diff options
| author | Marius Bakke <mbakke@fastmail.com> | 2018-03-08 21:21:05 +0100 |
|---|---|---|
| committer | Marius Bakke <mbakke@fastmail.com> | 2018-03-08 21:21:05 +0100 |
| commit | d8fa1890c705ca566a56b69a4880a10dc7cf0098 (patch) | |
| tree | c3f220949e5364d981a4895477249ad46852eea0 /gnu/packages | |
| parent | 5de561a79634e0814ea22f1cfece9a09efa120be (diff) | |
| parent | fee7f8a94ec64943109ba9c37f75c28749fb18bd (diff) | |
| download | guix-d8fa1890c705ca566a56b69a4880a10dc7cf0098.tar guix-d8fa1890c705ca566a56b69a4880a10dc7cf0098.tar.gz | |
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages')
37 files changed, 712 insertions, 152 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 78b7b64dd1..7623693722 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com> ;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org> -;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015, 2016 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com> ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr> @@ -75,6 +75,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-web) + #:use-module (gnu packages terminals) #:use-module (gnu packages texinfo) #:use-module (gnu packages groff) #:use-module (gnu packages pciutils) @@ -1855,7 +1856,7 @@ throughput (in the same interval).") (define-public thefuck (package (name "thefuck") - (version "3.19") + (version "3.25") (source (origin (method url-fetch) (uri (string-append "https://github.com/nvbn/thefuck/archive/" @@ -1863,7 +1864,7 @@ throughput (in the same interval).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "191zbvkyc02h0wwd46xwj4zzg7jhlr8xv0ji6knqkgjnk0nvqq01")) + "088bn2l1376qlndbpnjya4q1x3913nj3yj3wc7s2w3bz66d23skk")) (patches (search-patches "thefuck-test-environ.patch")))) (build-system python-build-system) (arguments @@ -1881,14 +1882,12 @@ throughput (in the same interval).") `(("python-colorama" ,python-colorama) ("python-decorator" ,python-decorator) ("python-psutil" ,python-psutil) + ("python-pyte" ,python-pyte) ("python-six" ,python-six))) (native-inputs `(("python-mock" ,python-mock) ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock) - ;; Requires setuptools >= 17.1 due to some features used, while our - ;; python currently only includes 12.0. TODO: Remove this input. - ("python-setuptools" ,python-setuptools))) + ("python-pytest-mock" ,python-pytest-mock))) (home-page "https://github.com/nvbn/thefuck") (synopsis "Correct mistyped console command") (description @@ -1993,12 +1992,10 @@ shortcut syntax and completion options.") (home-page "https://github.com/TrilbyWhite/interrobang") (license license:gpl3+)))) - - (define-public pam-krb5 (package (name "pam-krb5") - (version "4.7") + (version "4.8") (source (origin (method url-fetch) (uri (string-append @@ -2006,7 +2003,7 @@ shortcut syntax and completion options.") version ".tar.xz")) (sha256 (base32 - "0abf8cfpkprmhw5ca8iyqgrggh65lgqvmfllc1y6qz7zw1gas894")))) + "1qjp8i1s9bz7g6kiqrkzzkxn5pfspa4sy53b6z40fqmdf9przdfb")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2032,8 +2029,8 @@ It supports ticket refreshing by screen savers, configurable authorization handling, authentication of non-local accounts for network services, password changing, and password expiration, as well as all the standard expected PAM features. It works correctly with OpenSSH, even -with ChallengeResponseAuthentication and PrivilegeSeparation enabled, -and supports extensive configuration either by PAM options or in +with @code{ChallengeResponseAuthentication} and @code{PrivilegeSeparation} +enabled, and supports extensive configuration either by PAM options or in krb5.conf or both. PKINIT is supported with recent versions of both MIT Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") (home-page "http://www.eyrie.org/~eagle/software/pam-krb5") @@ -2043,8 +2040,6 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") ;; clause requiring us to give all recipients a copy. (license license:gpl1+))) -;;http://archives.eyrie.org/software/kerberos/pam-krb5-4.7.tar.xz - (define-public sunxi-tools (package (name "sunxi-tools") @@ -2067,7 +2062,8 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") ("cross-gcc" ,(cross-gcc "arm-linux-gnueabihf" #:xbinutils (cross-binutils "arm-linux-gnueabihf") #:libc (cross-libc "arm-linux-gnueabihf"))) - ("cross-libc" ,(cross-libc "arm-linux-gnueabihf")))) + ("cross-libc" ,(cross-libc "arm-linux-gnueabihf")) ; header files + ("cross-libc-static" ,(cross-libc "arm-linux-gnueabihf") "static"))) (inputs `(("libusb" ,libusb))) (build-system