1.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "13blvrlbw8194a96v38hnllnwvyhdw5x9m0dnkyw3xsi3jrhcxin"))))
+                "15s8lx3s0g9npwmys509ahrqc786lg2cid21civ3wm219i4gq2zb"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2813,13 +2831,13 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "2.13")
+    (version "2.14")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
-          (base32 "0i07p3dxxv2s2a4xmyhc3qxmwg86vakniq5jjjclmcq2sahvw5vj"))))
+          (base32 "081j1hpxcwadn606ch5lq279s66c1b0f0mjvap7yimnrljpigv79"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2928,13 +2946,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.2.12")
+    (version "2.2.14")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "12ka9cp591sc3hn5r6z4skbjzm3nfq338wlpjdmw6rz26mmr2c9s"))))
+                "0z307d7rx7blh2apc9dbw9vgad2ldbf9vbdjhmwlj0mwbs3nmqra"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2958,15 +2976,13 @@ engine (version 3.8.8.2) is included.")
 (define-public r-rcurl
   (package
     (name "r-rcurl")
-    (version "1.95-0.1.2")
+    (version "1.98-1.6")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/extra/src/"
-                                  "contrib/RCurl_" version ".tar.gz"))
+              (uri (cran-uri "RCurl" version))
               (sha256
                (base32
-                "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
+                "18nif4phr5vfhri07mnchiym0qfm31ak9nxvb2v9ac84mij6idbc"))))
     (properties `((upstream-name . "RCurl")))
     (build-system r-build-system)
     (arguments
@@ -2979,10 +2995,11 @@ engine (version 3.8.8.2) is included.")
                 (string-append "\
 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
-" m)))
-             #t)))))
+" m))))))))
+    (native-inputs
+     (list libxml2))
     (inputs
-     `(("libcurl" ,curl)))
+     (list curl))
     (propagated-inputs
      (list r-bitops))
     (home-page "http://www.omegahat.net/RCurl")
@@ -3122,14 +3139,14 @@ statements.")
 (define-public r-segmented
   (package
     (name "r-segmented")
-    (version "1.4-1")
+    (version "1.5-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "segmented" version))
        (sha256
         (base32
-         "1aagn2v48ncwxx79h601nlalbgc40fc81nqaw6nbncqkqm0zaxi3"))))
+         "1d8np6psnmqyq3bxxd17ivp6pq6p8rx5hal4bgz8ckc4d1i9lp6n"))))
     (build-system r-build-system)
     (propagated-inputs (list r-mass))
     (home-page "https://cran.r-project.org/web/packages/segmented")
@@ -3565,13 +3582,13 @@ using the multicore functionality of the parallel package.")
             "datatables-extensions/Select"))))
     (package
       (name "r-dt")
-      (version "0.22")
+      (version "0.23")
       (source (origin
                 (method url-fetch)
                 (uri (cran-uri "DT" version))
                 (sha256
                  (base32
-                  "16ah0h60ygvj49cs6cxxhdxx68cs6v6m35w5r1j5h8nxz171q61z"))
+                  "0w6wgiwa3zgldp175a3q7zfw853xqc7mfj34n6hja48ln7yf42in"))
                 (modules '((guix build utils)))
                 (snippet
                  '(for-each delete-file
@@ -3716,13 +3733,13 @@ analysis of large sparse or dense matrices.")
 (define-public r-glmnet
   (package
    (name "r-glmnet")
-   (version "4.1-3")
+   (version "4.1-4")
    (source
     (origin
      (method url-fetch)
      (uri (cran-uri "glmnet" version))
      (sha256
-      (base32 "0nij8v44b5dvp1vc843sfkl9ds83n6g687m2p37q1rdn82m3bg34"))))
+      (base32 "1y80a3b5s24ywhlil3r7b3a0vs9j59d7jkxrqa8zz09x1c5ggc7n"))))
    (build-system r-build-system)
    (native-inputs
     (list gfortran r-knitr))
@@ -3817,14 +3834,14 @@ the way current RNG settings can be changed.")
 (define-public r-rtsne
   (package
     (name "r-rtsne")
-    (version "0.15")
+    (version "0.16")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rtsne" version))
        (sha256
         (base32
-         "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
+         "1mgviwrqwapn8w7rq0sjxca5vi7ylgmm876ijwp22a3chbf5m82j"))))
     (properties `((upstream-name . "Rtsne")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3905,17 +3922,19 @@ message passing.")
