diff options
-rw-r--r-- | gnu/local.mk | 6 | ||||
-rw-r--r-- | gnu/packages/admin.scm | 4 | ||||
-rw-r--r-- | gnu/packages/bioconductor.scm | 110 | ||||
-rw-r--r-- | gnu/packages/bioinformatics.scm | 53 | ||||
-rw-r--r-- | gnu/packages/cran.scm | 156 | ||||
-rw-r--r-- | gnu/packages/fontutils.scm | 8 | ||||
-rw-r--r-- | gnu/packages/gl.scm | 3 | ||||
-rw-r--r-- | gnu/packages/java.scm | 55 | ||||
-rw-r--r-- | gnu/packages/linux.scm | 9 | ||||
-rw-r--r-- | gnu/packages/patches/jdk-currency-time-bomb.patch | 13 | ||||
-rw-r--r-- | gnu/packages/patches/jdk-currency-time-bomb2.patch | 13 | ||||
-rw-r--r-- | gnu/packages/patches/openjdk-currency-time-bomb.patch | 13 | ||||
-rw-r--r-- | gnu/packages/patches/openjdk-currency-time-bomb2.patch | 13 | ||||
-rw-r--r-- | gnu/packages/python-science.scm | 3 | ||||
-rw-r--r-- | gnu/packages/serialization.scm | 7 | ||||
-rw-r--r-- | gnu/packages/statistics.scm | 34 | ||||
-rw-r--r-- | gnu/packages/video.scm | 101 | ||||
-rw-r--r-- | gnu/packages/vim.scm | 4 |
18 files changed, 410 insertions, 195 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 62066a30dc..f1bdfc73e9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -7,7 +7,7 @@ # Copyright © 2016, 2017, 2018 Kei Kebreau <kkebreau@posteo.net> # Copyright © 2016, 2017 Rene Saavedra <rennes@openmailbox.org> # Copyright © 2016 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org> -# Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> +# Copyright © 2016-2024 Ricardo Wurmus <rekado@elephly.net> # Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> # Copyright © 2016, 2017, 2018, 2019 Alex Vong <alexvong1995@gmail.com> # Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il> @@ -1489,6 +1489,8 @@ dist_patch_DATA = \ %D%/packages/patches/java-xerces-build_dont_unzip.patch \ %D%/packages/patches/java-xerces-xjavac_taskdef.patch \ %D%/packages/patches/jbr-17-xcursor-no-dynamic.patch \ + %D%/packages/patches/jdk-currency-time-bomb.patch \ + %D%/packages/patches/jdk-currency-time-bomb2.patch \ %D%/packages/patches/jfsutils-add-sysmacros.patch \ %D%/packages/patches/jfsutils-gcc-compat.patch \ %D%/packages/patches/jfsutils-include-systypes.patch \ @@ -1741,6 +1743,8 @@ dist_patch_DATA = \ %D%/packages/patches/openboardview-use-system-mpc.patch \ %D%/packages/patches/openbox-python3.patch \ %D%/packages/patches/opencolorio-fix-build-with-gcc11.patch \ + %D%/packages/patches/openjdk-currency-time-bomb.patch \ + %D%/packages/patches/openjdk-currency-time-bomb2.patch \ %D%/packages/patches/openjdk-9-pointer-comparison.patch \ %D%/packages/patches/openjdk-9-setsignalhandler.patch \ %D%/packages/patches/openjdk-10-idlj-reproducibility.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 3f1de1e6b6..fcf05992d8 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -746,7 +746,7 @@ console.") (define-public btop (package (name "btop") - (version "1.2.13") + (version "1.3.0") (source (origin (method git-fetch) (uri (git-reference @@ -755,7 +755,7 @@ console.") (file-name (git-file-name name version)) (sha256 (base32 - "0aggzlxyfp213rknpbhkn8wbgzcnz181dyh9m2awz72w705axy8p")))) + "0fbrkzg03n2vamg1pfzdb8wxm3xffy6gp4izhqppl45zngy3c0s1")))) (build-system gnu-build-system) (arguments (list #:tests? #f ;no test suite diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7af5c42ce..69e6677062 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -157,6 +157,25 @@ descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.") (license license:artistic2.0))) +(define-public r-jaspar2020 + (package + (name "r-jaspar2020") + (version "0.99.10") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "JASPAR2020" version 'annotation)) + (sha256 + (base32 "0nrp63z7q2ivv5h87f7inpp2qll2dfgj4227l4rbnzii38a2vfdr")))) + (properties `((upstream-name . "JASPAR2020"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://jaspar.elixir.no/") + (synopsis "Data package for JASPAR database (version 2020)") + (description "Data package for JASPAR2020. To explore these databases, +utilize the TFBSTools package (version 1.23.1 or higher).") + (license license:gpl2))) + (define-public r-mafh5-gnomad-v3-1-2-grch38 (package (name "r-mafh5-gnomad-v3-1-2-grch38") @@ -1127,6 +1146,46 @@ Ensembl.") Ensembl.") (license license:artistic2.0))) +(define-public r-escape + (package + (name "r-escape") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "escape" version)) + (sha256 + (base32 "0bmin69ax7l5x3a0k9mv183277a0hl4znx02y79v2ilkgqkdm7fn")))) + (properties `((upstream-name . "escape"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel + r-broom + r-data-table + r-dplyr + r-ggplot2 + r-ggridges + r-gseabase + r-gsva + r-matrix + r-matrixgenerics + r-msigdbr + r-patchwork + r-reshape2 + r-rlang + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/escape") + (synopsis "Single cell analysis platform for enrichment") + (description + "R-escape streamlines gene set enrichment analysis for single-cell RNA +sequencing. Using raw count information, Seurat objects, or +@code{SingleCellExperiment} format, users can perform and visualize GSEA +across individual cells.") + (license license:gpl2))) + (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") @@ -5599,6 +5658,35 @@ identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-limma from Bioconductor. +(define-public r-dsb + (package + (name "r-dsb") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dsb" version)) + (sha256 + (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2")))) + (properties `((upstream-name . "dsb"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-magrittr r-mclust)) + (native-inputs (list r-knitr r-rmarkdown)) + (home-page "https://github.com/niaid/dsb") + (synopsis + "Normalize & denoise droplet single cell protein data (CITE-Seq)") + (description + "R-dsb improves protein expression analysis in droplet-based single-cell +studies. The package specifically addresses noise in raw protein UMI counts +from methods like CITE-seq. It identifies and removes two main sources of +noise—protein-specific noise from unbound antibodies and droplet/cell-specific +noise. The package is applicable to various methods, including CITE-seq, +REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette +for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb +in Python.") + (license license:cc0))) + (define-public r-dss (package (name "r-dss") @@ -7324,13 +7412,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.5") + (version "4.0.6") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "16cghh83v14jdq5n6xkm3jxj87n6l6zrxjgqdwb2ffgc26vkpb7w")))) + "0vksak7rv0agar0gplpj2fcp3183l3iyvbqjmx64c7dwpzjh3lb5")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7668,13 +7756,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "06xa3dcdk6jprvpyvr3pfbv6qv8xrqw2n6rrfp8q8qizx3ifj431")))) + "0y54kdgb77xqni46pgff1by2ska2jaxfcpq6gk86wb2rym37wlxj")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -13131,14 +13219,14 @@ accessiblity for new Bioconductor users is hopefully increased.") (define-public r-inspect (package (name "r-inspect") - (version "1.31.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0c7bw9cnav41vals2scv2gh5mj5nx2mgzagdb8g99sprdqv5924n")))) + "04znack6p50cmc2qyk4hf45m6v70p0bv7h3xs87j0x0h4mb920ch")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -13147,7 +13235,6 @@ accessiblity for new Bioconductor users is hopefully increased.") r-biocparallel r-deseq2 r-desolve - r-gdata r-genomeinfodb r-genomicalignments r-genomicfeatures @@ -13156,6 +13243,7 @@ accessiblity for new Bioconductor users is hopefully increased.") r-kernsmooth r-plgem r-proc + r-readxl r-rootsolve r-rsamtools r-rtracklayer @@ -13229,14 +13317,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j")))) + "0lvsw920i75di5pwq7yvk8wcxp01wrh7863xmwbrmk5jrvl3y4h4")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -21322,13 +21410,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0s7m3qdbgrqaq93k6rvyj34h36kdjvppn9ilflrcaa5w498fzfhf")))) + (base32 "0zlv45diasff5ipxp99dddswclrzzdcmkqp278fm2cj7aibvb3sd")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7dbebcf3da..f574fea0e9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2110,6 +2110,29 @@ matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.") (license license:expat))) +(define-public python-parabam + (package + (name "python-parabam") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "parabam" version)) + (sha256 + (base32 "1cy9q3gzdawi1kilycpd7waymjmrwsg8czwycfp13g301ir9xyp3")) + (modules '((guix build utils))) + (snippet + '(substitute* "setup.py" + (("'argparse',") ""))))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-pysam)) + (home-page "https://github.com/cancerit/parabam") + (synopsis "Parallel BAM File Analysis") + (description "Parabam is a tool for processing sequencing files in +parallel. It uses Python's native multiprocessing framework to apply a user +defined rule on an input file.") + (license license:gpl3))) + (define-public python-peaks2utr (package (name "python-peaks2utr") @@ -2424,6 +2447,30 @@ operations: @end itemize") (license license:asl2.0))) +(define-public python-telomerecat + (package + (name "python-telomerecat") + (version "4.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "telomerecat" version)) + (sha256 + (base32 "16mfdqmp0j6g3h26h59334w9lqb4qihqrlzwvgznj0fiqs1rkxn2")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-click python-numpy python-pandas + python-parabam python-pysam)) + (home-page "https://github.com/cancerit/telomerecat") + (synopsis "Telomere computational analysis tool") + (description "Telomerecat is a tool for estimating the average telomere +length (TL) for a paired end, whole genome sequencing (WGS) sample. + +Telomerecat is adaptable, accurate and fast. The algorithm accounts for +sequencing amplification artifacts, anneouploidy (common in cancer samples) +and noise generated by WGS. For a high coverage WGS BAM file of around 100GB +telomerecat can produce an estimate in ~1 hour.") + (license license:gpl3))) + (define-public python-bioframe (package (name "python-bioframe") @@ -20309,11 +20356,11 @@ translates between different variant encodings.") (license license:asl2.0)))) (define-public r-signac - (let ((commit "af4142724b72574d957f7fe3d422ed5828ec3ad0") + (let ((commit "8ecdde291676102bb3b503f48926c993354b5471") (revision "1")) (package (name "r-signac") - (version (git-version "1.9.0" revision commit)) + (version (git-version "1.12.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -20322,7 +20369,7 @@ translates between different variant encodings.") (file-name (git-file-name name version)) (sha256 (base32 - "0ps0lp1dcy20r6lakil6ih81m04r0s6fnirvfjf01sfs0gsyddww")))) + "0idkcqb1i13m164nxbdwgs3vflw0cxzm2ir84aw0i811vx9lqz8c")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) (inputs (list zlib)) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 85c527dc32..95bd62b5a7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -290,16 +290,17 @@ automatically pruning objects to maintain the constraints.") (define-public r-castor (package (name "r-castor") - (version "1.7.11") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "castor" version)) (sha256 (base32 - "1cxjgwbsacjcc10qdch6pndjxqnk20hhamxqg0lckszvkyb67yn3")))) + "0caw206hndfzypj33w6npvppdc5hhq1q71wriqd0ck9f238rfi3c")))) (properties `((upstream-name . "castor"))) (build-system r-build-system) - (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra)) + (propagated-inputs (list r-jsonlite r-matrix r-naturalsort r-rcpp + r-rspectra)) (home-page "https://cran.r-project.org/package=castor") (synopsis "Efficient phylogenetics on large trees") (description @@ -2117,13 +2118,13 @@ known as Dynamic Linear Models.") (define-public r-zcompositions (package (name "r-zcompositions") - (version "1.5") + (version "1.5.0-1") (source (origin (method url-fetch) (uri (cran-uri "zCompositions" version)) (sha256 (base32 - "1hfgw3h3si5qkynzc520648pskw26bckcji1qgi5fkag6fd8l08p")))) + "0sx6i03iyg4jxmjiyzkssz3i6c8nv29wwhbl7yd0wxapwpakmlj8")))) (properties `((upstream-name . "zCompositions"))) (build-system r-build-system) (propagated-inputs @@ -2268,14 +2269,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.5.5") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0nysan87vgy0pbcks3bychm84zcwx9pf4p250b45ghimhvxh5cvm")))) + "0xnjbxd1lkg85c2hsx7cgxqsqb3dc0pma8jwdlqfgg7d519d60xa")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -3485,13 +3486,13 @@ read a protected key.") (define-public r-astsa (package (name "r-astsa") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "astsa" version)) (sha256 - (base32 "0rv4fnz5bbd6f8b6fwa2ljdjq5yx0qi7hcbhrgvrbibl2pzfm7w7")))) + (base32 "0rnbacq5vbnlzfssj13ixgkg0d1wixh2m3dcsi66c63wx65rm3d3")))) (properties `((upstream-name . "astsa"))) (build-system r-build-system) (home-page "https://github.com/nickpoison/astsa/") @@ -3788,14 +3789,14 @@ sources.") (define-public r-reprex (package (name "r-reprex") - (version "2.0.2") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "14khx09yzn97xhags48lvym1g37h1l2ymvw6r1jlldhjc7i1cnx8")))) + "0ld90pkw2r7z115xdnyqk4p39vnxrc8jnn57sl4bkpg5frczw38a")))) (build-system r-build-system) (propagated-inputs (list r-callr @@ -5981,14 +5982,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.6.2") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx")))) + "1p4699p68k9f8d76bmgx5xabay6xjrcgajckzqxyn6icym8ipx8s")))) (build-system r-build-system) (properties ;; knitr depends on glue, so we can't add knitr here to build the @@ -6267,13 +6268,13 @@ value for each cluster in a dendrogram.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.11") + (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "0pzssba79z90rax2v02r5m1a6ysljfnvq03r6q2nr72rd0q7qxfz")))) + (base32 "1l1b0q2r6q2bjr4wvj98kp9844fyrsn2ppx339v05vmy8g65jwqc")))) (build-system r-build-system) (home-page "https://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -8356,20 +8357,20 @@ similar to finite mixture models.") (define-public r-rpostgresql (package (name "r-rpostgresql") - (version "0.7-5") + (version "0.7-6") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 - "18czy93l9dg321pbvrfmlwrjahpbkiw0sll4pkkqm55xapp02m3b")))) - (properties `((upstream-name . "RPostgreSQL"))) + "0b1dmx5pcd4v1xg25ihxilkga3zdblb1xy896ik5fdkaidq3jn9q")))) + (properties + '((upstream-name . "RPostgreSQL") + (updater-extra-inputs . ("postgresql")))) (build-system r-build-system) - (inputs - (list postgresql)) - (propagated-inputs - (list r-dbi)) + (inputs (list postgresql)) + (propagated-inputs (list r-dbi)) (home-page "https://github.com/tomoakin/RPostgreSQL") (synopsis "R interface to the PostgreSQL database system") (description @@ -8733,14 +8734,14 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.9.4") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "0gngsx87rcqijdr684bgpnazdlz3vj4brzw0fic0jdsrf1rb9aw1")))) + "1alcrw304bn6c2i64rxxjkzk3il19gq30gyj3sb4blradkjh1rni")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales r-withr)) @@ -14236,13 +14237,13 @@ libxlsxwriter.") (define-public r-writexls (package (name "r-writexls") - (version "6.4.0") + (version "6.5.0") (source (origin (method url-fetch) (uri (cran-uri "WriteXLS" version)) (sha256 (base32 - "1dqr98kx930y6mcvb9b39xiwshhs250gkd2vw2v6iil34sl90jv4")))) + "1rkc0r6l7cfz7h83i7gw6g0nlyy347mdh6bj73j0f8mdv3nmwwn4")))) (properties `((upstream-name . "WriteXLS"))) (build-system r-build-system) (inputs (list perl)) @@ -16136,13 +16137,13 @@ handle data from simple random samples as well as complex surveys.") (define-public r-tarchetypes (package (name "r-tarchetypes") - (version "0.7.10") + (version "0.7.11") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 - "14k9p98yv5vgpi1bxngqzmaibdx9h7wyn8k1hw5imvlg4cbwm675")))) + "1iqrz27n8ndazx97ngqbz5yz5ppyimpbxam30zgdwnnzf963s5ym")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) (propagated-inputs (list r-digest @@ -16170,13 +16171,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "0nbvyh1v88lz1fv09ap9p6qw4zw23f1rvmv2f01w1r17z53z7w3c")))) + "0kax8nj66jbcp8sbv7zl68hzf4clz5m50fibrcypnzvpamhafw1q")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url @@ -21690,14 +21691,14 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "2.0-6") + (version "2.0-7") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "0d0wlrwfpjvz02cwrqpg5bnrf8isz359dl9qqxn9yb6czpmp9ls5")))) + "1j1qa0lkb7ywh0q79dklhw4gvkxgvk3qhw3rx9srrlrc7jv22hml")))) (build-system r-build-system) (propagated-inputs (list r-bayesm r-mass r-robustbase r-tensora)) @@ -24037,14 +24038,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "0pjm4fnc30kv8xl6akh9y0jpqdsww83558cvyfl4j3xxnafrk8cs")))) + "0yh29d28i67z3wyif72lr35ki92rqv6rljdjwj28559f7n864yjv")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (propagated-inputs @@ -24533,14 +24534,14 @@ graphics using Vega.") (define-public r-gbm (package (name "r-gbm") - (version "2.1.8.1") + (version "2.1.9") (source (origin (method url-fetch) (uri (cran-uri "gbm" version)) (sha256 (base32 - "02z85d7zp3i5x8r8q005hyw2rx1ck7lw81q7a3lqwraj8l95c94d")))) + "1r5d8mkg4z14l3743h39r35r0qqjx5p40ixdkcc5iyjab0fzm24x")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-survival)) @@ -26498,14 +26499,14 @@ on graphs of millions of nodes (as long as they can fit in memory).") (define-public r-patchwork (package (name "r-patchwork") - (version "1.1.