diff options
Diffstat (limited to 'gnu')
32 files changed, 929 insertions, 366 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 5f72879658..3207cecb72 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -951,6 +951,7 @@ dist_patch_DATA = \ %D%/packages/patches/mcrypt-CVE-2012-4409.patch \ %D%/packages/patches/mcrypt-CVE-2012-4426.patch \ %D%/packages/patches/mcrypt-CVE-2012-4527.patch \ + %D%/packages/patches/meandmyshadow-define-paths-earlier.patch \ %D%/packages/patches/mesa-skip-disk-cache-test.patch \ %D%/packages/patches/meson-for-build-rpath.patch \ %D%/packages/patches/metabat-fix-compilation.patch \ @@ -972,7 +973,6 @@ dist_patch_DATA = \ %D%/packages/patches/mupen64plus-ui-console-notice.patch \ %D%/packages/patches/mupen64plus-video-z64-glew-correct-path.patch \ %D%/packages/patches/mutt-store-references.patch \ - %D%/packages/patches/myrepos-CVE-2018-7032.patch \ %D%/packages/patches/net-tools-bitrot.patch \ %D%/packages/patches/netcdf-date-time.patch \ %D%/packages/patches/netcdf-tst_h_par.patch \ diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92b67453f6..6ce5c0dc96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -363,13 +363,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.58.0") + (version "1.58.2") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) + "07smbb3c30pr5r425g181xsg0rs5jx6x2q6xpwb5dqgicxrz30ga")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 96ea07bdc4..1cf1de1ae5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6292,14 +6292,14 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-2") + (version "2.5-3") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c")))) + "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -7309,13 +7309,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.14.11") + (version "2.14.12") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0wz63hysspyjihqadg91dbvllc5a61zzjrsz0b9498lihqc6m1la")))) + "1ar8sqqgjdy00dbgrxnacqy6gwir5xax76yf0vjxi2vj2skqb0kn")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7338,7 +7338,7 @@ possible.") (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") - (version "0.99.1") + (version "1.1.0") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -7348,7 +7348,7 @@ possible.") version ".tar.gz")) (sha256 (base32 - "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r")))) + "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf")))) (properties `((upstream-name . "GenomeInfoDbData"))) (build-system r-build-system) @@ -7389,13 +7389,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.22.3") + (version "3.22.5") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0w3jv29n0kkaiig8dbbdqy2dkng8xfaihch82mj9ci5hphrx3nng")))) + "0pkcdkh8mwdaca6xa8a7vwdfh46r03rkxwkrf17pwwd4557j7lj7")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7455,13 +7455,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.36.3") + (version "3.36.5") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0iiifszr6hcqih6kszdsbkx3gacfg3d7v8hdx0lbjqnjqgqz7pwk")))) + "0d13w95si7l6fqfsdf6k50v4l573hhfva6mvd94v26iba24p2f6x")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7510,13 +7510,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.32.6") + (version "1.32.7") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0p58yk2i5gqvjlkx548mnrr49wvs0xfcl06l9rqj2hi6hkkbvnp3")))) + "1lh54asabrmk982636avpp1kcfzakwxi31cbj3jc8mkhar1mkyrx")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7716,13 +7716,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.6.5") + (version "0.6.6") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "10b03zrnvz5isfh4z55hasya2m71lrfx10l5lm2sdmqs0gwkanrd")))) + "0rkp0mfsq3wfnib389dh3i44ab0wiz8skkjcv4596dwgq50jqpf2")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7858,13 +7858,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.32.2") + (version "1.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0kfyyg1ib8fkq2hxraal10z4bx3rg8figdskw4yhn1mbh6l42q5f")))) + "06prj5iih3ywsgq00lgfl29p3f8j23a0kqqhzhqcgjrrwsp94588")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7899,7 +7899,7 @@ extracting the desired features in a convenient format.") (define-public r-go-db (package (name "r-go-db") - (version "3.5.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (string-append "https://www.bioconductor.org/packages/" @@ -7907,7 +7907,7 @@ extracting the desired features in a convenient format.") version ".tar.gz")) (sha256 (base32 - "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35")))) + "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j")))) (properties `((upstream-name . "GO.db"))) (build-system r-build-system) @@ -8777,14 +8777,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.63") + (version "1.66") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309")))) + "0rhnyhzfn93yp24jz9v6dzrmyizwzdw070a7idm0k33w1cm8sjqv")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -9359,13 +9359,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.6.1") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1hr2czi5ybdf7hdmqsv39d17f3mvmw94wa38bc14zzm9mgy9gfy7")))) + "1nla74d2sjs51yyvvxf038a03mhw9appvjzj60vr2vd3p5lhqn9k")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9733,14 +9733,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.6.3") + (version "2.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "15jhqg02ypmznc0wxksw56yij02csy678vqy531fdv86fsmypwa0")))) + "1civd8b1rd5n6ys52dazw5m1yy2wq7049dbbyhzv7pjpa1m2x1rm")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -10063,14 +10063,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1ss0xd5570x570v01r6lp64rr1apjrzp0j62520pvm3g8knjhfvs")))) + "0whmmbkq8bmc3ll20l4cv6hhxjgzbkrs97japljzg07ncn1fffsa")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -10378,14 +10378,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.6") + (version "0.6.7") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi")))) + "12nwidbnqmnfy5dnqga26byslvdnkrpz2fi19qfcby6xx0wbndk7")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 98a86b763f..72503254e6 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -211,16 +211,16 @@ COCOMO model or user-provided parameters.") (define-public cloc (package (name "cloc") - (version "1.78") + (version "1.80") (source (origin (method url-fetch) (uri (string-append - "https://github.com/AlDanial/cloc/releases/download/" version + "https://github.com/AlDanial/cloc/releases/download/v" version "/cloc-" version ".tar.gz")) (sha256 (base32 - "1j9lwy9xf43kpv1csqdxzch6y1hnsv881ddqd357f8v58dhr4s68")))) + "0rqxnaskg5b736asyzfda1113zvpkajyqjf49vl9wgzf1r9m6bq8")))) (build-system gnu-build-system) (inputs `(("coreutils" ,coreutils) @@ -231,8 +231,8 @@ COCOMO model or user-provided parameters.") ("perl-regexp-common" ,perl-regexp-common))) (arguments `(#:phases (modify-phases %standard-phases - (delete 'configure) - (delete 'build) + (delete 'configure) ; nothing to configure + (delete 'build) ; nothing to build (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out"))) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7f2123b90e..df869794db 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -166,19 +166,19 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "1l44pxjiz3g0jkk3v6rg5jps3llihfiah0qyv40s0bxvxa6gm8v9")))) + "1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-clipr" ,r-clipr) - ("r-knitr" ,r-knitr) + ("r-fs" ,r-fs) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-whisker" ,r-whisker) @@ -320,14 +320,14 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.1") + (version "5.2") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "0vm2065993wf4hdqarxqykhfz9aaj0rrb98alhkq4qw1d2kdrmdp")))) + "05b4yka5cirdgxd4d7iiaqvr428pk3j6n9q6dvg5j38kdj2h5sr7")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -492,13 +492,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1zm9qkyvy1fvcjvmgw51iqw8x1xzkpy7rx7xnchwfj0xpzal0ljx")))) + (base32 "0ai8igdkysmks1ihbp3h3s552da2hskxqwrvp4cx7vwn91x9f3wd")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -510,19 +510,21 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.0.