 (define-public r-bigmemory
   (package
     (name "r-bigmemory")
-    (version "4.5.36")
+    (version "4.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bigmemory" version))
        (sha256
         (base32
-         "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
+         "0hainqkm7cs8gjm42vkpdrr0284smsbwdfackp34yv7dhxy1avmm"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-bh r-rcpp r-bigmemory-sri))
+     (list r-bh r-bigmemory-sri r-rcpp r-uuid))
+    (inputs
+     (list `(,util-linux "lib"))) ;for -luuid
     (home-page "http://www.bigmemory.org")
     (synopsis "Manage large matrices with shared memory or memory-mapped files")
     (description "This package provides methods to create, store, access, and
@@ -4075,13 +4094,13 @@ t-probabilities, quantiles, random deviates and densities.")
 (define-public r-matrixstats
   (package
     (name "r-matrixstats")
-    (version "0.61.0")
+    (version "0.62.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "matrixStats" version))
               (sha256
                (base32
-                "16pxsba5i51ifbbgvxln2w6nigbwd3290b2ckgzn5bmib7nc1lyv"))))
+                "1jjfsi5vzx6js7phlnd3v64fd05fg0jyz8iq5pivy36jdmmh3ql5"))))
     (properties `((upstream-name . "matrixStats")))
     (build-system r-build-system)
     (arguments
@@ -4466,13 +4485,13 @@ package instead.")
 (define-public r-hmisc
   (package
     (name "r-hmisc")
-    (version "4.6-0")
+    (version "4.7-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Hmisc" version))
        (sha256
-        (base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c"))))
+        (base32 "1gc71wg6f17x6nriphs1kk39ix7lpqk32clk1qshqy8wl6f2vv19"))))
     (properties `((upstream-name . "Hmisc")))
     (build-system r-build-system)
     (native-inputs
@@ -4592,14 +4611,14 @@ Zurich, including many that are related to graphics.")
 (define-public r-gtools
   (package
     (name "r-gtools")
-    (version "3.9.2")
+    (version "3.9.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gtools" version))
        (sha256
         (base32
-         "0lx97yafrms2mjym8rhcq5586z7s1iqgy8qfm4px3xl1yn5qkc83"))))
+         "0pxg0ang9q26hlwgf53pp1hq6rlarq5rnrrr9dl14f5kgfnynpzc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/gtools")
     (synopsis "Various R programming tools")
@@ -4614,14 +4633,14 @@ tests for whether a value is missing, empty or contains only @code{NA} and
 (define-public r-gdata
   (package
     (name "r-gdata")
-    (version "2.18.0")
+    (version "2.18.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdata" version))
        (sha256
         (base32
-         "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
+         "1n9jw136kk5ld27qvny7cx2s8l34jdgmzlx40x62mmcqjddksbsy"))))
     (build-system r-build-system)
     (inputs
      (list perl))
@@ -4654,14 +4673,14 @@ including:
 (define-public r-gplots
   (package
     (name "r-gplots")
-    (version "3.1.1")
+    (version "3.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gplots" version))
        (sha256
         (base32
-         "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr"))))
+         "05k7a8x62qs5g6mps62vb3mwjdnfjzvjb20yws3x0r2j42g3p1cz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-catools r-gtools r-kernsmooth))
@@ -4997,14 +5016,14 @@ mixture models.")
 (define-public r-lars
   (package
     (name "r-lars")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "lars" version))
        (sha256
         (base32
-         "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
+         "17al1g0pvfz9frs2kxicqr8dyp7ciz3x87yx2l4lqd53ls6nm7n6"))))
     (build-system r-build-system)
     (inputs
      (list gfortran))
@@ -5044,14 +5063,14 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.")
 (define-public r-randomforest
   (package
     (name "r-randomforest")
-    (version "4.7-1")
+    (version "4.7-1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "randomForest" version))
        (sha256
         (base32
-         "04q6gb917md4yw837cf9vlx1q8ljl06jw7yhykzb6nl47w55jnkq"))))
+         "1micz9794j7xmj755ln2692rzip8azndflxgdg6xn3j86issi7pm"))))
     (properties `((upstream-name . "randomForest")))
     (build-system r-build-system)
     (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
@@ -5130,14 +5149,14 @@ models, generalized linear models and model-based clustering.")