gnu-build-system) @@ -2085,25 +2081,34 @@ Kerberos and Heimdal and FAST is supported with recent MIT Kerberos.") (lambda* (#:key make-flags #:allow-other-keys) (define (cross? x) (string-contains x "cross-arm-linux")) + (define (filter-environment! filter-predicate + environment-variable-names) + (for-each + (lambda (env-name) + (let* ((env-value (getenv env-name)) + (search-path (search-path-as-string->list env-value)) + (new-search-path (filter filter-predicate + search-path)) + (new-env-value (list->search-path-as-string + new-search-path ":"))) + (setenv env-name new-env-value))) + environment-variable-names)) (setenv "CROSS_C_INCLUDE_PATH" (getenv "C_INCLUDE_PATH")) (setenv "CROSS_CPLUS_INCLUDE_PATH" (getenv "CPLUS_INCLUDE_PATH")) (setenv "CROSS_LIBRARY_PATH" (getenv "LIBRARY_PATH")) - (for-each - (lambda (env-name) - (let* ((env-value (getenv env-name)) - (search-path (search-path-as-string->list env-value)) - (new-search-path (filter (lambda (e) (not (cross? e))) - search-path)) - (new-env-value (list->search-path-as-string - new-search-path ":"))) - (setenv env-name new-env-value))) - '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH" "LIBRARY_PATH")) + (filter-environment! cross? + '("CROSS_C_INCLUDE_PATH" "CROSS_CPLUS_INCLUDE_PATH" + "CROSS_LIBRARY_PATH")) + (filter-environment! (lambda (e) (not (cross? e))) + '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH" + "LIBRARY_PATH")) #t)) (replace 'build (lambda* (#:key make-flags #:allow-other-keys) (zero? (apply system* "make" "tools" "misc" make-flags)))) (add-after 'build 'build-armhf (lambda* (#:key make-flags #:allow-other-keys) + (setenv "LIBRARY_PATH" #f) (zero? (apply system* "make" "target-tools" make-flags)))) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 72dd9f8e13..07ae4b70ae 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -844,7 +844,6 @@ GLIBC/HURD for a Hurd host" (define glibc-2.26-patched (package (inherit glibc) - (replacement #f) (source (origin (inherit (package-source glibc)) (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 546b240f84..73765dafe7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10880,8 +10880,8 @@ memory usage and processing time is minimized.") (license license:expat))) (define-public r-dropbead - (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840") - (revision "1")) + (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") + (revision "2")) (package (name "r-dropbead") (version (string-append "0-" revision "." (string-take commit 7))) @@ -10894,7 +10894,7 @@ memory usage and processing time is minimized.") (file-name (git-file-name name version)) (sha256 (base32 - "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) + "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -12646,3 +12646,70 @@ contains analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.") (license license:expat))) + +(define-public pigx-rnaseq + (package + (name "pigx-rnaseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" + "releases/download/v" version + "/pigx_rnaseq-" version ".tar.gz")) + (sha256 + (base32 + "168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-tests? #f ; not supported + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + ;; Make sure the executable finds all R modules. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/pigx-rnaseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("snakemake" ,snakemake) + ("fastqc" ,fastqc) + ("multiqc" ,multiqc) + ("star" ,star) + ("trim-galore" ,trim-galore) + ("htseq" ,htseq) + ("samtools" ,samtools) + ("bedtools" ,bedtools) + ("r-minimal" ,r-minimal) + ("r-rmarkdown" ,r-rmarkdown) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gprofiler" ,r-gprofiler) + ("r-deseq2" ,r-deseq2) + ("r-dt" ,r-dt) + ("r-knitr" ,r-knitr) + ("r-pheatmap" ,r-pheatmap) + ("r-corrplot" ,r-corrplot) + ("r-reshape2" ,r-reshape2) + ("r-plotly" ,r-plotly) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-crosstalk" ,r-crosstalk) + ("r-tximport" ,r-tximport) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rjson" ,r-rjson) + ("salmon" ,salmon) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for RNA sequencing experiments") + (description "PiGX RNAseq is an analysis pipeline for preprocessing and +reporting for RNA sequencing experiments. It is easy to use and produces high +quality reports. The inputs are reads files from the sequencing experiment, +and a configuration file which describes the experiment. In addition to +quality control of the experiment, the pipeline produces a differential +expression report