diff options
| author | Mark H Weaver <mhw@netris.org> | 2018-04-30 04:03:54 -0400 |
|---|---|---|
| committer | Mark H Weaver <mhw@netris.org> | 2018-04-30 04:03:54 -0400 |
| commit | 3d5ad159b336a9903b31d0be7ae052dbc8d5bfcc (patch) | |
| tree | ee7dce4e436490a1db5f18e4bfad55511d2fff32 /gnu/packages | |
| parent | c77835db04ee20c0afe20600dc8f91a67bc2421e (diff) | |
| parent | 8c21c64e59d3f4d223d8aeef91f06fdde7de1ab7 (diff) | |
| download | guix-3d5ad159b336a9903b31d0be7ae052dbc8d5bfcc.tar.gz | |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages')
87 files changed, 2142 insertions, 946 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index d1af6d9474..a6abe86403 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -18,7 +18,7 @@ ;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au> ;;; Copyright © 2017 Ethan R. Jones <doubleplusgood23@gmail.com> ;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org> -;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr> ;;; @@ -58,6 +58,8 @@ #:use-module (gnu packages lua) #:use-module (gnu packages guile) #:use-module (gnu packages gettext) + #:use-module (gnu packages imagemagick) + #:use-module (gnu packages inkscape) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages perl-check) @@ -76,6 +78,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) + #:use-module (gnu packages qt) #:use-module (gnu packages terminals) #:use-module (gnu packages texinfo) #:use-module (gnu packages groff) @@ -242,16 +245,16 @@ services.") (define-public dfc (package (name "dfc") - (version "3.0.4") + (version "3.1.1") (source (origin (method url-fetch) (uri (string-append - "http://projects.gw-computing.net/attachments/download/79/dfc-" + "http://projects.gw-computing.net/attachments/download/615/dfc-" version ".tar.gz")) (sha256 (base32 - "0zk1ppx93ijimf4sbgqilxxikpsa2gmpbynknyh41xy7jbdjxp0b")))) + "0m1fd7l85ckb7bq4c5c3g257bkjglm8gq7x42pkmpp87fkknc94n")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; There are no tests. (native-inputs `(("gettext" ,gettext-minimal))) @@ -1142,6 +1145,51 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.") (string-append dir "/wpa_supplicant.conf"))) #t)))))))) +(define-public wpa-supplicant-gui + (package + (inherit wpa-supplicant) + (name "wpa-supplicant-gui") + (inputs `(("qtbase" ,qtbase) + ("qtsvg" ,qtsvg) + ,@(package-inputs wpa-supplicant))) + (native-inputs + ;; For icons. + `(("imagemagick" ,imagemagick) + ("inkscape" ,inkscape) + ,@(package-native-inputs wpa-supplicant))) + (arguments + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "wpa_supplicant/wpa_gui-qt4") + #t)) + (delete 'configure) + (replace 'build + (lambda _ + (invoke "qmake" "wpa_gui.pro") + (invoke "make" "-j" (number->string (parallel-job-count))) + (invoke "make" "-C" "icons"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (qt '("qtbase" "qtsvg"))) + (substitute* "wpa_gui.desktop" + (("Exec=wpa_gui") + (string-append "Exec=" out "/bin/wpa_gui"))) + (install-file "wpa_gui" (string-append out "/bin")) + (install-file "wpa_gui.desktop" + (string-append out "/share/applications")) + (copy-recursively "icons/hicolor" + (string-append out "/share/icons/hicolor")) + (wrap-program (string-append out "/bin/wpa_gui") + `("QT_PLUGIN_PATH" ":" prefix + ,(map (lambda (label) + (string-append (assoc-ref inputs label) + "/lib/qt5/plugins/")) + qt))) + #t)))))) + (synopsis "Graphical user interface for WPA supplicant"))) + (define-public wakelan (package (name "wakelan") @@ -1534,7 +1582,9 @@ of supported upstream metrics systems simultaneously.") (patches (search-patches "ansible-wrap-program-hack.patch")))) (build-system python-build-system) (native-inputs - `(("python2-pycrypto" ,python2-pycrypto) + `(("python2-bcrypt" ,python2-bcrypt) + ("python2-pycrypto" ,python2-pycrypto) + ("python2-pynacl" ,python2-pynacl) ("python2-httplib2" ,python2-httplib2) ("python2-passlib" ,python2-passlib) ("python2-nose" ,python2-nose) @@ -1899,7 +1949,7 @@ throughput (in the same interval).") (define-public thefuck (package (name "thefuck") - (version "3.25") + (version "3.26") (source (origin (method url-fetch) (uri (string-append "https://github.com/nvbn/thefuck/archive/" @@ -1907,7 +1957,7 @@ throughput (in the same interval).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "088bn2l1376qlndbpnjya4q1x3913nj3yj3wc7s2w3bz66d23skk")) + "0ddlf25ik97z34bcpc52xyfhlfm6a3hdi43l6cz4ggwcawdwvn1p")) (patches (search-patches "thefuck-test-environ.patch")))) (build-system python-build-system) (arguments @@ -1920,7 +1970,8 @@ throughput (in the same interval).") (add-installed-pythonpath inputs outputs) ;; Some tests need write access to $HOME. (setenv "HOME" "/tmp") - (zero? (system* "py.test" "-v"))))))) + (invoke "py.test" "-v") + #t))))) (propagated-inputs `(("python-colorama" ,python-colorama) ("python-decorator" ,python-decorator) @@ -2294,21 +2345,23 @@ Intel DRM Driver.") (define-public fabric (package (name "fabric") - (version "1.13.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (pypi-uri "Fabric" version)) (sha256 (base32 - "0k944dxr41whw7ib6380q9x15wyskx7fqni656icdn8rzshn9bwq")))) + "13r0b0hllgf8j9rh6x1knmbgvingbdmx046aazv6vck2ll120mw1")))) (build-system python-build-system) (arguments `(#:python ,python-2)) ; Python 2 only (native-inputs `(("python2-fudge" ,python2-fudge) ("python2-jinja2" ,python2-jinja2) - ("python2-nose" ,python2-nose))) + ("python2-nose" ,python2-nose) + ("python2-pynacl" ,python2-pynacl) + ("python2-bcrypt" ,python2-bcrypt))) (propagated-inputs `(("python2-paramiko" ,python2-paramiko))) (home-page "http://fabfile.org") @@ -2375,7 +2428,7 @@ you are running, what theme or icon set you are using, etc.") (define-public nnn (package (name "nnn") - (version "1.5") + (version "1.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/jarun/nnn/" @@ -2383,7 +2436,7 @@ you are running, what theme or icon set you are using, etc.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0zswf8lb29zr1z642i1d0zi1y2mxal8qjqdrpdiqjh197jamj3zm")))) + "0z3lqbfx3y1caxvn7yq90b7whwyq2y32zf8kyd976ilbxpxnxqpv")))) (build-system gnu-build-system) (inputs `(("ncurses" ,ncurses) ("readline" ,readline))) @@ -2606,4 +2659,6 @@ launch daemons into the relevant nodes.") "Spindle is a tool for improving the performance of dynamic library and Python loading in HPC environments.") (home-page "https://github.com/hpc/Spindle") + ;; This package supports x86_64 and PowerPC64 + (supported-systems '("x86_64-linux")) (license license:lgpl2.1))) diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm index 96fc34eb6e..105e3d1775 100644 --- a/gnu/packages/android.scm +++ b/gnu/packages/android.scm @@ -341,7 +341,7 @@ Images.") (define-public android-udev-rules (package (name "android-udev-rules") - (version "20171113") + (version "20180112") (source (origin (method git-fetch) @@ -350,7 +350,7 @@ Images.") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 - (base32 "11gcnk6wjc2sw05hwi4xphvx9ksmkpvsdziaczymqxkaads3f1dy")))) + (base32 "13gj79nnd04szqlrrzzkdr6wi1fky08pi7x8xfbg0jj3d3v0giah")))) (build-system trivial-build-system) (native-inputs `(("source" ,source))) (arguments diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index df1202087c..83fde34325 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -285,14 +285,15 @@ engineers, musicians, soundtrack editors and composers.") (define-public audacity (package (name "audacity") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/audacity/audacity/archive" "/Audacity-" version ".tar.gz")) (sha256 - (base32 "1n05r8b4rnf9fas0py0is8cm97s3h65dgvqkk040aym5d1x6wd7z")) + (base32 + "18q7i77ynihx7xp45lz2lv0k0wrh6736pcrivlpwrxjgbvyqx7km")) (patches (search-patches "audacity-build-with-system-portaudio.patch")) (modules '((guix build utils))) (snippet @@ -555,7 +556,7 @@ based on human speech recordings.") (define-public infamous-plugins (package (name "infamous-plugins") - (version "0.2.02") + (version "0.2.04") (source (origin (method url-fetch) (uri (string-append "https://github.com/ssj71/infamousPlugins/" @@ -563,10 +564,10 @@ based on human speech recordings.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0qm3ak07vc1l3f5c3c2lq9gkfknlxwn8ks03cysw1pk8hj7dwnv6")))) + "1n6rhqsmvad7692w2h01niw5gqg5yk7a09wxl5ivs77zyp93vf7z")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; There are no tests + `(#:tests? #f ; there are no tests #:phases (modify-phases %standard-phases (add-after 'unpack 'remove-compiler-flags @@ -581,7 +582,7 @@ based on human speech recordings.") "src/powercut/CMakeLists.txt" "src/powerup/CMakeLists.txt" "src/stuck/CMakeLists.txt") - (("-msse2 -mfpmath=sse") "")) + (("-msse2 -mfpmath=sse") "")) #t))))) (inputs `(("cairo" ,cairo) @@ -591,7 +592,7 @@ based on human speech recordings.") ("zita-resampler" ,zita-resampler))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://ssj71.github.io/infamousPlugins") + (home-page "https://ssj71.github.io/infamousPlugins") (synopsis "LV2 plugins for live use") (description "The infamous plugins are a collection of LV2 audio plugins for live diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index 77dcd78331..ebc8bdb5f2 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -34,7 +34,7 @@ (define-public fio (package (name "fio") - (version "3.5") + (version "3.6") (source (origin (method url-fetch) (uri (string-append @@ -42,7 +42,7 @@ "fio-" version ".tar.bz2")) (sha256 (base32 - "1rrzcrn07db4pffvi2q0d0k884bwcapx6r1rfv4yx9066snvx240")))) + "1d2jibp1b2dq97f22wj6pcjl7gbd2kmhfggj2c7q3j8v9axjqsh2")))) (build-system gnu-build-system) (arguments '(#:test-target "test" @@ -67,8 +67,9 @@ ;; The configure script doesn't understand some of the ;; GNU options, so we can't use #:configure-flags. (let ((out (assoc-ref outputs "out"))) - (zero? (system* "./configure" - (string-append "--prefix=" out)))))) + (invoke "./configure" + (string-append "--prefix=" out)) + #t))) ;; The main `fio` executable is fairly small and self contained. ;; Moving the auxiliary python and gnuplot scripts to a separate ;; output saves almost 400 MiB on the closure. diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 09581d9fde..76ff773ef1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -23,6 +23,8 @@ #:use-module (guix download) #:use-module (guix build-system r) #:use-module (gnu packages) + #:use-module (gnu packages cran) + #:use-module (gnu packages compression) #:use-module (gnu packages statistics) #:use-module (gnu packages bioinformatics)) @@ -70,3 +72,260 @@ the Human Protein Atlas project.") customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) + +(define-public r-diffbind + (package + (name "r-diffbind") + (version "2.6.6") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DiffBind" version)) + (sha256 + (base32 + "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp")))) + (properties `((upstream-name . "DiffBind"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-amap" ,r-amap) + ("r-biocparallel" ,r-biocparallel) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-genomicalignments" ,r-genomicalignments) + ("r-ggrepel" ,r-ggrepel) + ("r-gplots" ,r-gplots) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-rcolorbrewer" , r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-systempiper" ,r-systempiper) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "http://bioconductor.org/packages/DiffBind") + (synopsis "Differential binding analysis of ChIP-Seq peak data") + (description + "This package computes differentially bound sites from multiple +ChIP-seq experiments using affinity (quantitative) data. Also enables +occupancy (overlap) analysis and plotting functions.") + (license license:artistic2.0))) + +(define-public r-ripseeker + (package + (name "r-ripseeker") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RIPSeeker" version)) + (sha256 + (base32 + "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y")))) + (properties `((upstream-name . "RIPSeeker"))) + (build-system r-build-system) + (propagated-inputs + `(("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-genomicranges" ,r-genomicranges) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rsamtools" ,r-rsamtools) + ("r-genomicalignments" ,r-genomicalignments) + ("r-rtracklayer" ,r-rtracklayer))) + (home-page "http://bioconductor.org/packages/RIPSeeker") + (synopsis + "Identifying protein-associated transcripts from RIP-seq experiments") + (description + "This package infers and discriminates RIP peaks from RIP-seq alignments +using two-state HMM with negative binomial emission probability. While +RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides +a suite of bioinformatics tools integrated within this self-contained software +package comprehensively addressing issues ranging from post-alignments +processing to visualization and annotation.") + (license license:gpl2))) + +(define-public r-multtest + (package + (name "r-multtest") + (version "2.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "multtest" version)) + (sha256 + (base32 + "0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biobase" ,r-biobase) + ("r-mass" ,r-mass))) + (home-page "http://bioconductor.org/packages/multtest") + (synopsis "Resampling-based multiple hypothesis testing") + (description + "This package can do non-parametric bootstrap and permutation +resampling-based multiple testing procedures (including empirical Bayes +methods) for controlling the family-wise error rate (FWER), generalized +family-wise error rate (gFWER), tail probability of the proportion of +false positives (TPPFP), and false discovery rate (FDR). Several choices +of bootstrap-based null distribution are implemented (centered, centered +and scaled, quantile-transformed). Single-step and step-wise methods are +available. Tests based on a variety of T- and F-statistics (including +T-statistics based on regression parameters from linear and survival models +as well as those based on correlation parameters) are included. When probing +hypotheses with T-statistics, users may also select a potentially faster null +distribution which is multivariate normal with mean zero and variance +covariance matrix derived from the vector influence function. Results are +reported in terms of adjusted P-values, confidence regions and test statistic +cutoffs. The procedures are directly applicable to identifying differentially +expressed genes in DNA microarray experiments.") + (license license:lgpl3))) + +(define-public r-chippeakanno + (package + (name "r-chippeakanno") + (version "3.12.7") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPpeakAnno" version)) + (sha256 + (base32 + "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04")))) + (properties `((upstream-name . "ChIPpeakAnno"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) + ("r-biomart" ,r-biomart) + ("r-bsgenome" ,r-bsgenome) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-matrixstats" ,r-matrixstats) + ("r-annotationdbi" ,r-annotationdbi) + ("r-limma" ,r-limma) + ("r-multtest" ,r-multtest) + ("r-rbgl" ,r-rbgl) + ("r-graph" ,r-graph) + ("r-biocinstaller" ,r-biocinstaller) + ("r-regioner" ,r-regioner) + ("r-dbi" ,r-dbi) + ("r-ensembldb" ,r-ensembldb) + ("r-biobase" ,r-biobase) + ("r-seqinr" ,r-seqinr) + ("r-idr" ,r-idr) + ("r-genomicalignments" ,r-genomicalignments) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rsamtools" ,r-rsamtools) + ("r-venndiagram" ,r-venndiagram))) + (home-page "http://bioconductor.org/packages/ChIPpeakAnno") + (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") + (description + "The package includes functions to retrieve the sequences around the peak, +obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or +custom features such as most conserved elements and other transcription factor +binding sites supplied by users. Starting 2.0.5, new functions have been added +for finding the peaks with bi-directional promoters with summary statistics +(peaksNearBDP), for summarizing the occurrence of motifs in peaks +(summarizePatternInPeaks) and for adding other IDs to annotated peaks or +enrichedGO (addGeneIDs).") + (license license:gpl2+))) + +(define-public r-marray + (package + (name "r-marray") + (version "1.56.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "marray" version)) + (sha256 + (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limma" ,r-limma))) + (home-page "http://bioconductor.org/packages/marray") + (synopsis "Exploratory analysis for two-color spotted microarray data") + (description "This package contains class definitions for two-color spotted +microarray data. It also includes fuctions for data input, diagnostic plots, +normalization and quality checking.") + (license license:lgpl2.0+))) + +(define-public r-cghbase + (package + (name "r-cghbase") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CGHbase" version)) + (sha256 + (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm")))) + (properties `((upstream-name . "CGHbase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-marray" ,r-marray))) + (home-page "http://bioconductor.org/packages/CGHbase") + (synopsis "Base functions and classes for arrayCGH data analysis") + (description "This package contains functions and classes that are needed by +the @code{arrayCGH} packages.") + (license license:gpl2+))) + +(define-public r-cghcall + (package + (name "r-cghcall") + (version "2.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CGHcall" version)) + (sha256 + (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch")))) + (properties `((upstream-name . "CGHcall"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-cghbase" ,r-cghbase) + ("r-impute" ,r-impute) + ("r-dnacopy" ,r-dnacopy) + ("r-snowfall" ,r-snowfall))) + (home-page "http://bioconductor.org/packages/CGHcall") + (synopsis "Base functions and classes for arrayCGH data analysis") + (description "This package contains functions and classes that are needed by +@code{arrayCGH} packages.") + (license license:gpl2+))) + +(define-public r-qdnaseq + (package + (name "r-qdnaseq") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "QDNAseq" version)) + (sha256 + (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy")))) + (properties `((upstream-name . "QDNAseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-cghbase" ,r-cghbase) + ("r-cghcall" ,r-cghcall) + ("r-dnacopy" ,r-dnacopy) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-r-utils" ,r-r-utils) + ("r-rsamtools" ,r-rsamtools))) + (home-page "http://bioconductor.org/packages/QDNAseq") + (synopsis "Quantitative DNA sequencing for chromosomal aberrations") + (description "The genome is divided into non-overlapping fixed-sized bins, +number of sequence reads in each counted, adjusted with a simultaneous +two-dimensional loess correction for sequence mappability and GC content, and +filtered to remove spurious regions in the genome. Downstream steps of +segmentation and calling are also implemented via packages DNAcopy and CGHcall, +respectively.") + (license license:gpl2+))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5af4947b68..61e5d8bc34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -252,7 +252,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (define-public bamtools (package (name "bamtools") - (version "2.4.1") + (version "2.5.1") (source (origin (method url-fetch) (uri (string-append @@ -261,7 +261,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) + "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -285,7 +285,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.5") + (version "1.8") (source (origin (method url-fetch) (uri (string-append @@ -293,12 +293,11 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) - (patches (search-patches "bcftools-regidx-unsigned-char.patch")) + "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.5") + (delete-file-recursively "htslib-1.8") #t)))) (build-system gnu-build-system) (arguments @@ -339,7 +338,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (define-public bedops (package (name "bedops") - (version "2.4.14") + (version "2.4.33") (source (origin (method url-fetch) (uri (string-append "https://github.com/bedops/bedops/archive/v" @@ -347,7 +346,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) + "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m")))) (build-system gnu-build-system) (arguments '(#:tests? #f @@ -2089,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.") (define-public diamond (package (name "diamond") - (version "0.9.19") + (version "0.9.21") (source (origin (method url-fetch) (uri (string-append @@ -2098,7 +2097,7 @@ accurately delineate genomic rearrangements throughout the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0c4y8l90vdxmglb0w37y0413v11qzcwg8sdmy9k0c0gr3bsq7dzs")))) + "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2349,7 +2348,8 @@ dynamic programming or a variety of heuristics.") (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) (substitute* "src/CMakeLists.txt" (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") - (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) + (string-append (assoc-ref inputs "bamtools") "/lib")) + (("libprotobuf.a") "libprotobuf.so")) #t))))) (inputs `(("boost" ,boost) @@ -3462,7 +3462,7 @@ The main functions of FastQC are: (define-public htslib (package (name "htslib") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (string-append @@ -3470,7 +3470,7 @@ The main functions of FastQC are: version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy")))) + "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0")))) (build-system gnu-build-system) (inputs `(("openssl" ,openssl) @@ -4587,7 +4587,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.11.0") + (version "3.12.0") (source (origin (method url-fetch) @@ -4596,7 +4596,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i")))) + "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff")))) (build-system perl-build-system) (arguments `(#:phases @@ -4934,7 +4934,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) @@ -4943,7 +4943,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) + "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -5784,7 +5784,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.5.3a") + (version "2.6.0a") (source (origin (method url-fetch) (uri (string-append "https://github.com/alexdobin/STAR/archive/" @@ -5792,7 +5792,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a")) + "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56")) (modules '((guix build utils))) (snippet '(begin @@ -5979,13 +5979,13 @@ Cuffdiff or Ballgown programs.") (define-public taxtastic (package (name "taxtastic") - (version "0.6.4") + (version "0.8.5") (source (origin (method url-fetch) (uri (pypi-uri "taxtastic" version)) (sha256 (base32 - "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) + "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -6098,19 +6098,20 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-6") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w")))) + "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) + ("r-knitr" ,r-knitr) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) @@ -6266,14 +6267,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.3") + (version "1.