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 - "07npkbalfl2d9aix02m2srxgmd8ymar6v0x65ighg3nq9d7l4xp9")))) + "18b83gsv8idi5d062m9dvb46r7kxda97sa72pzllshhcaq9ylcfc")))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-gtable r-rlang)) @@ -31133,18 +31134,19 @@ machine learning, visually representing text and text analyses, and more.") (define-public r-topicmodels (package (name "r-topicmodels") - (version "0.2-15") + (version "0.2-16") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 - "1l3pmz6n0sd57bf3d16m9766285d2pmndmv36rf5pffpwiw0zdbi")))) - (properties `((upstream-name . "topicmodels"))) + "01g9avk0ldqnz15n8112vad31c1n7r6rih5dh6x3383vvmjrqp0d")))) + (properties + '((upstream-name . "topicmodels") + (updater-extra-inputs . ("gsl")))) (build-system r-build-system) - (inputs - (list gsl)) + (inputs (list gsl)) (propagated-inputs (list r-modeltools r-slam r-tm)) (home-page "https://cran.r-project.org/package=topicmodels") @@ -31432,14 +31434,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.26.28") + (version "2.32.5") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1s1xgvn5c1vjikm1dx9g0qm2k8m24clylgp7zssmfhx6sfb8v2lk")))) + "0wqps6xy2xypxsg3p3grdiw67a0xla3vh9x9hcf2ln03yhgkn4jl")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) @@ -32190,15 +32192,17 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.32.3") + (version "2.32.5") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "17alp92kj9mnlkzplk7zd83sv2zi2h7yc44fx5f7nz3dpwd9x7d2")))) - (properties `((upstream-name . "rstan"))) + "0m655pf0lrhqh2mzylximd2vch9wy252k4zwyfqn1sfwmx642dva")))) + (properties + '((upstream-name . "rstan") + (updater-extra-native-inputs . ("tzdata-for-tests")))) (build-system r-build-system) (arguments `(#:phases @@ -37115,13 +37119,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.17.1") + (version "0.17.2") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0q6px0l0ab3xcrf6ylnw9a3i50mnks3hlgqj424d6bpqdjqyh5s4")))) + "0kcny3wxc7qc2538hxxdzs9bw4pq55s4abhlnpf1r13b2gkns323")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -39518,14 +39522,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.6.4") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1pzgwljrk3maxcbmiy3yiccijm6c2ach8f9kzpqr7w5k5vkyhpvx")))) + "05rld34brjc32p9f9cbqyyh208rh9idnyih33cpw7bz7bfyicnqm")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -39549,14 +39553,14 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "0skfya3m9i36dd0jqvnnc72k1h3lb4s3fjkvg7na6aq6xgpjh4jv")))) + "1380waqavwga17fvdzfpag4snzynkykh3pnia5bi73476y7myj5h")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) @@ -39597,13 +39601,13 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "13i5yi23xsrks1dsw0k3cqzr2gqj8p23yajb3a7drim6d4rpsaxl")))) + (base32 "177q7x8l9asyidpc7j20xwpyk0bd9x9m20cy4qzlnnmr14anyvjm")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs @@ -39619,13 +39623,13 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "0v3ng20vrp5cvpbgipwwpvyhi995n2rp8jls0kklkrjax41x62cn")))) + (base32 "0qz5kps9819yfqjdqjmv7wx70ll7xayfxmd5dc867k14i41f91cm")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs @@ -39641,14 +39645,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "0hilnczvamdv3bi1v6hdki05h8qqh0wlgvh5ilh09113005fpz98")))) + "1sgzp0yr1jsmbyzyk26m762rhpxb89wrwqqvrrw3xr1ib0cg06ah")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) @@ -39665,14 +39669,14 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") (define-public r-paws-security-identity (package (name "r-paws-security-identity") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 - "081339201j19y8y28h0dhr876ii82zpfyqddc21lvmg27z53hj4x")))) + "01gh761ykc4h81whn649bm28b01njqm1kjqkn9l4n7hhnalddy06")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) @@ -39690,14 +39694,14 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "1x7ix8x0ks357b7gf2skixsd0najjbn8hnq7p6a354p5h7bz39b4")))) + "07nwa39mn749a9rqb683wf19kd8si7ksws87annbldmd57r072l8")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) @@ -39714,14 +39718,14 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "0cwmriprwrz446q4d5ljkpvwdhmamnl98g1ks6p35vbjiv4imk21")))) + "0zcw758xsw2360571dj215gyd1amaxx07i58h1r6r5zys940lxis")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) @@ -39738,14 +39742,14 @@ natural language processing, speech recognition, translation, and more.") (define-public r-paws-management (package (name "r-paws-management") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 - "0lp8s4caxppwxsra6ijcz1dzkmnznwrrs92y87387vq53y3icc6m")))) + "0k40lrgxx91bijj3648zsgj55x120mhmx8dyx3hm2yvh2k96ks7h")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) @@ -39762,14 +39766,14 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "1imq29nxy5hxz2vlijdj2jl0lllvm3plb3jwpvsx1wlcvhpz0in3")))) + "0qs6bp0vlbazxir9jmdcnazh90yrvhrw6k9046id73hw1j7h5zaf")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) @@ -39786,14 +39790,14 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "1rnjjdb4l7a943cawkkzfjkg8shy2vy5d9mcl2p5ms191lw056bn")))) + "0nlkbnyxd3znmvqxqb3w43sznacmikq32d9fihyc1dx7ghvmf61z")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs @@ -39810,14 +39814,14 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "0yr99328rwm6i95xhp4yds6dzfvrvbr7ys2hy17iqbyij958j0m4")))) + "0v2g1shv9m4h2fz2lvjad479g3nmxc92wlyrxj4s7fifzzs2pd97")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs @@ -39832,14 +39836,14 @@ services, including Simple Storage Service (S3).") (define-public r-paws-compute (package (name "r-paws-compute") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 - "0q0xikrq7095l8fhii2jyjxfbihhnlm7nzzbspfqdh8xbr7g4kld")))) + "1vsxwzqgk0004nmfy79pd0zc208fczay95p7h16mzqgds9586ma1")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm index 5bfdea1b27..8d3c017107 100644 --- a/gnu/packages/fontutils.scm +++ b/gnu/packages/fontutils.