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-rw-r--r--gnu/local.mk6
-rw-r--r--gnu/packages/admin.scm4
-rw-r--r--gnu/packages/bioconductor.scm110
-rw-r--r--gnu/packages/bioinformatics.scm53
-rw-r--r--gnu/packages/cran.scm156
-rw-r--r--gnu/packages/fontutils.scm8
-rw-r--r--gnu/packages/gl.scm3
-rw-r--r--gnu/packages/java.scm55
-rw-r--r--gnu/packages/linux.scm9
-rw-r--r--gnu/packages/patches/jdk-currency-time-bomb.patch13
-rw-r--r--gnu/packages/patches/jdk-currency-time-bomb2.patch13
-rw-r--r--gnu/packages/patches/openjdk-currency-time-bomb.patch13
-rw-r--r--gnu/packages/patches/openjdk-currency-time-bomb2.patch13
-rw-r--r--gnu/packages/python-science.scm3
-rw-r--r--gnu/packages/serialization.scm7
-rw-r--r--gnu/packages/statistics.scm34
-rw-r--r--gnu/packages/video.scm101
-rw-r--r--gnu/packages/vim.scm4
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
generated by cgit v1.2.3 (git 2.47.1) at 2025-02-04 11:43:53 +0000