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084")))) + "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6619,7 +6620,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.7.1") + (version "2.8.0") (source (origin (method url-fetch) @@ -6629,7 +6630,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f")) + "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -7604,13 +7605,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39")))) + "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -9077,14 +9078,14 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8")))) + "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy")))) (build-system python-build-system) (propagated-inputs `(("python-jinja2" ,python-jinja2) @@ -9652,13 +9653,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.2.1") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2")) + "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9688,11 +9689,15 @@ Main-Class: ModularityOptimizer\n"))) (propagated-inputs `(("r-ape" ,r-ape) ("r-caret" ,r-caret) + ("r-cluster" ,r-cluster) ("r-cowplot" ,r-cowplot) ("r-diffusionmap" ,r-diffusionmap) + ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-dtw" ,r-dtw) + ("r-fitdistrplus" ,r-fitdistrplus) ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) ("r-fpc" ,r-fpc) ("r-gdata" ,r-gdata) ("r-ggplot2" ,r-ggplot2) @@ -9704,13 +9709,16 @@ Main-Class: ModularityOptimizer\n"))) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-lars" ,r-lars) + ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-metap" ,r-metap) ("r-mixtools" ,r-mixtools) ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) + ("r-png" ,r-png) ("r-ranger" ,r-ranger) + ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) @@ -10185,14 +10193,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9")))) + "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10237,14 +10245,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.4") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b")))) + "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs @@ -10355,14 +10363,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g")))) + "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10391,14 +10399,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba")))) + "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0")))) (build-system r-build-system) (propagated-inputs `(("r-erma" ,r-erma) @@ -10608,13 +10616,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp")))) + "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10856,14 +10864,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x")))) + "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12826,7 +12834,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.10") + (version "0.0.15") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12834,7 +12842,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "13w99bkr0w4j28ms0yzpl1x6fkpdqay0vh495q3x20bcilsjwnf1")))) + "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm index ae9b3bc62d..9df4f097ac 100644 --- a/gnu/packages/bittorrent.scm +++ b/gnu/packages/bittorrent.scm @@ -315,8 +315,6 @@ Aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.") (base32 "0919cf7lfk1djdl003cahqjvafdliv7v2l8r5wg95n4isqggdk75")))) (build-system gnu-build-system) - (native-inputs - `(("intltool" ,intltool))) (inputs `(("curl" ,curl) ("gtk+" ,gtk+) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 5be77e550b..0db6ad3f6a 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -72,23 +72,6 @@ (base32 "0p2vhnc18cnbmb39vq4m7hzv4mhnm2l0a2s7gx3ar277fwng3hys")))) -;; The GRUB test suite fails with later versions of Qemu, so we -;; keep it at 2.10 for now. See -;; <https://lists.gnu.org/archive/html/bug-grub/2018-02/msg00004.html>. -;; TODO: When grub no longer needs this version, move to gnu/packages/debug.scm. -(define qemu-minimal-2.10 - (package - (inherit qemu-minimal) - (version "2.10.2") - (source (origin - (method url-fetch) - (uri (string-append "https://download.qemu.org/qemu-" - version ".tar.xz")) - (sha256 - (base32 - "17w21spvaxaidi2am5lpsln8yjpyp2zi3s3gc6nsxj5arlgamzgw")) - (patches (search-patches "qemu-glibc-2.27.patch")))))) - (define-public grub (package (name "grub") @@ -425,7 +408,7 @@ also initializes the boards (RAM etc).") (libexec (string-append out "/libexec")) (uboot-files (append (find-files "." ".*\\.(bin|efi|img|spl|itb|dtb)$") - (find-files "." "^MLO$")))) + (find-files "." "^(MLO|SPL)$")))) (mkdir-p libexec) (install-file ".config" libexec) (for-each @@ -480,6 +463,12 @@ also initializes the boards (RAM etc).") (define-public u-boot-nintendo-nes-classic-edition (make-u-boot-package "Nintendo_NES_Classic_Edition" "arm-linux-gnueabihf")) +(define-public u-boot-wandboard + (make-u-boot-package "wandboard" "arm-linux-gnueabihf")) + +(define-public u-boot-mx6cuboxi + (make-u-boot-package "mx6cuboxi" "arm-linux-gnueabihf")) + (define-public vboot-utils (package (name "vboot-utils") diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index e26a1bbf63..5d45d07288 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -394,7 +394,7 @@ capacity is user-selectable.") ("fontconfig" ,fontconfig) ("libexif" ,libexif) ("libjpeg" ,libjpeg) - ("ffmpeg" ,ffmpeg))) + ("ffmpeg" ,ffmpeg-3.4))) (native-inputs `(("pkg-config" ,pkg-config) ("flex" ,flex) diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index 057ee169dd..9f85781db2 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -1024,6 +1024,9 @@ COREUTILS-FINAL vs. COREUTILS, etc." (union-build (assoc-ref %outputs "debug") (list (assoc-ref %build-inputs "libc-debug"))) + (union-build (assoc-ref %outputs "static") + (list (assoc-ref %build-inputs + "libc-static"))) #t)))) (native-search-paths (package-native-search-paths gcc)) @@ -1036,7 +1039,7 @@ COREUTILS-FINAL vs. COREUTILS, etc." be installed in user profiles. This includes GCC, as well as libc (headers and binaries, plus debugging symbols in the 'debug' output), and Binutils.") (home-page "https://gcc.gnu.org/") - (outputs '("out" "debug")) + (outputs '("out" "debug" "static")) ;; The main raison d'être of this "meta-package" is (1) to conveniently ;; install everything that we need, and (2) to make sure ld-wrapper comes @@ -1045,7 +1048,8 @@ and binaries, plus debugging symbols in the 'debug' output), and Binutils.") ("ld-wrapper" ,(car (assoc-ref %final-inputs "ld-wrapper"))) ("binutils" ,binutils-final) ("libc" ,glibc-final) - ("libc-debug" ,glibc-final "debug"))))) + ("libc-debug" ,glibc-final "debug") + ("libc-static" ,glibc-final "static"))))) (define-public gcc-toolchain-4.8 (make-gcc-toolchain gcc-4.8)) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0ac35a909b..bc95fd2aa4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35,6 +35,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -113,16 +114,18 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (define-public r-selectr (package (name "r-selectr") - (version "0.3-2") + (version "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "selectr" version)) (sha256 (base32 - "0kdrj64rqg4z6hg92y9r2h602a2i73r5rnlpg23ys33d5d32n8jy")))) + "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b")))) (build-system r-build-system) - (propagated-inputs `(("r-stringr" ,r-stringr))) + (propagated-inputs + `(("r-stringr" ,r-stringr) + ("r-r6" ,r-r6))) (home-page "https://sjp.co.nz/projects/selectr/") (synopsis "Translate CSS selectors to XPath expressions") (description @@ -190,14 +193,14 @@ that.") (define-public r-readxl (package (name "r-readxl") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "1bf7gxw9r11m4llyymplxiaa4gzgyj4bwmwad5in756pzq3jzmpv")))) + "05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) @@ -404,14 +407,14 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-plogr (package (name "r-plogr") - (version "0.1-1") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "plogr" version)) (sha256 (base32 - "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/plogr") (synopsis "R bindings for the plog C++ logging library") @@ -424,13 +427,13 @@ error stream.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.15") + (version "0.12.16") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv")))) + (base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -448,14 +451,14 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see (define-public r-bindr (package (name "r-bindr") - (version "0.1") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "bindr" version)) (sha256 (base32 - "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc")))) + "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) (build-system r-build-system) (home-page "https://github.com/krlmlr/bindr") (synopsis "Parametrized active bindings") @@ -467,14 +470,14 @@ where the bound function accepts additional arguments.") (define-public r-bindrcpp (package (name "r-bindrcpp") - (version "0.2") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "bindrcpp" version)) (sha256 (base32 - "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh")))) + "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) (build-system r-build-system) (propagated-inputs `(("r-bindr" ,r-bindr) @@ -554,14 +557,14 @@ ellipses, circles, cylinders, arrows, ...") (define-public r-globaloptions (package (name "r-globaloptions") - (version "0.0.12") + (version "0.0.13") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 - "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0")))) + "04jvha0mafslqz5nr99xjylg9n2x31gj9v4mgyg7qcmfwpqyw3ch")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (home-page "https://github.com/jokergoo/GlobalOptions") @@ -936,19 +939,21 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-6") + (version "0.6-7") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "0fm6z049aaq2c9xagm8n64d9560hg9d8hyb0m359fii672nhkz6q")))) + "1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\""))) (inputs `(("openmpi" ,openmpi))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") (synopsis "R interface to message-passing interface (MPI)") (description @@ -1364,14 +1369,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz")))) + "11k9npmzp3nk2qx0h1dwwfc37j4ddd9y54bppxby0ffnb8qlpw1k")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -1411,14 +1416,14 @@ regression using Kernel Ridge Regression.") (define-public r-prodlim (package (name "r-prodlim") - (version "1.6.1") + (version "2018.04.18") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 - "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz")))) + "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb")))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth) @@ -1476,21 +1481,75 @@ Engineering and Computational Finance\" and for managing chronological and calendar objects.") (license license:gpl2+))) +(define-public r-magic + (package + (name "r-magic") + (version "1.5-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "magic" version)) + (sha256 + (base32 + "083cgpp3v03li0h8597b3g21pd9lkbmn9pyssblnhc800mpc52vz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind))) + (home-page "https://github.com/RobinHankin/magic.git") + (synopsis "Create and investigate magic squares") + (description + "This package provides a collection of efficient, vectorized algorithms +for the creation and investigation of magic squares and hypercubes, including +a variety of functions for the manipulation and analysis of arbitrarily +dimensioned arrays.") + (license license:gpl2))) + +(define-public r-geometry + (package + (name "r-geometry") + (version "0.3-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "geometry" version)) + (sha256 + (base32 + "0s09vi0rr0smys3an83mz6fk41bplxyz4myrbiinf4qpk6n33qib")))) + (build-system r-build-system) + (propagated-inputs `(("r-magic" ,r-magic))) + (home-page "http://geometry.r-forge.r-project.org/") + (synopsis "Mesh generation and surface tesselation") + (description + "This package makes the qhull library available in R, in a similar manner +as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace +intersections about a point, Voronoi diagrams, furthest-site Delaunay +triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, +and higher dimensions. It implements the Quickhull algorithm for computing +the convex hull. Qhull does not support constrained Delaunay triangulations, +or mesh generation of non-convex objects, but the package does include some R +functions that allow for this. Currently the package only gives access to +Delaunay triangulation and convex hull computation.") + ;; The Qhull sources are included and are distributed under a custom + ;; non-copyleft license. The R sources are released under GPL version 2. + (license (list license:gpl2 + (license:non-copyleft "http://www.qhull.org/COPYING.txt"))))) + (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.1.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y")))) + "1i2zcz20zy9xd42kdz09njbkq07mj2pp6f07z6dnwi5hrmvhbh9r")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-class" ,r-class) + ("r-geometry" ,r-geometry) ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp) ("r-robustbase" ,r-robustbase) @@ -1761,14 +1820,14 @@ color labels, layout, etc.") (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.4.6") + (version "0.9.4.7") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 - "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci")))) + "1qg80wmcrpkba9njvgjdg15bgw7ddks40kkfh5x61as9lhchy4i4")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") @@ -1986,14 +2045,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.10-1") + (version "0.10-2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1j9ddh9v9081zrqlpylsk13fldilhjdyaw6r6pa726fhgnrsf8a2")))) + "1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,gfortran))) @@ -2172,19 +2231,20 @@ plotting. a three dimensional point cloud.") (define-public r-ggridges (package (name "r-ggridges") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 - "0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3")))) + "1znvsbl3px8dddpjgdrygnpz4s685wizi0jnjvx2hrz58i0chjqj")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales))) + ("r-scales" ,r-scales) + ("r-withr" ,r-withr))) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description @@ -2511,14 +2571,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd")))) + "1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2555,14 +2615,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.3") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0mhxlr4709mca9jshnah5i7yjyy6k12s933619p7p9c8nbqj39cn")))) + "1pg4jfyvandjwz3lmr38pbqi9d045iwkk3xklhsfhhxq6aviq9p7")))) (build-system r-build-system) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") @@ -2577,14 +2637,14 @@ automatically.") (define-public r-metap (package (name "r-metap") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "06ny9zkilawdy0s8yiwhnygs3yppw89bbyf76zgdavykbzscz5lh")))) + "03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -2775,14 +2835,14 @@ Cambridge University Press, 1993.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4-12") + (version "0.4-13") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq")))) + "16aldg96z7amp5mr90nb8127yy04gxsihfr26km5p3cx3j117yv0")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -3323,14 +3383,14 @@ It also includes interpolation functions.") (define-public r-psych (package (name "r-psych") - (version "1.7.8") + (version "1.8.3.3") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k")))) + "1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3354,14 +3414,14 @@ serve as a useful front end for structural equation modeling.") (define-public r-gsubfn (package (name "r-gsubfn") - (version "0.6-6") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "gsubfn" version)) (sha256 (base32 - "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv")))) + "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) (propagated-inputs `(("r-proto" ,r-proto))) (home-page "http://gsubfn.googlecode.com") @@ -3704,3 +3764,212 @@ selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.") (license license:gpl3+))) + +(define-public r-openxlsx + (package + (name "r-openxlsx") + (version "4.0.17") + (source + (origin + (method url-fetch) + (uri (cran-uri "openxlsx" version)) + (sha256 + (base32 + "1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/awalker89/openxlsx") + (synopsis "Read, write and edit XLSX files") + (description + "This package simplifies the creation of Excel @code{.xlsx} files by +providing a high level interface to writing, styling and editing worksheets. +Through the use of Rcpp, read/write times are comparable to the @code{xlsx} +and @code{XLConnect} packages with the added benefit of removing the +dependency on Java.") + (license license:gpl3))) + +(define-public r-rio + (package + (name "r-rio") + (version "0.5.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "rio" version)) + (sha256 + (base32 + "158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-data-table" ,r-data-table) + ("r-foreign" ,r-foreign) + ("r-haven" ,r-haven) + ("r-openxlsx" ,r-openxlsx) + ("r-readxl" ,r-readxl) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/leeper/rio") + (synopsis "Swiss-army knife for data I/O") + (description + "This package provides streamlined data import and export infrastructure +by making assumptions that the user is probably willing to make: @code{import} +and @code{export} determine the data structure from the file extension, +reasonable defaults are used for data import and export (e.g., +@code{stringsAsFactors=FALSE}), web-based import is natively +supported (including from SSL/HTTPS), compressed files can be read directly +without explicit decompression, and fast import packages are used where +appropriate. An additional convenience function, @code{convert}, provides a +simple method for converting between file types.") + (license license:gpl2))) + +(define-public r-maptools + (package + (name "r-maptools") + (version "0.9-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "maptools" version)) + (sha256 + (base32 + "075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreign" ,r-foreign) + ("r-lattice" ,r-lattice) + ("r-sp" ,r-sp))) + (home-page "http://r-forge.r-project.org/projects/maptools/") + (synopsis "Tools for reading and handling spatial objects") + (description + "This package provides a set of tools for manipulating and reading +geographic data, in particular ESRI Shapefiles. It includes binary access to +GSHHG shoreline files. The package also provides interface wrappers for +exchanging spatial objects with other R packages.") + ;; The C source files from shapelib are released under the Expat license. + ;; The R code is released under GPL version 2 or later. + (license (list license:gpl2+ + license:expat)))) + +(define-public r-later + (package + (name "r-later") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "later" version)) + (sha256 + (base32 + "0z9jymmclkq9zcg1fd8p6gsnm5z1sn3n9pfz3bs03qjrkbizgrvz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) + (home-page "https://github.com/r-lib/later") + (synopsis "Utilities for delaying function execution") + (description + "This package provides tools to execute arbitrary R or C functions some +time after the current time, after the R execution stack has emptied.") + (license license:gpl2+))) + +(define-public r-promises + (package + (name "r-promises") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "promises" version)) + (sha256 + (base32 + "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-later" ,r-later) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) + (home-page "https://rstudio.github.io/promises") + (synopsis "Abstractions for promise-based asynchronous programming") + (description + "This package provides fundamental abstractions for doing asynchronous +programming in R using promises. Asynchronous programming is useful for +allowing a single R process to orchestrate multiple tasks in the background +while also attending to something else. Semantics are similar to JavaScript +promises, but with a syntax that is idiomatic R.") + (license license:expat))) + +(define-public r-dosnow + (package + (name "r-dosnow") + (version "1.0.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "doSNOW" version)) + (sha256 + (base32 + "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n")))) + (properties `((upstream-name . "doSNOW"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-snow" ,r-snow))) + (home-page "https://cran.r-project.org/web/packages/doSNOW") + (synopsis "Foreach parallel adaptor for the snow package") + (description + "This package provides a parallel backend for the @code{%dopar%} function +using the @code{snow} package.") + (license license:gpl2))) + +(define-public r-snowfall + (package + (name "r-snowfall") + (version "1.84-6.1") + (source (origin + (method url-fetch) + (uri (cran-uri "snowfall" version)) + (sha256 + (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) + (build-system r-build-system) + (propagated-inputs + `(("r-snow" ,r-snow))) + (home-page "http://cran.r-project.org/web/packages/snowfall/") + (synopsis "Easier cluster computing") + (description "This package is a usability wrapper around snow for easier +development of parallel R programs. This package offers e.g. extended error +checks, and additional functions. All functions work in sequential mode, too, +if no cluster is present or wished. The package is also designed as connector +to the cluster management tool @code{sfCluster}, but can also used without +it.") + (license license:gpl2+))) + +(define-public r-codedepends + (package + (name "r-codedepends") + (version "0.5-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "CodeDepends" version)) + (sha256 + (base32 + "03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc")))) + (properties `((upstream-name . "CodeDepends"))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-xml" ,r-xml))) + (home-page "http://cran.r-project.org/web/packages/CodeDepends") + (synopsis "Analysis of R code for reproducible research and code comprehension") + (description + "This package provides tools for analyzing R expressions or blocks of +code and determining the dependencies between them. It focuses on R scripts, +but can be used on the bodies of functions. There are many facilities +including the ability to summarize or get a high-level view of code, +determining dependencies between variables, code improvement suggestions.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index d3246ab36f..a9cc3acba0 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -616,7 +616,7 @@ HP@tie{}LaserJet, and possibly other printers. See @file{README} for details.") (define-public escpr (package (name "escpr") - (version "1.6.18") + (version "1.6.20") ;; XXX: This currently works. But it will break as soon as a newer ;; version is available since the URLs for older versions are not ;; preserved. An alternative source will be added as soon as @@ -624,12 +624,12 @@ HP@tie{}LaserJet, and possibly other printers. See @file{README} for details.") (source (origin (method url-fetch) ;; The uri has to be chopped up in order to satisfy guix lint. - (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/06/86/80/" - "9955e43f3aead20366851d24cea65de779cf5aa7/" - "epson-inkjet-printer-escpr-1.6.18-1lsb3.2.tar.gz")) + (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/07/16/23/" + "804253d188a31ae6a0f2722648248ef952afedfb/" + "epson-inkjet-printer-escpr-1.6.20-1lsb3.2.tar.gz")) (sha256 (base32 - "137jf52dhi5v2rkmlw4b73f7r7f98m61dpgsb7yvqs2f0yhsjsb3")))) + "19800pl7kbbgdzbsy9ijmd7dm3ly4kr2h1dxypqpd075g6n0i770")))) (build-system gnu-build-system) (arguments `(#:configure-flags diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 01b897da22..441a6977f6 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -846,7 +846,7 @@ types are supported, as is encryption.") (define-public rocksdb (package (name "rocksdb") - (version "5.10.4") + (version "5.12.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/facebook/rocksdb" @@ -854,7 +854,7 @@ types are supported, as is encryption.