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 - "10iz8057mixl9j73pq2cbp4ib6dadfsgi3fcsjjm7l3wwb9issd9")))) + "1i1rrax7x7r2bplig5cfc50lx85jc4n9a3qmvbdviaj22wr2lghs")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) + ("r-prettyunits" ,r-prettyunits) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot) ("r-withr" ,r-withr))) @@ -537,14 +539,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "1rjj229nq9fsl4ki4m75ybsavjgpqqhsr1zjzapwicsrxv6212px")))) + "0mm0avvan528zbrcrxigl5fkd7za01fb0qhlqrqvm3ar0115cqa8")))) (build-system r-build-system) (propagated-inputs `(("r-desc" ,r-desc) @@ -564,13 +566,13 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.18") + (version "0.12.19") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "006kpg2ph109rh1l13lqk26pp4as4fvl5661vrcczjygacgd1v7w")))) + (base32 "10mmiaawv9iwglc6z4y51mdpsfb1sivqmwr6xnfqkllcnpabdbk3")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -790,14 +792,14 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.8.0") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "1virn3c232xwcq3d0hhkgjh5gpzl01s39iwii5gxcm9mnsxjzdrh")))) + "1jiani6zwfajky2vafvay2hq158nh99rdrk3j00lycspds9v35fd")))) (build-system r-build-system) (propagated-inputs `(("r-fpc" ,r-fpc) @@ -889,14 +891,14 @@ in main memory.") (define-public r-ffbase (package (name "r-ffbase") - (version "0.12.3") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 - "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5")))) + "1h5x6rbb1nrpzf4ywkizn8ij0bz3mlz46byh46ylxhicg1ribi24")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) @@ -934,14 +936,14 @@ quantities.") (define-public r-reshape (package (name "r-reshape") - (version "0.8.7") + (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 - "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig")))) + "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) @@ -1348,17 +1350,18 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.0-9") + (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6")))) + "12hckg3y5j3zh9q1gwxkc27q813p2r42iqp7wdfiq6nj55jrh6w6")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) + ("r-npsurv" ,r-npsurv) ("r-survival" ,r-survival))) (home-page "http://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") @@ -1626,14 +1629,14 @@ calendar objects.") (define-public r-magic (package (name "r-magic") - (version "1.5-8") + (version "1.5-9") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 - "083cgpp3v03li0h8597b3g21pd9lkbmn9pyssblnhc800mpc52vz")))) + "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind))) @@ -2226,14 +2229,14 @@ acceptance regions, log-ratio plots and Q-Q plots.") (define-public r-sm (package (name "r-sm") - (version "2.2-5.5") + (version "2.2-5.6") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 - "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3")))) + "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") @@ -2316,14 +2319,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.11-0") + (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1v50yn4bsjzdyk7r90isn6dxmpkapillrhpx3gqsshd180vwzqk9")))) + "17d3g14xkxa1a5z5gd3gk1xjqfkjg1ik3i12q0arina8frql3jhd")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (home-page "https://github.com/joshuaulrich/xts") @@ -2501,14 +2504,14 @@ plotting. a three dimensional point cloud.") (define-public r-ggridges (package (name "r-ggridges") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 - "1znvsbl3px8dddpjgdrygnpz4s685wizi0jnjvx2hrz58i0chjqj")))) + "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2548,14 +2551,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg")))) + "1r2yih4c0bdmbx0qrarlf0m1p5z30sri755zmdazsq2pw76zp07g")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -2703,20 +2706,19 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and (define-public r-webshot (package (name "r-webshot") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 - "07r71zzmggp4jf92x4ws4wg6v1x98vaj01lsar85bnb30n5vx8gh")))) + "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr")))) (build-system r-build-system) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-processx" ,r-processx) - ("r-withr" ,r-withr))) + `(("r-callr" ,r-callr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description @@ -2763,14 +2765,14 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.3") + (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 - "1r11dd49ngmjgbjdv28a9c1jp8cg1l50x0acbsamzz576p8i2wl9")))) + "0991ywgc2dsraba91kkj37akhfzhzn02cnz7c88hhdis9kag3pwv")))) (build-system r-build-system) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") @@ -2847,14 +2849,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1bgpr5i5399jf9n6pg2mm4aamisbhppg082ad0wv1j4g0rlxf1gy")))) + "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -2962,14 +2964,14 @@ generation, and 2D/3D network visualization.") (define-public r-ttr (package (name "r-ttr") - (version "0.23-3") + (version "0.23-4") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1")))) + "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -3170,14 +3172,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.9") + (version "1.8.10") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "1fg8vjpal33y51iqzglk1yvy46d7js0l0wfbdy698lq8a06hq19p")))) + "00lvqp5bb3iak5myiz4rqm887bkq9sdh7aybmz84mmfni6q01m28")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs @@ -3240,14 +3242,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.4") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "1hd23b8v2kpqp5gr0va8p2q7j8w9rik6ks7zrr4b8mb2mwrakk74")))) + "10jl5l3xnigiq95829ssq69xbim97k851187dghc30awszcx4clh")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -3296,14 +3298,14 @@ sample Robust Rank-Order Distributional Test.") (define-public r-expm (package (name "r-expm") - (version "0.999-2") + (version "0.999-3") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 - "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q")))) + "04k4a6g071jkjc0d30ncmf713dj16brcs9m6pj43hnycc1caq6si")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) @@ -3361,14 +3363,14 @@ creation and manipulation of WAVE audio files.") (define-public r-np (package (name "r-np") - (version "0.60-8") + (version "0.60-9") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 - "17h67a510wh83800ri6g02wvznrlhigxni8shyijz1iaxcpk8k4j")))) + "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -3500,14 +3502,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb")))) + "1fbk5i6w6cpam8s3acf4bgdp8hajn4digjjix3i6i4q3p2rvn6zx")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs @@ -3523,14 +3525,14 @@ environment within Shiny.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "0.9.5") + (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "0mbxfqn79nphii4hb6kxl2wc0w0ra16y378rp2yw9a9926zdb7mb")) + "1f98ahki0kyb27gl55a859zb0lsvk9gddd9f54y767xfs6h89cgk")) (modules '((guix build utils))) (snippet '(begin @@ -3564,7 +3566,9 @@ environment within Shiny.") ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles) ("r-shinyace" ,r-shinyace) + ("r-summarytools" ,r-summarytools) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-writexl" ,r-writexl))) @@ -4059,14 +4063,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "0.9-3") + (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0hxbv01im9zk1qrwgigpc510w6x0kzdzip4gx2jzfqmmwr8m17r8")))) + "1753kgyc4kmbb5h6knz5wgvvvj8v77kzm8lz0kwz05m5k3spa24k")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -4087,14 +4091,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.7.4") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "125zc499gj702x2bch95lsfzk2qb4dzv3604x9afym2i3ylrmm64")))) + "0xhwn37makzm85zb6w5acc7svzibxcnz69rks0kxw22vapkxwz1i")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -4236,14 +4240,14 @@ quizzes to create self-paced tutorials for learning about R and R packages.") (define-public r-analytics (package (name "r-analytics") - (version "2.0") + (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "analytics" version)) (sha256 (base32 - "1jkdjqc3fnvvsgi6x9ncf36rxzq0a55cmgkcv92mfmpcramg2lk6")))) + "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) @@ -4256,7 +4260,8 @@ quizzes to create self-paced tutorials for learning about R and R packages.") ("r-robust" ,r-robust) ("r-trend" ,r-trend) ("r-tsa" ,r-tsa) - ("r-urca" ,r-urca))) + ("r-urca" ,r-urca) + ("r-vim" ,r-vim))) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description @@ -4536,14 +4541,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "135qj7bcc3mwn0vg55hiiadf66lx6zaxvkicfmfw9x0zr7ah2r6x")))) + "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -4578,14 +4583,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "1s6p4cj909kc635fh5xpl87bqlcdj3dn3r1wk5g40abimk2b0pva")))) + "0h222q80li8rs3cv4c5lvv3g91ygd51w43ay6fwyk9q9d315vwrj")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) @@ -4668,14 +4673,14 @@ functions.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.9-0") + (version "0.10-1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "067w0w6kza0hkzcnx58danl83yfvl9yjacr47mnid2bg856gdd1b")))) + "0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -5219,14 +5224,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.12.1") + (version "1.13.0") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "05ad69a6fxy9k903cw3h4q59ch2jv6qfg9yjdbw3cgiiazcafrlj")))) + "0ain17clympkx09ym7gydylcd93096dxzqx1qzci310yq2l7fknm")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -5857,13 +5862,13 @@ detection.") (define-public r-abps (package (name "r-abps") - (version "0.2") + (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "ABPS" version)) (sha256 - (base32 "1k3f5i34f4w2khkszb4qhwwcpiy7gsfh82vjr6rypwg6rx5rjclq")))) + (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab))) @@ -6401,14 +6406,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.2.4") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "01g6albv9whpdsj4j7c3q02pwdlkscjl5d2l8z96qafw7n9gml6g")))) + "0kdyy4qp332c4yyvp1cnh48h6ks6ffir5rjcv0py0vm3m8c3hh61")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -6693,3 +6698,530 @@ component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.") (license license:gpl3))) + +(define-public r-ini + (package + (name "r-ini") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ini" version)) + (sha256 + (base32 + "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) + (build-system r-build-system) + (home-page "https://github.com/dvdscripter/ini") + (synopsis "Read and write configuration files") + (description + "This package provides tools to parse simple @code{.ini} configuration +files to an structured list. Users can manipulate this resulting list with +@code{lapply()} functions. This same structured list can be used to write +back to file after modifications.") + (license license:gpl3))) + +(define-public r-gh + (package + (name "r-gh") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gh" version)) + (sha256 + (base32 + "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k")))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-ini" ,r-ini) + ("r-jsonlite" ,r-jsonlite))) + (home-page "https://github.com/r-lib/gh#readme") + (synopsis "Access the GitHub API via R") + (description + "This package provides a minimal R client to access the GitHub API.") + (license license:expat))) + +(define-public r-fs + (package + (name "r-fs") + (version "1.