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017 Leo Famulari <leo@famulari.name> ;;; Copyright © 2017 Nikita <nikita@n0.is> ;;; Copyright © 2017, 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2018, 2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018, 2019, 2020, 2021, 2023 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2019, 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2020 Roel Janssen <roel@gnu.org> @@ -232,7 +232,11 @@ them as it goes.") (when tests? (setenv "HOME" "/tmp") (invoke "pytest" "-vv" "--dist" "loadfile" "-n" - (number->string (parallel-job-count)))))) + (number->string (parallel-job-count)) + ;; This test fails because of a different date in the + ;; copyright header of an expected file since an + ;; update to ffmpeg. + "-k" "not test_alt_missing_glyph")))) (add-after 'check 'wrap (assoc-ref %standard-phases 'wrap)) (add-before 'wrap 'wrap-PATH diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index 7998142b4d..49dc878c02 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -421,6 +421,9 @@ svga,swrast,virgl,zink"))) ;; When cross compiling, we use cmake to find llvm, not ;; llvm-config, because llvm-config cannot be executed ;; see https://github.com/llvm/llvm-project/issues/58984 + (substitute* "meson.build" + (("method : host_machine\\.system.*") + "method : 'cmake',\n")) (setenv "CMAKE" (search-input-file native-inputs "/bin/cmake"))))) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index e2c2a041a9..3fa80dcfe7 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -100,13 +100,14 @@ (define-public icedtea-7 (let* ((version "2.6.13") - (drop (lambda (name hash) + (drop (lambda* (name hash #:optional (patches '())) (origin (method url-fetch) (uri (string-append "http://icedtea.classpath.org/download/drops" "/icedtea7/" version "/" name ".tar.bz2")) - (sha256 (base32 hash)))))) + (sha256 (base32 hash)) + (patches patches))))) (package (name "icedtea") (version version) @@ -614,7 +615,8 @@ "110j7jlz47x2gg6f7653x12mssan5kvj9l9h1m1c8c92drfxbqyk")) ("jdk-drop" ,(drop "jdk" - "0d1mca38ksxvdskp9im3pp7fdijhj1n3lwq9w13r9s4v3qyskgdd")) + "0d1mca38ksxvdskp9im3pp7fdijhj1n3lwq9w13r9s4v3qyskgdd" + (search-patches "jdk-currency-time-bomb.patch"))) ("langtools-drop" ,(drop "langtools" "0nq5236fzxn3p6x8cgncl56mzcmsj07q9gymysnws4c8byc6n0qj")) @@ -687,13 +689,14 @@ IcedTea build harness.") (define-public icedtea-8 (let* ((version "3.19.0") - (drop (lambda (name hash) + (drop (lambda* (name hash #:optional (patches '())) (origin (method url-fetch) (uri (string-append "http://icedtea.classpath.org/download/drops" "/icedtea8/" version "/" name ".tar.xz")) - (sha256 (base32 hash)))))) + (sha256 (base32 hash)) + (patches patches))))) (package (inherit icedtea-7) (version "3.19.0") (source (origin @@ -839,7 +842,8 @@ new Date();")) "1pc0pv4v2mn2mjc0vp19d94v2150xigyhxsmckqasy647zcm6w0r")) ("jdk-drop" ,(drop "jdk" - "1742lcm55l8zhi522x83v65ccr0rd6511q9rj7crw44x3ymdrhrv")) + "1742lcm55l8zhi522x83v65ccr0rd6511q9rj7crw44x3ymdrhrv" + (search-patches "jdk-currency-time-bomb2.patch"))) ("langtools-drop" ,(drop "langtools" "08iz7p2xcddlphipf6gahyabr5cawlnydap12p1n4f0md069b50b")) @@ -869,14 +873,14 @@ new Date();")) (changeset "jdk-9+181"))) (file-name (hg-file-name name version)) (modules '((guix build utils))) - (snippet `(begin - (for-each delete-file - (find-files "." ".*.(bin|exe|jar)$")))) + (snippet '(for-each delete-file + (find-files "." ".*.(bin|exe|jar)$"))) (sha256 (base32 "1v92nzdqx07c35x945awzir4yk0fk22vky6fpp8mq9js930sxsz0")) (patches (search-patches "openjdk-9-pointer-comparison.patch" - "openjdk-9-setsignalhandler.patch")))) + "openjdk-9-setsignalhandler.patch" + "openjdk-currency-time-bomb.patch")))) (build-system gnu-build-system) (outputs '("out" "jdk" "doc")) (arguments @@ -911,8 +915,7 @@ new Date();")) ;; This file was "fixed" by patch-source-shebangs, but it requires ;; this exact first line. (substitute* "jdk/make/data/blacklistedcertsconverter/blacklisted.certs.pem" - (("^#!.*") "#! java BlacklistedCertsConverter SHA-256\n")) - #t)) + (("^#!.*") "#! java BlacklistedCertsConverter SHA-256\n")))) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) ;; TODO: unbundle libpng and lcms @@ -928,14 +931,12 @@ new Date();")) "--disable-hotspot-gtest" "--with-giflib=system" "--with-libjpeg=system" - (string-append "--prefix=" (assoc-ref outputs "out"))) - #t)) + (string-append "--prefix=" (assoc-ref outputs "out"))))) (add-before 'build 'write-source-revision-file (lambda _ (with-output-to-file ".src-rev" (lambda _ - (display ,version))) - #t)) + (display ,version))))) (replace 'build (lambda* (#:key make-flags parallel-build? #:allow-other-keys) (apply invoke "make" @@ -978,8 +979,7 @@ new Date();")) "warning: failed to substitute: ~a~%" file)))) (find-files "." - "\\.c$|\\.h$")) - #t))) + "\\.c$|\\.h$"))))) ;; By default OpenJDK only generates an empty keystore. In order to ;; be able to use certificates in Java programs we need to generate a ;; keystore from a set of certificates. For convenience we use the @@ -1073,8 +1073,7 @@ new Date();")) (symlink (string-append lib-jdk "/server/libjvm.so") (string-append lib-jdk "/libjvm.so")) (symlink (string-append lib-out "/server/libjvm.so") - (string-append lib-out "/libjvm.so"))) - #t)) + (string-append lib-out "/libjvm.so"))))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -1084,8 +1083,7 @@ new Date();")) #:directories? #t)))) (copy-recursively (string-append images "/images/jdk") jdk) (copy-recursively (string-append images "/images/jre") out) - (copy-recursively (string-append images "/images/docs") doc)) - #t)) + (copy-recursively (string-append images "/images/docs") doc)))) (add-after 'install 'strip-zip-timestamps (lambda* (#:key outputs #:allow-other-keys) (for-each (lambda (zip) @@ -1102,8 +1100,7 @@ new Date();")) (with-directory-excursion dir (let ((files (find-files "." ".