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hp7jxr99vyc57n708hiqk4lks9a9zmjgfjc21mx6v1rmabj2944")) + "1jcwgsjhk4hdfr2wf549blkgb89vwcdb5i2ahhqs6zf3mm20i3bf")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 1f238637a4..2ff26aebae 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -169,7 +170,7 @@ tools that process C/C++ code.") (inputs `(("custom-qemu" ;; The afl-qemu tool builds qemu 2.10.0 with a few patches applied. - ,(package (inherit (@@ (gnu packages bootloaders) qemu-minimal-2.10)) + ,(package (inherit qemu-minimal-2.10) (name "afl-qemu") (inputs `(("afl-src" ,source) diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm index d09280a3d4..ec85831d64 100644 --- a/gnu/packages/dictionaries.scm +++ b/gnu/packages/dictionaries.scm @@ -211,7 +211,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.") (define-public grammalecte (package (name "grammalecte") - (version "0.6.3.1") + (version "0.6.4") (source (origin (method url-fetch/zipbomb) @@ -219,21 +219,8 @@ It comes with a German-English dictionary with approximately 270,000 entries.") "Grammalecte-fr-v" version ".zip")) (sha256 (base32 - "0jlzrhpx9qvjdq679w188p86x09yfjf3l0h4scjl9w26yyp53gr8")))) + "13var1gi3gb2bwi7k21bn2pla0rs17cd7kc3mc5a2nsyqgsrzxfw")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-setup - ;; Fix typos in "setup.py". In particular, add the new - ;; "graphspell" module introduced in 0.6.2. Reported upstream: - ;; <https://www.dicollecte.org/thread.php?prj=fr&t=709> - (lambda _ - (substitute* "setup.py" - (("packages=\\['grammalecte', 'grammalecte.fr'\\],") - "packages=['grammalecte', 'grammalecte.fr', 'grammalecte.graphspell'],") - (("_dictionaries/French.bdic") "graphspell/_dictionaries/fr.bdic")) - #t))))) (home-page "https://www.dicollecte.org") (synopsis "French spelling and grammar checker") (description "Grammalecte is a grammar checker dedicated to the French diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index 595000bf88..d7bf726830 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at> ;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com> +;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,6 +36,7 @@ #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages base) + #:use-module (gnu packages check) #:use-module (gnu packages databases) #:use-module (gnu packages docbook) #:use-module (gnu packages gettext) @@ -502,3 +504,29 @@ your data as it changes, without having to re-checksum unchanged data. Duperemove can also take input from the @command{fdupes} program.") (license license:gpl2))) + +(define-public ranger + (package + (name "ranger") + (version "1.9.1") + (source (origin + (method url-fetch) + (uri (string-append "https://ranger.github.io/" + "ranger-" version ".tar.gz")) + (sha256 + (base32 + "1lnzkrxcnlwnyi3z0v8ybyp8d5rm26qm35rr68kbs2lbs06inha0")))) + (build-system python-build-system) + (native-inputs ;for tests + `(("python-pytest" ,python-pytest) + ("python-pylint" ,python-pylint) + ("python-flake8" ,python-flake8) + ("which" ,which))) + (arguments '(#:test-target "test")) + (home-page "https://ranger.github.io/") + (synopsis "Console file manager") + (description "ranger is a console file manager with Vi key bindings. It +provides a minimalistic and nice curses interface with a view on the directory +hierarchy. It ships with @code{rifle}, a file launcher that is good at +automatically finding out which program to use for what file type.") + (license license:gpl3))) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index e8fb1e64d6..58f06c3106 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org> ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> -;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -107,29 +107,54 @@ of categories with some of the activities available in that category. (define-public gcompris-qt (package (name "gcompris-qt") - (version "0.70") + (version "0.90") (source (origin (method url-fetch) (uri (string-append - "http://gcompris.net/download/qt/src/gcompris-qt-" + "https://gcompris.net/download/qt/src/gcompris-qt-" version ".tar.xz")) (sha256 (base32 - "01r7i8dmwb2nlfyp0y0mzs8yydmvn5gq7xn1w7g21lysak1mliwa")))) + "1i5adxnhig849qxwi3c4v7r84q6agx1zxkd69fh4y7lcmq2qiaza")))) (build-system cmake-build-system) (arguments - ;; Qml_box2d is unmaintained and not actually required for building - '(#:configure-flags (list "-DQML_BOX2D_MODULE=disabled") + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/gcompris-qt") + `("QT_PLUGIN_PATH" ":" prefix + ,(map (lambda (label) + (string-append (assoc-ref inputs label) + "/lib/qt5/plugins")) + '("qtbase" "qtdeclarative" "qtmultimedia" "qtsvg"))) + `("QML2_IMPORT_PATH" ":" prefix + ,(map (lambda (label) + (string-append (assoc-ref inputs label) + "/lib/qt5/qml")) + '("qtdeclarative" "qtgraphicaleffects" + "qtmultimedia" "qtquickcontrols")))) + #t)))) + #:configure-flags (list "-DQML_BOX2D_MODULE=disabled") #:tests? #f)) ; no test target (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) ("gettext" ,gettext-minimal) - ("perl" ,perl))) + ("perl" ,perl) + ("qttools" ,qttools))) (inputs `(("python-2" ,python-2) - ("qt" ,qt))) ; Cannot find qtquick at runtime with modular qt. - (home-page "http://gcompris.net/index-en.html") + ("qtbase" ,qtbase) + ("qtdeclarative" ,qtdeclarative) + ("qtgraphicaleffects" ,qtgraphicaleffects) + ("qtmultimedia" ,qtmultimedia) + ("qtquickcontrols" ,qtquickcontrols) + ("qtsensors" ,qtsensors) + ("qtsvg" ,qtsvg) + ("qtxmlpatterns" ,qtxmlpatterns))) + (home-page "https://gcompris.net/index-en.html") (synopsis "Educational games for small children") (description "Gcompris offers a large collection of educational games for small diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index bc98284686..3bd15989ad 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org> -;;; Copyright © 2014, 2015, 2016, 2017 Alex Kost <alezost@gmail.com> +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Alex Kost <alezost@gmail.com> ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017 Chris Marusich <cmmarusich@gmail.com> @@ -321,14 +321,14 @@ editor (without an X toolkit)" ) (define-public geiser (package (name "geiser") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/geiser/" version "/geiser-" version ".tar.gz")) (sha256 (base32 - "0phz9d8wjk4p13vqannv0003fwh8qqrp0gfzcs2hgq1mrmv1srss")))) + "0pj3l7p8d60c9b4vfprnv6g5l61d74pls4b5dvd84cn4ky9mzwjv")))) (build-system gnu-build-system) (arguments '(#:phases @@ -412,7 +412,7 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.") (define-public emacs-with-editor (package (name "emacs-with-editor") - (version "2.7.0") + (version "2.7.2") (source (origin (method url-fetch) (uri (string-append @@ -421,7 +421,7 @@ configuration files, such as .gitattributes, .gitignore, and .git/config.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0kah7pv211zx9fsb5g4hd51bqcq2bxd1chdykd488ihvfz1l5y14")))) + "1jqi3axcs0cb1pcv1jxxc2a09v6psrm33wwl6hmyshzl8kbxs2mv")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-dash" ,emacs-dash))) @@ -561,7 +561,7 @@ support for Git-SVN.") (define-public emacs-magit-popup (package (name "emacs-magit-popup") - (version "2.12.0") + (version "2.12.3") (source (origin (method url-fetch) (uri (string-append @@ -570,7 +570,7 @@ support for Git-SVN.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1dnk611f7lww6rb03hk8ijg2jwxx9f26pjfff4bwjmnjz7hnd6vz")))) + "1kz6vj67awkwf9y2wj6m3l2him3znm08z6bkdvnmfr6rwd96dr39")))) (build-system emacs-build-system) (arguments `(#:phases @@ -4536,6 +4536,31 @@ main features of Vim, and provides facilities for writing custom extensions.") (license license:gpl3+))) +(define-public emacs-evil-collection + (let ((commit "f40704a57fd33b4bfad64147a2b771fc8961fdfc") + (revision "1")) + (package + (name "emacs-evil-collection") + (version (git-version "20180425" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-evil/evil-collection") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0qn19k0f3isnbi1hkmcf3qjxbyvp23m5ak5ny7623qgwb2nwz1l5")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-evil" ,emacs-evil))) + (home-page "https://github.com/emacs-evil/evil-collection") + (synopsis "Collection of Evil bindings for many major and minor modes") + (description "This is a collection of Evil bindings for the parts of +Emacs that Evil does not cover properly by default, such as @code{help-mode}, +@code{M-x calendar}, Eshell and more.") + (license license:gpl3+)))) + (define-public emacs-goto-chg (package (name "emacs-goto-chg") @@ -4627,14 +4652,14 @@ passive voice.") (name "emacs-org") ;; emacs-org-contrib inherits from this package. Please update its sha256 ;; checksum as well. - (version "9.1.10") + (version "9.1.11") (source (origin (method url-fetch) (uri (string-append "http://elpa.gnu.org/packages/org-" version ".tar")) (sha256 (base32 - "01vvq6m7r2ifyflvq5ga241qvl4j62smz0zr6jljk56b6nqi20lm")))) + "0i27g5qbkfqbxhgiz917pjwkxg3rwid99d0ickwx43bzq0zi7c1m")))) (build-system emacs-build-system) (home-page "https://orgmode.org/") (synopsis "Outline-based notes management and organizer") @@ -4648,14 +4673,14 @@ reproducible research.") (package (inherit emacs-org) (name "emacs-org-contrib") - (version "20180416") + (version "20180423") (source (origin (method url-fetch) (uri (string-append "https://orgmode.org/elpa/org-plus-contrib-" version ".tar")) (sha256 (base32 - "1f5zdfsa1fcf66hk3w57wh5385069yg0b86h57jgkcbmxkcmj6ij")))) + "1aggvdy74q8p79xyc19zring5gjvlzp6lbsq8ar319zkmcjrapqd")))) (arguments `(#:modules ((guix build emacs-build-system) (guix build utils) @@ -5201,6 +5226,34 @@ To make YASnippet aware of these snippets, add the above directory to Yasnippet.") (license license:gpl2+)))) +(define-public emacs-helm-system-packages + (let ((commit "986b7bd360a705053500c4ce2c9bea03dd7b24a6") + (revision "1")) + (package + (name "emacs-helm-system-packages") + (version (git-version "1.9.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-helm/helm-system-packages") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "19iklhpxgh5xx6h4dysf58nd46lmyb46xj601lf7kbwl6yq0y61f")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-helm" ,emacs-helm))) + (home-page "https://github.com/emacs-helm/helm-system-packages") + (synopsis "Helm System Packages is an interface to your package manager") + (description "List all available packages in Helm (with installed +packages displayed in their own respective face). Fuzzy-search, mark and +execute the desired action over any selections of packages: Install, +uninstall, display packages details (in Org Mode) or insert details at point, +find files owned by packages... And much more, including performing all the +above over the network.") + (license license:gpl3+)))) + (define-public emacs-memoize (package (name "emacs-memoize") @@ -6834,15 +6887,17 @@ well as Github-style emojis like @code{:smile:}. It provides a minor mode (define-public emacs-websocket (package (name "emacs-websocket") - (version "1.8") + (version "1.10") (source (origin - (method url-fetch) - (uri (string-append "https://elpa.gnu.org/packages/websocket-" - version ".tar")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/ahyatt/emacs-websocket.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0dcxmnnm8z7cvsc7nkb822a1g6w03klp7cijjnfq0pz84p3w9cd9")))) + "1dgrf7na6r6mmkknphzshlbd5fnzisg0qn0j7vfpa38wgsymaq52")))) (build-system emacs-build-system) (home-page "http://elpa.gnu.org/packages/websocket.html") (synopsis "Emacs WebSocket client and server") @@ -6906,8 +6961,8 @@ want to use it.") (license license:gpl3+))) (define-public emacs-slack - (let ((commit "92724604879149cf331fa8778d089813a9d4ce1a") - (revision "3")) + (let ((commit "d90395482d26175ce38fd935e978c428be8af9a0") + (revision "4")) (package (name "emacs-slack") (version (string-append "0-" revision "." (string-take commit 7))) @@ -6919,7 +6974,7 @@ want to use it.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1fdf8s3ca356k7m7f5kqzfamfl2nrqjj2pynjv3kkrr0ad15nxmw")))) + "14f6wjcbl09cfd3yngr6m1k1d4nr764im666mbnqbk9nmqf50nib")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-alert" ,emacs-alert) @@ -7943,3 +7998,25 @@ name and password. To skip it press a @key{Return} key. You could get a Epkg package list by invoking @code{epkg-list-packages} in Emacs.") (license license:gpl3+)))) + +(define-public emacs-elisp-slime-nav + (package + (name "emacs-elisp-slime-nav") + (version "0.9") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/purcell/elisp-slime-nav/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1vq7ym1q47p97gxrv45c9gm96d23xbp237vkmakikj6grngxjfb2")))) + (build-system emacs-build-system) + (home-page "https://github.com/purcell/elisp-slime-nav") + (synopsis "Make @code{M-.} and @code{M-,} work for elisp like they do in SLIME") + (description + "This package provides SLIME's convenient @code{M-.}and @code{M-,} navigation +in @code{emacs-lisp-mode}, together with an elisp equivalent of +@code{slime-describe-symbol}.") + (license license:gpl3+))) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index a502af9c09..7943d51cf4 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -186,7 +186,7 @@ ("bluez" ,bluez) ("curl" ,curl) ("eudev" ,eudev) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("font-wqy-microhei" ,font-wqy-microhei) ("freetype" ,freetype) ("glew" ,glew) @@ -1046,7 +1046,7 @@ emulation community. It provides highly accurate emulation.") (define-public retroarch (package (name "retroarch") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) @@ -1054,7 +1054,7 @@ emulation community. It provides highly accurate emulation.") version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1wykv0w0kdlh7lh0k1ig0lpk5vh4c7r19jlfa9103jmjlryrq679")))) + (base32 "1y9fakr41h6xpddpkj12mcw1kgldvy76nzvxm5jk5v7iyiks4c6k")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no tests diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index e6a29554f1..ed0239a613 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 David Thompson <davet@gnu.org> -;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016, 2017 Theodoros Foradis <theodoros@foradis.org> ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> @@ -585,7 +585,9 @@ as well as pick-place files.") (file-name (git-file-name name version)) (snippet ;; Remove bundled catch since we provide our own. - '(delete-file "libfive/test/catch.hpp")))) + '(begin + (delete-file "libfive/test/catch.hpp") + #t)))) (build-system cmake-build-system) (arguments `(#:test-target "libfive-test" diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index ae5deeccb5..ef2be9ad41 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -49,6 +49,7 @@ #:use-module (gnu packages llvm) #:use-module (gnu packages lua) #:use-module (gnu packages pdf) + #:use-module (gnu packages perl) #:use-module (gnu packages photo) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) @@ -176,7 +177,7 @@ removable devices or support for multimedia.") (define-public terminology (package (name "terminology") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri @@ -184,25 +185,17 @@ removable devices or support for multimedia.") "terminology/terminology-" version ".tar.xz")) (sha256 (base32 - "05ncxvzb9rzkyjvd95hzn8lswqdwr8cix6rd54nqn9559jibh4ns")) + "0kw34l5lahn1qaks3ah6x8k41d6hfywpqfak2p7qq1z87zj506mx")) (modules '((guix build utils))) ;; Remove the bundled fonts. ;; TODO: Remove bundled lz4. (snippet '(begin (delete-file-recursively "data/fonts") - (substitute* '("data/Makefile.in" "data/Makefile.am") - (("fonts") "")) - (substitute* "configure" - (("data/fonts/Makefile") "") - (("\\\"data/fonts/Makefile") "# \"data/fonts/Makefile")) - (substitute* '("data/themes/Makefile.in" - "data/themes/Makefile.am" - "data/themes/nyanology/Makefile.in" - "data/themes/nyanology/Makefile.am") - (("-fd \\$\\(top_srcdir\\)/data/fonts") "")) + (substitute* "data/meson.build" + (("subdir\\('fonts'\\)") "")) #t)))) - (build-system gnu-build-system) + (build-system meson-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -211,6 +204,7 @@ removable devices or support for multimedia.") (lambda _ (setenv "HOME" "/tmp") #t))))) (native-inputs `(("gettext" ,gettext-minimal) + ("perl" ,perl) ("pkg-config" ,pkg-config))) (inputs `(("efl" ,efl))) @@ -257,7 +251,7 @@ Libraries with some extra bells and whistles.") (define-public enlightenment (package (name "enlightenment") - (version "0.22.2") + (version "0.22.3") (source (origin (method url-fetch) (uri @@ -265,7 +259,7 @@ Libraries with some extra bells and whistles.") name "/" name "-" version ".tar.xz")) (sha256 (base32 - "0b33w75s4w7xmz9cv8dyp8vy2gcffnrvjys20fhcpw26abw1wn2d")))) + "16zydv7z94aw3rywmb9gr8ya85k7b75h22wng95lfx1x0y1yb0ad")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--enable-mount-eeze") diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 2dad010587..49e391f9db 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -348,7 +348,7 @@ of a the system to know what users are logged in, and where.") (define-public packagekit (package (name "packagekit") - (version "1.1.5") + (version "1.1.10") (source (origin (method url-fetch) (uri (string-append @@ -357,7 +357,7 @@ of a the system to know what users are logged in, and where.") "PackageKit-" version ".tar.xz")) (sha256 (base32 - "035pqxgkyki813hyw2frrbpfllq113zfk5qcp9wvsq5lsp74ix2h")))) + "1msfmb22cm4s3l6vsbr86b8s0v897sy6gcga3qg87z7640a0di2b")))) (build-system gnu-build-system) (arguments `(#:tests? #f diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 3b7db9caef..3ff27b4a1b 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> +;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1059,16 +1060,34 @@ games.") (define-public godot (package (name "godot") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/godotengine/godot/archive/" version "-stable.tar.gz")) - (file-name (string-append name "-" version)) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0k8c12nzhl98i9il9s3awbwdamkrwxk0s47jr7n8a3z93rpszd2p")))) + "0ldnk3j4w2kh454mzclmq8nk7zqrn758yrqq85i4kzljpkf93g0m")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Drop libraries that we take from Guix. Note that some + ;; of these may be modified; see "thirdparty/README.md". + (with-directory-excursion "thirdparty" + (for-each delete-file-recursively + '("freetype" + "libogg" + "libpng" + "libtheora" + "libvorbis" + "libvpx" + "libwebp" + "openssl" + "opus" + "zlib")) + #t))))) (build-system scons-build-system) (arguments `(#:scons ,scons-python2 @@ -1086,6 +1105,7 @@ games.") "builtin_libpng=no" "builtin_libtheora=no" "builtin_libvorbis=no" + "builtin_libvpx=no" "builtin_libwebp=no" "builtin_openssl=no" "builtin_opus=no" @@ -1141,6 +1161,7 @@ games.") ("glu" ,glu) ("libtheora" ,libtheora) ("libvorbis" ,libvorbis) + ("libvpx" ,libvpx) ("libwebp" ,libwebp) ("libx11" ,libx11) ("libxcursor" ,libxcursor) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index f1f76258f9..b62d679a91 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4913,7 +4913,8 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.") ,(origin (method url-fetch) (uri (string-append "https://bitbucket.org/shlomif/shlomif-cmake-modules/" - "raw/default/shlomif-cmake-modules/Shlomif_Common.cmake")) + "raw/c505713d7a7cda608f97f01577e5868a711b883e/" + "shlomif-cmake-modules/Shlomif_Common.cmake")) (sha256 (base32 "0kx9s1qqhhzprp1w3b67xmsns0n0v506bg5hgrshxaxpy6lqiwb2")))))) (home-page "http://www.shlomifish.org/open-source/projects/fortune-mod/") diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 9f31d90619..75ed83f8a4 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -500,14 +500,14 @@ development.") (define-public r-maps (package (name "r-maps") - (version "3.2.0") + (version "3.3.0") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 - "0577f3b5d3a7djl7r0miy9mzr6xq6jb32p8nyrma7m2azasbwyj3")))) + "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") @@ -519,14 +519,14 @@ Projection code and larger maps are in separate packages ('mapproj' and (define-public r-mapproj (package (name "r-mapproj") - (version "1.2-5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 - "0rjz37r4rizk2c6jaf54f0kfb60dqv6b262cnhiwjl55d4x6l0pk")))) + "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps))) (home-page "https://cran.r-project.org/web/packages/mapproj") diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 4c9cdef7cf..319c2e6fd0 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -533,7 +533,7 @@ and keep up to date translations of documentation.") (define-public gnome-disk-utility (package (name "gnome-disk-utility") - (version "3.26.2") + (version "3.28.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -541,7 +541,7 @@ and keep up to date translations of documentation.") name "-" version ".tar.xz")) (sha256 (base32 - "1wjnw9hpjqyhrr116491rfzd0837g6jqvzq2z1ndx2sdqv19caxa")))) + "09dmknfas8iifv6k5jb4a9ag57s8awrn0f26fd1qlg0mbfjlnfd6")))) (build-system meson-build-system) (native-inputs `(("glib:bin" ,glib "bin") @@ -725,7 +725,7 @@ forgotten when the session ends.") (define-public evince (package (name "evince") - (version "3.28.0") + (version "3.28.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -733,7 +733,7 @@ forgotten when the session ends.") name "-" version ".tar.xz")) (sha256 (base32 - "1a3kcls18dcz1lj8hrx8skcli9xxfyi71c17xjwayh71cm5jc8zs")))) + "1qbk1x2c7iacmmfwjzh136v2sdacrkqn9d6bnqid7xn9hlnx4m89")))) (build-system glib-or-gtk-build-system) (arguments `(#:configure-flags '("--disable-nautilus") @@ -2062,7 +2062,7 @@ libraries written in C.") (define-public vte (package (name "vte") - (version "0.50.2") + (version "0.52.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -2070,7 +2070,7 @@ libraries written in C.") name "-" version ".tar.xz")) (sha256 (base32 - "1kq9bxf7waap190zx5k78d21y3l31npblrnhfkxz4j7zz9mk3pbr")))) + "1lva70inb5y8p42rg95fb88z2ybwcz0lybla3ixbgp2sj0s4rzdh")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -2730,7 +2730,7 @@ more fun.") (define-public gnome-terminal (package (name "gnome-terminal") - (version "3.26.2") + (version "3.28.1") (source (origin (method url-fetch) @@ -2739,7 +2739,7 @@ more fun.") name "-" version ".tar.xz")) (sha256 (base32 - "1c05f2lrlm8jfx2394k6nabg4ml07lqasxaja5v98mhlm0aa96rs")))) + "1hqwh12hiy73mazqgvyrq8jk4c669x2fb4nh8mwby3qbk8ca19pp")))) (build-system glib-or-gtk-build-system) (arguments '(#:configure-flags @@ -6302,7 +6302,7 @@ existing databases over the internet.") (define-public gnome-tweak-tool (package (name "gnome-tweak-tool") - (version "3.24.1") + (version "3.26.4") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/gnome-tweak-tool/" @@ -6312,7 +6312,7 @@ existing databases over the internet.") (search-patch "gnome-tweak-tool-search-paths.patch"))) (sha256 (base32 - "0rgmm7n6jwc5hz64sprm4jxnky62hw839a7r18rn1mj884vnn8hr")))) + "1pq5a0kzh1sz7s7ax5c7p6212k9d51nk5bfvjfyqn99cs928187x")))) (build-system glib-or-gtk-build-system) (arguments `(#:configure-flags '("--localstatedir=/tmp" @@ -6320,6 +6320,16 @@ existing databases over the internet.") #:imported-modules ((guix build python-build-system) ,@%glib-or-gtk-build-system-modules) #:phases (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key outputs #:allow-other-keys) + (invoke "meson" "build" + "--prefix" (assoc-ref outputs "out")))) + (replace 'check + (lambda _ (invoke "ninja" "-C" "build" "test"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "ninja" "-C" "build" "install"))) (add-after 'install 'wrap-program (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -6330,17 +6340,21 @@ existing databases over the internet.") (add-after 'install 'wrap (@@ (guix build python-build-system) wrap))))) (native-inputs - `(("intltool" ,intltool) + `(("gtk+:bin" ,gtk+ "bin") ; For gtk-update-icon-cache + ("intltool" ,intltool) + ("meson" ,meson-for-build) + ("ninja" ,ninja) ("pkg-config" ,pkg-config))) (inputs - `(("python" ,python-2) - ("python2-pygobject" ,python2-pygobject) - ("gnome-desktop" ,gnome-desktop) - ("libsoup" ,libsoup) - ("libnotify" ,libnotify) + `(("gnome-desktop" ,gnome-desktop) + ("gtk+" ,gtk+) ("gobject-introspection" ,gobject-introspection) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) - ("gtk+" ,gtk+))) + ("libnotify" ,libnotify) + ("libsoup" ,libsoup) + ("nautilus" ,nautilus) + ("python" ,python) + ("python-pygobject" ,python-pygobject))) (synopsis "Customize advanced GNOME 3 options") (home-page "https://wiki.gnome.org/action/show/Apps/GnomeTweakTool") (description diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index 939bdf9148..c74ccc9229 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -88,7 +88,7 @@ `(("exiv2" ,exiv2) ("bzip2" ,bzip2) ("flac" ,flac) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("file" ,file) ;libmagic, for the MIME plug-in ("glib" ,glib) ("gstreamer" ,gstreamer) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 80bae77ca3..17207e2173 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -797,7 +797,7 @@ passphrase when @code{gpg} is run and needs it."))) (define-public paperkey (package (name "paperkey") - (version "1.3") + (version "1.5") (source (origin (method url-fetch) (uri (string-append "http://www.jabberwocky.com/" @@ -805,7 +805,7 @@ passphrase when @code{gpg} is run and needs it."))) version ".tar.gz")) (sha256 (base32 - "1yybj8bj68v4lxwpn596b6ismh2fyixw5vlqqg26byrn4d9dfmsv")))) + "1prd2jaf4zjad3xhv160hmi5n408ssljfg7iz90jxs9w111pjwy4")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 485aa02c46..c6fc68468f 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -195,7 +195,7 @@ ;; https://github.com/golang/go/issues/24046 ("gcc:lib" ,gcc-6 "lib"))) (native-inputs - `(("pkg-config" ,%pkg-config) + `(("pkg-config" ,pkg-config) ("which" ,which) ("net-base" ,net-base) ("perl" ,perl))) @@ -214,7 +214,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") (package (inherit go-1.4) (name "go") - (version "1.9.4") + (version "1.9.5") (source (origin (method url-fetch) @@ -222,7 +222,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") name version ".src.tar.gz")) (sha256 (base32 - "01nw8rfvf10naja0wq0kabsm012sbqq76hd4b8c7g28n6ggshwq5")))) + "1g4zqhbh1yw3gnb400szzwrdz0k5s3h0h5nc35xgmn5v69zvphpi")))) (arguments (substitute-keyword-arguments (package-arguments go-1.4) ((#:phases phases) @@ -292,6 +292,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") ("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)") ("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)") ("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)") + ("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)") ("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)") ("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)") ("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)") @@ -382,7 +383,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") (package (inherit go-1.9) (name "go") - (version "1.10") + (version "1.10.1") (source (origin (method url-fetch) @@ -390,7 +391,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") name version ".src.tar.gz")) (sha256 (base32 - "093z1h0gmi458kv7smpx0ph6jm7ss9mzxa432kysbz85jhl4kppk")))) + "1p1xyyxicp752n9wj10sljjl6mjxpfsplkhx74fzzjrwdkzlk52q")))) (arguments (substitute-keyword-arguments (package-arguments go-1.9) ((#:phases phases) @@ -460,6 +461,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") ("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)") ("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)") ("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)") + ("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)") ("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)") ("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)") ("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)") diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 74fbe9e84e..a9ee949855 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -98,23 +98,24 @@ more.") (define-public r-igraph (package (name "r-igraph") - (version "1.1.