comparing samples in an easily configurable manner.") + (license license:gpl3+))) diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 7c0faca9a2..2abb44fdb8 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr> -;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -90,8 +90,8 @@ makes a few sacrifices to acquire fast full and incremental build times.") It can compile code written in C, C++, Fortran, Java, Rust, and other languages. Meson provides features comparable to those of the Autoconf/Automake/make combo. Build specifications, also known as @dfn{Meson -files}, are written in a custom domain-specific language (DSL) that resembles -Python.") +files}, are written in a custom domain-specific language (@dfn{DSL}) that +resembles Python.") (license license:asl2.0))) (define-public meson-for-build diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 50b4afcaf0..73d3efd9e1 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -16,7 +16,7 @@ ;;; Copyright © 2016 Troy Sankey <sankeytms@gmail.com> ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> -;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu> ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> @@ -202,14 +202,14 @@ multi-paradigm automated test framework for C++ and Objective-C.") (define-public cmdtest (package (name "cmdtest") - (version "0.29") + (version "0.32") (source (origin (method url-fetch) (uri (string-append "http://git.liw.fi/cmdtest/snapshot/" name "-" version ".tar.gz")) (sha256 (base32 - "1i6gi4yp4qqx1liax098c7nwdb24pghh11xqlrcs7lnhh079rqhb")))) + "1jmfiyrrqmpvwdb273bkb8hjaf4rwx9njblx29pmr7giyahskwi5")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -271,13 +271,13 @@ format.") (define-public cppcheck (package (name "cppcheck") - (version "1.81") + (version "1.82") (source (origin (method url-fetch) (uri (string-append "https://github.com/danmar/cppcheck/archive/" version ".tar.gz")) (sha256 - (base32 "0miamqk7pa2dzmnmi5wb6hjp2a3zya1x8afnlcxby8jb6gp6wf8j")) + (base32 "0zywpd9hbsx23aj33pk5mbr0fz1ijhqzxlnqgwjfwgg6g2k48i2j")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (home-page "http://cppcheck.sourceforge.net") diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 8d9c661302..13a89c7bcc 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -139,10 +139,10 @@ highlighting your own code that seemed comprehensible when you wrote it.") (home-page "https://www.gnu.org/software/global/") (synopsis "Cross-environment source code tag system") (description - "GLOBAL is a source code tagging system that functions in the same way -across a wide array of environments, such as different text editors, shells -and web browsers. The resulting tags are useful for quickly moving around in -a large, deeply nested project.") + "GNU GLOBAL is a source code tagging system that functions in the same +way across a wide array of environments, such as different text editors, +shells and web browsers. The resulting tags are useful for quickly moving +around in a large, deeply nested project.") (license license:gpl3+))) (define-public sloccount diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index c38f40f618..fe9fbebcc2 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -673,27 +673,32 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%" (define glibc-final ;; The final glibc, which embeds the statically-linked Bash built above. - (package (inherit glibc-final-with-bootstrap-bash) - (name "glibc") - (inputs `(("static-bash" ,static-bash-for-glibc) - ,@(alist-delete - "static-bash" - (package-inputs glibc-final-with-bootstrap-bash)))) - - ;; This time we need 'msgfmt' to install all the libc.mo files. - (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash) - ("gettext" ,gettext-boot0))) - - ;; The final libc only refers to itself, but the 'debug' output contains - ;; references to GCC-BOOT0 and to the Linux headers. XXX: Would be great - ;; if 'allowed-references' were per-output. - (arguments - `(#:allowed-references - ,(cons* `(,gcc-boot0 "lib") (kernel-headers-boot0) - static-bash-for-glibc - (package-outputs glibc-final-with-bootstrap-bash)) + ;; Use 'package/inherit' so we get the 'replacement' of 'glibc', if any. + (let ((glibc (package-with-bootstrap-guile glibc))) + (package/inherit glibc + (name "glibc") + (inputs `(("static-bash" ,static-bash-for-glibc) + ,@(alist-delete + "static-bash" + (package-inputs glibc-final-with-bootstrap-bash)))) + + ;; This time we need 'msgfmt' to install all the libc.mo files. + (native-inputs `(,@(package-native-inputs