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "fs" version)) + (sha256 + (base32 + "0kqqaqqml8x3r1mdld40iwns0ylj2f52qsdh1vcn39f7w7c2ka8j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://fs.r-lib.org") + (synopsis "Cross-platform file system operations based on libuv") + (description + "This package provides a cross-platform interface to file system +operations, built on top of the libuv C library.") + (license license:gpl3))) + +(define-public r-clisymbols + (package + (name "r-clisymbols") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "clisymbols" version)) + (sha256 + (base32 + "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/clisymbols") + (synopsis "Unicode symbols at the R prompt") + (description + "This package provides a small subset of Unicode symbols, that are useful +when building command line applications. They fall back to alternatives on +terminals that do not support Unicode.") + (license license:expat))) + +(define-public r-usethis + (package + (name "r-usethis") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "usethis" version)) + (sha256 + (base32 + "1gadckx3sxz9gxvpkprj9x7zcgg2nz5m4q0vi76ya9li1v03rwwn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-clipr" ,r-clipr) + ("r-clisymbols" ,r-clisymbols) + ("r-crayon" ,r-crayon) + ("r-curl" ,r-curl) + ("r-desc" ,r-desc) + ("r-fs" ,r-fs) + ("r-gh" ,r-gh) + ("r-git2r" ,r-git2r) + ("r-glue" ,r-glue) + ("r-rlang" ,r-rlang) + ("r-rprojroot" ,r-rprojroot) + ("r-rstudioapi" ,r-rstudioapi) + ("r-whisker" ,r-whisker))) + (home-page "https://github.com/r-lib/usethis") + (synopsis "Automate R package and project setup") + (description + "This package helps you to automate R package and project setup tasks +that are otherwise performed manually. This includes setting up unit testing, +test coverage, continuous integration, Git, GitHub integration, licenses, +Rcpp, RStudio projects, and more.") + (license license:gpl3))) + +(define-public r-sessioninfo + (package + (name "r-sessioninfo") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "sessioninfo" version)) + (sha256 + (base32 + "01c0m8yzadpwd825hky6as0f8ka4xyz7zfy0ih2iy7qqw11w6qn5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-withr" ,r-withr))) + (home-page "https://github.com/r-lib/sessioninfo#readme") + (synopsis "R session information") + (description + "This package provides tools to query and print information about the +current R session. It is similar to @code{utils::sessionInfo()}, but includes +more information about packages, and where they were installed from.") + (license license:gpl2))) + +(define-public r-remotes + (package + (name "r-remotes") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "remotes" version)) + (sha256 + (base32 + "1xkzlciv68jyf4j8hads0i47nxbgsy1kv7258c6zzyq66z0amhss")))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/remotes#readme") + (synopsis "R package installation from remote repositories") + (description + "Download and install R packages stored in GitHub, BitBucket, or plain +subversion or git repositories. This package is a lightweight replacement of +the @code{install_*} functions in the @code{devtools} package. Indeed most of +the code was copied over from @code{devtools}.") + (license license:gpl2+))) + +(define-public r-xopen + (package + (name "r-xopen") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "xopen" version)) + (sha256 + (base32 + "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-processx" ,r-processx))) + (home-page "https://github.com/r-lib/xopen#readme") + (synopsis "Open system files, URLs, anything") + (description + "This package provides a cross-platform solution to open files, +directories or URLs with their associated programs.") + (license license:expat))) + +(define-public r-rcmdcheck + (package + (name "r-rcmdcheck") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rcmdcheck" version)) + (sha256 + (base32 + "13liz9lmx9xgc0f7pjiz3sp8ygvazx2zslbiwz3p9fimfsx1yfsg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-desc" ,r-desc) + ("r-digest" ,r-digest) + ("r-pkgbuild" ,r-pkgbuild) + ("r-prettyunits" ,r-prettyunits) + ("r-r6" ,r-r6) + ("r-rprojroot" ,r-rprojroot) + ("r-withr" ,r-withr) + ("r-xopen" ,r-xopen))) + (home-page "https://github.com/r-Lib/rcmdcheck#readme") + (synopsis "Run R CMD check from R and capture results") + (description + "Run @code{R CMD check} from R programmatically, and capture the results +of the individual checks.") + (license license:expat))) + +(define-public r-rapportools + (package + (name "r-rapportools") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rapportools" version)) + (sha256 + (base32 + "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-pander" ,r-pander) + ("r-plyr" ,r-plyr) + ("r-reshape" ,r-reshape))) + (home-page "https://cran.r-project.org/web/packages/rapportools/") + (synopsis "Miscellaneous helper functions with sane defaults for reporting") + (description + "This package provides helper functions that act as wrappers to more +advanced statistical methods with the advantage of having sane defaults for +quick reporting.") + (license license:agpl3+))) + +(define-public r-pander + (package + (name "r-pander") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pander" version)) + (sha256 + (base32 + "0gd7rqkpbraznip8jmri9lqa8ajg1sryyplhd6m633wg91whiipi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-rcpp" ,r-rcpp))) + (home-page "https://rapporter.github.io/pander") + (synopsis "Render R objects into Pandoc's markdown") + (description + "The main aim of the pander R package is to provide a minimal and easy +tool for rendering R objects into Pandoc's markdown. The package is also +capable of exporting/converting complex Pandoc documents (reports) in various +ways.") + ;; This package is licensed under either the AGPLv3+ or the very rarely + ;; used OSL 3.0. + (license license:agpl3+))) + +(define-public r-summarytools + (package + (name "r-summarytools") + (version "0.8.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "summarytools" version)) + (sha256 + (base32 + "0z836m6ib9bznwcawn6xf8gck05ydxwi3bx4jbrbyqql4kci8zwb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-lubridate" ,r-lubridate) + ("r-matrixstats" ,r-matrixstats) + ("r-pander" ,r-pander) + ("r-pryr" ,r-pryr) + ("r-rapportools" ,r-rapportools) + ("r-rcurl" ,r-rcurl))) + (home-page "https://github.com/dcomtois/summarytools") + (synopsis "Tools to quickly and neatly summarize data") + (description + "This package provides tools for data frame summaries, cross-tabulations, +weight-enabled frequency tables and common univariate statistics in concise +tables available in a variety of formats (plain ASCII, Markdown and HTML). A +good point-of-entry for exploring data, both for experienced and new R +users.") + (license license:gpl2))) + +(define-public r-lsei + (package + (name "r-lsei") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "lsei" version)) + (sha256 + (base32 + "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://www.stat.auckland.ac.nz/~yongwang") + (synopsis "Solve regression problems under equality/inequality constraints") + (description + "It contains functions that solve least squares linear regression +problems under linear equality/inequality constraints. Functions for solving +quadratic programming problems are also available, which transform such +problems into least squares ones first.") + (license license:gpl2+))) + +(define-public r-npsurv + (package + (name "r-npsurv") + (version "0.