 (define-public r-mclust
   (package
     (name "r-mclust")
-    (version "5.4.9")
+    (version "5.4.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mclust" version))
        (sha256
         (base32
-         "0s4mva0n04f3pl41msmzhlh7pnk0zbmf06n826smxkw6mz327wb5"))))
+         "0wh6nsbma4b0wsmqm2ynbznl2wlwdly4vg583f6z0zd1qkrvn6ra"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
@@ -5222,14 +5241,14 @@ regression methodology including model selections and multivariate statistics.")
 (define-public r-pcapp
   (package
     (name "r-pcapp")
-    (version "1.9-74")
+    (version "2.0-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pcaPP" version))
        (sha256
         (base32
-         "1dlrz5plb8b89vr3j6sn9jwryyhcwflqkiilxkybbr379m1pp0sh"))))
+         "06hjhr0dzdp5yhd421q9scbv6w6bchicbn2bl7am490ncgrf544n"))))
     (properties `((upstream-name . "pcaPP")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5244,14 +5263,14 @@ analysis} (PCA) by projection pursuit.")
 (define-public r-rrcov
   (package
     (name "r-rrcov")
-    (version "1.6-2")
+    (version "1.7-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rrcov" version))
        (sha256
         (base32
-         "18x8y2b9n2plpn4086nkjk9c27p7gb78kbrv5pj9r8fb0idl5rn5"))))
+         "1z98j9973hl19b70dcwfcf55ifxr2a9v53daaq2sagynh95aik6b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-lattice r-mvtnorm r-pcapp r-robustbase))
@@ -5507,18 +5526,24 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.88")
+    (version "5.93")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
-        (base32 "0grsha18zkiil0qnxc1d7kc3w26i6aaa4av9n9ahdm8yf59yah0r"))))
+        (base32 "0fg5x6sa8mz2hh9nak0wajh4l6h03x216462vs94rgq0ln24kafl"))))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list gfortran))
+     (list gfortran
+           r-r-rsp)) ;for vignettes
     (propagated-inputs
-     (list r-matrix r-matrixmodels r-sparsem))
+     (list r-mass r-matrix r-matrixmodels r-sparsem r-survival))
     (home-page "https://www.r-project.org")
     (synopsis "Quantile regression")
     (description
@@ -5532,14 +5557,14 @@ expected shortfall risk are also included.")
 (define-public r-nloptr
   (package
     (name "r-nloptr")
-    (version "2.0.0")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nloptr" version))
        (sha256
         (base32
-         "16k124ll14p3ygny6i1zd7yza83bv2sk87x922n1bfn9rx4k3jk5"))))
+         "1mqnjswm0dl6vqc8b2s5k3n1mhanaha3l33vh68dh6zx8q9aq9kv"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr ; for building vignettes
@@ -5642,13 +5667,13 @@ Companion to Applied Regression, Third Edition, Sage.")
 (define-public r-car
   (package
     (name "r-car")
-    (version "3.0-12")
+    (version "3.0-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "car" version))
        (sha256
-        (base32 "00kk8l71508f73kyn21is1mx6kjbrzdq3ls94c5ajhiqmvpsd6dq"))))
+        (base32 "1ss7kvi5hf9s4b6i7y06zl4iip1w1h8ff4zzf529wk18h3dfhnnk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-abind
@@ -5792,14 +5817,14 @@ multivariate case.")
 (define-public r-tclust
   (package
     (name "r-tclust")
-    (version "1.4-2")
+    (version "1.5-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tclust" version))
        (sha256
         (base32
-         "1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m"))))
+         "09zk38gih67a8lk72k46mfgv21jpnxh2nzrxc5ypdc2bfwq8nckk"))))
     (build-system r-build-system)
     ;; These are all suggested packages, not build dependencies.
     (propagated-inputs
@@ -6454,14 +6479,14 @@ mediation and estimating power.")
 (define-public r-clubsandwich
   (package
     (name "r-clubsandwich")
-    (version "0.5.5")
+    (version "0.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "clubSandwich" version))
        (sha256
         (base32
-         "1ifnc2rg5agf7lpilmm27iq0af7ghfhkvwykajhvykgf6h4clvhf"))))
+         "0mll8q61vnb980dck8ihxcy89z8m7f8i16mqdvr4l2ljywkhpzvd"))))
     (properties `((upstream-name . "clubSandwich")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6603,14 +6628,14 @@ or eta squared effect size.")