glibc-final-with-bootstrap-bash) + ("gettext" ,gettext-boot0))) + + (propagated-inputs + (package-propagated-inputs glibc-final-with-bootstrap-bash)) + + ;; The final libc only refers to itself, but the 'debug' output contains + ;; references to GCC-BOOT0 and to the Linux headers. XXX: Would be great + ;; if 'allowed-references' were per-output. + (arguments + `(#:allowed-references + ,(cons* `(,gcc-boot0 "lib") (kernel-headers-boot0) + static-bash-for-glibc + (package-outputs glibc-final-with-bootstrap-bash)) - ,@(package-arguments glibc-final-with-bootstrap-bash))))) + ,@(package-arguments glibc-final-with-bootstrap-bash)))))) (define gcc-boot0-wrapped ;; Make the cross-tools GCC-BOOT0 and BINUTILS-BOOT0 available under the diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 423d3989aa..d44ae2d259 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -99,7 +99,7 @@ (zero? (system* "./configure" (string-append "--prefix=" out))))))))) - (home-page "http://zlib.net/") + (home-page "https://zlib.net/") (synopsis "Compression library") (description "zlib is designed to be a free, general-purpose, legally unencumbered -- @@ -844,14 +844,14 @@ extract such file systems.") (define-public pigz (package (name "pigz") - (version "2.3.3") + (version "2.4") (source (origin (method url-fetch) (uri (string-append "http://zlib.net/pigz/" name "-" version ".tar.gz")) (sha256 (base32 - "172hdf26k4zmm7z8md7nl0dph2a7mhf3x7slb9bhfyff6as6g2sf")))) + "0wsgw5vwl23jrnpsvd8v3xcp5k4waw5mk0164fynjhkv58i1dy54")))) (build-system gnu-build-system) (arguments `(#:phases @@ -869,7 +869,7 @@ extract such file systems.") #:make-flags (list "CC=gcc") #:test-target "tests")) (inputs `(("zlib" ,zlib))) - (home-page "http://zlib.net/pigz/") + (home-page "https://zlib.net/pigz/") (synopsis "Parallel implementation of gzip") (description "This package provides a parallel implementation of gzip that exploits diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f8d17e1ad2..c4cf394e6e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2738,3 +2738,189 @@ ordered factor data types.") "This package provides tools for the computation of matrix and scalar exponentiation.") (license license:gpl2))) + +(define-public r-heatmaply + (package + (name "r-heatmaply") + (version "0.14.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "heatmaply" version)) + (sha256 + (base32 + "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-colorspace" ,r-colorspace) + ("r-dendextend" ,r-dendextend) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-magrittr" ,r-magrittr) + ("r-plotly" ,r-plotly) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-seriation" ,r-seriation) + ("r-viridis" ,r-viridis) + ("r-webshot" ,r-webshot))) + (home-page "https://cran.r-project.org/package=heatmaply") + (synopsis "Interactive cluster heat maps using plotly") + (description + "This package enables you to create interactive cluster heatmaps that can +be saved as a stand-alone HTML file, embedded in R Markdown documents or in a +Shiny app, and made available in the RStudio viewer pane. Hover the mouse +pointer over a cell to show details or drag a rectangle to zoom. A heatmap is +a popular graphical method for visualizing high-dimensional data, in which a +table of numbers is encoded as a grid of colored cells. The rows and columns +of the matrix are ordered to highlight patterns and are often accompanied by +dendrograms.") + ;; Either version of the license. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-cgdsr + (package + (name "r-cgdsr") + (version "1.2.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "cgdsr" version)) + (sha256 + (base32 + "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23")))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo))) + (home-page "https://github.com/cBioPortal/cgdsr") + (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") + (description + "This package provides a basic set of R functions for querying the Cancer +Genomics Data Server (CGDS), hosted by the Computational Biology Center at +Memorial-Sloan-Kettering Cancer Center (MSKCC).") + (license license:lgpl3))) + +(define-public r-import + (package + (name "r-import") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "import" version)) + (sha256 + (base32 + "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji")))) + (build-system r-build-system) + (home-page "https://github.com/smbache/import") + (synopsis "Import mechanism for R") + (description + "This is an alternative mechanism for importing objects from packages. +The syntax allows for importing multiple