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "npsurv" version)) + (sha256 + (base32 + "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lsei" ,r-lsei))) + (home-page "https://www.stat.auckland.ac.nz/~yongwang") + (synopsis "Nonparametric survival analysis") + (description + "This package contains functions for non-parametric survival analysis of +exact and interval-censored observations.") + (license license:gpl2+))) + +(define-public r-clusteval + (package + (name "r-clusteval") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "clusteval" version)) + (sha256 + (base32 + "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mvtnorm" ,r-mvtnorm) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/clusteval/") + (synopsis "Evaluation of clustering algorithms") + (description + "This R package provides a suite of tools to evaluate clustering +algorithms, clusterings, and individual clusters.") + (license license:expat))) + +(define-public r-tweedie + (package + (name "r-tweedie") + (version "2.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "tweedie" version)) + (sha256 + (base32 + "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/tweedie/") + (synopsis "Evaluation of Tweedie exponential family models") + (description + "Maximum likelihood computations for Tweedie families, including the +series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and +the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), +and related methods.") + (license license:gpl2+))) + +(define-public r-rcppgsl + (package + (name "r-rcppgsl") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppGSL" version)) + (sha256 + (base32 + "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m")))) + (properties `((upstream-name . "RcppGSL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("gsl" ,gsl))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://cran.r-project.org/web/packages/RcppGSL/") + (synopsis "Rcpp integration for GSL vectors and matrices") + (description + "The GNU Scientific Library (or GSL) is a collection of numerical +routines for scientific computing. It is particularly useful for C and C++ +programs as it provides a standard C interface to a wide range of mathematical +routines. There are over 1000 functions in total with an extensive test +suite. The RcppGSL package provides an easy-to-use interface between GSL data +structures and R using concepts from Rcpp which is itself a package that eases +the interfaces between R and C++.") + (license license:gpl2+))) + +(define-public r-mvabund + (package + (name "r-mvabund") + (version "3.13.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mvabund" version)) + (sha256 + (base32 + "1z8bj9zbc8h7w1xki9sc2p2rq6lv8gbcmiy9819z54d7lx1i9cnj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcppgsl" ,r-rcppgsl) + ("r-statmod" ,r-statmod) + ("r-tweedie" ,r-tweedie))) + (home-page "https://cran.r-project.org/web/packages/mvabund/") + (synopsis "Statistical methods for analysing multivariate abundance data") + (description + "This package provides a set of tools for displaying, modeling and +analysing multivariate abundance data in community ecology.") + (license license:lgpl2.1+))) + +(define-public r-afex + (package + (name "r-afex") + (version "0.22-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "afex" version)) + (sha256 + (base32 + "065wbxljl77zqvc2c4gpfpfyc6mbnnrf24q399q9bxmrz3sapj8n")))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-lme4" ,r-lme4) + ("r-lmertest" ,r-lmertest) + ("r-pbkrtest" ,r-pbkrtest) + ("r-reshape2" ,r-reshape2))) + (home-page "https://afex.singmann.science/") + (synopsis "Analysis of factorial experiments") + (description + "This package provides convenience functions for analyzing factorial +experiments using ANOVA or mixed models.") + (license license:gpl2+))) + +(define-public r-lmertest + (package + (name "r-lmertest") + (version "3.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lmerTest" version)) + (sha256 + (base32 + "0pia69sc8bn37mkiprdf91iilziqb865f94k6x6c26i33fg7rq4m")))) + (properties `((upstream-name . "lmerTest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-numderiv" ,r-numderiv))) + (home-page "https://github.com/runehaubo/lmerTestR") + (synopsis "Tests in linear mixed effects models") + (description + "This package provides p-values in type I, II or III anova and summary +tables for @code{lmer} model fits via Satterthwaite's degrees of freedom +method. A Kenward-Roger method is also available via the @code{pbkrtest} +package. Model selection methods include step, drop1 and anova-like tables +for random effects (ranova). Methods for Least-Square means (LS-means) and +tests of linear contrasts of fixed effects are also available.") + (license license:gpl2+))) + +(define-public r-r2glmm + (package + (name "r-r2glmm") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "r2glmm" version)) + (sha256 + (base32 + "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-afex" ,r-afex) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-lmertest" ,r-lmertest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-pbkrtest" ,r-pbkrtest))) + (home-page "https://github.com/bcjaeger/r2glmm") + (synopsis "Compute R squared for mixed (multilevel) models") + (description + "This package computes model and semi partial R squared with confidence +limits for the linear and generalized linear mixed model (LMM and GLMM). The +R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM +using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et +al. (2016)).") + (license license:gpl2))) diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 6d45dc0cc5..2fb87251f4 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -51,7 +51,7 @@ (package (name "curl") (version "7.59.0") - (replacement curl-7.61.1) + (replacement curl-7.62.0) (source (origin (method url-fetch) (uri (string-append "https://curl.haxx.se/download/curl-" @@ -141,10 +141,10 @@ tunneling, and so on.") "See COPYING in the distribution.")) (home-page "https://curl.haxx.se/"))) -(define-public curl-7.61.1 +(define-public curl-7.62.0 (package (inherit curl) - (version "7.61.1") + (version "7.62.0") (source (origin (method url-fetch) @@ -152,7 +152,7 @@ tunneling, and so on.") version ".tar.xz")) (sha256 (base32 - "148qv1f32290r9pwg07mccawihz4srznkzsdwdl2xllvlgb16n9x")))))) + "1hbm29r3pirhn4gkcnd94ylc4jzgn3v3v7qbay9awxg7bwx69dfs")))))) (define-public kurly (package diff --git a/gnu/packages/electronics.scm b/gnu/packages/electronics.scm index 4aaf050faf..bc30e619ec 100644 --- a/gnu/packages/electronics.scm +++ b/gnu/packages/electronics.scm @@ -202,7 +202,7 @@ format support.") (define-public sigrok-cli (package (name "sigrok-cli") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (string-append @@ -210,7 +210,7 @@ format support.") version ".tar.gz")) (sha256 (base32 - "072ylscp0ppgii1k5j07hhv7dfmni4vyhxnsvxmgqgfyq9ldjsan")))) + "15vpn1psriadcbl6v9swwgws7dva85ld03yv6g1mgm27kx11697m")))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs @@ -226,7 +226,7 @@ format support.") (define-public pulseview (package (name "pulseview") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (string-append @@ -234,9 +234,20 @@ format support.") version ".tar.gz")) (sha256 (base32 - "1f8f2342d5yam98mmcb8f9g2vslcwv486bmi4x45pxn68l82ky3q")))) + "0bvgmkgz37n2bi9niskpl05hf7rsj1lj972fbrgnlz25s4ywxrwy")))) + (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DCMAKE_CXX_FLAGS=-fext-numeric-literals"))) + `(#:configure-flags '("-DENABLE_TESTS=y") + #:phases + (modify-phases %standard-phases + (add-after 'install 'remove-empty-doc-directory + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion (string-append out "/share") + ;; Use RMDIR to never risk silently deleting files. + (rmdir "doc/pulseview") + (rmdir "doc")) + #t)))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs @@ -247,7 +258,6 @@ format support.") ("libsigrokdecode" ,libsigrokdecode) ("qtbase" ,qtbase) ("qtsvg" ,qtsvg))) - (build-system cmake-build-system) (home-page "https://www.sigrok.org/wiki/PulseView") (synopsis "Qt based logic analyzer, oscilloscope and MSO GUI for sigrok") (description "PulseView is a Qt based logic analyzer, oscilloscope and MSO GUI diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 438e9df1fc..232adfb081 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -117,8 +117,8 @@ ;; Building from recent Git because the official 5.0 release no longer builds. (define-public dolphin-emu - (let ((commit "5f0d825f40b8aabe13eaef32d44ab667ff8e8c28") - (revision "3")) + (let ((commit "22ddd11573fd8d3e43a879804e7a64e50928435d") + (revision "4")) (package (name "dolphin-emu") (version (git-version "5.0" revision commit)) @@ -144,7 +144,7 @@ #t)) (sha256 (base32 - "0dh7mih16aif9ynbgcsn7n10f89g8d232i86xqfp2rijsdggcmzl")))) + "01l6r8spaslqc73m3y7hfb2jx5a4848vdkman6x6w2arpb8bywzl")))) (build-system cmake-build-system) (arguments '(#:tests? #f @@ -153,7 +153,8 @@ (add-before 'configure 'fixgcc7 (lambda _ (unsetenv "C_INCLUDE_PATH") - (unsetenv "CPLUS_INCLUDE_PATH"))) + (unsetenv "CPLUS_INCLUDE_PATH") + #t)) (add-before 'configure 'generate-fonts&hardcore-libvulkan-path (lambda* (#:key inputs outputs #:allow-other-keys) (let ((fontfile @@ -195,7 +196,7 @@ ("bluez" ,bluez) ("curl" ,curl) ("eudev" ,eudev) - ("ffmpeg" ,ffmpeg-3.4) + ("ffmpeg" ,ffmpeg) ("font-wqy-microhei" ,font-wqy-microhei) ("freetype" ,freetype) ("glew" ,glew) @@ -1185,7 +1186,7 @@ play them on systems for which they were never designed!") (define-public mame (package (name "mame") - (version "0.202") + (version "0.203") (source (origin (method git-fetch) @@ -1195,7 +1196,7 @@ play them on