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9")))) + "1hcr6b1lz030lgay1bz8y8sxaf2j93ds8n8gsqr6qhssz141hd2m")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (inputs `(("gmp" ,gmp) - ("libxml2" ,libxml2))) + ("glpk" ,glpk) + ("libxml2" ,libxml2) + ("zlib" ,zlib))) (propagated-inputs - `(("r-irlba" ,r-irlba) - ("r-magrittr" ,r-magrittr) + `(("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-pkgconfig" ,r-pkgconfig))) (home-page "http://igraph.org") diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm index 58b0abcecf..cb72d25921 100644 --- a/gnu/packages/gstreamer.scm +++ b/gnu/packages/gstreamer.scm @@ -404,7 +404,7 @@ distribution problems in some jurisdictions, e.g. due to patent threats.") ("python" ,python))) (inputs `(("gst-plugins-base" ,gst-plugins-base) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("orc" ,orc) ("zlib" ,zlib))) (home-page "https://gstreamer.freedesktop.org/") diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index d9379b3bec..c9497225a9 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1501,7 +1501,7 @@ users and in some situations.") (description "Sly is a 2D/3D game engine written in Guile Scheme. Sly features a functional reactive programming interface and live coding capabilities.") - (home-page "http://dthompson.us/pages/software/sly.html") + (home-page "https://dthompson.us/projects/sly.html") (license license:gpl3+))) (define-public g-wrap diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index ae7ae0f519..1f0a9e46e1 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -59,7 +59,7 @@ (define-public feh (package (name "feh") - (version "2.25.1") + (version "2.26") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -67,7 +67,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc")))) + "11kckzwk3b734l0n4j41k40liq1v2lbbj1gzir5qc386g7fvzmmi")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure)) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index d312fb79de..a6d8b320da 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -716,7 +716,8 @@ supplies a generic doubly-linked list and some string functions.") (for-each (lambda (dir) (delete-file-recursively (string-append "Source/" dir))) - '("LibJPEG" "LibJXR" "LibOpenJPEG" "LibPNG" "LibRawLite" + '("LibJPEG" "LibOpenJPEG" "LibPNG" "LibRawLite" + ;; "LibJXR" "LibWebP" "OpenEXR" "ZLib")))) (patches (search-patches "freeimage-unbundle.patch" "freeimage-CVE-2015-0852.patch" @@ -752,14 +753,15 @@ supplies a generic doubly-linked list and some string functions.") ;; We need '-fpermissive' for Source/FreeImage.h. ;; libjxr doesn't have a pkg-config file. (string-append "CFLAGS+=-O2 -fPIC -fvisibility=hidden -fpermissive " - "-I" (assoc-ref %build-inputs "libjxr") "/include/jxrlib")) + ;"-I" (assoc-ref %build-inputs "libjxr") "/include/jxrlib" + )) #:tests? #f)) ; no check target (native-inputs `(("pkg-config" ,pkg-config) ("unzip" ,unzip))) (inputs `(("libjpeg" ,libjpeg) - ("libjxr" ,libjxr) + ;("libjxr" ,libjxr) ("libpng" ,libpng) ("libraw" ,libraw) ("libtiff" ,libtiff) @@ -836,16 +838,18 @@ multi-dimensional image processing.") (define-public libwebp (package (name "libwebp") - (version "0.6.1") + (version "1.0.0") (source (origin - (method url-fetch) - (uri (string-append - "http://downloads.webmproject.org/releases/webp/libwebp-" version - ".tar.gz")) + ;; No tarballs are provided for >0.6.1. + (method git-fetch) + (uri (git-reference + (url "https://chromium.googlesource.com/webm/libwebp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1ayq2zq0zbgf5yizbm32zh7p1vb8kibw74am6am1n5cz5mw3ql06")))) + "1w8jzdbr1s4238ygyrlxryycss3f2z6d9amxdq8m82nl3l6skar4")))) (build-system gnu-build-system) (inputs `(("freeglut" ,freeglut) @@ -853,10 +857,18 @@ multi-dimensional image processing.") ("libjpeg" ,libjpeg) ("libpng" ,libpng) ("libtiff" ,libtiff))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) (arguments '(#:configure-flags '("--enable-libwebpmux" "--enable-libwebpdemux" - "--enable-libwebpdecoder"))) + "--enable-libwebpdecoder") + #:phases (modify-phases %standard-phases + (add-after 'unpack 'bootstrap + (lambda _ + (invoke "autoreconf" "-vif")))))) (home-page "https://developers.google.com/speed/webp/") (synopsis "Lossless and lossy image compression") (description diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index e1c49d1385..2b266748ae 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -65,18 +65,17 @@ (define-public quassel (package (name "quassel") - (version "0.12.4") + (version "0.12.5") (source (origin (method url-fetch) (uri (string-append "http://quassel-irc.org/pub/quassel-" version ".tar.bz2")) - (patches (search-patches "quassel-fix-tls-check.patch")) (sha256 (base32 - "0ka456fb8ha3w7g74xlzfg6w4azxjjxgrhl4aqpbwg3lnd6fbr4k")) + "1qkl3sb4ijx4k17m0c42j2p5bc4jymypwhmplm942rbrzm6mg50q")) (modules '((guix build utils))) - ;; We don't want to install the bundles scripts + ;; We don't want to install the bundled scripts. (snippet '(begin (delete-file-recursively "data/scripts") @@ -105,7 +104,7 @@ ("qtscript" ,qtscript) ("snorenotify" ,snorenotify) ("zlib" ,zlib))) - (home-page "http://quassel-irc.org/") + (home-page "https://quassel-irc.org/") (synopsis "Distributed IRC client") (description "Quassel is a distributed IRC client, meaning that one or more clients can attach to and detach from the central core. It resembles the diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 4f882c3e6f..7000e5a475 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -8150,70 +8150,50 @@ by technical operatives or consultants working with enterprise platforms.") algorithms and xxHash hashing algorithm.") (license license:asl2.0))) -(define-public java-bouncycastle-bcprov +(define-public java-bouncycastle (package - (name "java-bouncycastle-bcprov") - (version "1.58") + (name "java-bouncycastle") + (version "1.59") (source (origin (method url-fetch) - (uri "https://bouncycastle.org/download/bcprov-jdk15on-158.tar.gz") + (uri (string-append "https://github.com/bcgit/bc-java/archive/r" + (substring version 0 1) "rv" + (substring version 2 4) ".tar.gz")) (sha256 (base32 - "1hgkg96llbvgs8i0krwz2n0j7wlg6jfnq8w8kg0cc899j0wfmf3n")))) + "1bwl499whlbq896w18idqw2dkp8v0wp0npv9g71i5fgf8xjh0k3q")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file + (find-files "." "\\.jar$")) + #t)))) (build-system ant-build-system) (arguments - `(#:jar-name "bouncycastle-bcprov.jar" - #:tests? #f; no tests - #:source-dir "src" + `(#:jdk ,icedtea-8 #:phases (modify-phases %standard-phases - (add-before 'configure 'unzip-src + (replace 'build (lambda _ - (mkdir-p "src") - (with-directory-excursion "src" - (invoke "unzip" "../src.zip")) - #t))))) - (native-inputs - `(("unzip" ,unzip) - ("junit" ,java-junit))) - (home-page "https://www.bouncycastle.org") - (synopsis "Cryptographic library") - (description "Bouncy Castle Provider (bcprov) is a cryptographic library -for the Java programming language.") - (license license:expat))) - -(define-public java-bouncycastle-bcpkix - (package - (name "java-bouncycastle-bcpkix") - (version "1.58") - (source (origin - (method url-fetch) - (uri "https://bouncycastle.org/download/bcpkix-jdk15on-158.tar.gz") - (sha256 - (base32 - "0is7qay02803s9f7lhnfcjlz61ni3hq5d7apg0iil7nbqkbfbcq2")))) - (build-system ant-build-system) - (arguments - `(#:jar-name "bouncycastle-bcpkix.jar" - #:tests? #f; no tests - #:source-dir "src" - #:phases - (modify-phases %standard-phases - (add-before 'configure 'unzip-src + (invoke "ant" "-f" "ant/jdk15+.xml" "build-provider") + (invoke "ant" "-f" "ant/jdk15+.xml" "build") + #t)) + (replace 'check (lambda _ - (mkdir-p "src") - (with-directory-excursion "src" - (invoke "unzip" "../src.zip")) - #t))))) + (invoke "ant" "-f" "ant/jdk15+.xml" "test"))) + (replace 'install + (install-jars "build/artifacts/jdk1.5/jars"))))) + (inputs + `(("java-javax-mail" ,java-javax-mail))) (native-inputs `(("unzip" ,unzip) - ("junit" ,java-junit))) - (inputs - `(("bcprov" ,java-bouncycastle-bcprov))) + ("junit" ,java-junit) + ("java-native-access" ,java-native-access) + ("java-native-access-platform" ,java-native-access-platform))) (home-page "https://www.bouncycastle.org") (synopsis "Cryptographic library") - (description "Bouncy Castle Java API for PKIX, CMS, EAC, TSP, PKCS, OCSP, -CMP, and CRMF.") + (description "Bouncy Castle is a cryptographic library for the Java +programming language.") (license license:expat))) (define-public java-lmax-disruptor @@ -8636,8 +8616,7 @@ protocol-independent framework to build mail and messaging applications.") ("powermock-junit4-common" ,java-powermock-modules-junit4-common) ("powermock-junit4" ,java-powermock-modules-junit4) ("powermock-support" ,java-powermock-api-support) - ("bouncycastle" ,java-bouncycastle-bcprov) - ("bouncycastle-bcpkix" ,java-bouncycastle-bcpkix))) + ("java-bouncycastle" ,java-bouncycastle))) (home-page "https://kafka.apache.org") (synopsis "Distributed streaming platform") (description "Kafka is a distributed streaming platform, which means: @@ -9610,3 +9589,225 @@ Java method invocation.") and mappings for a number of commonly used platform functions, including a large number of Win32 mappings as well as a set of utility classes that simplify native access."))) + +(define-public java-jsch-agentproxy-core + (package + (name "java-jsch-agentproxy-core") + (version "0.0.8") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ymnk/jsch-agent-proxy/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02iqg6jbc1kxvfzqcg6wy9ygqxfm82bw5rf6vnswqy4y572niz4q")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "jsch-agentproxy-core.jar" + #:source-dir "jsch-agent-proxy-core/src/main/java" + #:tests? #f)); no tests + (home-page "https://github.com/ymnk/jsch-agent-proxy") + (synopsis "Core component of the proxy to ssh-agent and Pageant in Java") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included Putty. It will be easily integrated into JSch, and users +will be allowed to use these programs for authentication.") + (license license:bsd-3))) + +(define-public java-jsch-agentproxy-sshagent + (package + (inherit java-jsch-agentproxy-core) + (name "java-jsch-agentproxy-sshagent") + (arguments + `(#:jar-name "jsch-agentproxy-sshagent.jar" + #:source-dir "jsch-agent-proxy-sshagent/src/main/java" + #:tests? #f)); no tests + (inputs + `(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core))) + (synopsis "Proxy to ssh-agent") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included in Putty. This component contains the code for a proxy to +ssh-agent."))) + +(define-public java-jsch-agentproxy-usocket-jna + (package + (inherit java-jsch-agentproxy-core) + (name "java-jsch-agentproxy-usocket-jna") + (arguments + `(#:jar-name "jsch-agentproxy-usocket-jna.jar" + #:source-dir "jsch-agent-proxy-usocket-jna/src/main/java" + #:tests? #f)); no tests + (inputs + `(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core) + ("java-native-access" ,java-native-access))) + (synopsis "USocketFactory implementation using JNA") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included in Putty. This component contains an implementation of +USocketFactory using @dfn{JNA} (Java Native Access)."))) + +(define-public java-jsch-agentproxy-pageant + (package + (inherit java-jsch-agentproxy-core) + (name "java-jsch-agentproxy-pageant") + (arguments + `(#:jar-name "jsch-agentproxy-pageant.jar" + #:source-dir "jsch-agent-proxy-pageant/src/main/java" + #:tests? #f)); no tests + (inputs + `(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core) + ("java-native-access" ,java-native-access) + ("java-native-access-platform" ,java-native-access-platform))) + (synopsis "Proxy to pageant") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included in Putty. This component contains the code for a proxy to +pageant."))) + +(define-public java-jsch-agentproxy-usocket-nc + (package + (inherit java-jsch-agentproxy-core) + (name "java-jsch-agentproxy-usocket-nc") + (arguments + `(#:jar-name "jsch-agentproxy-usocket-nc.jar" + #:source-dir "jsch-agent-proxy-usocket-nc/src/main/java" + #:tests? #f)); no tests + (inputs + `(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core))) + (synopsis "USocketFactory implementation using netcat") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included in Putty. This component contains an implementation of +USocketFactory using netcat."))) + +(define-public java-jsch-agentproxy-connector-factory + (package + (inherit java-jsch-agentproxy-core) + (name "java-jsch-agentproxy-connector-factory") + (arguments + `(#:jar-name "jsch-agentproxy-connector-factory.jar" + #:source-dir "jsch-agent-proxy-connector-factory/src/main/java" + #:tests? #f)); no tests + (inputs + `(("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core) + ("java-jsch-agentproxy-sshagent" ,java-jsch-agentproxy-sshagent) + ("java-jsch-agentproxy-usocket-jna" ,java-jsch-agentproxy-usocket-jna) + ("java-jsch-agentproxy-pageant" ,java-jsch-agentproxy-pageant) + ("java-jsch-agentproxy-usocket-nc" ,java-jsch-agentproxy-usocket-nc))) + (synopsis "Connector factory for jsch agent proxy") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included in Putty. This component contains a connector factory."))) + +(define-public java-jsch-agentproxy-jsch + (package + (inherit java-jsch-agentproxy-core) + (name "java-jsch-agentproxy-jsch") + (arguments + `(#:jar-name "jsch-agentproxy-jsch.jar" + #:source-dir "jsch-agent-proxy-jsch/src/main/java" + #:tests? #f)); no tests + (inputs + `(("java-jsch" ,java-jsch) + ("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core))) + (synopsis "JSch integration library for agentproxy") + (description "jsch-agent-proxy is a proxy program to OpenSSH's ssh-agent +and Pageant included in Putty. This component contains a library to use +jsch-agent-proxy with JSch."))) + +(define-public java-apache-ivy + (package + (name "java-apache-ivy") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://apache//ant/ivy/" version + "/apache-ivy-" version "-src.tar.gz")) + (sha256 + (base32 + "1xkfn57g2m7l6y0xdq75x5rnrgk52m9jx2xah70g3ggl8750hbr0")) + (patches + (search-patches + "java-apache-ivy-port-to-latest-bouncycastle.patch")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "ivy.jar" + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'build 'remove-example + (lambda _ + (delete-file-recursively "src/example") + #t)) + (add-before 'build 'copy-resources + (lambda _ + (with-directory-excursion "src/java" + (for-each (lambda (file) + (install-file file (string-append "../../build/classes/" (dirname file)))) + (append + (find-files "." ".*.css") + (find-files "." ".*.ent") + (find-files "." ".*.html") + (find-files "." ".*.properties") + (find-files "." ".*.xsd") + (find-files "." ".*.xsl") + (find-files "." ".*.xml")))))) + (add-before 'build 'fix-vfs + (lambda _ + (substitute* + '("src/java/org/apache/ivy/plugins/repository/vfs/VfsRepository.java" + "src/java/org/apache/ivy/plugins/repository/vfs/VfsResource.java") + (("import org.apache.commons.vfs") "import org.apache.commons.vfs2")) + #t)) + (add-before 'install 'copy-manifest + (lambda _ + (install-file "META-INF/MANIFEST.MF" "build/classes/META-INF") + #t)) + (add-before 'install 'repack + (lambda _ + (invoke "jar" "-cmf" "build/classes/META-INF/MANIFEST.MF" "build/jar/ivy.jar" + "-C" "build/classes" ".") + #t)) + (add-after 'install 'install-bin + (lambda* (#:key outputs #:allow-other-keys) + (let* ((bin (string-append (assoc-ref outputs "out") "/bin")) + (ivy (string-append bin "/ivy")) + (jar (string-append (assoc-ref outputs "out") "/share/java/ivy.jar"))) + (mkdir-p bin) + (with-output-to-file ivy + (lambda _ + (display (string-append + "#!" (which "sh") "\n" + "if [[ -z $CLASSPATH ]]; then\n" + " cp=\"" (getenv "CLASSPATH") ":" jar "\"\n" + "else\n" + " cp=\"" (getenv "CLASSPATH") ":" jar ":$CLASSPATH\"\n" + "fi\n" + (which "java") " -cp $cp org.apache.ivy.Main $@\n")))) + (chmod ivy #o755) + #t)))))) + (inputs + `(("java-bouncycastle" ,java-bouncycastle) + ("java-commons-cli" ,java-commons-cli) + ("java-commons-collections" ,java-commons-collections) + ("java-commons-httpclient" ,java-commons-httpclient) + ("java-commons-lang" ,java-commons-lang) + ("java-commons-vfs" ,java-commons-vfs) + ("java-jakarta-oro" ,java-jakarta-oro) + ("java-jsch" ,java-jsch) + ("java-jsch-agentproxy-core" ,java-jsch-agentproxy-core) + ("java-jsch-agentproxy-connector-factory" ,java-jsch-agentproxy-connector-factory) + ("java-jsch-agentproxy-jsch" ,java-jsch-agentproxy-jsch) + ("java-junit" ,java-junit))) + (home-page "https://ant.apache.org/ivy") + (synopsis "Dependency manager for the Java programming language") + (description "Ivy is a tool for managing (recording, tracking, resolving +and reporting) project dependencies. It is characterized by the following: + +@itemize +@item flexibility and configurability - Ivy is essentially process agnostic + and is not tied to any methodology or structure. Instead it provides the + necessary flexibility and configurability to be adapted to a broad range + of dependency management and build processes. +@item tight integration with Apache Ant - while available as a standalone tool, + Ivy works particularly well with Apache Ant providing a number of + powerful Ant tasks ranging from dependency resolution to dependency + reporting and publication. +@end itemize") + (license license:asl2.0))) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 7a44abdec2..6fb1eee6cc 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -384,7 +384,7 @@ ;; Julia is not officially released for ARM and MIPS. ;; See https://github.com/JuliaLang/julia/issues/10639 (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux")) - (home-page "http://julialang.org/") + (home-page "https://julialang.org/") (synopsis "High-performance dynamic language for technical computing") (description "Julia is a high-level, high-performance dynamic programming language for diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 50f44b5d65..65119e85df 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -359,14 +359,14 @@ CorelDRAW documents of all versions.") (define-public libetonyek (package (name "libetonyek") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (string-append "http://dev-www.libreoffice.org/src/" name "/" name "-" version ".tar.xz")) (sha256 (base32 - "1b1lqy6g7flximlv0bp8jbsivyhdp679yj0d0q4jzm968h6y3nv9")))) + "0bfq9rwm040xhh7b3v0gsdavwvnrz4hkwnhpggarxk70mr3j7jcx")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-mdds=1.2"))) @@ -611,14 +611,14 @@ spreadsheet documents.") (define-public libstaroffice (package (name "libstaroffice") - (version "0.0.5") + (version "0.0.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/fosnola/libstaroffice/releases/download/" version "/libstaroffice-" version ".tar.xz")) (sha256 (base32 - "10m9imcgqf7kdhn1a5ara62fdayidwm7qzj3binsls40snnhfm9i")))) + "1i0ykl0c94lc1qzb5mbyf9jr7qw8p38ja424whmhgrllh7ny203b")))) (build-system gnu-build-system) (inputs `(("librevenge" ,librevenge) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a3b3ab262e..b92b146f3b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -27,6 +27,7 @@ ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2017 nee <nee-git@hidamari.blue> ;;; Copyright © 2017 Dave Love <fx@gnu.org> +;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -391,8 +392,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.16.3") -(define %linux-libre-hash "1wmx0ph8nbwidlx1dh8bi4p97b84nif9ymv00mafnn6iykdfdin0") +(define %linux-libre-version "4.16.6") +(define %linux-libre-hash "069bxqx27xib1gz4aayy8ar2hfp68cpdi8h51g6453k0w14pkchn") (define-public linux-libre (make-linux-libre %linux-libre-version @@ -400,8 +401,8 @@ It has been modified to remove all non-free binary blobs.") %linux-compatible-systems #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.35") -(define %linux-libre-4.14-hash "0dfzc2290zks1a63zld8ac0xarc8gxwwh4wsr71y8mas7gfmyqzj") +(define %linux-libre-4.14-version "4.14.38") +(define %linux-libre-4.14-hash "09lmz8zbd3c1qf8z3d2lkhcqcwawajh76s85zdhgqdmd2idpwach") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version @@ -410,14 +411,14 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.95" - "06i756gbglxa2m4lib4p0fff5m2fm4s6f9aqc58i8lihnjqpkldk" + (make-linux-libre "4.9.97" + "1xc3mj1qi51n1kr5bxmdf1rlpyj78x9imhfc7gihn8qjc6zsf1sp" %intel-compatible-systems #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.128" - "1aqz5skyz534bcpnn6w9madg6kadgyjjypah9dhmqf841rygb6rk" + (make-linux-libre "4.4.130" + "15cayafj7d9y5fs9flg115kzrcrjycbvax9hgfzz6yym94v9k8lk" %intel-compatible-systems #:configuration-file kernel-config)) @@ -2898,7 +2899,7 @@ arrays when needed.") (define-public multipath-tools (package (name "multipath-tools") - (version "0.7.4") + (version "0.7.6") (source (origin (method url-fetch) (uri (string-append "https://git.opensvc.com/?p=multipath-tools/" @@ -2906,7 +2907,7 @@ arrays when needed.