objects from a package with a single +command in an expressive way. The import package bridges some of the gap +between using @code{library} (or @code{require}) and direct (single-object) +imports. Furthermore the imported objects are not placed in the current +environment. It is also possible to import objects from stand-alone @code{.R} +files.") + (license license:expat))) + +(define-public r-shinyace + (package + (name "r-shinyace") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyAce" version)) + (sha256 + (base32 + "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9")))) + (properties `((upstream-name . "shinyAce"))) + (build-system r-build-system) + (propagated-inputs + `(("r-shiny" ,r-shiny))) + (home-page "http://cran.r-project.org/web/packages/shinyAce") + (synopsis "Ace editor bindings for Shiny") + (description + "This package provides Ace editor bindings to enable a rich text editing +environment within Shiny.") + (license license:expat))) + +(define-public r-radiant-data + (package + (name "r-radiant-data") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "radiant.data" version)) + (sha256 + (base32 + "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete files that are under CC-NC-SA. + (delete-file-recursively "inst/app/tools/help") + #t)))) + (properties `((upstream-name . "radiant.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-broom" ,r-broom) + ("r-car" ,r-car) + ("r-curl" ,r-curl) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-import" ,r-import) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-markdown" ,r-markdown) + ("r-pryr" ,r-pryr) + ("r-psych" ,r-psych) + ("r-readr" ,r-readr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-shinyace" ,r-shinyace) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/radiant-rstats/radiant.data") + (synopsis "Data menu for Radiant: business analytics using R and Shiny") + (description + "The Radiant Data menu includes interfaces for loading, saving, viewing, +visualizing, summarizing, transforming, and combining data. It also contains +functionality to generate reproducible reports of the analyses conducted in +the application.") + (license license:agpl3))) + +(define-public r-algdesign + (package + (name "r-algdesign") + (version "1.1-7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "AlgDesign" version)) + (sha256 + (base32 + "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz")))) + (properties `((upstream-name . "AlgDesign"))) + (build-system r-build-system) + (home-page "https://github.com/jvbraun/AlgDesign") + (synopsis "Algorithmic experimental design") + (description + "This package provides tools to calculate exact and approximate theory +experimental designs for D, A, and I criteria. Very large designs may be +created. Experimental designs may be blocked or blocked designs created from +a candidate list, using several criteria. The blocking can be done when whole +and within plot factors interact.") + (license license:gpl2+))) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index b498aabf4d..7716205947 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -258,7 +258,7 @@ the wrong hands.") (define-public keyutils (package (name "keyutils") - (version "1.5.9") + (version "1.5.10") (source (origin (method url-fetch) @@ -267,7 +267,7 @@ the wrong hands.") version ".tar.bz2")) (sha256 (base32 - "1bl3w03ygxhc0hz69klfdlwqn33jvzxl1zfl2jmnb2v85iawb8jd")) + "1dmgjcf7mnwc6h72xkvpaqpzxw8vmlnsmzz0s27pg0giwzm3sp0i")) (modules '((guix build utils))) ;; Create relative symbolic links instead of absolute ones to /lib/* (snippet '(substitute* "Makefile" (("\\$\\(LNS\\) \\$\\(LIBDIR\\)/") diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 6b566b0097..112c656ff8 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -85,10 +86,11 @@ program to exhibit a bug.") ;; home-page pointing to a bsd-2 license. (license bsd-3))) +;; Newer versions depend on LLVM and Clang >= 4, which have yet to be packaged. (define-public c-reduce (package (name "c-reduce") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) @@ -97,12 +99,12 @@ program to exhibit a bug.") "creduce-" version ".tar.gz"))) (sha256 (base32 - "1r23lhzq3dz8vi2dalxk5las8bf0av2w94hxxbs61pr73m77ik9d")))) + "0pf5q0n8vkdcr1wrkxn2jzxv0xkrir13bwmqfw3jpbm3dh2c3b6d")))) (build-system gnu-build-system) (inputs `(("astyle" ,astyle) - ("llvm" ,llvm) - ("clang" ,clang) + ("llvm" ,llvm-3.9.1) + ("clang" ,clang-3.9.1) ("flex" ,flex) ("indent" ,indent) ("perl" ,perl) @@ -131,7 +133,7 @@ program to exhibit a