systems for which they were never designed!") (file-name (git-file-name name version)) (sha256 (base32 - "1v9gm124p65nbj678gfkcvwphp9qc15ky2p12ca6g3rllma94di5")) + "19ccqc00024fbjyk0k5d9xljhwq7wsrp7phwm2jmn0h77mgdj844")) (modules '((guix build utils))) (snippet ;; Remove bundled libraries. diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index b195019866..f250719bbd 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -107,7 +107,7 @@ single file can be mounted.") (define-public disorderfs (package (name "disorderfs") - (version "0.5.4") + (version "0.5.5") (source (origin (method git-fetch) @@ -117,7 +117,7 @@ single file can be mounted.") (file-name (git-file-name name version)) (sha256 (base32 - "1mw4ix9h17ikki8p2rxdvzp87rcm1c7by5lvfn5gxlxr7hlj9f8g")))) + "18c32qcdzbxrzg7srnqnw1ls9yqqxyk9b996yxr6w2znw6x6n8v4")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -126,7 +126,7 @@ single file can be mounted.") ("attr" ,attr))) (arguments `(#:phases (modify-phases %standard-phases - (delete 'configure)) + (delete 'configure)) ; no configure script #:make-flags (let ((out (assoc-ref %outputs "out"))) (list (string-append "PREFIX=" out))) #:test-target "test" diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm index c9454aa324..9ab2e35255 100644 --- a/gnu/packages/fpga.scm +++ b/gnu/packages/fpga.scm @@ -121,14 +121,15 @@ For synthesis, the compiler generates netlists in the desired format.") (name "yosys") (version "0.7") (source (origin - (method url-fetch) - (uri - (string-append "https://github.com/cliffordwolf/yosys/archive/" - name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/cliffordwolf/yosys.git") + (commit (string-append "yosys-" version)) + (recursive? #t))) ; for the ‘iverilog’ submodule (sha256 (base32 - "0vkfdn4phvkjqlnpqlr6q5f97bgjc3312vj5jf0vf85zqv88dy9x")) - (file-name (string-append name "-" version "-checkout.tar.gz")) + "1ssrpgw0j9qlm52g1hsbb9fsww4vnwi0l7zvvky7a8w7wamddky0")) + (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 53e7a79ce6..0467872fcd 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -572,7 +572,7 @@ automata. The following features are available: (define-public meandmyshadow (package (name "meandmyshadow") - (version "0.4.1") + (version "0.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/meandmyshadow/" @@ -580,38 +580,24 @@ automata. The following features are available: "-src.tar.gz")) (sha256 (base32 - "0wl5dc75qy001s6043cx0vr2l5y2qfv1cldqnwill9sfygqj9p95")))) + "1b6qf83vdfv8jwn2jq9ywmda2qn2f5914i7mwfy04m17wx593m3m")) + (patches (search-patches + ;; This will not be needed in the next release. + "meandmyshadow-define-paths-earlier.patch")))) (build-system cmake-build-system) (arguments - '(#:tests? #f ; there are no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-sdl'paths - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "cmake/Modules/FindSDL_gfx.cmake" - (("/usr/local/include/SDL") - (string-append (assoc-ref inputs "sdl") - "/include/SDL"))) - ;; Because SDL provides lib/libX11.so.6 we need to explicitly - ;; link with libX11, even though we're using the GL backend. - (substitute* "CMakeLists.txt" - (("\\$\\{X11_LIBRARIES\\}") "-lX11")) - #t))))) + `(#:tests? #f)) ; there are no tests (native-inputs `(("pkg-config" ,pkg-config))) (inputs - `(("sdl" ,(sdl-union (list sdl - sdl-image - sdl-gfx - sdl-mixer - sdl-ttf))) - ("libx11" ,libx11) ; needed by sdl's libX11 + `(("curl" ,curl) ("libarchive" ,libarchive) - ("openssl" ,openssl) - ("mesa" ,mesa) - ("glu" ,glu) - ("curl" ,curl))) - (home-page "http://meandmyshadow.sourceforge.net/") + ("lua" ,lua) + ("sdl" ,(sdl-union (list sdl2 + sdl2-image + sdl2-mixer + sdl2-ttf))))) + (home-page "https://acmepjz.github.io/meandmyshadow/") (synopsis "Puzzle/platform game") (description "Me and My Shadow is a puzzle/platform game in which you try to reach the exit by solving puzzles. Spikes, moving blocks, fragile blocks @@ -3658,18 +3644,18 @@ throwing people around in pseudo-randomly generated buildings.") (define-public hyperrogue (package (name "hyperrogue") - (version "10.4t") + (version "10.4x") ;; When updating this package, be sure to update the "hyperrogue-data" ;; origin in native-inputs. (source (origin (method url-fetch) (uri (string-append - "http://www.roguetemple.com/z/hyper/" + "https://www.roguetemple.com/z/hyper/" name (string-join (string-split version #\.) "") "-src.tgz")) (sha256 (base32 - "0phqhmnzmc16a23qb4fkil0flzb86kibdckf1r35nc3l0k4193nn")))) + "0khk7xqdw4aiw1wnf1xrhmd7fklnzmpdavd7ix4mkm510dr5wklm")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -3741,12 +3727,12 @@ throwing people around in pseudo-randomly generated buildings.") (method url-fetch) (uri (string-append - "http://www.roguetemple.com/z/hyper/" name + "https://www.roguetemple.com/z/hyper/" name (string-join (string-split version #\.) "") "-win.zip")) (sha256 (base32 - "1xd9v8zzgi8m5ar8g4gy1xx5zqwidz3gn1knz0lwib3kbxx4drpg")))) + "1dv3kdv1n5imh3n9900b55rf0wwbjj7243lhsbk7lcjqsqxia39q")))) ("unzip" ,unzip))) (inputs `(("font-dejavu" ,font-dejavu) @@ -3756,7 +3742,7 @@ throwing people around in pseudo-randomly generated buildings.") sdl-gfx sdl-mixer sdl-ttf))))) - (home-page "http://www.roguetemple.com/z/hyper/") + (home-page "https://www.roguetemple.com/z/hyper/") (synopsis "Non-euclidean graphical rogue-like game") (description "HyperRogue is a game in which the player collects treasures and fights diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 60d3ee7ad9..82e8173210 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -510,12 +510,23 @@ in the style of communicating sequential processes (@dfn{CSP}).") (substitute* (find-files "cmd" "\\.go") (("/lib(64)?/ld-linux.*\\.so\\.[0-9]") loader)) #t))) + ;; Prevent installation of the build cache, which contains store + ;; references to most of the tools used to build Go and would + ;; unnecessarily increase the size of Go's closure if it was + ;; installed. + ;; TODO This should be moved into the 'install' phase when Go 1.9 is + ;; removed. + (add-before 'install 'delete-extraneous-files + (lambda _ + (delete-file-recursively "../pkg/obj") + #t)) (replace 'set-bootstrap-variables (lambda* (#:key outputs inputs #:allow-other-keys) ;; Tell the build system where to find the bootstrap Go. (let ((go (assoc-ref inputs "go"))) (setenv "GOROOT_BOOTSTRAP" go) - (setenv "GOGC" "400")))))))))) + (setenv "GOGC" "400") + #t))))))))) (define-public go go-1.9) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index fb9b0eeedf..856bbc0eed 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -357,10 +357,10 @@ (method url-fetch) ;; No versioned URL, see <https://www.agner.org/optimize/> for updates. (uri "https://www.agner.org/optimize/objconv.zip") - (file-name "objconv-2018-08-15.zip") + (file-name "objconv-2018-10-07.zip") (sha256 (base32 - "09y4pwxfs6fl47cyingbf95i2rxx74wmycl9fd4ldcgvpx9bzdrx")))) + "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs")))) ("dsfmt" ,(origin (method url-fetch) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 437f3672c2..6a3a59590e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2110,16 +2110,14 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.1.5") + (version "2.1.8") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "18cv7c2gvagbmggfbsy2xk9bpn47izd0qrmqnc3q7afvj6pr6nf9")))) + (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z")))) (build-system r-build-system) - (propagated-inputs - `(("r-quadprog" ,r-quadprog))) - (home-page "https://cran.r-project.org/web/packages/pracma") + (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") (description "This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 0090fe12ce..de33d737e2 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -1648,7 +1648,7 @@ notifications, and Python scripting support.") (define-public libqmatrixclient (package (name "libqmatrixclient") - (version "0.3.0.2") + (version "0.4.0") (source (origin (method git-fetch) @@ -1658,7 +1658,7 @@ notifications, and Python scripting support.") (file-name (git-file-name name version)) (sha256 (base32 - "03pxmr4wa818fgqddkr2fkwz6pda538x3ic9yq7c40x98zqf55w5")))) + "1llzqjagvp91kcg26q5c4qw9aaz7wna3rh6k06rc3baivrjqf3cn")))) (build-system cmake-build-system) (inputs `(("qtbase" ,qtbase))) @@ -1676,7 +1676,7 @@ QMatrixClient project.") (define-public quaternion (package (name "quaternion") - (version "0.0.9.2") + (version "0.0.9.3") (source (origin (method git-fetch) @@ -1686,31 +1686,31 @@ QMatrixClient project.") (file-name (git-file-name name version)) (sha256 (base32 - "0zrr4khbbdf5ziq65gi0cb1yb1d0y5rv18wld22w1x96f7fkmrib")))) + "1hr9zqf301rg583n9jv256vzj7y57d8qgayk7c723bfknf1s6hh3")))) (build-system cmake-build-system) (inputs `(("libqmatrixclient" ,libqmatrixclient) ("qtbase" ,qtbase) - ("qtdeclarative" ,qtdeclarative))) + ("qtdeclarative" ,qtdeclarative) + ("qtquickcontrols" ,qtquickcontrols) + ("qtsvg" ,qtsvg) + ("qttools" ,qttools))) (arguments `(#:tests? #f ; No tests #:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-libqmatrixclient-dynamic-linking - ;; Upstream recommends statically linking with - ;; libqmatrixclient. Patch the source so that we can dynamically - ;; link instead. In a future release, when upstream moves to - ;; dynamic linking, remove this phase. - (lambda _ - (substitute* "CMakeLists.txt" - (("^add_subdirectory\\(lib\\)" all) - (string-append "#" all))) - (for-each - (lambda (file) - (substitute* file - (("#include \"lib/([^\"]*)\"" all header) - (string-append "#include <" header ">")))) - (find-files "client" "\\.