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "02lk453wa2gfxkl8zmdws15nkcibln2yw76zm779pkngkhggl6w8")) + "0zkcayi3mmp43ji2zid1gprgsvqhjjapsw7jjd60sf75prf50h2r")) (modules '((guix build utils))) (snippet '(begin @@ -3306,7 +3307,8 @@ disks and SD cards. This package provides the userland utilities.") (("alarm\\(2\\)") "alarm(5)")) #t))) #:make-flags (list (string-append "PREFIX=" - (assoc-ref %outputs "out"))) + (assoc-ref %outputs "out")) + "CC=gcc") #:tests? #f)) ;no tests (home-page (package-home-page linux-libre)) (synopsis "Free-fall protection for spinning laptop hard drives") @@ -4301,20 +4303,20 @@ available in the kernel Linux.") (define-public cpuid (package (name "cpuid") - (version "20170122") + (version "20180419") (source (origin (method url-fetch) (uri (string-append "http://www.etallen.com/cpuid/cpuid-" version ".src.tar.gz")) (sha256 (base32 - "0ra8ph9m1dckqaikfnbsh408fp2w9k49fkl423fl2hvhwsm14xk6")))) + "0cnxj72pjalsszhn862r6shw64zbrkw0k3mm36fn93bivswjnj12")))) (build-system gnu-build-system) (arguments '(#:make-flags '("CC=gcc") - #:tests? #f ; no tests + #:tests? #f ; no tests #:phases (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) ; no configure script (add-before 'install 'fix-makefile (lambda* (#:key outputs #:allow-other-keys) (substitute* "Makefile" @@ -4628,3 +4630,98 @@ the @code{coretemp} module and sets the fan speed using the @code{applesmc} module. It can be executed as a daemon or in the foreground with root privileges.") (license license:gpl3+))) + +(define-public psm2 + (package + (name "psm2") + (version "10.3-46") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/intel/opa-psm2.git") + (commit (string-append "PSM2_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0wadphv4rl5p38x6a3dgpbijlzqdvcn02cfafnp72nh9faz0zvlx")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags + `(,(string-append "LDFLAGS=-Wl,-rpath=" %output "/lib")) + #:tests? #f + #:phases (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'patch-Makefiles + (lambda _ + (substitute* "Makefile" + (("/lib64") "/lib") + (("/usr") "")) + (substitute* "compat/Makefile" + (("/lib64") "/lib") + (("/usr") "")) + #t)) + (replace 'install + (lambda _ + (setenv "DESTDIR" %output) + (invoke "make" "install") + #t))))) + (inputs + `(("rdma-core" ,rdma-core) + ("numactl" ,numactl))) + (synopsis "Intel Performance Scaled Messaging 2 (PSM2) library") + (description + "This package is low-level user-level Intel's communications interface. +The PSM2 API is a high-performance vendor-specific protocol that provides a +low-level communications interface for the Intel Omni-Path family of +high-speed networking devices.") + (home-page "https://github.com/intel/opa-psm2") + ;; Only the x86_64 architecure is supported. + (supported-systems '("x86_64-linux")) + (license (list license:bsd-3 license:gpl2)))) ; dual + +(define-public libpfm4 + (package + (name "libpfm4") + (version "4.9.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/perfmon2/" + name "/libpfm-" version ".tar.gz")) + (sha256 + (base32 + "1qp4g4n6dw42p2w5rkwzdb7ynk8h7g5vg01ybpmvxncgwa7bw3yv")))) + (build-system gnu-build-system) + (arguments + '(#:modules ((guix build utils) + (guix build gnu-build-system)) + #:phases (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (setenv "CC" "gcc") + (invoke "make") + #t))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (invoke "make" + (string-append "PREFIX=" out) + "install") + #t)))))) + (synopsis "Performance event monitoring library") + (description + "This package provides a library called libpfm4, which is used to develop +monitoring tools exploiting the performance monitoring events such as those +provided by the Performance Monitoring Unit (PMU) of modern processors. + +Libpfm4 helps convert from an event name, expressed as a string, to the event +encoding that is either the raw event as documented by the hardware vendor or +the OS-specific encoding. In the latter case, the library is able to prepare +the OS-specific data structures needed by the kernel to setup the event. + +libpfm4 provides support for the @code{perf_events} interface, which was +introduced in Linux 2.6.31.") + (home-page "http://perfmon2.sourceforge.net/") + (license license:expat))) diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm index 8166fb8d71..af576c44f7 100644 --- a/gnu/packages/lxde.scm +++ b/gnu/packages/lxde.scm @@ -48,7 +48,7 @@ (define-public libfm (package (name "libfm") - (version "1.2.5") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/pcmanfm/" @@ -56,7 +56,7 @@ "%29/LibFM/" name "-" version ".tar.xz")) (sha256 (base32 - "0nlvfwh09gbq8bkbvwnw6iqr918rrs9gc9ljb9pjspyg408bn1n7")))) + "151jyy8ipmp2h829gd9s4s429qafv1zxl7j6zaj1k1gzm9s5rmnb")))) (build-system gnu-build-system) (inputs `(("glib" ,glib) ("gtk+" ,gtk+-2))) @@ -205,26 +205,25 @@ speed up the access to freedesktop.org defined application menus.") (define-public pcmanfm (package (name "pcmanfm") - (version "1.2.5") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/" name "/" "PCManFM%20%2B%20Libfm%20%28tarball%20release" "%29/PCManFM/" name "-" version ".tar.xz")) - (patches (search-patches "pcmanfm-CVE-2017-8934.patch")) (sha256 (base32 - "0rxdh0dfzc84l85c54blq42gczygq8adhr3l9hqzy1dp530cm1hc")))) + "1ywgfyklms5hqkapsbjps4kyx20ac0d1qk16ww74yagkyfdkwsas")))) (build-system gnu-build-system) (inputs `(("gtk+" ,gtk+-2) - ("gvfs" ,gvfs) ;for trash and mount support + ("gvfs" ,gvfs) ; for trash and mount support ("libfm" ,libfm) ("libx11" ,libx11))) (native-inputs `(("intltool" ,intltool) ("libtool" ,libtool) ("pkg-config" ,pkg-config))) (propagated-inputs - `(("lxmenu-data" ,lxmenu-data))) ;for "Open With..." application list + `(("lxmenu-data" ,lxmenu-data))) ; for "Open With..." application list (synopsis "LXDE file manager") (description "PCMan is a lightweight GTK+ based file manager, compliant with freedesktop.org standard.") diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index d9b54d692f..fb511b4949 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org> ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com> +;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -689,3 +690,46 @@ mining and data analysis.") (define-public python2-scikit-learn (package-with-python2 python-scikit-learn)) + +(define-public python-autograd + (let* ((commit "442205dfefe407beffb33550846434baa90c4de7") + (revision "0") + (version (git-version "0.0.0" revision commit))) + (package + (name "python-autograd") + (home-page "https://github.com/HIPS/autograd") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (sha256 + (base32 + "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4")) + (file-name (git-file-name name version)))) + (version version) + (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) + (propagated-inputs + `(("python-future" ,python-future) + ("python-numpy" ,python-numpy))) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "py.test" "-v")))))) + (synopsis "Efficiently computes derivatives of NumPy code") + (description "Autograd can automatically differentiate native Python and +NumPy code. It can handle a large subset of Python's features, including loops, +ifs, recursion and closures, and it can even take derivatives of derivatives +of derivatives. It supports reverse-mode differentiation +(a.k.a. backpropagation), which means it can efficiently take gradients of +scalar-valued functions with respect to array-valued arguments, as well as +forward-mode differentiation, and the two can be composed arbitrarily. The +main intended application of Autograd is gradient-based optimization.") + (license license:expat)))) + +(define-public python2-autograd + (package-with-python2 python-autograd)) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index fb13ec1fdb..8980b3df74 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -747,14 +747,14 @@ invoking @command{notifymuch} from the post-new hook.") (define-public notmuch (package (name "notmuch") - (version "0.26.1") + (version "0.26.2") (source (origin (method url-fetch) (uri (string-append "https://notmuchmail.org/releases/notmuch-" version ".tar.gz")) (sha256 (base32 - "0dx8nhdmkaqabxcgxfa757m99fi395y76h9ynx8539yh9m7y9xyk")))) + "0fqf6wwvqlccq9qdnd0mky7fx0kbkczd28blf045s0vsvdjii70h")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2f6c6d6277..a2bf14ea84 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1779,7 +1779,7 @@ arising after the discretization of partial differential equations.") (define-public mumps (package (name "mumps") - (version "5.0.2") + (version "5.1.2") (source (origin (method url-fetch) @@ -1787,7 +1787,7 @@ arising after the discretization of partial differential equations.") version ".tar.gz")) (sha256 (base32 - "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp")) + "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b")) (patches (search-patches "mumps-build-parallelism.patch")))) (build-system gnu-build-system) (inputs @@ -2208,16 +2208,18 @@ implemented in ANSI C, and MPI for communications.") (define-public scotch (package (name "scotch") - (version "6.0.4") + (version "6.0.5a") (source (origin (method url-fetch) (uri (string-append "https://gforge.inria.fr/frs/download.php/" "latestfile/298/scotch_" version ".tar.gz")) (sha256 - (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm")) + (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av")) (patches (search-patches "scotch-test-threading.patch" - "pt-scotch-build-parallelism.patch")))) + "scotch-build-parallelism.patch" + "scotch-graph-induce-type-64.patch" + "scotch-graph-diam-64.patch")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) @@ -3845,14 +3847,14 @@ analysed.") (define-public r-subplex (package (name "r-subplex") - (version "1.5-2") + (version "1.5-4") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 - "1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g")))) + "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm index 5c832f9d13..d2ce394a03 100644 --- a/gnu/packages/mes.scm +++ b/gnu/packages/mes.scm @@ -60,16 +60,15 @@ extensive examples, including parsers for the Javascript and C99 languages.") (let ((triplet "i686-unknown-linux-gnu")) (package (name "mes") - (version "0.12") + (version "0.13") (source (origin (method url-fetch) (uri (string-append "https://gitlab.com/janneke/mes" - "/repository/archive.tar.gz?ref=v" - version)) - (file-name (string-append name "-" version ".tar.gz")) + "/-/archive/v" version + "/mes-" version ".tar.gz")) (sha256 (base32 - "0lbwmyl5262z28kpac6kmxxx8aglzy8n6bsicp5lyzkmzkzvjnh2")))) + "0db4f32rak839ff3n7ywkkng9672457pd2pvvgvcsyndqmmdsqw0")))) (build-system gnu-build-system) (supported-systems '("i686-linux" "x86_64-linux")) (propagated-inputs diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index b3205c7ae2..c31e3604c8 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -802,7 +802,7 @@ protocols.") (define-public c-toxcore (package (name "c-toxcore") - (version "0.1.11") + (version "0.2.2") (source (origin (method url-fetch) @@ -811,7 +811,10 @@ protocols.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "040vwihl1r5159vzimmnff75iqfg53vhnfi5wcb3cd0c2r51idl5")))) + "18bfqx0ylbas9gs91rkspf04l5fjjcl0mxm1gfs2d59bv65mvcm3")))) + (arguments + `(#:tests? #f)) ; FIXME: Testsuite seems to stay stuck on test 3. Disable + ; for now. (build-system cmake-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -829,23 +832,26 @@ messenger protocol.") (define-public utox (package (name "utox") - (version "0.16.1") + (version "0.17.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/uTox/uTox/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/uTox/uTox.git") + (commit "v0.17.0") + (recursive? #t))) ;; Needed for 'minini' git submodule. + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "14xl72y4w1x2kk0cvkcr9pmywllm0r9w2grjqiknwn95pw6yxz6q")))) + "12wbq883il7ikldayh8hm0cjfrkp45vn05xx9s1jbfz6gmkidyar")))) (build-system cmake-build-system) (arguments - `(#:phases + `(#:configure-flags '("-DENABLE_TESTS=on") + #:phases (modify-phases %standard-phases (add-before 'build 'patch-absolute-filename-libgtk-3 (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "../uTox-0.16.1/src/xlib/gtk.c" + (substitute* "../source/src/xlib/gtk.c" (("libgtk-3.so") (string-append (assoc-ref inputs "gtk+") "/lib/libgtk-3.so"))))) @@ -884,14 +890,14 @@ instant messenger with audio and video chat capabilities.") (define-public qtox (package (name "qtox") - (version "1.13.0") + (version "1.15.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/qTox/qTox/archive/v" version ".tar.gz")) (sha256 (base32 - "0dyplmlqhg4zbg7hdzp3iqppn9xgp7pds5k6w6byjcqhb9zv91ca")) + "0bmnx6m33qn9nx40yy268x4wnvv2y7bvm41hzrlbhsiaph7kg583")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (arguments @@ -913,7 +919,7 @@ instant messenger with audio and video chat capabilities.") ,(list (string-append (assoc-ref inputs "qtsvg") "/lib/qt5/plugins/")))))))))) (inputs - `(("ffmpeg" ,ffmpeg) + `(("ffmpeg" ,ffmpeg-3.4) ("filteraudio" ,filteraudio) ("glib" ,glib) ("gtk+" ,gtk+-2) @@ -1520,14 +1526,14 @@ building the IRC clients and bots.") (define-public toxic (package (name "toxic") - (version "0.8.0") + (version "0.8.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/JFreegman/toxic/archive/v" version ".tar.gz")) (sha256 (base32 - "0166lqb47f4kj34mhi57aqmnk9mh4hsicmbdsj6ag54sy1zicy20")) + "1dx6z7k0zpsd7dpysdy23f0hnm49qlikb0mq8fg0y01dsz9vxgak")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 0e2acedf7f..a9d317eb7b 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -88,7 +88,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.20.18") + (version "0.20.19") (source (origin (method url-fetch) (uri @@ -97,7 +97,7 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "0d6lz8ykyvxkl0fwnd9c5vzbbhmjh1yzv7rzhprlzfchmv12sn3a")))) + "1hsng4mnaz1jr2s3fy3q78vf2f6102lwphjdls7qln0pj8dyzk81")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index c8f2fd84b4..6f17fa799e 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1601,7 +1601,7 @@ is subjective.") (define-public tuxguitar (package (name "tuxguitar") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (string-append @@ -1609,7 +1609,7 @@ is subjective.") version "/tuxguitar-" version "-src.tar.gz")) (sha256 (base32 - "041275vwfr82kass7wiq9g2y82w9qrbzfinzcvfij2f2q45njwmc")) + "1yd5wv17sh6i8pkndxayfd6r2k1ccgnc4w3nda3lpniv8cpjzz3k")) (modules '((guix build utils))) (snippet '(begin @@ -1691,7 +1691,7 @@ is subjective.") #t)))))) (inputs `(("java-swt" ,java-swt))) - (home-page "http://tuxguitar.pw") + (home-page "http://tuxguitar.com.ar/") (synopsis "Multitrack tablature editor and player") (description "TuxGuitar is a guitar tablature editor with player support through midi. @@ -1883,17 +1883,17 @@ browser.") (define-public drumstick (package (name "drumstick") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/drumstick/" version "/drumstick-" version ".tar.bz2")) (sha256 (base32 - "13pkfqrav30bbcddgf1imd7jk6lpqbxkz1qv31718pdl446jq7df")))) + "0avwxr6n9ra7narxc5lmkhdqi8ix10gmif8rpd06wp4g9iv46xrn")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; no test target + `(#:tests? #f ; no test target #:configure-flags '("-DLIB_SUFFIX=") #:phases (modify-phases %standard-phases @@ -1909,11 +1909,10 @@ browser.") (inputs `(("qtbase" ,qtbase) ("qtsvg" ,qtsvg) - ("alsa-lib" ,alsa-lib) - ("fluidsynth" ,fluidsynth))) + ("alsa-lib" ,alsa-lib))) (native-inputs `(("pkg-config" ,pkg-config) - ("libxslt" ,libxslt) ;for xsltproc + ("libxslt" ,libxslt) ; for xsltproc ("docbook-xsl" ,docbook-xsl) ("doxygen" ,doxygen))) (home-page "http://drumstick.sourceforge.net/") @@ -2150,14 +2149,14 @@ computer's keyboard.") (define-public aj-snapshot (package (name "aj-snapshot") - (version "0.9.7") + (version "0.9.8") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/aj-snapshot/" "aj-snapshot-" version ".tar.bz2")) (sha256 (base32 - "0yxccgp9qw2cyqv719wlbq8wfsr5ga8czvwa7bmb8dh5s11n3rn8")))) + "0wilky1g2mb88v2z0520s7sw1dsn10iwanc8id5p6z1xsnhg7b6p")))) (build-system gnu-build-system) (inputs `(("minixml" ,minixml) @@ -2393,7 +2392,7 @@ tune-in sender list from @url{http://opml.radiotime.com}.") ("curl" ,curl) ("libgcrypt" ,libgcrypt) ("json-c" ,json-c) - ("ffmpeg" ,ffmpeg))) + ("ffmpeg" ,ffmpeg-3.4))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://6xq.net/projects/pianobar/") @@ -2785,21 +2784,13 @@ available memory.") name "-" version ".tar.bz2")) (sha256 (base32 - "026v977kwb0wbmlmf6mnik328plxg8wykfx9ryvqhirac0aq39pk")) - (modules '((guix build utils))) - (snippet - ;; Remove use of __DATE__ and __TIME__ for reproducibility. - '(begin - (substitute* "main.c" - (("printf \\(\" Built : %s\", __DATE__\\);") "") - (("printf \\(\" %s\", __TIME__\\);") "")) - #t)))) + "026v977kwb0wbmlmf6mnik328plxg8wykfx9ryvqhirac0aq39pk")))) (build-system gnu-build-system) (inputs `(("alsa-lib" ,alsa-lib) ("curl" ,curl) ("faad2" ,faad2) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("file" ,file) ("jack" ,jack-1) ("libid3tag" ,libid3tag) diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm index 848399a8a1..1a79066eac 100644 --- a/gnu/packages/node.scm +++ b/gnu/packages/node.scm @@ -43,14 +43,14 @@ (define-public node (package (name "node") - (version "9.10.0") + (version "9.11.1") (source (origin (method url-fetch) (uri (string-append "http://nodejs.org/dist/v" version "/node-v" version ".tar.gz")) (sha256 (base32 - "0xld7jh3fx85az7s5zbbsbccnfjwp99xxfn5w0gh2zfc5dalwrg5")) + "1vjh9zvw7wkdz6b0l99ya7mqjk0l8lbg9isr1q8rxwp400dhkk32")) (modules '((guix build utils))) (snippet `(begin diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 7e35af5dfd..ea90e78547 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2017 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> +;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -93,8 +94,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "0.14.0") - (commit "486de7377f25438b0f44fd93f97e9ef822d558b8") - (revision 10)) + (commit "ab85cf7185da366da56314c53d8e43276e1cccc4") + (revision 11)) (package (name "guix") @@ -110,7 +111,7 @@ (commit commit))) (sha256 (base32 - "12ghbby83w335g7vbg7h52hjaal5l6mc6qmldlx8029340br8h1w")) + "1c00yr2vgsdl3kmlbjppyws47ssahamdx88y0wg26x73px71rd19")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments @@ -534,13 +535,13 @@ transactions from C or Python.") (define-public diffoscope (package (name "diffoscope") - (version "90") + (version "93") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "0hhg26vi0z2q4gwklwq4k16hibc4kq16jvyzp6zhr4kspi07wl6i")))) + "0g90nf7817jk03hzk36l3hymky4xqs50iynfld3r0in7hffly5nj")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 66d9e933e7..1dfafac4e7 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> -;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> +;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. @@ -47,7 +47,7 @@ (define-public parallel (package (name "parallel") - (version "20180322") + (version "20180422") (source (origin (method url-fetch) @@ -55,7 +55,7 @@ version ".tar.bz2")) (sha256 (base32 - "15v46pv4z98xm3fkwy7335faw4r7pilrxp4xis5a4zi4319sv2b3")))) + "0xsfpbxwgd4197gra981iv0nmjfk58c0d88dxx6dh6yrqz523klx")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch b/gnu/packages/patches/bcftools-regidx-unsigned-char.patch deleted file mode 100644 index af5bc160f5..0000000000 --- a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: Fix test-regidx argument parsing on archs with unsigned char - On architectures where char is unsigned "c >= 0" was always true. -Author: Adrian Bunk <bunk@debian.org> -Bug-Debian: https://bugs.debian.org/865060 - ---- a/test/test-regidx.c -+++ b/test/test-regidx.c -@@ -336,7 +336,7 @@ - {"seed",1,0,'s'}, - {0,0,0,0} - }; -- char c; -+ int c; - int seed = (int)time(NULL); - while ((c = getopt_long(argc, argv, "hvs:",loptions,NULL)) >= 0) - { diff --git a/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch b/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch index f210799254..429087c661 100644 --- a/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch +++ b/gnu/packages/patches/ceph-skip-collect-sys-info-test.patch @@ -1,14 +1,13 @@ This test fails because /etc/os-release is not available. diff --git a/src/test/common/test_util.cc b/src/test/common/test_util.cc -index 288dd37db1..95b6cd4b30 100644 +index 64eace923c..6daf4aa514 100644 --- a/src/test/common/test_util.cc +++ b/src/test/common/test_util.cc -@@ -31,19 +31,3 @@ TEST(util, unit_to_bytesize) - +@@ -32,17 +32,3 @@ TEST(util, unit_to_bytesize) ASSERT_EQ(65536ll, unit_to_bytesize(" 64K", &cerr)); } -- + -#if defined(__linux__) -TEST(util, collect_sys_info) -{ @@ -18,12 +17,8 @@ index 288dd37db1..95b6cd4b30 100644 - collect_sys_info(&sys_info, cct); - - ASSERT_TRUE(sys_info.find("distro") != sys_info.end()); -- ASSERT_TRUE(sys_info.find("distro_version") != sys_info.end()); - ASSERT_TRUE(sys_info.find("distro_description") != sys_info.end()); - - cct->put(); -} -#endif --- -2.11.1 - diff --git a/gnu/packages/patches/freeimage-unbundle.patch b/gnu/packages/patches/freeimage-unbundle.patch index 2727d9fbda..ca907d3276 100644 --- a/gnu/packages/patches/freeimage-unbundle.patch +++ b/gnu/packages/patches/freeimage-unbundle.patch @@ -25,7 +25,7 @@ diff -rupN FreeImage/gensrclist.sh FreeImage-new/gensrclist.sh #!/bin/sh -DIRLIST=". Source Source/Metadata Source/FreeImageToolkit Source/LibJPEG Source/LibPNG Source/LibTIFF4 Source/ZLib Source/LibOpenJPEG Source/OpenEXR Source/OpenEXR/Half Source/OpenEXR/Iex Source/OpenEXR/IlmImf Source/OpenEXR/IlmThread Source/OpenEXR/Imath Source/OpenEXR/IexMath Source/LibRawLite Source/LibRawLite/dcraw Source/LibRawLite/internal Source/LibRawLite/libraw Source/LibRawLite/src Source/LibWebP Source/LibJXR Source/LibJXR/common/include Source/LibJXR/image/sys Source/LibJXR/jxrgluelib" -+DIRLIST=". Source Source/Metadata Source/FreeImageToolkit" ++DIRLIST=". Source Source/Metadata Source/FreeImageToolkit Source/LibJXR Source/LibJXR/common/include Source/LibJXR/image/sys Source/LibJXR/jxrgluelib" echo "VER_MAJOR = 3" > Makefile.srcs echo "VER_MINOR = 17.0" >> Makefile.srcs @@ -90,8 +90,8 @@ diff -rupN FreeImage/Makefile.gnu FreeImage-new/Makefile.gnu -# LibJXR -CXXFLAGS += -D__ANSI__ -CXXFLAGS += $(INCLUDE) -+override CFLAGS += $(INCLUDE) -D__ANSI__ -I/usr/include/jxrlib $(shell pkg-config --cflags OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib) -+override LDFLAGS += -ljpeg -ljpegxr -ljxrglue $(shell pkg-config --libs OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib) ++override CFLAGS += $(INCLUDE) -D__ANSI__ $(shell pkg-config --cflags OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib) ++override LDFLAGS += -ljpeg $(shell pkg-config --libs OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib) ifeq ($(shell sh -c 'uname -m 2>/dev/null || echo not'),x86_64) - CFLAGS += -fPIC @@ -215,18 +215,6 @@ diff -rupN FreeImage/Source/FreeImage/PluginJPEG.cpp FreeImage-new/Source/FreeIm } #include "FreeImage.h" -diff -rupN FreeImage/Source/FreeImage/PluginJXR.cpp FreeImage-new/Source/FreeImage/PluginJXR.cpp ---- FreeImage/Source/FreeImage/PluginJXR.cpp 2015-03-02 02:07:08.000000000 +0100 -+++ FreeImage-new/Source/FreeImage/PluginJXR.cpp 2015-09-05 02:13:52.043353343 +0200 -@@ -23,7 +23,7 @@ - #include "Utilities.h" - #include "../Metadata/FreeImageTag.h" - --#include "../LibJXR/jxrgluelib/JXRGlue.h" -+#include <JXRGlue.h> - - // ========================================================== - // Plugin Interface diff -rupN FreeImage/Source/FreeImage/PluginPNG.cpp FreeImage-new/Source/FreeImage/PluginPNG.cpp --- FreeImage/Source/FreeImage/PluginPNG.cpp 2015-03-10 20:16:12.000000000 +0100 +++ FreeImage-new/Source/FreeImage/PluginPNG.cpp 2015-09-05 02:13:52.044353363 +0200 diff --git a/gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch b/gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch new file mode 100644 index 0000000000..506de833dd --- /dev/null +++ b/gnu/packages/patches/java-apache-ivy-port-to-latest-bouncycastle.patch @@ -0,0 +1,81 @@ +From 29055a825af5405e44ffcd59a776f8952bdc7203 Mon Sep 17 00:00:00 2001 +From: Julien Lepiller <julien@lepiller.eu> +Date: Fri, 15 Dec 2017 16:03:23 +0100 +Subject: [PATCH] Port to latest bouncycastle. + +--- + .../bouncycastle/OpenPGPSignatureGenerator.java | 34 ++++++++++------------ + 1 file changed, 16 insertions(+), 18 deletions(-) + +diff --git a/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java b/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java +index af7beae..34c204f 100644 +--- a/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java ++++ b/src/java/org/apache/ivy/plugins/signer/bouncycastle/OpenPGPSignatureGenerator.java +@@ -41,6 +41,11 @@ import org.bouncycastle.openpgp.PGPSecretKeyRingCollection; + import org.bouncycastle.openpgp.PGPSignature; + import org.bouncycastle.openpgp.PGPSignatureGenerator; + import org.bouncycastle.openpgp.PGPUtil; ++import org.bouncycastle.openpgp.operator.PBESecretKeyDecryptor; ++import org.bouncycastle.openpgp.operator.bc.BcPBESecretKeyDecryptorBuilder; ++import org.bouncycastle.openpgp.operator.bc.BcPGPDigestCalculatorProvider; ++import org.bouncycastle.openpgp.operator.bc.BcPGPContentSignerBuilder; ++import org.bouncycastle.openpgp.operator.bc.BcKeyFingerprintCalculator; + + public class OpenPGPSignatureGenerator implements SignatureGenerator { + +@@ -101,11 +106,15 @@ public class OpenPGPSignatureGenerator implements SignatureGenerator { + pgpSec = readSecretKey(keyIn); + } + +- PGPPrivateKey pgpPrivKey = pgpSec.extractPrivateKey(password.toCharArray(), +- BouncyCastleProvider.PROVIDER_NAME); +- PGPSignatureGenerator sGen = new PGPSignatureGenerator(pgpSec.getPublicKey() +- .getAlgorithm(), PGPUtil.SHA1, BouncyCastleProvider.PROVIDER_NAME); +- sGen.initSign(PGPSignature.BINARY_DOCUMENT, pgpPrivKey); ++ PBESecretKeyDecryptor decryptor = ++ new BcPBESecretKeyDecryptorBuilder(new BcPGPDigestCalculatorProvider()) ++ .build(password.toCharArray()); ++ PGPPrivateKey pgpPrivKey = pgpSec.extractPrivateKey(decryptor); ++ BcPGPContentSignerBuilder builder = new BcPGPContentSignerBuilder( ++ pgpSec.getPublicKey().getAlgorithm(), PGPUtil.SHA1); ++ ++ PGPSignatureGenerator sGen = new PGPSignatureGenerator(builder); ++ sGen.init(PGPSignature.BINARY_DOCUMENT, pgpPrivKey); + + in = new FileInputStream(src); + out = new BCPGOutputStream(new ArmoredOutputStream(new FileOutputStream(dest))); +@@ -116,22 +125,10 @@ public class OpenPGPSignatureGenerator implements SignatureGenerator { + } + + sGen.generate().encode(out); +- } catch (SignatureException e) { +- IOException ioexc = new IOException(); +- ioexc.initCause(e); +- throw ioexc; + } catch (PGPException e) { + IOException ioexc = new IOException(); + ioexc.initCause(e); + throw ioexc; +- } catch (NoSuchAlgorithmException e) { +- IOException ioexc = new IOException(); +- ioexc.initCause(e); +- throw ioexc; +- } catch (NoSuchProviderException e) { +- IOException ioexc = new IOException(); +- ioexc.initCause(e); +- throw ioexc; + } finally { + if (out != null) { + try { +@@ -156,7 +153,8 @@ public class OpenPGPSignatureGenerator implements SignatureGenerator { + + private PGPSecretKey readSecretKey(InputStream in) throws IOException, PGPException { + in = PGPUtil.getDecoderStream(in); +- PGPSecretKeyRingCollection pgpSec = new PGPSecretKeyRingCollection(in); ++ PGPSecretKeyRingCollection pgpSec = new PGPSecretKeyRingCollection(in, ++ new BcKeyFingerprintCalculator()); + + PGPSecretKey key = null; + for (Iterator it = pgpSec.getKeyRings(); key == null && it.hasNext();) { +-- +2.15.1 diff --git a/gnu/packages/patches/pcmanfm-CVE-2017-8934.patch b/gnu/packages/patches/pcmanfm-CVE-2017-8934.patch deleted file mode 100644 index 489d22c83b..0000000000 --- a/gnu/packages/patches/pcmanfm-CVE-2017-8934.patch +++ /dev/null @@ -1,56 +0,0 @@ -From bc8c3d871e9ecc67c47ff002b68cf049793faf08 Mon Sep 17 00:00:00 2001 -From: Andriy Grytsenko <andrej@rep.kiev.ua> -Date: Sun, 14 May 2017 21:35:40 +0300 -Subject: [PATCH] Fix potential access violation, use runtime user dir instead - of tmp dir. - ---- - NEWS | 4 ++++ - src/single-inst.c | 7 ++++++- - 2 files changed, 10 insertions(+), 1 deletion(-) - -diff --git a/NEWS b/NEWS -index 8c2049a..876f7f3 100644 ---- a/NEWS -+++ b/NEWS -@@ -1,3 +1,7 @@ -+* Fixed potential access violation, use runtime user dir instead of tmp dir -+ for single instance socket. -+ -+ - Changes on 1.2.5 since 1.2.4: - - * Removed options to Cut, Remove and Rename from context menu on mounted -diff --git a/src/single-inst.c b/src/single-inst.c -index 62c37b3..aaf84ab 100644 ---- a/src/single-inst.c -+++ b/src/single-inst.c -@@ -2,7 +2,7 @@ - * single-inst.c: simple IPC mechanism for single instance app - * - * Copyright 2010 Hong Jen Yee (PCMan) <pcman.tw@gmail.com> -- * Copyright 2012 Andriy Grytsenko (LStranger) <andrej@rep.kiev.ua> -+ * Copyright 2012-2017 Andriy Grytsenko (LStranger) <andrej@rep.kiev.ua> - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by -@@ -404,11 +404,16 @@ static void get_socket_name(SingleInstData* data, char* buf, int len) - } - else - dpynum = 0; -+#if GLIB_CHECK_VERSION(2, 28, 0) -+ g_snprintf(buf, len, "%s/%s-socket-%s-%d", g_get_user_runtime_dir(), -+ data->prog_name, host ? host : "", dpynum); -+#else - g_snprintf(buf, len, "%s/.