*" #:directories? #t))) (apply invoke "zip" "-0" "-X" zip files))))) - (find-files (assoc-ref outputs "doc") ".*.zip$")) - #t))))) + (find-files (assoc-ref outputs "doc") ".*.zip$"))))))) (inputs `(("alsa-lib" ,alsa-lib) ("cups" ,cups) @@ -1157,7 +1154,8 @@ new Date();")) (patches (search-patches "openjdk-10-idlj-reproducibility.patch" "openjdk-10-pointer-comparison.patch" - "openjdk-10-setsignalhandler.patch")))) + "openjdk-10-setsignalhandler.patch" + "openjdk-currency-time-bomb2.patch")))) (arguments (substitute-keyword-arguments (package-arguments openjdk9) ((#:phases phases) @@ -1179,8 +1177,7 @@ new Date();")) ;; This file was "fixed" by patch-source-shebangs, but it requires ;; this exact first line. (substitute* "make/data/blacklistedcertsconverter/blacklisted.certs.pem" - (("^#!.*") "#! java BlacklistedCertsConverter SHA-256\n")) - #t)) + (("^#!.*") "#! java BlacklistedCertsConverter SHA-256\n")))) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (invoke "bash" "./configure" @@ -1229,7 +1226,9 @@ new Date();")) "1prvqy0ysz0999wrhsrbz6vrknpqfihl9l74l16ph93g89dqi5ia")) (modules '((guix build utils))) (snippet - '(for-each delete-file (find-files "." "\\.(bin|exe|jar)$"))))) + '(for-each delete-file (find-files "." "\\.(bin|exe|jar)$"))) + (patches (search-patches + "openjdk-currency-time-bomb2.patch")))) (build-system gnu-build-system) (outputs '("out" "jdk" "doc")) (arguments diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2ce25bfa00..a96c817729 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -7497,15 +7497,16 @@ running boot option, and more.") (define-public sysstat (package (name "sysstat") - (version "12.4.4") + (version "12.7.5") (source (origin (method url-fetch) - (uri (string-append "http://pagesperso-orange.fr/sebastien.godard/" + (uri (string-append "https://sysstat.github.io/sysstat-packages/" "sysstat-" version ".tar.xz")) (sha256 - (base32 "091xjip7l52dxal8dsfh5chksr4g9gclnssw3hjjxy84kr3yf4lm")))) + (base32 "0ssdrm3k0fclq5b5i0aznfwdkbac9l9cf88idaq3pls9lm040rjp")))) (build-system gnu-build-system) + (native-inputs (list gettext-minimal)) (arguments `(#:tests? #f ; no test suite. ;; Without this flag, it tries to install the man pages with group 'root' @@ -7522,7 +7523,7 @@ running boot option, and more.") (substitute* "Makefile" (("mkdir -p \\$\\(DESTDIR\\)\\$\\(SA_DIR\\)") ""))))))) - (home-page "http://sebastien.godard.pagesperso-orange.fr/") + (home-page "https://sysstat.github.io") (synopsis "Performance monitoring tools for Linux") (description "The sysstat utilities are a collection of performance monitoring tools for Linux. These include @code{mpstat}, @code{iostat}, diff --git a/gnu/packages/patches/jdk-currency-time-bomb.patch b/gnu/packages/patches/jdk-currency-time-bomb.patch new file mode 100644 index 0000000000..8e6bce6fcd --- /dev/null +++ b/gnu/packages/patches/jdk-currency-time-bomb.patch @@ -0,0 +1,13 @@ +Fix a time bomb present in the jdk "drop" of IcedTea. + +--- a/make/tools/src/build/tools/generatecurrencydata/GenerateCurrencyData.java ++++ b/make/tools/src/build/tools/generatecurrencydata/GenerateCurrencyData.java +@@ -284,7 +284,7 @@ public class GenerateCurrencyData { + String timeString = currencyInfo.substring(4, length - 4); + long time = format.parse(timeString).getTime(); + if (Math.abs(time - System.currentTimeMillis()) > ((long) 10) * 365 * 24 * 60 * 60 * 1000) { +- throw new RuntimeException("time is more than 10 years from present: " + time); ++ System.err.println("note: time is more than 10 years from \"present\": " + time); + } + specialCaseCutOverTimes[specialCaseCount] = time; + specialCaseOldCurrencies[specialCaseCount] = oldCurrency; diff --git a/gnu/packages/patches/jdk-currency-time-bomb2.patch b/gnu/packages/patches/jdk-currency-time-bomb2.patch new file mode 100644 index 0000000000..94454626c4 --- /dev/null +++ b/gnu/packages/patches/jdk-currency-time-bomb2.patch @@ -0,0 +1,13 @@ +Fix a time bomb present in the jdk "drop" of IcedTea 8. + +--- a/make/src/classes/build/tools/generatecurrencydata/GenerateCurrencyData.java ++++ b/make/src/classes/build/tools/generatecurrencydata/GenerateCurrencyData.java +@@ -284,7 +284,7 @@ public class GenerateCurrencyData { + String timeString = currencyInfo.substring(4, length - 4); + long time = format.parse(timeString).getTime(); + if (Math.abs(time - System.currentTimeMillis()) > ((long) 10) * 365 * 24 * 60 * 60 * 1000) { +- throw new RuntimeException("time is more than 10 years from present: " + time); ++ System.err.println("note: time is more than 10 years from \"present\": " + time); + } + specialCaseCutOverTimes[specialCaseCount] = time; + specialCaseOldCurrencies[specialCaseCount] = oldCurrency; diff --git a/gnu/packages/patches/openjdk-currency-time-bomb.patch b/gnu/packages/patches/openjdk-currency-time-bomb.patch new file mode 100644 index 0000000000..7738eb1595 --- /dev/null +++ b/gnu/packages/patches/openjdk-currency-time-bomb.patch @@ -0,0 +1,13 @@ +Fix a time bomb present in the OpenJDK tools. + +--- a/jdk/make/src/classes/build/tools/generatecurrencydata/GenerateCurrencyData.java ++++ b/jdk/make/src/classes/build/tools/generatecurrencydata/GenerateCurrencyData.java +@@ -285,7 +285,7 @@ public class GenerateCurrencyData { + String timeString = currencyInfo.substring(4, length - 4); + long time = format.parse(timeString).getTime(); + if (Math.abs(time - System.currentTimeMillis()) > ((long) 10) * 365 * 24 * 60 * 60 * 