(cpp|h)$")) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/quaternion") + `("QT_PLUGIN_PATH" ":" prefix + (,(string-append (assoc-ref inputs "qtsvg") + "/lib/qt5/plugins"))) + `("QML2_IMPORT_PATH" ":" prefix + ,(map (lambda (label) + (string-append (assoc-ref inputs label) + "/lib/qt5/qml")) + '("qtdeclarative" "qtquickcontrols")))) #t))))) (home-page "https://matrix.org/docs/projects/client/quaternion.html") (synopsis "Graphical client for the Matrix instant messaging protocol") diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index b69be2965f..fe8610ab94 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -90,7 +90,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.20.21") + (version "0.20.23") (source (origin (method url-fetch) (uri @@ -99,7 +99,7 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "1p2qrhdb1gzfv3y5dvvbc9s2wwmhg3azvzf8r02hzhk5q96pc8l3")))) + "1smg6hab4kwrzsw1k7vlpya3ampdk8psnmkrzxlgb43j4fgmygjh")))) (build-system gnu-build-system) (arguments `(#:phases @@ -165,7 +165,7 @@ protocol.") (define-public mpd-mpc (package (name "mpd-mpc") - (version "0.30") + (version "0.31") (source (origin (method url-fetch) (uri @@ -174,10 +174,12 @@ protocol.") "/mpc-" version ".tar.xz")) (sha256 (base32 - "1kkzhrypkp0v6xv4d6db415pd0h6jqki29kfpsnfkvrhhh55pz35")))) + "0b9bsn4sl26xc6wdcms51x9yxznkxkppaycn8gnv4rd1m21kwdv2")))) (build-system meson-build-system) (inputs `(("libmpdclient" ,libmpdclient))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("python-sphinx" ,python-sphinx))) (synopsis "Music Player Daemon client") (description "MPC is a minimalist command line interface to MPD, the music player daemon.") diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 5a0c464252..5504742fa8 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -538,7 +538,7 @@ and up to 1 Mbit/s downstream.") (define-public whois (package (name "whois") - (version "5.3.2") + (version "5.4.0") (source (origin (method url-fetch) @@ -546,7 +546,7 @@ and up to 1 Mbit/s downstream.") name "_" version ".tar.xz")) (sha256 (base32 - "0m3352d5b0ragygbqjbaimghrbx4va2rixa34j5a1g3jj6l4nwbr")))) + "0y73b3z1akni620s1hlrijwdrk95ca1c8csjds48vpd6z86awx9p")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no test suite diff --git a/gnu/packages/patches/meandmyshadow-define-paths-earlier.patch b/gnu/packages/patches/meandmyshadow-define-paths-earlier.patch new file mode 100644 index 0000000000..505cbd23fe --- /dev/null +++ b/gnu/packages/patches/meandmyshadow-define-paths-earlier.patch @@ -0,0 +1,50 @@ +From: Tobias Geerinckx-Rice <me@tobias.gr> +Date: Wed, 31 Oct 2018 02:24:26 +0100 +Subject: [PATCH] gnu: meandmyshadow: Define paths earlier. + +The following patch was taken verbatim from the upstream repository[0] +and will be included in the next release. + +[0]: https://github.com/acmepjz/meandmyshadow/pull/29 +--- +From 4847e6b5755258a1e0534f2d4b91dce2ce3b459e Mon Sep 17 00:00:00 2001 +From: Dmitry Marakasov <amdmi3@amdmi3.ru> +Date: Wed, 24 Oct 2018 23:31:19 +0300 +Subject: [PATCH] Define paths earlier in CMakeLists.txt + +At the very least, paths should be defined before Configure_File(), otherwise empty DATAROOTDIR is substituted in config.h +--- + CMakeLists.txt | 13 +++++++------ + 1 file changed, 7 insertions(+), 6 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index e79639a..6321d9d 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -2,6 +2,13 @@ Project (meandmyshadow) + CMake_Minimum_Required (VERSION 3.1)
+ Set (CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
++#Path options
++Set (BINDIR "bin" CACHE STRING "Where to install binaries")
++Set (DATAROOTDIR "${CMAKE_INSTALL_PREFIX}/share" CACHE STRING "Sets the root of data directories to a non-default location")
++Set (ICONDIR "${DATAROOTDIR}/icons" CACHE STRING "Sets the icon directory for desktop entry to a non-default location.")
++Set (DESKTOPDIR "${DATAROOTDIR}/applications" CACHE STRING "Sets the desktop file directory for desktop entry to a non-default location.")
++
++#Options
+ Option (DEBUG_MODE "Compile the game with debug mode enabled" OFF)
+ Option (DISABLED_DEBUG_STUFF "Enable this you'll see a lot of annoying script debug messages which will lag the game." OFF)
+
+@@ -164,12 +171,6 @@ Target_Link_Libraries ( + ${LUA_LIBRARIES}
+ )
+
+-#Path options
+-Set (BINDIR "bin" CACHE STRING "Where to install binaries")
+-Set (DATAROOTDIR "${CMAKE_INSTALL_PREFIX}/share" CACHE STRING "Sets the root of data directories to a non-default location")
+-Set (ICONDIR "${DATAROOTDIR}/icons" CACHE STRING "Sets the icon directory for desktop entry to a non-default location.")
+-Set (DESKTOPDIR "${DATAROOTDIR}/applications" CACHE STRING "Sets the desktop file directory for desktop entry to a non-default location.")
+-
+ #Install locations
+ Install (DIRECTORY ${PROJECT_SOURCE_DIR}/data DESTINATION ${DATAROOTDIR}/meandmyshadow/)
+ Install (FILES AUTHORS DESTINATION ${DATAROOTDIR}/meandmyshadow/)
diff --git a/gnu/packages/patches/myrepos-CVE-2018-7032.patch b/gnu/packages/patches/myrepos-CVE-2018-7032.patch deleted file mode 100644 index ce9493e5f9..0000000000 --- a/gnu/packages/patches/myrepos-CVE-2018-7032.patch +++ /dev/null @@ -1,69 +0,0 @@ -http://source.myrepos.branchable.com/?p=source.git;a=patch;h=40a3df21c73f1bb1b6915cc6fa503f50814664c8 -This can be removed with the next release. It was modified slightly to apply - -From 40a3df21c73f1bb1b6915cc6fa503f50814664c8 Mon Sep 17 00:00:00 2001 -From: Paul Wise <pabs3@bonedaddy.net> -Date: Sun, 11 Feb 2018 21:57:49 +0800 -Subject: [PATCH] Mitigate vulnerabilities caused by some git remotes being - able to execute code - -Set GIT_PROTOCOL_FROM_USER=0 with git versions newer than 2.12. - -Prevent remote websites from causing cloning of local repositories. - -Manually whitelist known-safe protocols (http, https, git, ssh) -when using git versions older than 2.12. - -Fixes: CVE-2018-7032 -Fixes: https://bugs.debian.org/840014 -Suggestions-by: Jakub Wilk <jwilk@jwilk.net> -Reported-by: Jakub Wilk <jwilk@jwilk.net> ---- - webcheckout | 22 +++++++++++++++++++++- - 1 file changed, 21 insertions(+), 1 deletion(-) - -diff --git a/webcheckout b/webcheckout -index e98da5c..de497ba 100755 ---- a/webcheckout -+++ b/webcheckout -@@ -71,6 +71,16 @@ use Getopt::Long; - use warnings; - use strict; - -+# Mitigate some git remote types being dangerous -+my $git_unsafe = 1; -+my $git_version = `git --version`; -+$git_version =~ s{^git version }{}; -+my ($major, $minor) = split(/\./, $git_version); -+if (int($major) >= 2 && int($minor) >= 12) { -+ $ENV{GIT_PROTOCOL_FROM_USER} = 0; -+ $git_unsafe = 0; -+} -+ - # What to download. - my $url; - -@@ -89,7 +99,17 @@ my $destdir; - - # how to perform checkouts - my %handlers=( -- git => sub { doit("git", "clone", shift, $destdir) }, -- svn => sub { doit("svn", "checkout", shift, $destdir) }, -- bzr => sub { doit("bzr", "branch", shift, $destdir) }, -+ git => sub { -+ my $git_url = shift; -+ # Reject unsafe URLs with older versions of git -+ # that do not already check the URL safety. -+ if ($git_unsafe && $git_url !~ m{^(?:(?:https?|git|ssh):[^:]|(?:[-_.A-Za-z0-9]+@)?[-_.A-Za-z0-9]+:(?!:|//))}) { -+ print STDERR "potentially unsafe git URL, may fail, touch local files or execute arbitrary code\n"; -+ return 1; -+ } -+ # Reject cloning local directories too, webcheckout is for remote repos -+ doit(qw(git -c protocol.file.allow=user clone --), $git_url, $destdir) -+ }, -+ svn => sub { doit(qw(svn checkout --), shift, $destdir) }, -+ bzr => sub { doit(qw(bzr branch --), shift, $destdir) }, - ); --- -2.11.0 - diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm index ad429854a2..bdb5dbbdad 100644 --- a/gnu/packages/pretty-print.scm +++ b/gnu/packages/pretty-print.scm @@ -244,7 +244,7 @@ seen in a terminal.") (define-public highlight (package (name "highlight") - (version "3.42") + (version "3.47") (source (origin (method url-fetch) @@ -252,7 +252,7 @@ seen in a terminal.") version ".tar.bz2")) (sha256 (base32 - "07iihzy8ckzdrxqd6bzbij4hy4mmlixibjnjviqfihd0hh1q30m5")))) + "0xidf8755lnx55x6p4ajgg4l145akjqswny41483fvg5lpa41i6f")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index f71b8a3467..1a70f943a3 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -637,7 +637,7 @@ PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") (define-public python-pynacl (package (name "python-pynacl") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) @@ -648,7 +648,7 @@ PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") #t)) (sha256 (base32 - "1ada3qr83cliap6dk897vnvjkynij1kjqbwizdbgarazlyh8zlz0")))) + "0330wyvggm19xhmwmz9rrr97lzbv3siwfy50gmax3vvgs7nh0q8c")))) (build-system python-build-system) (arguments `(#:phases diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fbb280224a..a65573fbb8 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12824,15 +12824,17 @@ embeddable JavaScript engine.") (define-public python-jsonrpclib-pelix (package (name "python-jsonrpclib-pelix") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (pypi-uri "jsonrpclib-pelix" version)) (sha256 (base32 - "1qs95vxplxwspbrqy8bvc195s58iy43qkf75yrjfql2sim8b25sl")))) + "0f83z5zi7w32vprhk1dyc94ir1bh4hdd57bjdbwkq9ykng8qilhl")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; no tests in PyPI tarball (home-page "https://github.com/tcalmant/jsonrpclib/") (synopsis "JSON-RPC 2.0 client library for Python") (description @@ -14433,14 +14435,14 @@ This Python package wraps the Blosc library.") (define-public python-partd (package (name "python-partd") - (version "0.3.8") + (version "0.3.9") (source (origin (method url-fetch) (uri (pypi-uri "partd" version)) (sha256 (base32 - "03s0i5qfgkx6y24bmfgyd5hnsjznkbbfafwb2khf7k9790f1yab7")))) + "0sz6rwlnl4fqq220pyz863cnv0gjdxl4m7lscl71ishl5z0xkmhz")))) (build-system python-build-system) (propagated-inputs `(("python-blosc" ,python-blosc) diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm index 3fa0e0242a..6198925727 100644 --- a/gnu/packages/sdl.scm +++ b/gnu/packages/sdl.