%s-socket-%s-%d-%s", - g_get_tmp_dir(), - data->prog_name, - host ? host : "", - dpynum, - g_get_user_name()); -+#endif - } - --- -2.1.4 - diff --git a/gnu/packages/patches/pt-scotch-build-parallelism.patch b/gnu/packages/patches/pt-scotch-build-parallelism.patch deleted file mode 100644 index 2ac5f27f52..0000000000 --- a/gnu/packages/patches/pt-scotch-build-parallelism.patch +++ /dev/null @@ -1,13 +0,0 @@ -Building with -j may cause the esmumps_main target to fail with a "no rule for -dependency libptesmumps.a" error. Fix the dependency name. - ---- scotch_6.0.4/src/esmumps/Makefile 2012-12-01 08:29:29.000000000 -0600 -+++ scotch_6.0.4/src/esmumps/Makefile 2015-06-15 17:29:23.279605734 -0500 -@@ -160,6 +160,6 @@ - order.h \ - symbol.h \ - esmumps.h \ -- lib$(ESMUMPSLIB)$(LIB) \ -+ libesmumps$(LIB) \ - $(libdir)/lib$(SCOTCHLIB)$(LIB) \ - $(libdir)/lib$(SCOTCHLIB)errexit$(LIB) diff --git a/gnu/packages/patches/qemu-CVE-2018-7550.patch b/gnu/packages/patches/qemu-CVE-2018-7550.patch deleted file mode 100644 index 43f111e206..0000000000 --- a/gnu/packages/patches/qemu-CVE-2018-7550.patch +++ /dev/null @@ -1,66 +0,0 @@ -Fix CVE-2018-7550: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7550 - -Patch copied from upstream source repository: - -https://git.qemu.org/?p=qemu.git;a=patch;h=2a8fcd119eb7c6bb3837fc3669eb1b2dfb31daf8 - -From 2a8fcd119eb7c6bb3837fc3669eb1b2dfb31daf8 Mon Sep 17 00:00:00 2001 -From: Jack Schwartz <jack.schwartz@oracle.com> -Date: Thu, 21 Dec 2017 09:25:15 -0800 -Subject: [PATCH] multiboot: bss_end_addr can be zero - -The multiboot spec (https://www.gnu.org/software/grub/manual/multiboot/), -section 3.1.3, allows for bss_end_addr to be zero. - -A zero bss_end_addr signifies there is no .bss section. - -Suggested-by: Daniel Kiper <daniel.kiper@oracle.com> -Signed-off-by: Jack Schwartz <jack.schwartz@oracle.com> -Reviewed-by: Daniel Kiper <daniel.kiper@oracle.com> -Reviewed-by: Prasad J Pandit <pjp@fedoraproject.org> -Signed-off-by: Kevin Wolf <kwolf@redhat.com> ---- - hw/i386/multiboot.c | 18 ++++++++++-------- - 1 file changed, 10 insertions(+), 8 deletions(-) - -diff --git a/hw/i386/multiboot.c b/hw/i386/multiboot.c -index 46d9c68bf5..bb8d8e4629 100644 ---- a/hw/i386/multiboot.c -+++ b/hw/i386/multiboot.c -@@ -233,12 +233,6 @@ int load_multiboot(FWCfgState *fw_cfg, - mh_entry_addr = ldl_p(header+i+28); - - if (mh_load_end_addr) { -- if (mh_bss_end_addr < mh_load_addr) { -- fprintf(stderr, "invalid mh_bss_end_addr address\n"); -- exit(1); -- } -- mb_kernel_size = mh_bss_end_addr - mh_load_addr; -- - if (mh_load_end_addr < mh_load_addr) { - fprintf(stderr, "invalid mh_load_end_addr address\n"); - exit(1); -@@ -249,8 +243,16 @@ int load_multiboot(FWCfgState *fw_cfg, - fprintf(stderr, "invalid kernel_file_size\n"); - exit(1); - } -- mb_kernel_size = kernel_file_size - mb_kernel_text_offset; -- mb_load_size = mb_kernel_size; -+ mb_load_size = kernel_file_size - mb_kernel_text_offset; -+ } -+ if (mh_bss_end_addr) { -+ if (mh_bss_end_addr < (mh_load_addr + mb_load_size)) { -+ fprintf(stderr, "invalid mh_bss_end_addr address\n"); -+ exit(1); -+ } -+ mb_kernel_size = mh_bss_end_addr - mh_load_addr; -+ } else { -+ mb_kernel_size = mb_load_size; - } - - /* Valid if mh_flags sets MULTIBOOT_HEADER_HAS_VBE. --- -2.17.0 - diff --git a/gnu/packages/patches/quassel-fix-tls-check.patch b/gnu/packages/patches/quassel-fix-tls-check.patch deleted file mode 100644 index 057bc02a14..0000000000 --- a/gnu/packages/patches/quassel-fix-tls-check.patch +++ /dev/null @@ -1,25 +0,0 @@ -This allows quasselclient to connect to SSL-enabled quasselcore instances. - -The check in qglobal.h requires -fPIC (not -fPIE as it is now). When this check -fails SSL / TLS is disabled. - -This patch comes from the upstream source repository [0] and can be -removed when the next version is packaged. - -[0] https://github.com/quassel/quassel/commit/4768c9e99f99b581d4e32e797db91d0182391696 - ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -428,6 +428,11 @@ endif() - cmake_push_check_state(RESET) - set(CMAKE_REQUIRED_INCLUDES ${QT_INCLUDES} ${Qt5Core_INCLUDE_DIRS}) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Core_EXECUTABLE_COMPILE_FLAGS}") -+ -+if (USE_QT5 AND Qt5_POSITION_INDEPENDENT_CODE) -+ set(CMAKE_REQUIRED_FLAGS "-fPIC -DQT_NO_VERSION_TAGGING") -+endif() -+ - check_cxx_source_compiles(" - #include \"qglobal.h\" - #if defined QT_NO_SSL - diff --git a/gnu/packages/patches/scotch-build-parallelism.patch b/gnu/packages/patches/scotch-build-parallelism.patch new file mode 100644 index 0000000000..a669f1dbeb --- /dev/null +++ b/gnu/packages/patches/scotch-build-parallelism.patch @@ -0,0 +1,39 @@ +Fixes make with -j, otherwise scotch.h may not be generated by the time make +tries to compile library_graph_diam.o et al. + +Reported upstream at +https://gforge.inria.fr/tracker/index.php?func=detail&aid=21651&group_id=248&atid=1081 + +diff --git a/src/libscotch/Makefile b/src/libscotch/Makefile +index 9898894..b0ee14c 100644 +--- a/src/libscotch/Makefile ++++ b/src/libscotch/Makefile +@@ -2229,6 +2229,28 @@ library_graph_color_f$(OBJ) : library_graph_color_f.c \ + common.h \ + scotch.h + ++library_graph_diam$(OBJ) : library_graph_diam.c \ ++ module.h \ ++ common.h \ ++ graph.h \ ++ scotch.h ++ ++library_graph_diam_f$(OBJ) : library_graph_diam.c \ ++ module.h \ ++ common.h \ ++ scotch.h ++ ++library_graph_induce$(OBJ) : library_graph_diam.c \ ++ module.h \ ++ common.h \ ++ graph.h \ ++ scotch.h ++ ++library_graph_induce_f$(OBJ) : library_graph_diam.c \ ++ module.h \ ++ common.h \ ++ scotch.h ++ + library_graph_io_chac$(OBJ) : library_graph_io_chac.c \ + module.h \ + common.h \ diff --git a/gnu/packages/patches/scotch-graph-diam-64.patch b/gnu/packages/patches/scotch-graph-diam-64.patch new file mode 100644 index 0000000000..2ae31e3c3b --- /dev/null +++ b/gnu/packages/patches/scotch-graph-diam-64.patch @@ -0,0 +1,27 @@ +Fixes test_scotch_graph_diam test with -DINTSIZE64. + +Reported upstream at +https://gforge.inria.fr/tracker/index.php?func=detail&aid=21650&group_id=248&atid=1081 + +--- scotch-6.0.5a/src/libscotch/library.h ++++ scotch-6.0.5a/src/libscotch/library.h +@@ -187,6 +187,7 @@ SCOTCH_Num SCOTCH_graphBase (SCOTCH_Graph * const, const SCO + int SCOTCH_graphCheck (const SCOTCH_Graph * const); + void SCOTCH_graphSize (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const); + void SCOTCH_graphData (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num * const, SCOTCH_Num ** const, SCOTCH_Num ** const); ++SCOTCH_Num SCOTCH_graphDiamPV (SCOTCH_Graph * const); + void SCOTCH_graphStat (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const); + int SCOTCH_graphCoarsen (const SCOTCH_Graph * const, const SCOTCH_Num, const double, const SCOTCH_Num, SCOTCH_Graph * const, SCOTCH_Num * const); + int SCOTCH_graphCoarsenMatch (const SCOTCH_Graph * const, SCOTCH_Num * const, const double, const SCOTCH_Num, SCOTCH_Num * const); +--- scotch-6.0.5a/src/libscotch/library_graph_diam.c ++++ scotch-6.0.5a/src/libscotch/library_graph_diam.c +@@ -72,8 +72,7 @@ + + SCOTCH_Num + SCOTCH_graphDiamPV ( +-SCOTCH_Graph * const grafptr, +-const SCOTCH_Num baseval) ++SCOTCH_Graph * const grafptr) + { + return ((SCOTCH_Num) graphDiamPV ((Graph * const) grafptr)); + } diff --git a/gnu/packages/patches/scotch-graph-induce-type-64.patch b/gnu/packages/patches/scotch-graph-induce-type-64.patch new file mode 100644 index 0000000000..d2eee52a7b --- /dev/null +++ b/gnu/packages/patches/scotch-graph-induce-type-64.patch @@ -0,0 +1,19 @@ +Fixes return type of SCOTCH_graphInduceList and SCOTCH_graphInducePart +so that the definition matches with -DINTSIZE64. + +Reported upstream at +https://gforge.inria.fr/tracker/index.php?func=detail&aid=21608&group_id=248&atid=1081 + +--- scotch_6.0.5a/src/libscotch/library.h.orig 2018-02-11 10:52:38.000000000 -0600 ++++ scotch_6.0.5a/src/libscotch/library.h 2018-02-23 16:56:41.000000000 -0600 +@@ -199,8 +199,8 @@ + int SCOTCH_graphGeomSaveChac (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const); + int SCOTCH_graphGeomSaveMmkt (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const); + int SCOTCH_graphGeomSaveScot (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const); +-int SCOTCH_graphInduceList (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, SCOTCH_Graph * const); +-int SCOTCH_graphInducePart (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_GraphPart2 * const, const SCOTCH_GraphPart2, SCOTCH_Graph * const); ++SCOTCH_Num SCOTCH_graphInduceList (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, SCOTCH_Graph * const); ++SCOTCH_Num SCOTCH_graphInducePart (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_GraphPart2 * const, const SCOTCH_GraphPart2, SCOTCH_Graph * const); + + int SCOTCH_graphMapInit (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Arch * const, SCOTCH_Num * const); + void SCOTCH_graphMapExit (const SCOTCH_Graph * const, SCOTCH_Mapping * const); diff --git a/gnu/packages/patches/zsh-CVE-2018-7548.patch b/gnu/packages/patches/zsh-CVE-2018-7548.patch deleted file mode 100644 index 1ee15fad73..0000000000 --- a/gnu/packages/patches/zsh-CVE-2018-7548.patch +++ /dev/null @@ -1,48 +0,0 @@ -Fix CVE-2018-7548: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7548 - -Patch copied from upstream source repository: - -https://sourceforge.net/p/zsh/code/ci/110b13e1090bc31ac1352b28adc2d02b6d25a102 - -From 110b13e1090bc31ac1352b28adc2d02b6d25a102 Mon Sep 17 00:00:00 2001 -From: Joey Pabalinas <joeypabalinas@gmail.com> -Date: Tue, 23 Jan 2018 22:28:08 -0800 -Subject: [PATCH] 42313: avoid null-pointer deref when using ${(PA)...} on an - empty array result - ---- - ChangeLog | 5 +++++ - Src/subst.c | 2 +- - 2 files changed, 6 insertions(+), 1 deletion(-) - -#diff --git a/ChangeLog b/ChangeLog -#index d2ba94afc..3037edda4 100644 -#--- a/ChangeLog -#+++ b/ChangeLog -#@@ -1,3 +1,8 @@ -#+2018-01-23 Barton E. Schaefer <schaefer@zsh.org> -#+ -#+ * Joey Pabalinas: 42313: Src/subst.c: avoid null-pointer deref -#+ when using ${(PA)...} on an empty array result -#+ -# 2018-01-23 Oliver Kiddle <okiddle@yahoo.co.uk> -# -# * 42317: Completion/Linux/Command/_cryptsetup, -diff --git a/Src/subst.c b/Src/subst.c -index d027e3d83..a265a187e 100644 ---- a/Src/subst.c -+++ b/Src/subst.c -@@ -2430,7 +2430,7 @@ paramsubst(LinkList l, LinkNode n, char **str, int qt, int pf_flags, - val = aval[0]; - isarr = 0; - } -- s = dyncat(val, s); -+ s = val ? dyncat(val, s) : dupstring(s); - /* Now behave po-faced as if it was always like that... */ - subexp = 0; - /* --- -2.16.2 - diff --git a/gnu/packages/patches/zsh-CVE-2018-7549.patch b/gnu/packages/patches/zsh-CVE-2018-7549.patch deleted file mode 100644 index abefcdf2f9..0000000000 --- a/gnu/packages/patches/zsh-CVE-2018-7549.patch +++ /dev/null @@ -1,56 +0,0 @@ -Fix CVE-2018-7549: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7549 - -Patch copied from upstream source repository: - -https://sourceforge.net/p/zsh/code/ci/c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd - -From c2cc8b0fbefc9868fa83537f5b6d90fc1ec438dd Mon Sep 17 00:00:00 2001 -From: Stephane Chazelas <stephane.chazelas@gmail.com> -Date: Fri, 22 Dec 2017 22:17:09 +0000 -Subject: [PATCH] Avoid crash copying empty hash table. - -Visible with typeset -p. ---- - ChangeLog | 2 ++ - Src/params.c | 11 +++++++---- - 2 files changed, 9 insertions(+), 4 deletions(-) - -#diff --git a/ChangeLog b/ChangeLog -#index f74c26b88..e3628cfa7 100644 -#--- a/ChangeLog -#+++ b/ChangeLog -#@@ -1,5 +1,7 @@ -# 2018-01-04 Peter Stephenson <p.stephenson@samsung.com> -# -#+ * Stephane: 42159: Src/params.c: avoid crash copying empty hash table. -#+ -# * Sebastian: 42188: Src/Modules/system.c: It is necessary to -# close the lock descriptor in some failure cases. -# -diff --git a/Src/params.c b/Src/params.c -index 31ff0445b..de7730ae7 100644 ---- a/Src/params.c -+++ b/Src/params.c -@@ -549,10 +549,13 @@ scancopyparams(HashNode hn, UNUSED(int flags)) - HashTable - copyparamtable(HashTable ht, char *name) - { -- HashTable nht = newparamtable(ht->hsize, name); -- outtable = nht; -- scanhashtable(ht, 0, 0, 0, scancopyparams, 0); -- outtable = NULL; -+ HashTable nht = 0; -+ if (ht) { -+ nht = newparamtable(ht->hsize, name); -+ outtable = nht; -+ scanhashtable(ht, 0, 0, 0, scancopyparams, 0); -+ outtable = NULL; -+ } - return nht; - } - --- -2.16.2 - diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 832efc2b78..9c17733d4c 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -96,7 +96,7 @@ warning content is outputted via diag.") (define-public perl-test-base (package (name "perl-test-base") - (version "0.88") + (version "0.89") (source (origin (method url-fetch) @@ -104,7 +104,7 @@ warning content is outputted via diag.") "Test-Base-" version ".tar.gz")) (sha256 (base32 - "0fch1cvivnszbnwhpfmwv1rin04j5xkj1n1ylfmlxg6bm72qqdjj")))) + "056hibgg3i2b89mwr76vyxi6ayb3hqjqcwicvn3s5lximsma3517")))) (build-system perl-build-system) (native-inputs `(("perl-algorithm-diff" ,perl-algorithm-diff) @@ -317,7 +317,7 @@ structures without getting caught in an infinite loop.") (define-public perl-test-differences (package (name "perl-test-differences") - (version "0.63") + (version "0.64") (source (origin (method url-fetch) @@ -325,7 +325,7 @@ structures without getting caught in an infinite loop.") "Test-Differences-" version ".tar.gz")) (sha256 (base32 - "0rhs4q6qn64ji06ns7lwl6iiiw3mggvd9xk9nkiqvx1jihbplrbw")))) + "0xmj5vgklq4yqvi7l63ky1k6g7fhww68llpmw9rhlaihqbcrsicz")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) @@ -798,7 +798,7 @@ If used in a subtest, the remainder of the subtest will be skipped.") (define-public perl-test-notabs (package (name "perl-test-notabs") - (version "2.00") + (version "2.02") (source (origin (method url-fetch) @@ -808,7 +808,7 @@ If used in a subtest, the remainder of the subtest will be skipped.") ".tar.gz")) (sha256 (base32 - "127kpl1va267qar2ia4c22xb96jby2jqnda3sj5pjgmxg8si26cg")))) + "0c306p9qdpa2ycii3c50hml23mwy6bjxpry126g1dw11hyiwcxgv")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Test-NoTabs/") @@ -869,14 +869,14 @@ usually called epsilon. This module provides such a function for use with (define-public perl-test-output (package (name "perl-test-output") - (version "1.03") + (version "1.031") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/B/BD/BDFOY/" "Test-Output-" version ".tar.gz")) (sha256 (base32 - "12991jnzj4cbw9whhprmqvnzd1ayii84g2mh8vxbjngwqrjsy41i")))) + "193y1xjvgc1p9pdgdwps2127knvpz9wc1xh6gmr74y3ihmqz7f7q")))) (build-system perl-build-system) (propagated-inputs `(("perl-capture-tiny" ,perl-capture-tiny) @@ -894,7 +894,7 @@ as flexible as possible to the tester.") (define-public perl-test-pod (package (name "perl-test-pod") - (version "1.51") + (version "1.52") (source (origin (method url-fetch) @@ -902,7 +902,7 @@ as flexible as possible to the tester.") "Test-Pod-" version ".tar.gz")) (sha256 (base32 - "1yvy5mc4j3s2h4aizryvark2nm58g2c6zhw9mlx9wmsavz7d78f1")))) + "1z75x1pxwp8ajwq9iazlg2c3wd7rdlim08yclpdg32qnc36dpa30")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) (home-page "http://search.cpan.org/dist/Test-Pod/") @@ -1077,14 +1077,14 @@ makes fork(2) safe to use in test cases.") (define-public perl-test-simple (package (name "perl-test-simple") - (version "1.302122") + (version "1.302136") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/E/EX/EXODIST/" "Test-Simple-" version ".tar.gz")) (sha256 (base32 - "117m707cbvrh01s3w6g371i9xvpnklifiqpcmky4f49jgck8izgm")))) + "0inlv8f4rbhsw6qnqhf1w6ay153xbw27fldmb2pmg4ihn19mr6ld")))) (build-system perl-build-system) (synopsis "Basic utilities for writing tests") (description diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index c3609dfd58..c4228e4e05 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -162,7 +162,7 @@ ;; Fixes CVE-2018-6797, CVE-2018-6798, and CVE-2018-6913. ;; See <https://metacpan.org/changes/release/SHAY/perl-5.26.2>. -(define-public perl-5.26.2 +(define perl-5.26.2 (package (inherit perl) (version "5.26.2") @@ -386,7 +386,7 @@ error when it would have happened.") (define-public perl-bareword-filehandles (package (name "perl-bareword-filehandles") - (version "0.005") + (version "0.006") (source (origin (method url-fetch) @@ -395,7 +395,7 @@ error when it would have happened.") version ".tar.gz")) (sha256 (base32 - "0fdirls2pg7d6ymvlzzz59q3dy6hgh08k0qpr2mw51w127s8rav6")))) + "1yxz6likpfshpyfrgwyi7dw6ig1wjhh0vnvbcs6ypr62pv00fv5d")))) (build-system perl-build-system) (native-inputs `(("perl-b-hooks-op-check" ,perl-b-hooks-op-check) @@ -453,7 +453,7 @@ all known commands are checked.") (define-public perl-b-hooks-endofscope (package (name "perl-b-hooks-endofscope") - (version "0.21") + (version "0.24") (source (origin (method url-fetch) @@ -461,7 +461,7 @@ all known commands are checked.") "B-Hooks-EndOfScope-" version ".tar.gz")) (sha256 (base32 - "0b70vbpabsy9ia366k330cz1zbdyb1pwhb0l7j28pmpih045iwwh")))) + "1imcqxp23yc80a7p0h56sja9glbrh4qyhgzljqd4g9habpz3vah3")))) (build-system perl-build-system) (propagated-inputs `(("perl-module-runtime" ,perl-module-runtime) @@ -611,7 +611,7 @@ Agency.") (define-public perl-business-isbn (package (name "perl-business-isbn") - (version "3.003") + (version "3.004") (source (origin (method url-fetch) @@ -619,7 +619,7 @@ Agency.") "Business-ISBN-" version ".tar.gz")) (sha256 (base32 - "1i2bxzqkki257rqbswa4ryj1grmwa5s47wrxln2ff5mha1ry31gm")))) + "07l3zfv8hagv37i3clvj5a1zc2jarr5phg80c93ks35zaz6llx9i")))) (build-system perl-build-system) (propagated-inputs `(("perl-business-isbn-data" ,perl-business-isbn-data) @@ -721,7 +721,7 @@ algorithm to keep the most used entries in the cache.") (define-public perl-capture-tiny (package (name "perl-capture-tiny") - (version "0.46") + (version "0.48") (source (origin (method url-fetch) @@ -730,7 +730,7 @@ algorithm to keep the most used entries in the cache.") version ".tar.gz")) (sha256 (base32 - "05bhlx6d4nzamhkkh0pkckg7wlvaq6mazf7q1fbb5wpp1j1nlyjx")))) + "069yrikrrb4vqzc3hrkkfj96apsh7q0hg8lhihq97lxshwz128vc")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Capture-Tiny/") (synopsis "Capture STDOUT and STDERR from Perl, XS or external programs") @@ -1121,7 +1121,7 @@ to the calling program.") (define-public perl-class-inspector (package (name "perl-class-inspector") - (version "1.31") + (version "1.32") (source (origin (method url-fetch) @@ -1129,7 +1129,7 @@ to the calling program.") "Class-Inspector-" version ".tar.gz")) (sha256 (base32 - "1sqfjgzxx1f951fykc6vgfvys4j8rxaw2zf3jq26yrvs3ygn8pq6")))) + "0d85rihxahdvhj8cysqrgg0kbmcqghz5hgy41dbkxr1qaf5xrynf")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Class-Inspector/") (synopsis "Get information about a class and its structure") @@ -1321,14 +1321,14 @@ arrays for their internal representation.") (define-public perl-clone (package (name "perl-clone") - (version "0.38") + (version "0.39") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/G/GA/GARU/" "Clone-" version ".tar.gz")) (sha256 (base32 - "1s5xrv9zlckqqzyhxi0l9lwj9m6na2bz5hqxrkva2v7gnx5m7c4z")))) + "0bgsidb96gxzf3zhy6v1ksj1c200vxbwykk32fqm1mj97rl4dc5c")))) (build-system perl-build-system) (synopsis "Recursively copy Perl datatypes") (description @@ -2713,7 +2713,7 @@ variable in a subroutines scope to one of your choosing.") (define-public perl-devel-overloadinfo (package (name "perl-devel-overloadinfo") - (version "0.004") + (version "0.005") (source (origin (method url-fetch) @@ -2721,7 +2721,7 @@ variable in a subroutines scope to one of your choosing.") "Devel-OverloadInfo-" version ".tar.gz")) (sha256 (base32 - "0zckjhzdqa6smpp98y15mqafsyzwjxwrvk10snzhn2sb0r889s43")))) + "1rx6g8pyhi7lx6z130b7vlf8syzrq92w9ky8mpw4d6bwlkzy5zcb")))) (build-system perl-build-system) (native-inputs `(("perl-test-fatal" ,perl-test-fatal))) @@ -3026,14 +3026,14 @@ separator.") (define-public perl-error (package (name "perl-error") - (version "0.17023") + (version "0.17025") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/S/SH/SHLOMIF/" "Error-" version ".tar.gz")) (sha256 (base32 - "0dsxic78mxy30qvbbdzfyp501hbkwhnbmafqfxipr0yqfy8f2j5g")))) + "1bzgzmf1v4md02vadm46b4j4ilqxrcrfasvbzymhrznlsd54g7vc")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) (home-page "http://search.cpan.org/dist/Error/") @@ -3371,7 +3371,7 @@ type.") (define-public perl-file-find-rule (package (name "perl-file-find-rule") - (version "0.33") + (version "0.34") (source (origin (method url-fetch) @@ -3379,7 +3379,7 @@ type.") "File-Find-Rule-" version ".tar.gz")) (sha256 (base32 - "0w73b4jr2fcrd74a1w3b2jryq3mqzc8z5mk7ia9p85xn3qmpa5r4")))) + "1znachnhmi1w5pdqx8dzgfa892jb7x8ivrdy4pzjj7zb6g61cvvy")))) (build-system perl-build-system) (propagated-inputs `(("perl-text-glob" ,perl-text-glob) @@ -3636,7 +3636,7 @@ distributions. It is a companion module to File::ShareDir.") (define-public perl-file-sharedir-install (package (name "perl-file-sharedir-install") - (version "0.11") + (version "0.13") (source (origin (method url-fetch) @@ -3644,7 +3644,7 @@ distributions. It is a companion module to File::ShareDir.") "File-ShareDir-Install-" version ".tar.gz")) (sha256 (base32 - "1j0cw1aq9fdv9kl1a6fnfa4zihsvmcqzy9sb0xk0i9pyx5r8ggrj")))) + "1yc0wlkav2l2wr36a53n4mnhsy2zv29z5nm14mygxgjwv7qgvgj5")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) @@ -4522,17 +4522,17 @@ logging mechanism.") (define-public perl-log-any-adapter-log4perl (package (name "perl-log-any-adapter-log4perl") - (version "0.08") + (version "0.09") (source (origin (method url-fetch) (uri (string-append - "mirror://cpan/authors/id/D/DA/DAGOLDEN/Log-Any-Adapter-Log4perl-" + "mirror://cpan/authors/id/P/PR/PREACTION/Log-Any-Adapter-Log4perl-" version ".tar.gz")) (sha256 (base32 - "0xf4fnrsznvg0hf36q481124ja1hp3lybki1xjgnk82z9990jmxn")))) + "19f1drqnzr6g4xwjm6jk4iaa3zmiax8bzxqch04f4jr12bjd75qi")))) (build-system perl-build-system) (propagated-inputs `(("perl-log-any" ,perl-log-any) @@ -4981,7 +4981,7 @@ messages.") (define-public perl-mime-types (package (name "perl-mime-types") - (version "2.16") + (version "2.17") (source (origin (method url-fetch) @@ -4989,7 +4989,7 @@ messages.") "MIME-Types-" version ".tar.gz")) (sha256 (base32 - "0nkv99yd8bxa6h8c52nd07142f0mdzjnhcdw66s3wljmzsi9z8hk")))) + "1xlg7q6h8zyb8534sy0iqn90py18kilg419q6051bwqz5zadfkp0")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/MIME-Types/") (synopsis "Definition of MIME types") @@ -5127,7 +5127,7 @@ debug options. (define-public perl-module-find (package (name "perl-module-find") - (version "0.12") + (version "0.13") (source (origin (method url-fetch) @@ -5135,7 +5135,7 @@ debug options. "Module-Find-" version ".tar.gz")) (sha256 (base32 - "1lc33jdv4pgmm7nkr9bff0lhwjhhw91kaf6iiy2n7i7mw8dfv47l")))) + "0s45y5lvd9k89g7lds83c0bn1p29c13hfsbrd7x64jfaf8h8cisa")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Module-Find/") (synopsis "Find and use installed modules in a (sub)category") @@ -6258,7 +6258,7 @@ and libraries based on OpenSSL.") (define-public perl-multidimensional (package (name "perl-multidimensional") - (version "0.013") + (version "0.014") (source (origin (method url-fetch) @@ -6267,7 +6267,7 @@ and libraries based on OpenSSL.") version ".tar.gz")) (sha256 (base32 - "02p5zv68i39hnkmzzxsk1fi7xy56pfcsslrd7yqwzhq74czcw81x")))) + "0prchsg547ziysjl8ghiid6ph3m2xnwpsrwrjymibga7fhqi9sqj")))) (build-system perl-build-system) (native-inputs `(("perl-b-hooks-op-check" ,perl-b-hooks-op-check) @@ -7172,7 +7172,7 @@ and @code{deserialize_regexp}.") (define-public perl-safe-isa (package (name "perl-safe-isa") - (version "1.000008") + (version "1.000010") (source (origin (method url-fetch) @@ -7180,7 +7180,7 @@ and @code{deserialize_regexp}.") "Safe-Isa-" version ".tar.gz")) (sha256 (base32 - "08r74hwxq5b3bibnbwjr9anybg15l3zqdgcirpw1xm2qpvcxgdkx")))) + "0sm6p1kw98s7j6n92vvxjqf818xggnmjwci34xjmw7gzl2519x47")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Safe-Isa/") (synopsis "Call isa, can, does, and DOES safely") @@ -7452,7 +7452,7 @@ run from within a source-controlled directory.") (define-public perl-strictures-2 (package (inherit perl-strictures) - (version "2.000003") + (version "2.000004") (source (origin (method url-fetch) @@ -7460,7 +7460,7 @@ run from within a source-controlled directory.") "strictures-" version ".tar.gz")) (sha256 (base32 - "08mgvf1d2651gsg3jgjfs13878ndqa4ji8vfsda9f7jjd84ymy17")))))) + "0lzp0q6kwk6vgf7zdlvy9zz28fj6n1b776irm556c7gylcq29113")))))) (define-public perl-string-camelcase (package @@ -7691,7 +7691,7 @@ return value is the sub.") (define-public perl-sub-quote (package (name "perl-sub-quote") - (version "2.005000") + (version "2.005001") (source (origin (method url-fetch) @@ -7700,7 +7700,7 @@ return value is the sub.") version ".tar.gz")) (sha256 (base32 - "1zv45cvj4ifkbr61ydcpphnj6lvib37gfxwfh40h0yzf3c8lbca4")))) + "01xsvfdpxzimsbrp9mqipsr93y83nhj21q05g8v1bw6yfl3lzayn")))) (build-system perl-build-system) (native-inputs `(("perl-test-fatal" ,perl-test-fatal))) @@ -7873,7 +7873,7 @@ of a system.") (define-public perl-task-weaken (package (name "perl-task-weaken") - (version "1.05") + (version "1.06") (source (origin (method url-fetch) @@ -7881,7 +7881,7 @@ of a system.") "Task-Weaken-" version ".tar.gz")) (sha256 (base32 - "0p5ryr3421p5rqj6dk5dcvxsml5gl9skbn7gv4szk50fimrvzww5")))) + "1gk6rmnp4x50lzr0vfng41khf0f8yzxlm0pad1j69vxskpdzx0r3")))) (build-system perl-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -8261,7 +8261,7 @@ to tabs.") (define-public perl-text-glob (package (name "perl-text-glob") - (version "0.09") + (version "0.11") (source (origin (method url-fetch) @@ -8269,7 +8269,7 @@ to tabs.") "Text-Glob-" version ".tar.gz")) (sha256 (base32 - "0lr76wrsj8wcxrq4wi8z1640w4dmdbkznp06q744rg3g0bd238d5")))) + "11sj62fynfgwrlgkv5a051cq6yn0pagxqjsz27dxx8phsd4wv706")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) (home-page "http://search.cpan.org/dist/Text-Glob/") @@ -8791,7 +8791,7 @@ variable conform.") (define-public perl-type-tiny (package (name "perl-type-tiny") - (version "1.002001") + (version "1.002002") (source (origin (method url-fetch) @@ -8799,7 +8799,7 @@ variable conform.") "Type-Tiny-" version ".tar.gz")) (sha256 (base32 - "1p8krim8kvw123nady96fagi8sk2pj1z8jkr4r8n45ihyamfxjck")))) + "0b48v28rvl20969gyr62yg6gr6a2nj9qik0bixavbjdmk67hqnx8")))) (build-system perl-build-system) (native-inputs `(("perl-test-warnings" ,perl-test-warnings))) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 437acd305d..2c0c2313f4 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -69,14 +69,14 @@ (define-public libraw (package (name "libraw") - (version "0.18.8") + (version "0.18.9") (source (origin (method url-fetch) (uri (string-append "https://www.libraw.org/data/LibRaw-" version ".tar.gz")) (sha256 (base32 - "1qi0fkw2zmd0yplrf79z7lgpz0hxl45dj5rdgpaj7283jzys9b2n")))) + "0kmjfdr409k9q9n17k9ywims5z4kqc16s81ba7y09n7669q1gvyj")))) (build-system gnu-build-system) (home-page "https://www.libraw.org") (synopsis "Raw image decoder") @@ -330,7 +330,7 @@ photographic equipment.") (define-public darktable (package (name "darktable") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) (uri (string-append @@ -339,7 +339,7 @@ photographic equipment.") version "/darktable-" version ".tar.xz")) (sha256 (base32 - "10asz918kv2248px3w9bn5k8cfrad5xrci58x9y61l0yf5hcpk0r")))) + "1lq3xp7hhfhfwqrz0f2mrp3xywnpvb0nlw6lbm5cgx22s5xzri8x")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; There are no tests. diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 69b6ffd3f4..48e84521c5 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -620,6 +620,9 @@ Networking and Cryptography library. These libraries have a stated goal of improving usability, security and speed.") (license license:asl2.0))) +(define-public python2-pynacl + (package-with-python2 python-pynacl)) + (define-public python2-pgpdump (package (name "python2-pgpdump") @@ -715,28 +718,28 @@ Python.") (define-public python-josepy (package (name "python-josepy") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "josepy" version)) (sha256 (base32 - "1k0ahzzaq2rrjiifwbhbp7vm8z4zk0ipgiqwicil80kzlf6bhj4z")))) + "11khz8malzrv375b27jjkv66z6z6khdx1v5mkkr4vq16gp3n4p7v")))) (build-system python-build-system) (arguments - ;; The tests require pytest >= 3.2, which is not yet packaged. + ;; The tests require flake8 >= 3.5, which is not yet packaged. '(#:tests? #f)) (propagated-inputs `(("python-cryptography" ,python-cryptography) ("python-pyopenssl" ,python-pyopenssl) ("python-six" ,python-six))) -;; TODO Enable when we have pytest >= 3.2. +;; TODO Enable when we have flake8 >= 3.5. ; (native-inputs ; `(("python-coverage" ,python-coverage) ; ("python-flake8" ,python-flake8) ; ("python-isort" ,python-isort) ; ("python-mock" ,python-mock) -; ("python-pytest" ,python-pytest-3.0) +; ("python-pytest" ,python-pytest) ; ("python-pytest-cov" ,python-pytest-cov) ; ("python-pytest-cache" ,python-pytest-cache) ; ("python-pytest-flake8" ,python-pytest-flake8))) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d15ad92a56..6e8d9ab954 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -44,6 +44,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system python) + #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -214,13 +215,13 @@ and written in Python.") (define-public python-html5-parser (package (name "python-html5-parser") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (pypi-uri "html5-parser" version)) (sha256 (base32 - "1d8sxhl41ffh7qlk7wlsy17xw6slzx5v1yna9s72wx5qrpaa3wxr")))) + "01mx33sx4dhl4kj6wc48nj6jz7ry60rkhjv0s6k8h5xmjf5yy0x9")))) (build-system python-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -998,13 +999,13 @@ facilities for defining, registering and looking up components.") (define-public python-ndg-httpsclient (package (name "python-ndg-httpsclient") - (version "0.4.4") + (version "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "ndg_httpsclient" version)) (sha256 (base32 - "0sl5ak1r1xil9ms0a9fh9fm6ncml65kgnjpjfic9dhnaimwx997v")))) + "12q8rjvsvjphj6lvvcka2izdjr36a5lgkygajwx6p4wh0x1za2f0")))) (build-system python-build-system) (arguments '(;; The tests appear to require networking. @@ -1024,7 +1025,9 @@ of the SSL peer.") (define-public python2-ndg-httpsclient (package (inherit python-ndg-httpsclient) (name "python2-ndg-httpsclient") - (arguments `(#:python ,python-2)) + (arguments + (substitute-keyword-arguments (package-arguments python-ndg-httpsclient) + ((#:python _) python-2))) (propagated-inputs `(("python2-pyopenssl" ,python2-pyopenssl))))) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e342d62a03..37434c4758 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1290,14 +1290,14 @@ after Andy Lester’s Perl module WWW::Mechanize.") (define-public python-simplejson (package (name "python-simplejson") - (version "3.13.2") + (version "3.14.0") (source (origin (method url-fetch) (uri (pypi-uri "simplejson" version)) (sha256 (base32 - "02jg5nixffqyicfqdl4dil82fh1z9p2as758wp0nqwalw0hcykjc")))) + "1lkv3xlf7ryzi69zqfdbkvpxdfy1rg1rq2yzcnxgf4km5m6difqy")))) (build-system python-build-system) (home-page "http://simplejson.readthedocs.org/en/latest/") (synopsis @@ -2525,13 +2525,13 @@ sources.") (define-public python-sphinx-1.6 (package (inherit python-sphinx) (name "python-sphinx") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "1rj6f3i8hmrx2qlkshi5kp5xcy98dlynwlyl05yvflj5f66dp2xg")))) + "0gjakw9fv5pwqb5yyclxycs36sapxizk1vx6mkcdizmzgzcfy0gi")))) (arguments `(#:phases (modify-phases %standard-phases @@ -2638,14 +2638,14 @@ and several other projects.") (define-public python-rst.linker (package (name "python-rst.linker") - (version "1.7") + (version "1.9") (source (origin (method url-fetch) (uri (pypi-uri "rst.linker" version)) (sha256 (base32 - "0bh4lnj2p1nh0wf5pgxgfbrp27xhb1rinahkb5j7s3qprq6qn0sr")))) + "16crgnai6020vdmnpwdimw1vm3jb74ysfyb3kmcidb0lgma5xq2d")))) (build-system python-build-system) (propagated-inputs `(("python-dateutil" ,python-dateutil) @@ -3876,28 +3876,28 @@ multivalue dictionary that retains the order of insertions and deletions.") (define-public python-autopep8 (package - (name "python-autopep8") - (version "1.3.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "autopep8" version)) - (sha256 - (base32 - "1p9pa1ffg4iy96l918808jggg9a69iaka5awmj8xid36yc5mk0ky")))) - (build-system python-build-system) - (propagated-inputs - `(("python-pycodestyle" ,python-pycodestyle))) - (home-page "https://github.com/hhatto/autopep8") - (synopsis "Format Python code according to the PEP 8 style guide") - (description - "@code{autopep8} automatically formats Python code to conform to + (name "python-autopep8") + (version "1.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "autopep8" version)) + (sha256 + (base32 + "192bvhzi4d0claqxgzymvv7k3qnj627742bc8sgxpzjj42pd9112")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pycodestyle" ,python-pycodestyle))) + (home-page "https://github.com/hhatto/autopep8") + (synopsis "Format Python code according to the PEP 8 style guide") + (description + "@code{autopep8} automatically formats Python code to conform to the PEP 8 style guide. It uses the pycodestyle utility to determine what parts of the code needs to be formatted. @code{autopep8} is capable of fixing most of the formatting issues that can be reported by pycodestyle.") - (license (license:non-copyleft - "https://github.com/hhatto/autopep8/blob/master/LICENSE")))) + (license (license:non-copyleft + "https://github.com/hhatto/autopep8/blob/master/LICENSE")))) (define-public python2-autopep8 (package-with-python2 python-autopep8)) @@ -8264,13 +8264,13 @@ anymore.") (define-public python2-pathlib2 (package (name "python2-pathlib2") - (version "2.3.0") + (version "2.3.2") (source (origin (method url-fetch) (uri (pypi-uri "pathlib2" version)) (sha256 (base32 - "1cx5gs2v9j2vnzmcrbq5l8fq2mwrr1h6pyf1sjdji2w1bavm09fk")))) + "10yb0iv5x2hs631rcppkhbddx799d3h8pcwmkbh2a66ns3w71ccf")))) (build-system python-build-system) ;; We only need the the Python 2 variant, since for Python 3 our minimum ;; version is 3.4 which already includes this package as part of the @@ -10482,14 +10482,14 @@ a file-like object from which an arbitrarly-sized key can be read.") (define-public python-qrcode (package (name "python-qrcode") - (version "5.3") + (version "6.0") (source (origin (method url-fetch) (uri (pypi-uri "qrcode" version)) (sha256 (base32 - "0kljfrfq0c2rmxf8am57333ia41kd0snbm2rnqbdy816hgpcq5a1")))) + "1gz1g2n9kqwqkak78aavr354z1v3yyiksk7q6xp5hi1zr6s0syq3")))) (build-system python-build-system) (arguments ;; FIXME: Tests require packaging 'pymaging'. @@ -12788,14 +12788,14 @@ and works only with Python 2 and NumPy < 1.9.") (define-public python-yapf (package (name "python-yapf") - (version "0.20.1") + (version "0.21.0") (source (origin (method url-fetch) (uri (pypi-uri "yapf" version)) (sha256 (base32 - "0s7l6afzxvpx39kzd0lwshlaxw8m4fwh4iy0rlmav4vipr3g46dx")))) + "144gc7d6b1415vh02409rnb8qd5kxi6mxlr7y64d5cizgxbf72kx")))) (build-system python-build-system) (home-page "https://github.com/google/yapf") (synopsis "Formatter for Python code") @@ -13263,7 +13263,7 @@ in Python. You can simply type pybtex instead of bibtex.") (sha256 (base32 "09vagxgbq78wvq4xbikmn2hpqqsa2i96kqsmphf7dqynfv0dlsd5")))) (build-system python-build-system) - (inputs `(("python-six" ,python-six))) + (propagated-inputs `(("python-six" ,python-six))) (home-page "https://github.com/tadeck/onetimepass/") (synopsis "One-time password library") (description "Python one-time password library for HMAC-based (HOTP) and diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 98bb5bd110..c15e677438 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -4079,14 +4079,14 @@ support to both Ruby and JRuby. It uses @code{unf_ext} on CRuby and (define-public ruby-domain-name (package (name "ruby-domain-name") - (version "0.5.20170404") + (version "0.5.20180417") (source (origin (method url-fetch) (uri (rubygems-uri "domain_name" version)) (sha256 (base32 - "12hs8yijhak7p2hf1xkh98g0mnp5phq3mrrhywzaxpwz1gw5r3kf")))) + "0abdlwb64ns7ssmiqhdwgl27ly40x2l27l8hs8hn0z4kb3zd2x3v")))) (build-system ruby-build-system) (arguments `(#:phases @@ -4585,14 +4585,14 @@ files and use the data therein.") (define-public ruby-ascii85 (package (name "ruby-ascii85") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (rubygems-uri "Ascii85" version)) (sha256 (base32 - "0j95sbxd18kc8rhcnvl1w37kflqpax1r12h1x47gh4xxn3mz4m7q")))) + "0658m37jjjn6drzqg1gk4p6c205mgp7g1jh2d00n4ngghgmz5qvs")))) (build-system ruby-build-system) (native-inputs `(("bundler" ,bundler))) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index 50b5368a3b..dba5067e9e 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015, 2016 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net> @@ -302,7 +302,7 @@ Scheme and C programs and between Scheme and Java programs.") version ".tar.gz")) (sha256 (base32 - "09m7pahjsp7wxzd20cdph9j3mgf2nq5dyckcjljcd40m25v85kks")))) + "0bvq79vxcpgwydwi923cxb5w9isx2x8r3d0xndbdhacmmsw1m811")))) (build-system gnu-build-system) (arguments `(#:test-target "test" diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm index 72abfbf699..43cf2795dd 100644 --- a/gnu/packages/sdl.scm +++ b/gnu/packages/sdl.scm @@ -505,7 +505,7 @@ sound and device input (keyboards, joysticks, mice, etc.).") (string-append "--with-libsdl2-mixer-prefix=" (assoc-ref %build-inputs "sdl2-mixer"))))) (native-inputs - `(("guile" ,guile-2.0) + `(("guile" ,guile-2.2) ("pkg-config" ,pkg-config))) (inputs `(("sdl2" ,sdl2) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 5527e8ab79..8b41c8d613 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -292,20 +292,18 @@ history mechanism, job control and a C-like syntax.") (define-public zsh (package (name "zsh") - (version "5.4.2") + (version "5.5.1") (source (origin (method url-fetch) (uri (list (string-append "http://www.zsh.org/pub/zsh-" version - ".tar.gz") + ".tar.xz") (string-append "http://www.zsh.org/pub/old/zsh-" version - ".tar.gz"))) - (patches (search-patches "zsh-CVE-2018-7548.patch" - "zsh-CVE-2018-7549.patch")) + ".tar.xz"))) (sha256 (base32 - "1jdcfinzmki2w963msvsanv29vqqfmdfm4rncwpw0r3zqnrcsywm")))) + "105aqkdfsdxc4531anrj2zis2ywz6icagjam9lsc235yzh48ihz1")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-tcsetpgrp" "--enable-pcre") #:phases diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index 521be54c49..38d4a3a6bd 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -302,7 +302,7 @@ resolution scaling on graphical console window resize.") (define-public virt-viewer (package (name "virt-viewer") - (version "5.0") + (version "6.0") (source (origin (method url-fetch) (uri (string-append @@ -310,7 +310,7 @@ resolution scaling on graphical console window resize.") "virt-viewer-" version ".tar.gz")) (sha256 (base32 - "0blbp1wkw8ahss9va0bmcz2yx18j0mvm6fzrzhh2ly3sja5ysb8b")))) + "1chqrf658niivzfh85cbwkbv9vyg8sv1mv3i31vawkfsfdvvsdwh")))) (build-system gnu-build-system) (inputs `(("gtk+" ,gtk+) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index d712e06431..112ccb3280 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -258,8 +258,20 @@ Additionally, various channel-specific options can be negotiated.") (substitute* (find-files "." "\\.scm$") (("\"libguile-ssh\"") (string-append "\"" libdir "/libguile-ssh\""))) - #t))))) - + #t)))) + (add-after 'install 'remove-bin-directory + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (examples (string-append + out "/share/guile-ssh/examples"))) + (mkdir-p examples) + (rename-file (string-append bin "/ssshd.scm") + (string-append examples "/ssshd.scm")) + (rename-file (string-append bin "/sssh.scm") + (string-append examples "/sssh.scm")) + (delete-file-recursively bin) + #t)))) ;; Tests are not parallel-safe. #:parallel-tests? #f)) (native-inputs `(("autoconf" ,autoconf) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5069ef7c5d..51f5ad91b1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -361,14 +361,14 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") (define-public r-cluster (package (name "r-cluster") - (version "2.0.7") + (version "2.0.7-1") (source (origin (method url-fetch) (uri (cran-uri "cluster" version)) (sha256 (base32 - "0nf2hnsv5rhw6399b4gk1rj5c8hfc6ajfnkh3qbwfx3cz4asrg45")))) + "1grxbifbc4nwig25dmjgkympnbzb4al0w6k1c0ibdhpk1h4l20di")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -402,14 +402,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-69") + (version "0.8-70") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k")))) + "11mql8q3i1q593dvd351fhvkvfab25li80d1ahl4xjjzy52qdkc6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -488,14 +488,14 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-131.1") + (version "3.1-137") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 (base32 - "1xafi670a9jzb52kqxkacxfmy0viac3aql5byfq86kgkgla2sg0y")))) + "11vyxxc0n36vb8d8g02zr0402ymicvbifwdsqm7gy9iqqnwrn101")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -593,14 +593,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "2.41-3") + (version "2.42-3") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk")))) + "15pasbfzmg2r5bfpsadp9ia4cpybqz6n1kwm7ma02ykzf7bk4xx0")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -2694,13 +2694,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz")))) + "0hknfqcgijdapx1ryy20zy68qmm8wsb1hjx4n4hmkgl552z82q5d")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2766,13 +2766,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.10") + (version "3.98-1.11") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "1faza9bbllp67lf1yv1sllxc3iv8llz52m9diazhq322iqbh97m1")))) + "18izvlg2x9mzr6yb3yf02ghwbyn00frki3av4lpc44r22m4djnsh")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -2820,28 +2820,17 @@ plotted and compared with the asymptotic curve.") (define-public r-lambda-r (package (name "r-lambda-r") - (version "1.2") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "lambda.r" version)) (sha256 (base32 - "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x")))) + "05cfaq9dbgdnmmj3d6ggmsw300qgiw8k7f6h6k0ylv63cf3v6pkq")))) (properties `((upstream-name . "lambda.r"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'check 'delete-test-log - ;; The test report contains time stamps and is not important for - ;; the installed package. - (lambda* (#:key outputs #:allow-other-keys) - (delete-file-recursively - (string-append (assoc-ref outputs "out") - "/site-library/lambda.r/unitTests")) - #t))))) - (native-inputs - `(("r-runit" ,r-runit))) + (propagated-inputs + `(("r-formatr" ,r-formatr))) (home-page "https://cran.r-project.org/web/packages/lambda.r") (synopsis "Functional programming extension for R") (description @@ -2854,13 +2843,13 @@ safety.") (define-public r-futile-options (package (name "r-futile-options") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "futile.options" version)) (sha256 (base32 - "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f")))) + "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s")))) (properties `((upstream-name . "futile.options"))) (build-system r-build-system) @@ -3410,13 +3399,13 @@ want to migrate to S4.") (define-public r-r-oo (package (name "r-r-oo") - (version "1.21.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (cran-uri "R.oo" version)) (sha256 (base32 - "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34")))) + "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0")))) (properties `((upstream-name . "R.oo"))) (build-system r-build-system) (propagated-inputs @@ -4222,13 +4211,13 @@ series of numeric vectors/matrices and factors.") (define-public r-ztable (package (name "r-ztable") - (version "0.1.5") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "ztable" version)) (sha256 (base32 - "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r")))) + "1hk5k9614n52dpfrhdws06w4gvwhnz8q47x4cwxx88qmrzm8z2m3")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ztable") (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") @@ -4281,14 +4270,14 @@ closely-packed, non-overlapping points.") (define-public r-sourcetools (package (name "r-sourcetools") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "sourcetools" version)) (sha256 (base32 - "0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69")))) + "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sourcetools") (synopsis "Tools for reading, tokenizing and parsing R code") @@ -4697,14 +4686,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.92-8") + (version "0.93-0") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "080ynchq8pvhnmbivj4fp74n0x9lyr9923sg0s9gq5irgm68kgxw")))) + "130pzibn5cb8mycv8byc6npzcpddghz8m7jqwk15qmx4g3cj8zgy")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -5071,14 +5060,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-16") + (version "1.1-17") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "0p5x9ki4dq8058mc7k9wdnlh60z1xa3wk2nmf71wl7w59m4szh92")))) + "0czwdy1s8h3slaw73pz0h8qmqczf5135fz6i46i2dv1ql2pbq49x")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -5123,24 +5112,50 @@ modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.") (license license:gpl2+))) +(define-public r-cardata + (package + (name "r-cardata") + (version "3.