1000) { +- throw new RuntimeException("time is more than 10 years from present: " + time); ++ System.err.println("note: time is more than 10 years from \"present\": " + time); + } + specialCaseCutOverTimes[specialCaseCount] = time; + specialCaseOldCurrencies[specialCaseCount] = oldCurrency; diff --git a/gnu/packages/patches/openjdk-currency-time-bomb2.patch b/gnu/packages/patches/openjdk-currency-time-bomb2.patch new file mode 100644 index 0000000000..d2ea04d63b --- /dev/null +++ b/gnu/packages/patches/openjdk-currency-time-bomb2.patch @@ -0,0 +1,13 @@ +Fix a time bomb present in the OpenJDK tools. + +--- a/make/jdk/src/classes/build/tools/generatecurrencydata/GenerateCurrencyData.java ++++ b/make/jdk/src/classes/build/tools/generatecurrencydata/GenerateCurrencyData.java +@@ -285,7 +285,7 @@ public class GenerateCurrencyData { + String timeString = currencyInfo.substring(4, length - 4); + long time = format.parse(timeString).getTime(); + if (Math.abs(time - System.currentTimeMillis()) > ((long) 10) * 365 * 24 * 60 * 60 * 1000) { +- throw new RuntimeException("time is more than 10 years from present: " + time); ++ System.err.println("note: time is more than 10 years from \"present\": " + time); + } + specialCaseCutOverTimes[specialCaseCount] = time; + specialCaseOldCurrencies[specialCaseCount] = oldCurrency; diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 262d5b7b98..8065de0e99 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023, 2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> @@ -1374,6 +1374,7 @@ Mathematics (GLM) library to Python.") "test_shutdown" "test_shutdown_localcluster" "test_teardown_failure_doesnt_crash_scheduler" + "test_tell_workers_when_peers_have_left" "test_threadpoolworkers_pick_correct_ioloop" "test_tls_listen_connect" "test_tls_temporary_credentials_functional" diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 3ff3b57cb2..ccafb8e802 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com> ;;; Copyright © 2023 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -512,16 +513,16 @@ character limit for implicit keys.") (define-public yaml-cpp (package (name "yaml-cpp") - (version "0.6.3") + (version "0.8.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/jbeder/yaml-cpp") - (commit (string-append "yaml-cpp-" version)))) + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0ykkxzxcwwiv8l8r697gyqh1nl582krpvi7m7l6b40ijnk4pw30s")))) + (base32 "0whdn6pqa56532ml20h89p6rchcrrazdrvi5fz6zpmrkl15yiki7")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DYAML_BUILD_SHARED_LIBS=ON"))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 906ec456b6..80d8ff2f93 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1431,13 +1431,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.81.0-1") + (version "1.84.0-0") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "0r7zjxpbm2paliplprwf9769a57clqaiskiiadiy10gissnqn77m")))) + "1b7igvvy9f13l969a26j2bdzib2laq3m4w1x0xsxjb2pbxsn1dkg")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -1782,13 +1782,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "14l0dz36wav2jbz0dd3w34va68lrhr7fgd9dqf1v4nawdvff23ia")))) + "02mz53g8lk26yi0js6qq57ijhl1mw7xm82vwbwzbvi62bm5l58r4")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -3033,13 +3033,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "2.1.4") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "03gbzf29kdvf4rdqgdq2jm7c9ifjla3qzpiyqzw1x9jgijj4y54q")))) + "02p1jjal73j39r49ba4jlvbx8bdqmm96nsdp47igyv54w1gmm9hg")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -3048,9 +3048,9 @@ time-of-day values, based on the @code{difftime} class.") r-crayon r-hms r-lifecycle - r-tibble r-r6 r-rlang + r-tibble r-tzdb r-vroom)) (native-inputs @@ -3373,13 +3373,13 @@ engine (version 3.8.8.2) is included.") (define-public r-rcurl (package (name "r-rcurl") - (version "1.98-1.13") + (version "1.98-1.14") (source (origin (method url-fetch) (uri (cran-uri "RCurl" version)) (sha256 (base32 - "01pkmip1sllislmp34c25i9m9mlrid9b48xfjbf93sml55ijz985")))) + "1kq3ydvm7hvy8pxk9iy13pkq5mxyxqlx4mpjsadzl7a7jj32gbgf")))) (properties `((upstream-name . "RCurl"))) (build-system r-build-system) (arguments @@ -3393,10 +3393,8 @@ engine (version 3.8.8.2) is included.") certs = Sys.getenv(\"CURL_CA_BUNDLE\") if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) } " m)))))))) - (native-inputs - (list libxml2)) (inputs - (list curl)) + (list curl libxml2)) (propagated-inputs (list r-bitops)) (home-page "https://www.omegahat.net/RCurl") @@ -4182,13 +4180,13 @@ computation, bagged clustering, naive Bayes classifier, and more.") (define-public r-bigmemory-sri (package (name "r-bigmemory-sri") - (version "0.1.6") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "bigmemory.sri" version)) (sha256 - (base32 "03468ak0lgd9m0f7synxms2zzr8f7n2nm1gmhcraj3nfcv4nmyiv")))) + (base32 "0wbpk3naipl0ab3wnixnp2n874kazrapv1c31fi3cxm19b94x6h2")))) (properties `((upstream-name . "bigmemory.sri"))) (build-system r-build-system) @@ -4202,14 +4200,14 @@ bigmemory and synchronicity packages.") (define-public r-synchronicity (package (name "r-synchronicity") - (version "1.3.5") + (version "1.3.10") (source (origin (method url-fetch) (uri (cran-uri "synchronicity" version)) (sha256 (base32 - "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx")))) + "12svf4xzb9s3m1h2ddqgl6q2v57ifsj2p80j8cg2k0543a43pww2")))) (build-system r-build-system) (propagated-inputs (list r-bh r-bigmemory-sri r-rcpp r-uuid)) @@ -4224,14 +4222,14 @@ message passing.") (define-public r-bigmemory (package (name "r-bigmemory") - (version "4.6.1") + (version "4.6.4") (source (origin (method url-fetch) (uri (cran-uri "bigmemory" version)) (sha256 (base32 - "0hainqkm7cs8gjm42vkpdrr0284smsbwdfackp34yv7dhxy1avmm")))) + "0b80c2nsgphgr3cnvf75a0z3bzqx4q1a4dplq0h2izc71mn5fgzy")))) (build-system r-build-system) (propagated-inputs (list r-bh r-bigmemory-sri r-rcpp r-uuid)) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index d751442561..7f98e2ca5b 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2025,41 +2025,22 @@ audio/video codec library.") (arguments (substitute-keyword-arguments (package-arguments ffmpeg) ((#:configure-flags _ '()) + ;; The base configure flags preserved from ffmpeg appear first. #~(list "--disable-static" "--enable-shared" "--disable-stripping" - ;; The following variables are configure flags used by - ;; ffmpeg-jami. They're from the - ;; jami/daemon/contrib/src/ffmpeg/rules.mak file. We try to - ;; keep it as close to the official Jami package as possible, - ;; to provide all the codecs and extra features that are - ;; expected (see: + + ;; Extra Guix-added flags that make sense for this custom + ;; package; these could be contributed upstream. + "--disable-doc" + + ;; The following flags are those specified by Jami. + ;; They're from the jami/daemon/contrib/src/ffmpeg/rules.mak + ;; file. We try to keep it as close to the official Jami + ;; package as possible, to provide all the codecs and extra + ;; features that are expected (see: ;; https://review.jami.net/plugins/gitiles/jami-daemon/+/ ;; refs/heads/master/contrib/src/ffmpeg/rules.mak). - ;; An exception are the ffnvcodec-related switches, which is - ;; not packaged in Guix and would not work with Mesa. - #$@(if (string-contains (%current-system) "linux") - '("--enable-pic" - "--extra-cxxflags=-fPIC" - "--extra-cflags=-fPIC" - "--target-os=linux" - "--enable-indev=v4l2" - "--enable-indev=xcbgrab" - "--enable-vdpau" - "--enable-hwaccel=h264_vdpau" - "--enable-hwaccel=mpeg4_vdpau" - "--enable-vaapi" - "--enable-hwaccel=h264_vaapi" - "--enable-hwaccel=mpeg4_vaapi" - "--enable-hwaccel=h263_vaapi" - "--enable-hwaccel=vp8_vaapi" - "--enable-hwaccel=mjpeg_vaapi" - "--enable-hwaccel=hevc_vaapi" - "--enable-encoder=h264_vaapi" - "--enable-encoder=vp8_vaapi" - "--enable-encoder=mjpeg_vaapi" - "--enable-encoder=hevc_vaapi") - '()) "--disable-everything" "--enable-zlib" "--enable-gpl" @@ -2068,6 +2049,7 @@ audio/video codec library.") "--disable-filters" "--disable-programs" "--disable-postproc" + "--disable-protocols" "--enable-protocol=crypto" "--enable-protocol=file" @@ -2083,17 +2065,18 @@ audio/video codec library.") "--disable-muxers" "--enable-muxer=rtp" "--enable-muxer=g722" + "--enable-muxer=g723_1" "--enable-muxer=g726" "--enable-muxer=g726le" "--enable-muxer=h263" "--enable-muxer=h264" "--enable-muxer=hevc" "--enable-muxer=matroska" - "--enable-muxer=wav" "--enable-muxer=webm" "--enable-muxer=ogg" "--enable-muxer=pcm_s16be" "--enable-muxer=pcm_s16le" + "--enable-muxer=wav" "--enable-demuxer=rtp" "--enable-demuxer=mjpeg" "--enable-demuxer=mjpeg_2000" @@ -2193,18 +2176,6 @@ audio/video codec library.") "--enable-encoder=pcm_s32le" "--enable-encoder=pcm_s64le" - "--enable-decoder=pcm_s16be" - "--enable-decoder=pcm_s16be_planar" - "--enable-decoder=pcm_s16le_planar" - "--enable-decoder=pcm_s24be" - "--enable-decoder=pcm_s24le_planar" - "--enable-decoder=pcm_s32be" - "--enable-decoder=pcm_s32le_planar" - "--enable-decoder=pcm_s64be" - "--enable-decoder=pcm_s8" - "--enable-decoder=pcm_s8_planar" - "--enable-decoder=pcm_u16be" - ;; Encoders/decoders for images. "--enable-encoder=gif" "--enable-decoder=gif" @@ -2231,6 +2202,20 @@ audio/video codec library.") "--enable-filter=transpose" "--enable-filter=pad" + ;; Decoders for ringtones and audio streaming. + "--enable-decoder=pcm_s16be" + "--enable-decoder=pcm_s16be_planar" + "--enable-decoder=pcm_s16le_planar" + "--enable-decoder=pcm_s24be" + "--enable-decoder=pcm_s24le_planar" + "--enable-decoder=pcm_s32be" + "--enable-decoder=pcm_s32le_planar" + "--enable-decoder=pcm_s64be" + "--enable-decoder=pcm_s8" + "--enable-decoder=pcm_s8_planar" + "--enable-decoder=pcm_u16be" + + ;; More filters. "--enable-filter=afir" "--enable-filter=split" "--enable-filter=drawbox" @@ -2244,7 +2229,35 @@ audio/video codec library.") "--enable-filter=lut" "--enable-filter=negate" "--enable-filter=colorkey" - "--enable-filter=transpose")))))) + "--enable-filter=transpose" + + "--enable-libfreetype" + + #$@(if (string-contains (%current-system) "linux") + ;; Leave out the '--enable-cuvid' ... '--enable-encoder=hevc_nvenc' + ;; flags, as there's no support for ffnvcodec in Guix; + ;; it would not work with Mesa anyway. + '("--enable-pic" + "--extra-cxxflags=-fPIC" + "--extra-cflags=-fPIC" + "--target-os=linux" + "--enable-indev=v4l2" + "--enable-indev=xcbgrab" + "--enable-vdpau" + "--enable-hwaccel=h264_vdpau" + "--enable-hwaccel=mpeg4_vdpau" + "--enable-vaapi" + "--enable-hwaccel=h264_vaapi" + "--enable-hwaccel=mpeg4_vaapi" + "--enable-hwaccel=h263_vaapi" + "--enable-hwaccel=vp8_vaapi" + "--enable-hwaccel=mjpeg_vaapi" + "--enable-hwaccel=hevc_vaapi" + "--enable-encoder=h264_vaapi" + "--enable-encoder=vp8_vaapi" + "--enable-encoder=mjpeg_vaapi" + "--enable-encoder=hevc_vaapi") + '()))))))) (define-public ffmpegthumbnailer (package diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index e301088394..55c896f373 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -769,7 +769,7 @@ is based on Vim's builtin plugin support.") (define-public neovim (package (name "neovim") - (version "0.9.4") + (version "0.9.5") (source (origin (method git-fetch) (uri (git-reference @@ -778,7 +778,7 @@ is based on Vim's builtin plugin support.") (file-name (git-file-name name version)) (sha256 (base32 - "0wj1p5x88s58f22crdyzwlfiqgnwlqdkbw4wxllf0v5hg16gbnhp")))) + "1j3z7jay0m6g06v04falrzr062g07xr4svbrc3hywlqi2h6rrvk5")))) (build-system cmake-build-system) (arguments (list #:modules |