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2017 Sou Bunnbu <iyzsong@member.fsf.org> ;;; Copyright © 2015 Alex Kost <alezost@gmail.com> ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> +;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> ;;; @@ -102,7 +102,7 @@ joystick, and graphics hardware.") (define-public sdl2 (package (inherit sdl) (name "sdl2") - (version "2.0.8") + (version "2.0.9") (source (origin (method url-fetch) (uri @@ -110,7 +110,7 @@ joystick, and graphics hardware.") version ".tar.gz")) (sha256 (base32 - "1v4js1gkr75hzbxzhwzzif0sf9g07234sd23x1vdaqc661bprizd")))) + "1c94ndagzkdfqaa838yqg589p1nnqln8mv0hpwfhrkbfczf8cl95")))) (arguments (substitute-keyword-arguments (package-arguments sdl) ((#:configure-flags flags) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 04979ffe25..3ca0d01d35 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -339,14 +339,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-50") + (version "7.3-51") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "16hasv9k4n773jsyzvh8s3gbga49hwdj8n5hxij6zqisy4i0kxq6")))) + "0yp5ssfm9mahrp30y1hkqgjg70mzs6w065ba8h7j5ky1z6msdsdy")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -532,14 +532,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-24") + (version "1.8-25") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "15b76m1f0hz8dbmj9shqvslihdx5b7c48vck9grj5xs1z2y45r9c")))) + "1y2rq6v45pr2wcxihhgmingcdvcsilim2cvskrlb7k2n00qg6v2q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -725,13 +725,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.16") + (version "0.6.18") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "1lhs59pdjhpb63jyy98pi1shk9shw044k6vl0mvw0f40v08326ar")))) + (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1059,13 +1059,13 @@ legends.") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.0.0") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "0kb977hizsvk3b1k3zr717q78bpmbabhl8cj9a3w717nkq1zas67")))) + (base32 "1msy36r21nlmnpyaw2m9k0ykmnd19b9il01b65w457pfw75prrs9")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -1249,16 +1249,14 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.11") + (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "1k8vcd4vsgg0hf7kdz8rlqp1dx4ygvg35aj4n3ay50kdnpzhaj5h")))) + "11rpn40153kcvqqrfhg2ldqfs68frg6yzsl0k3rxnlnv4c0v008g")))) (build-system r-build-system) - (propagated-inputs - `(("r-stringr" ,r-stringr))) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") (description @@ -1310,13 +1308,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw")))) + "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") @@ -1423,13 +1421,13 @@ from knitr Rmarkdown.") (define-public r-microbenchmark (package (name "r-microbenchmark") - (version "1.4-4") + (version "1.4-6") (source (origin (method url-fetch) (uri (cran-uri "microbenchmark" version)) (sha256 (base32 - "0fv2w2vsiz18imf4115nd9chhmf275w2mb49pn7pkxi6z3bamc9c")))) + "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/microbenchmark/") (synopsis "Accurate timing functions for R") @@ -1526,13 +1524,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v")))) + "1cafy5xsjx6m08s45456mjsal7mfxzwpbrds0p4z3gwam948gpzy")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -1553,13 +1551,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.2.2") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8")))) + "1jgshp0x8a65rwyvk31slnfp7l153dk5826y2rxcd5lpclby3d85")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1575,13 +1573,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.2.2") + (version "0.3.0.1") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0cqd894wzi53rs53prg0j7i75h0yzgi0127fzjqbdbhczwh984f9")))) + "0j7kp6h25wbkvpzr7dpc0zgdpjiwsjjlgprj3mv7bgfalfq1si99")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1617,13 +1615,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.7.6") + (version "0.7.7") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0c43h13s5mr0fklikbbm89gs6z5n66rkjzdv6w3w6kl5af5wr2fl")))) + "196lwck3i3m25jnn1f1nrda9svnjqqi89s0is79gbrphamddnlq5")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -1767,13 +1765,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.11.4") + (version "1.11.8") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "1mc1drqj5i5ar2za3nkh5j70y37s7z7xwqri2r2b72zkqggg3k7x")))) + "1nb6wngrk1a30m984524gf26fa1nwgyf4y4an94dibcwb5jp8hnw")))) (build-system r-build-system) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") @@ -1913,13 +1911,13 @@ inference for statistical models.") (define-public r-coda (package (name "r-coda") - (version "0.19-1") + (version "0.19-2") (source (origin (method url-fetch) (uri (cran-uri "coda" version)) (sha256 (base32 - "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) + "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -2212,14 +2210,14 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "1jwx5rgm0ypd9a3v4jd9za4a644rdzhk1n4dvmgkj9hdpwsida3z")))) + "1xymqncf8byqxzpx64zlp6vbx7gry572jkr2ax0zlavr8bli861x")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") @@ -2350,13 +2348,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5")))) + "0d6r0in13k0rcyr6asanwy0a9dv4lizq6l2w913rr222pq6vrrck")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") @@ -2368,22 +2366,29 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.13.6") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "1d9n49djydywfyp9w3njgxs5lag4ac7719wmxy1lkgcmn3l9sx5r")))) + "1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) + `(("r-callr" ,r-callr) + ("r-cli" ,r-cli) + ("r-digest" ,r-digest) ("r-git2r" ,r-git2r) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-memoise" ,r-memoise) + ("r-pkgbuild" ,r-pkgbuild) + ("r-pkgload" ,r-pkgload) + ("r-rcmdcheck" ,r-rcmdcheck) + ("r-remotes" ,r-remotes) ("r-rstudioapi" ,r-rstudioapi) - ("r-whisker" ,r-whisker) + ("r-sessioninfo" ,r-sessioninfo) + ("r-usethis" ,r-usethis) ("r-withr" ,r-withr))) (home-page "https://github.com/hadley/devtools") (synopsis "Tools to make developing R packages easier") @@ -2459,13 +2464,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.7-3") + (version "3.7-4") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "18702y1gbyis56mh219z5ww0nrkh6qx7bgqv3khyn80g2giwk7cf")))) + "1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2942,13 +2947,13 @@ multiple breakpoints are allowed.") (define-public r-snow (package (name "r-snow") - (version "0.4-2") + (version "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "snow" version)) (sha256 (base32 - "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf")))) + "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/snow") (synopsis "Support for simple parallel computing in R") @@ -3034,14 +3039,14 @@ parallel.") (define-public r-doparallel (package (name "r-doparallel") - (version "1.0.11") + (version "1.0.14") (source (origin (method url-fetch) (uri (cran-uri "doParallel" version)) (sha256 (base32 - "0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc")))) + "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb")))) (properties `((upstream-name . "doParallel"))) (build-system r-build-system) (propagated-inputs @@ -3634,14 +3639,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw")))) + "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw")))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue) @@ -4231,13 +4236,13 @@ mechanism.