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "carData" version)) + (sha256 + (base32 + "193pdwgw6gk19v7swk1kwphg3vqdmpsgi555g9nyz93sa39j7r8j")))) + (properties `((upstream-name . "carData"))) + (build-system r-build-system) + (home-page "https://r-forge.r-project.org/projects/car/") + (synopsis "Data Sets for the book Companion to Applied Regression") + (description + "This package provides datasets to accompany J. Fox and S. Weisberg, An R +Companion to Applied Regression, Third Edition, Sage.") + (license license:gpl2+))) + (define-public r-car (package (name "r-car") - (version "2.1-6") + (version "3.0-0") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 - "14l4d9j87xnb0bz2wgqqbxnlnbcdfb5vx2fw6kdxj91kyrk6lhnj")))) + "1ks2jaav8lbxhzw56vpbnysjk3pvpmqh6avd574k0bha1226k81h")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) + `(("r-abind" ,r-abind) + ("r-cardata" ,r-cardata) + ("r-lme4" ,r-lme4) + ("r-maptools" ,r-maptools) + ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) + ("r-nlme" ,r-nlme) ("r-nnet" ,r-nnet) ("r-pbkrtest" ,r-pbkrtest) - ("r-quantreg" ,r-quantreg))) + ("r-quantreg" ,r-quantreg) + ("r-rio" ,r-rio))) (home-page "https://r-forge.r-project.org/projects/car/") (synopsis "Companion to applied regression") (description @@ -5247,14 +5262,14 @@ first and second order derivatives.") (define-public r-sn (package (name "r-sn") - (version "1.5-1") + (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 - "0l7qlah6dwkp8jswnr2mn3phlm15naba5zkmv0g5pcqy5ix0gz7w")))) + "16gwr68zzj5v83bqfmzxnzwig3dnjrkxdhs6clri1caqkvrq6aig")))) (build-system r-build-system) (propagated-inputs `(("r-mnormt" ,r-mnormt) diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm index 9882a4ec34..11f6f9d7e8 100644 --- a/gnu/packages/storage.scm +++ b/gnu/packages/storage.scm @@ -51,14 +51,14 @@ (define-public ceph (package (name "ceph") - (version "12.2.4") + (version "12.2.5") (source (origin (method url-fetch) (uri (string-append "https://download.ceph.com/tarballs/ceph-" version ".tar.gz")) (sha256 (base32 - "13hv8scaxc1gdvrhzbfnsk4yy3pla6n1i4j4j4zf7schmbf0j8mp")) + "1ydc3mfvc0vpnpfnfmissvsrsj4jyxgzc2pcl1a4vdr3bwkcglp3")) (patches (search-patches "ceph-skip-unittest_blockdev.patch" "ceph-skip-collect-sys-info-test.patch" diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 93390df946..0a90610ecb 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -860,8 +860,6 @@ implements arithmetic over the Galois Field GF(256).") `(#:import-path "github.com/vitrun/qart/qr" #:unpack-path "github.com/vitrun/qart")) (synopsis "Qart component for generating QR codes") - (description "This package, a component of @code{qart}, provides -@code{qr}, for QR code generation.") (description "This package provides a library for embedding human-meaningful graphics in QR codes. However, instead of scribbling on redundant pieces and relying on error correction to preserve the meaning, diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 06e8e47323..2536754eb7 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -239,14 +239,16 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (define-public mg (package (name "mg") - (version "20171014") + (version "20180408") (source (origin - (method url-fetch) - (uri (string-append "https://homepage.boetes.org/software/mg/mg-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/hboetes/mg") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0hakfikzsml7z0hja8m8mcahrmfy2piy81bq9nccsjplyfc9clai")) + "06w86xk7sjl2x2h3z6msn8kpmwj05qdimcym77wzhz5s94dzh1bl")) (modules '((guix build utils))) (snippet '(begin (substitute* "GNUmakefile" @@ -262,10 +264,9 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on ;; No test suite available. '(#:tests? #f #:make-flags (list (string-append "prefix=" %output) - "CURSES_LIBS=-lncurses" "CC=gcc") #:phases (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) ; no configure script (add-before 'build 'correct-location-of-difftool (lambda _ (substitute* "buffer.c" @@ -294,7 +295,7 @@ team.") (define-public ghostwriter (package (name "ghostwriter") - (version "1.6.1") + (version "1.6.2") (source (origin (method git-fetch) (uri (git-reference @@ -303,7 +304,7 @@ team.") (file-name (git-file-name name version)) (sha256 (base32 - "1ihdr4xk0j83q83xknbikxb7yf9qhlkgvc89w33lhj090cv376gd")))) + "0251563zy0q69fzfacvalpx43y15cshb0bhshyd4w37061gh1c12")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 78532ec268..5734bf62d6 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -135,7 +135,7 @@ libenca and several charset conversion libraries and tools.") (define-public utf8proc (package (name "utf8proc") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) @@ -144,9 +144,9 @@ libenca and several charset conversion libraries and tools.") version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0q1jhdkk4f9b0zb8s2ql3sba3br5nvjsmbsaybmgj064k9hwbk15")))) + (base32 "1cnpigrazhslw65s4j1a56j7p6d7d61wsxxjf1218i9mkwv2yw17")))) (build-system gnu-build-system) - (inputs ;test data that is otherwise downloaded with curl + (inputs ; test data that is otherwise downloaded with curl `(("NormalizationTest.txt" ,(origin (method url-fetch) @@ -176,7 +176,7 @@ libenca and several charset conversion libraries and tools.") (substitute* "data/GraphemeBreakTest.txt" (("÷") "/") (("×") "+"))))))) - (home-page "http://julialang.org/utf8proc/") + (home-page "https://julialang.org/utf8proc/") (synopsis "C library for processing UTF-8 Unicode data") (description "utf8proc is a small C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index ef891a8b17..0c84c29fe8 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at> ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com> +;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1910,3 +1911,52 @@ repository is the centre, directories are branches and files are leaves. Contributors to the source code appear and disappear as they contribute to specific files and directories.") (license license:gpl3+))) + +(define-public src + (package + (name "src") + (version "1.18") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.catb.org/~esr/src/src-" version ".tar.gz")) + (sha256 + (base32 + "0n0skhvya8w2az45h2gsafxy8m2mvqas64nrgxifcmrzfv0rf26c")))) + (build-system gnu-build-system) + (arguments + '(#:make-flags + (list (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ; no 'configure' script + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (prog (string-append out "/bin/src")) + (rcs (assoc-ref inputs "rcs"))) + (wrap-program prog + `("PATH" ":" prefix (,(string-append rcs "/bin")))) + #t))) + (replace 'check + (lambda _ + (setenv "HOME" (getenv "TMPDIR")) + (invoke "git" "config" "--global" "user.name" "guix") + (invoke "git" "config" "--global" "user.email" "guix") + (invoke "./srctest")))))) + (native-inputs + ;; For testing. + `(("git" ,git) + ("perl" ,perl))) + (inputs + `(("python" ,python-wrapper) + ("rcs" ,rcs))) + (synopsis "Simple revision control") + (home-page "http://www.catb.org/~esr/src/") + (description + "SRC (or src) is simple revision control, a version-control system for +single-file projects by solo developers and authors. It modernizes the +venerable RCS, hence the anagrammatic acronym. The design is tuned for use +cases like all those little scripts in your @file{~/bin} directory, or a +directory full of HOWTOs.") + (license license:bsd-2))) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index ad7e12079a..85efda65ec 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2017 Chris Marusich <cmmarusich@gmail.com> ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017 Ethan R. Jones <doubleplusgood23@gmail.com> -;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org> +;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org> ;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net> ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2018 Roel Janssen <roel@gnu.org> @@ -598,14 +598,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).") (define-public ffmpeg (package (name "ffmpeg") - (version "3.4.2") + (version "4.0") (source (origin (method url-fetch) (uri (string-append "https://ffmpeg.org/releases/ffmpeg-" version ".tar.xz")) (sha256 (base32 - "0h6prjn1ijkzzhkyj8mazp0wpx7m0n9ycadjxagf9czqirbyk4ib")))) + "0gx4ngnhi5glmxh38603qy5n6vq8bl1cr4sqd1xff95i82pmv57d")))) (build-system gnu-build-system) (inputs `(("fontconfig" ,fontconfig) @@ -771,6 +771,18 @@ convert and stream audio and video. It includes the libavcodec audio/video codec library.") (license license:gpl2+))) +(define-public ffmpeg-3.4 + (package + (inherit ffmpeg) + (version "3.4.2") + (source (origin + (method url-fetch) + (uri (string-append "https://ffmpeg.org/releases/ffmpeg-" + version ".tar.xz")) + (sha256 + (base32 + "0h6prjn1ijkzzhkyj8mazp0wpx7m0n9ycadjxagf9czqirbyk4ib")))))) + (define-public ffmpeg-2.8 (package (inherit ffmpeg) @@ -791,25 +803,6 @@ audio/video codec library.") flag)) ,flags)))))) -;; Annoyingly enough, the latest mpv release does not build with the stable -;; release of ffmpeg. Use a git commit until the situation is fixed. -(define-public ffmpeg-git - (let ((commit "3f887440677328c9cfed97ad81d14051ffa32aae") - (revision "1")) - (package - (inherit ffmpeg) - (name "ffmpeg-git") - (version (string-append "3.4-" revision "." (string-take commit 9))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/FFmpeg/FFmpeg.git") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "1b7n3g4m2rbvrwsgbfl8wl91z42g1ld42clwxs8qpl9ny5rwz6sq"))))))) - (define-public vlc (package (name "vlc") @@ -1033,7 +1026,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") (inputs `(("alsa-lib" ,alsa-lib) ("enca" ,enca) - ("ffmpeg" ,ffmpeg-git) + ("ffmpeg" ,ffmpeg) ("jack" ,jack-1) ("ladspa" ,ladspa) ("lcms" ,lcms) @@ -1162,7 +1155,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2018.04.16") + (version "2018.04.25") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -1170,7 +1163,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "046zg8pww2xg1yibh7c1a8jcg8f1znr4hsz1l1da03djcp6na99d")))) + "17zxgwfcy7c6gdyxdgh02f5zi52gvmy0zpccfj6zjkhw5iqj1vbw")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion @@ -1319,7 +1312,7 @@ audio, images) from the Web. It can use either mpv or vlc for playback.") (define-public youtube-viewer (package (name "youtube-viewer") - (version "3.3.3") + (version "3.3.4") (source (origin (method url-fetch) (uri (string-append @@ -1328,7 +1321,7 @@ audio, images) from the Web. It can use either mpv or vlc for playback.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1j572his6qmazlmyrbnfq62s9bqml875ay7wy26byy9hfc7m0vgk")))) + "1dqaxkz5svv0lmxds6lppcpzhkq6gar2raw9gx6imrd7yz02fpgn")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) @@ -1857,7 +1850,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.") #t))))) (inputs `(("alsa-lib" ,alsa-lib) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("fftw" ,fftw) ("libxml2" ,libxml2) ("jack" ,jack-1) @@ -2093,7 +2086,7 @@ making @dfn{screencasts}.") ;; As a result, they are omitted. Please add them back if problems appear. (inputs `(("alsa-lib" ,alsa-lib) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("glu" ,glu) ("jack" ,jack-1) ("libxi" ,libxi) @@ -2806,7 +2799,7 @@ It counts more than 100 plugins.") ("pkg-config" ,pkg-config))) (inputs `(("libjpeg" ,libjpeg) - ("ffmpeg" ,ffmpeg) + ("ffmpeg" ,ffmpeg-3.4) ("sqlite" ,sqlite))) (arguments '(#:phases (modify-phases %standard-phases @@ -2864,3 +2857,41 @@ the results, download the highest-rated result in the requested language and save it to the appropriate filename.") (license license:gpl3+) (home-page "https://github.com/alexanderwink/subdl")))) + +(define-public l-smash + (package + (name "l-smash") + (version "2.14.5") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/" name "/" name "/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0dary0h65kq6sv93iabv25djlvzr5ckdcp3ywagbix44wqfw7xz6")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no tests + #:make-flags + (list (string-append "LDFLAGS=-Wl,-L.,-rpath=" + (assoc-ref %outputs "out") "/lib")) + #:phases + (modify-phases %standard-phases + ;; configure fails if it is followed by CONFIG_SHELL + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (invoke "./configure" (string-append "--prefix=" out) + "--disable-static"))))))) + (native-inputs + `(("which" ,which))) + (home-page "https://l-smash.github.io/l-smash/") + (synopsis "MP4 multiplexer and demultiplexer library") + (description + "L-SMASH is a cross-platform library that handles the ISO base media file +format and some of its derived file formats, including MP4. It operates as a +multiplexer and demultiplexer, and can mux video and audio in several formats +using standalone executable files.") + (license license:isc))) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 0b373b1407..9dd8bb8971 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -5,9 +5,10 @@ ;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> ;;; Copyright © 2017 Andy Patterson <ajpatter@uwaterloo.ca> -;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com> +;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org> +;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,9 +41,11 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) + #:use-module (gnu packages gettext) #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) + #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages libusb) @@ -65,9 +68,11 @@ #:use-module (gnu packages xdisorg) #:use-module (gnu packages xml) #:use-module (guix build-system gnu) + #:use-module (guix build-system go) #:use-module (guix build-system python) #:use-module (guix download) - #:use-module ((guix licenses) #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+)) + #:use-module ((guix licenses) #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+ + asl2.0)) #:use-module (guix packages) #:use-module (guix utils) #:use-module (srfi srfi-1)) @@ -85,16 +90,14 @@ (define-public qemu (package (name "qemu") - (version "2.11.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (string-append "https://download.qemu.org/qemu-" version ".tar.xz")) (sha256 (base32 - "11l6cs6mib16rgdrnqrhkqs033fjik316gkgfz3asbmxz38lalca")) - (patches (search-patches "qemu-glibc-2.27.patch" - "qemu-CVE-2018-7550.patch")))) + "1z66spkm1prvhbq7h5mfnp0i6mmamsb938fqmdfvyrgzc7rh34z6")))) (build-system gnu-build-system) (arguments '(;; Running tests in parallel can occasionally lead to failures, like: @@ -173,6 +176,7 @@ exec smbd $@"))) `(("alsa-lib" ,alsa-lib) ("attr" ,attr) ("glib" ,glib) + ("gtk+" ,gtk+) ("libaio" ,libaio) ("libattr" ,attr) ("libcap" ,libcap) ; virtfs support requires libcap & libattr @@ -187,19 +191,20 @@ exec smbd $@"))) ;; ("pciutils" ,pciutils) ("pixman" ,pixman) ("pulseaudio" ,pulseaudio) - ("sdl" ,sdl) + ("sdl2" ,sdl2) ("spice" ,spice) ("usbredir" ,usbredir) ("util-linux" ,util-linux) ;; ("vde2" ,vde2) ("virglrenderer" ,virglrenderer) ("zlib" ,zlib))) - (native-inputs `(("glib:bin" ,glib "bin") ; gtester, etc. + (native-inputs `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") ; gtester, etc. ("perl" ,perl) ("flex" ,flex) ("bison" ,bison) ("pkg-config" ,pkg-config) - ("python" ,python-2) ; incompatible with Python 3 according to error message + ("python-wrapper" ,python-wrapper) ("texinfo" ,texinfo))) (home-page "https://www.qemu.org") (synopsis "Machine emulator and virtualizer") @@ -234,10 +239,35 @@ server and embedded PowerPC, and S390 guests.") ''("--target-list=i386-softmmu,x86_64-softmmu,mips64el-softmmu,arm-softmmu,aarch64-softmmu")))) ;; Remove dependencies on optional libraries, notably GUI libraries. + (native-inputs (fold alist-delete (package-native-inputs qemu) + '("gettext"))) (inputs (fold alist-delete (package-inputs qemu) - '("libusb" "mesa" "sdl" "spice" "virglrenderer" + '("libusb" "mesa" "sdl2" "spice" "virglrenderer" "gtk+" "usbredir" "libdrm" "libepoxy" "pulseaudio"))))) +;; The GRUB test suite fails with later versions of Qemu, so we +;; keep it at 2.10 for now. See +;; <https://lists.gnu.org/archive/html/bug-grub/2018-02/msg00004.html>. +;; This package is hidden since we do not backport updates to it. +(define-public qemu-minimal-2.10 + (hidden-package + (package + (inherit qemu-minimal) + (version "2.10.2") + (source (origin + (method url-fetch) + (uri (string-append "https://download.qemu.org/qemu-" + version ".tar.xz")) + (sha256 + (base32 + "17w21spvaxaidi2am5lpsln8yjpyp2zi3s3gc6nsxj5arlgamzgw")) + (patches + (search-patches "qemu-glibc-2.27.patch")))) + ;; qemu-minimal-2.10 needs Python 2. Remove below once no longer necessary. + (native-inputs `(("python-2" ,python-2) + ,@(fold alist-delete (package-native-inputs qemu) + '("python-wrapper"))))))) + (define-public libosinfo (package (name "libosinfo") @@ -524,7 +554,7 @@ virtualization library.") (define-public virt-manager (package (name "virt-manager") - (version "1.4.3") + (version "1.5.1") (source (origin (method url-fetch) (uri (string-append "https://virt-manager.org/download/sources" @@ -532,7 +562,7 @@ virtualization library.") version ".tar.gz")) (sha256 (base32 - "093azs8p4p7y4nf5j25xpsvdxww7gky1g0hs8mkcvmpxl2wjd0jj")))) + "1ardmd4sxdmd57y7qpka44gf09c1yq2g0xs074d3k1h925crv27f")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -777,3 +807,60 @@ monitor/GPU.") ;; This package requires SSE instructions. (supported-systems '("i686-linux" "x86_64-linux")) (license gpl2+))) + +(define-public runc + (package + (name "runc") + (version "1.0.0-rc5") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/opencontainers/runc/releases/" + "download/v" version "/runc.tar.xz")) + (sha256 + (base32 + "081avdzwnqpk368wbaihlzsypaxpj42d7699h7jgp0fks14x4103")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/opencontainers/runc" + #:install-source? #f + ;; XXX: 20/139 tests fail due to missing /var, cgroups and apparmor in + ;; the build environment. + #:tests? #f + #:phases + (modify-phases %standard-phases + (replace 'unpack + (lambda* (#:key source import-path #:allow-other-keys) + ;; Unpack the tarball into 'runc' instead of 'runc-1.0.0-rc5'. + (let ((dest (string-append "src/" import-path))) + (mkdir-p dest) + (invoke "tar" "-C" (string-append "src/" import-path) + "--strip-components=1" + "-xvf" source)))) + (replace 'build + (lambda* (#:key import-path #:allow-other-keys) + (chdir (string-append "src/" import-path)) + ;; XXX: requires 'go-md2man'. + ;; (invoke "make" "man") + (invoke "make"))) + ;; (replace 'check + ;; (lambda _ + ;; (invoke "make" "localunittest"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (invoke "make" "install" "install-bash" + (string-append "PREFIX=" out)))))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libseccomp" ,libseccomp))) + (synopsis "Open container initiative runtime") + (home-page "https://www.opencontainers.org/") + (description + "@command{runc} is a command line client for running applications +packaged according to the +@uref{https://github.com/opencontainers/runtime-spec/blob/master/spec.md, Open +Container Initiative (OCI) format} and is a compliant implementation of the +Open Container Initiative specification.") + (license asl2.0))) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 2fc930aa9e..fb06196ec4 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu> +;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,9 +33,11 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages check) + #:use-module (gnu packages autotools) #:use-module (gnu packages compression) #:use-module (gnu packages gettext) #:use-module (gnu packages gnupg) + #:use-module (gnu packages libevent) #:use-module (gnu packages linux) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -207,6 +210,39 @@ example for writing your own. For example, @command{vpnc-script-sshd} contains the entire VPN in a network namespace accessible only through SSH.") (license license:gpl2+)))) +(define-public ocproxy + (package + (name "ocproxy") + (version "1.60") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/cernekee/ocproxy/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1b4rg3xq5jnrp2l14sw0msan8kqhdxmsd7gpw9lkiwvxy13pcdm7")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (inputs + `(("libevent" ,libevent))) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autogen + (lambda _ (invoke "sh" "autogen.sh")))))) + (home-page "https://github.com/cernekee/ocproxy") + (synopsis "OpenConnect proxy") + (description + "User-level @dfn{SOCKS} and port forwarding proxy for OpenConnect based +on LwIP. When using ocproxy, OpenConnect only handles network activity that +the user specifically asks to proxy, so the @dfn{VPN} interface no longer +\"hijacks\" all network traffic on the host.") + (license license:bsd-3))) + (define-public openconnect (package (name "openconnect") @@ -243,7 +279,7 @@ and probably others.") (define-public openvpn (package (name "openvpn") - (version "2.4.5") + (version "2.4.6") (source (origin (method url-fetch) (uri (string-append @@ -251,7 +287,7 @@ and probably others.") version ".tar.xz")) (sha256 (base32 - "17njq59hsraqyxrbhkrxr7dvx0p066s3pn8w1mi0yd9jldis7h23")))) + "09lck4wmkas3iyrzaspin9gn3wiclqb1m9sf8diy7j8wakx38r2g")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-iproute2=yes"))) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 12b1f93015..ac9f6f2f25 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -160,7 +160,7 @@ interpretation of the specifications for these languages.") (define-public vulkan-icd-loader (package (name "vulkan-icd-loader") - (version "1.1.70.0") + (version "1.1.73.0") (source (origin (method url-fetch) @@ -169,7 +169,7 @@ interpretation of the specifications for these languages.") "archive/sdk-" version ".tar.gz")) (sha256 (base32 - "15qkh77596v3xivnbb3l0q9zbmmsdglnaza2m1g7f8q7bbigyc5x")))) + "1qb34j2zrc04fgs96m3k76vi4nx3sygbdcyg7pbwasr45cbdhsxb")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;FIXME: 23/39 tests fail. Try "tests/run_all_tests.sh". @@ -182,6 +182,7 @@ interpretation of the specifications for these languages.") #t))) #:configure-flags (list "-DBUILD_LAYERS=OFF" ; FIXME: Fails to build. + "-DBUILD_TESTS=OFF" ; FIXME: Needs 'googletest' submodule. (string-append "-DCMAKE_INSTALL_LIBDIR=" (assoc-ref %outputs "out") "/lib")))) (inputs `(("glslang" ,glslang) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 88c3b4aa1c..a8f28040b0 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3784,15 +3784,19 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.3.6.2") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0h3hkw575b211bxma23inbq1565wkhiapgasd539h219apqs534f")))) + "1pndv0h870ygibk0bmg9ayzkls60jqscrsyk39k29gy2pvm9ha5y")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-later" ,r-later) + ("r-promises" ,r-promises))) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description @@ -3892,13 +3896,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.0") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "09lkmzh35l1420sg0dyh4vgyishqx3g8xmgs2y9z7lbi09xgwwwr")))) + "04c4d0mfcy3dkdlbxnaccpdgxvyxfdwfmmh5djim6v9hyg0j2z8s")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -5432,13 +5436,13 @@ responsive, and powerful applications with minimal effort.") (define-public r-shinydashboard (package (name "r-shinydashboard") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 - "14zi7g5wrngy6lwi9xpvaid7727m6rfdijbb89al9likfhjqzqqy")))) + "10yqcqqcxgfqwkmscqwvvgr710im583qsqnsqkfpisjvkqp10yqb")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 7486d8f29d..dc74c9f59e 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -496,7 +496,7 @@ of the screen selected by mouse.") (define-public slop (package (name "slop") - (version "7.3.49") + (version "7.4") (source (origin (method url-fetch) (uri (string-append @@ -505,7 +505,7 @@ of the screen selected by mouse.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0gxi174vi13ldjaf776s2jcdyy379lnwwml29nk1bkzj5d5gpghm")))) + "1kpdrikgpjb4fpxalb6pjcih5njv1w9cnrjj5612ywdv1q5mjs48")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target @@ -529,7 +529,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "5.4.68") + (version "5.5") (source (origin (method url-fetch) (uri (string-append @@ -538,7 +538,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0f54s7csrxjd5r9anqqa92diwmzdplpws3llmbr6g3c0l6bp8815")))) + "02blbimjdckbcb04crhv0k2vxnp3rcgskyq66sk0v13l2h52849v")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target |