 (define-public r-logspline
   (package
     (name "r-logspline")
-    (version "2.1.16")
+    (version "2.1.17")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "logspline" version))
         (sha256
           (base32
-            "12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l"))))
+            "05c8l22zcvb086909h9vw7icphww703vkcxp2h881y4n1232pdq3"))))
     (properties `((upstream-name . "logspline")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
@@ -6778,14 +6803,14 @@ Michael Lim & Trevor Hastie (2015)")
 (define-public r-datasaurus
   (package
     (name "r-datasaurus")
-    (version "0.1.4")
+    (version "0.1.6")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "datasauRus" version))
         (sha256
           (base32
-            "1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl"))))
+            "0vgylf3bab0xcfg08xwvfq9yhxy6w0fxi7wp4kkxfyjb0pw15qxk"))))
     (properties `((upstream-name . "datasauRus")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
@@ -6894,13 +6919,13 @@ Calculates confidence intervals for the difference in proportion.")
 (define-public r-desctools
   (package
     (name "r-desctools")
-    (version "0.99.44")
+    (version "0.99.45")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "DescTools" version))
         (sha256
-          (base32 "04wp3sp6sahgq167465y38y13h1ia5a4zqazysacpjxd1if0578j"))))
+          (base32 "01gbmikpzjmymvb7p76k7wqvfvwznl6v0qa78jy7bi6fzmbp1zld"))))
     (properties `((upstream-name . "DescTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6910,9 +6935,11 @@ Calculates confidence intervals for the difference in proportion.")
             r-exact
             r-expm
             r-gld
+            r-httr
             r-mass
             r-mvtnorm
             r-rcpp
+            r-readxl
             r-rstudioapi))
     (native-inputs (list gfortran))
     (home-page "https://andrisignorell.github.io/DescTools/")
@@ -7016,13 +7043,13 @@ the presence of variance components/nonparametric terms for models fit with
 (define-public r-binom
   (package
     (name "r-binom")
-    (version "1.1-1")
+    (version "1.1-1.1")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "binom" version))
         (sha256
-          (base32 "0mjj92dqf5q69jxzqya4izb1mly3mkydbnmlm4wb3zqqg82a324c"))))
+          (base32 "1yxyhsd0savwirlmgnq6973slfakqyfvjm0zz60cmc9v490my8gf"))))
     (properties `((upstream-name . "binom")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/package=binom")
diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
index 2c82390ba6..620822b870 100644
--- a/guix/build-system/r.scm
+++ b/guix/build-system/r.scm
@@ -61,7 +61,7 @@ release corresponding to NAME and VERSION."
                          "/src/contrib/"
                          name "_" version ".tar.gz")
           ;; TODO: use %bioconductor-version from (guix import cran)
-          (string-append "https://bioconductor.org/packages/3.14"
+          (string-append "https://bioconductor.org/packages/3.15"
                          type-url-part
                          "/src/contrib/"
                          name "_" version ".tar.gz"))))
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index e848ebc789..4e1ce7c010 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -156,9 +156,9 @@ package definition."
 (define %cran-canonical-url "https://cran.r-project.org/package=")
 (define %bioconductor-url "https://bioconductor.org/packages/")
 
-;; The latest Bioconductor release is 3.14.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.15.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.14")
+(define %bioconductor-version "3.15")
 
 (define* (bioconductor-packages-list-url #:optional type)
   (string-append "https://bioconductor.org/packages/"
author	Ricardo Wurmus <rekado@elephly.net>	2022-05-29 11:49:03 +0200
committer	Ricardo Wurmus <rekado@elephly.net>	2022-05-29 11:49:03 +0200
commit	e640da33f3f142f24af8c63b6e1350865096bae1 (patch)
tree	17ed9611de1e4946bace8e6d22270c6ebe36bbe9
parent	926fcb488b756fb5d6c4c129c4348650919e5835 (diff)
parent	89e926201234a4fe5474dc97504474323dd03f0a (diff)
download	guix-patches-e640da33f3f142f24af8c63b6e1350865096bae1.tar guix-patches-e640da33f3f142f24af8c63b6e1350865096bae1.tar.gz