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-3") + (version "1.8-4") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "15jmkgwvq2mm9f09vijgx7sff8pszh90fndcwhk2vw9i0p183di0")))) + "1pywcp86kqijdrvl42qwdy75szrag9pzj0p88zbrj2r1klb8rn5i")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -4735,14 +4740,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-2") + (version "0.93-3") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "1632p73iv9iqqm0v3k9rfv9way0him3fl35si1nly9wi5kpq5ci7")))) + "1nqh1qg1qd1qrxl1w585dqx7ql55qzjny1r4f9hqxpwd7lml07cc")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -5084,17 +5089,19 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "1.0.4") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4")))) + "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("r-knitr" ,r-knitr) ; for building vignettes + ("pkg-config" ,pkg-config) + ("gfortran" ,gfortran))) (inputs `(("nlopt" ,nlopt))) (home-page "https://cran.r-project.org/web/packages/nloptr") @@ -5165,14 +5172,14 @@ bootstrap test for generalized linear mixed models.") (define-public r-cardata (package (name "r-cardata") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "carData" version)) (sha256 (base32 - "193pdwgw6gk19v7swk1kwphg3vqdmpsgi555g9nyz93sa39j7r8j")))) + "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v")))) (properties `((upstream-name . "carData"))) (build-system r-build-system) (home-page "https://r-forge.r-project.org/projects/car/") diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 8780bb2829..084017dbde 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -338,7 +338,7 @@ as existing hashing techniques, with provably negligible risk of collisions.") (define-public oniguruma (package (name "oniguruma") - (version "6.8.2") + (version "6.9.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/kkos/" @@ -346,7 +346,7 @@ as existing hashing techniques, with provably negligible risk of collisions.") "/onig-" version ".tar.gz")) (sha256 (base32 - "00s9gjgb3srn5sbmx4x9bssn52mi04d868ghizssdhjlddgxmsmd")))) + "1jg76i2ksf3s4bz4h3g2f9ac19q31lzxs11j900w7qqc0mgb5gwi")))) (build-system gnu-build-system) (home-page "https://github.com/kkos/oniguruma") (synopsis "Regular expression library") diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index ccb1f5dacc..df0b2f0122 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1730,7 +1730,7 @@ modification time.") (define-public myrepos (package (name "myrepos") - (version "1.20171231") + (version "1.20180726") (source (origin (method git-fetch) @@ -1739,8 +1739,7 @@ modification time.") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 - (base32 "10q7lpx152xnkk701fscn4dq99q9znnmv3bc2482khhjg7z8rps0")) - (patches (search-patches "myrepos-CVE-2018-7032.patch")))) + (base32 "0jphw61plm8cgklja6hs639xhdvxgvjwbr6jpvjwpp7hc5gmhms5")))) (build-system gnu-build-system) (inputs `(("perl" ,perl))) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 4fcd15e4aa..34af248eb7 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -67,6 +67,7 @@ #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages assembly) #:use-module (gnu packages audio) #:use-module (gnu packages autotools) #:use-module (gnu packages avahi) @@ -96,6 +97,7 @@ #:use-module (gnu packages glib) #:use-module (gnu packages guile) #:use-module (gnu packages gnome) + #:use-module (gnu packages gnunet) #:use-module (gnu packages gnupg) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) @@ -139,8 +141,7 @@ #:use-module (gnu packages xdisorg) #:use-module (gnu packages xiph) #:use-module (gnu packages xml) - #:use-module (gnu packages xorg) - #:use-module (gnu packages assembly)) + #:use-module (gnu packages xorg)) (define-public aalib (package @@ -2911,25 +2912,27 @@ It counts more than 100 plugins.") (define-public motion (package (name "motion") - (version "4.1.1") + (version "4.2") (home-page "https://motion-project.github.io/") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Motion-Project/motion/archive/" - "release-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/Motion-Project/motion.git") + (commit (string-append "release-" version)))) (sha256 (base32 - "1qm4i8zrqafl60sv2frhixvkd0wh0r5jfcrj5i6gha7yplsvjx10")) - (file-name (string-append name "-" version ".tar.gz")))) + "0c0q6dl4v561m5y8bp0c0h4p3s52fjgcdnsrrf5ygdi288d3rfxv")) + (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf-wrapper) ("automake" ,automake) + ("gettext" ,gettext-minimal) ("pkg-config" ,pkg-config))) (inputs `(("libjpeg" ,libjpeg) ("ffmpeg" ,ffmpeg-3.4) + ("libmicrohttpd" ,libmicrohttpd) ("sqlite" ,sqlite))) (arguments '(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 29d03f6a15..447a899544 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3874,13 +3874,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.10") + (version "0.11") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0yz3igqsiyqnjj1ngh199zicg3spx4kbmvl0wc8i8xahk6l9g06v")))) + "0yj3p1risf269n25dd56lqv82dsxv6a0aq4bcc1ddn9wv7h2xdfi")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) @@ -3932,13 +3932,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "04c4d0mfcy3dkdlbxnaccpdgxvyxfdwfmmh5djim6v9hyg0j2z8s")))) + "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -5607,13 +5607,13 @@ responsive, and powerful applications with minimal effort.") (define-public r-shinydashboard (package (name "r-shinydashboard") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 - "10yqcqqcxgfqwkmscqwvvgr710im583qsqnsqkfpisjvkqp10yqb")))) + "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. @@ -5633,6 +5633,7 @@ responsive, and powerful applications with minimal effort.") (dump-port minified port)))))))))) (propagated-inputs `(("r-htmltools" ,r-htmltools) + ("r-promises" ,r-promises) ("r-shiny" ,r-shiny))) (native-inputs `(("uglify-js" ,uglify-js))) @@ -5645,6 +5646,35 @@ application framework for R, making it easy to create attractive dashboards.") ;; later. (license l:gpl2+))) +(define-public r-shinyfiles + (package + (name "r-shinyfiles") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyFiles" version)) + (sha256 + (base32 + "1cbg09l7w2zbgxb4qjm9p873p0lzrihlzsk5xxi3cpxdckn6zsrm")))) + (properties `((upstream-name . "shinyFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fs" ,r-fs) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/thomasp85/shinyFiles") + (synopsis "Server-side file system viewer for Shiny") + (description + "This package provides functionality for client-side navigation of the +server side file system in shiny apps. In case the app is running locally +this gives the user direct access to the file system without the need to +\"download\" files to a temporary location. Both file and folder selection as +well as file saving is available.") + (license l:gpl2+))) + (define-public r-crosstalk (package (name "r-crosstalk") diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index c5238a8a65..d1890c8b32 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -143,14 +143,14 @@ HTML/CSS applications to full-fledged web browsers.") (define-public webkitgtk-2.22 (package/inherit webkitgtk (name "webkitgtk") - (version "2.22.2") + (version "2.22.3") (source (origin (method url-fetch) (uri (string-append "https://www.webkitgtk.org/releases/" name "-" version ".tar.xz")) (sha256 (base32 - "1flrbr8pzbrlwv09b4pmgh6vklw7jghd2lgrhcb72vl9s7a8fm1l")))) + "0wnddhm2bihmmkmi919lyxskvjk2wrzx6azkiypyjfwm08lm9zcx")))) (native-inputs `(("gcc" ,gcc-7) ; webkitgtk-2.22 requires gcc-6 or newer ,@(package-native-inputs webkitgtk))) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 169cc6e3c5..60b2a81de8 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -225,7 +225,7 @@ integrate Windows applications into your desktop.") (define-public wine-staging-patchset-data (package (name "wine-staging-patchset-data") - (version "3.18") + (version "3.19") (source (origin (method git-fetch) @@ -235,7 +235,7 @@ integrate Windows applications into your desktop.") (file-name (git-file-name name version)) (sha256 (base32 - "18g1lmqzkc7ngppynimfvza1gkdhqlnjbvnckmaws847ns4i0kzp")))) + "0nmlhc6jamz0zb4b1w165l8j1a1b0j5ad1sv06aasc9jy8s12b22")))) (build-system trivial-build-system) (native-inputs `(("bash" ,bash) @@ -281,7 +281,7 @@ integrate Windows applications into your desktop.") (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "0xqs76hxcym8nb95r7l72xx0msbscp7fhkr1wrv4r0923d5x9s4v")))) + "0slwgbxclx2dx0glj8az3mv0bqxmx119v9s0jvg1b5zhmqkcc8gg")))) (inputs `(("autoconf" ,autoconf) ; for autoreconf ("gtk+" ,gtk+) ("libva" ,libva) diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm index 9a1bece63f..43b0d2723a 100644 --- a/gnu/packages/xiph.scm +++ b/gnu/packages/xiph.scm @@ -441,7 +441,7 @@ encoding Opus files and streams.") (define-public icecast (package (name "icecast") - (version "2.4.3") + (version "2.4.4") (source (origin (method url-fetch) (uri (string-append @@ -449,7 +449,7 @@ encoding Opus files and streams.") version ".tar.gz")) (sha256 (base32 - "14n5vm2xnyn8y7kl46lnnlgv6v5fjykhc57ffdsh0qaxfs6a8p68")))) + "0i2d9rhav0x6js2qhjf5iy6j2a7f0d11ail0lfv40hb1kygrgda9")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 6f9c266fff..a4909d4a69 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5936,7 +5936,7 @@ basic eye-candy effects.") (define-public xpra (package (name "xpra") - (version "2.4") + (version "2.4.1") (source (origin (method url-fetch) @@ -5944,7 +5944,7 @@ basic eye-candy effects.") version ".tar.xz")) (sha256 (base32 - "0blzx231sr1ri1zwzpwzf611sq9104bv3ccvnap9pbvfrc05sfwx")))) + "1bhk6vydsrhlngvrv5w55arqf69cr3yw84xscnnl7km2g1iswkrs")))) (build-system python-build-system) (inputs `(("ffmpeg" ,ffmpeg) ("flac" ,flac) |