bug.") "file-which" "getopt-tabular" "regex-common" "sys-cpu"))))) #t))))) - (home-page "http://embed.cs.utah.edu/creduce") + (home-page "https://embed.cs.utah.edu/creduce") (synopsis "Reducer for interesting code") (description "C-Reduce is a tool that takes a large C or C++ program that has a diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index a6f398ac3b..c2c162c75c 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -6787,8 +6787,8 @@ want to use it.") (license license:gpl3+))) (define-public emacs-slack - (let ((commit "02ee1d7339e48c64946041f6f4e09447c3f53e82") - (revision "2")) + (let ((commit "92724604879149cf331fa8778d089813a9d4ce1a") + (revision "3")) (package (name "emacs-slack") (version (string-append "0-" revision "." (string-take commit 7))) @@ -6800,7 +6800,7 @@ want to use it.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0grx95xxf314m2k35m1kf20l2pwc6j11ibvrngx4pis7wqwjas3h")))) + "1fdf8s3ca356k7m7f5kqzfamfl2nrqjj2pynjv3kkrr0ad15nxmw")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-alert" ,emacs-alert) diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm index 5309510d40..192f84c36c 100644 --- a/gnu/packages/flashing-tools.scm +++ b/gnu/packages/flashing-tools.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis <manolis837@gmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> -;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017 Jonathan Brielmaier <jonathan.brielmaier@web.de> ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu> @@ -402,7 +402,10 @@ dump Intel Firmware Descriptor data of an image file.") Management Engine (ME). You need to @code{sudo rmmod mei_me} and @code{sudo rmmod mei} before using this tool. Also pass @code{iomem=relaxed} to the Linux kernel command line.") - (license license:gpl2))) + (license license:gpl2) + + ;; This is obviously an Intel thing, plus it requires <cpuid.h>. + (supported-systems '("x86_64-linux" "i686-linux")))) (define-public me-cleaner (package @@ -420,7 +423,7 @@ Management Engine (ME). You need to @code{sudo rmmod mei_me} and (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'create-setup.py + (add-after 'unpack 'create-setup.py (lambda _ (call-with-output-file "setup.py" (lambda (port) @@ -433,4 +436,7 @@ setup(name='me_cleaner', version='~a', scripts=['me_cleaner.py']) (synopsis "Intel ME cleaner") (description "This package provides tools for disabling Intel ME as far as possible (it only edits ME firmware image files).") - (license license:gpl3+))) + (license license:gpl3+) + + ;; This is an Intel thing. + (supported-systems '("x86_64-linux" "i686-linux")))) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 8af4f8dc83..aa9e466ebb 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2017 Brendan Tildesley <brendan.tildesley@openmailbox.org> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017 Mohammed Sadiq <sadiq@sadiqpk.org> +;;; Copyright © 2018 Charlie Ritter <chewzerita@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -55,6 +56,27 @@ #:use-module (gnu packages python) #:use-module (gnu packages xorg)) +(define-public font-ibm-plex + (package + (name "font-ibm-plex") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/IBM/plex/releases/download/" + "v" version "/OpenType.zip")) + (sha256 + (base32 + "0nzxw9z6waixslam248yr26ci3fbk83c7jf6m90hncnaj6zxx795")))) + (build-system font-build-system) + (home-page "https://github.com/IBM/plex") + (synopsis "IBM Plex typeface") + (description "This package provides the Plex font family. It comes in a +Sans, Serif, Mono and Sans Condensed, all with roman and true italics. The +fonts have been designed to work well in user interface (UI) environments as +well as other mediums.") + (license license:silofl1.1))) + (define-public font-inconsolata (package (name "font-inconsolata") diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index a64407a36f..30a22d7d59 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -499,7 +499,7 @@ has an ease of use unmatched by other C++ callback libraries.") (define glibmm (package (name "glibmm") - (version "2.50.1") + (version "2.54.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/glibmm/" @@ -507,10 +507,13 @@ has an ease of use unmatched by other C++ callback libraries.") "/glibmm-" version ".tar.xz")) (sha256 (base32 - "1926b3adx903hzvdp8glblsgjyadzqnwgkj8hg605d4wv98m1n0z")))) + "0jkapw18icz59cmlmsl00nwwz0wh291kb4hc9z9hxmq45drqrhkw")))) (build-system gnu-build-system) (arguments - `(#:phases + `(;; XXX: Some tests uses C++14 features. Remove this when the default + ;; compiler is >= GCC6. + #:configure-flags '("CXXFLAGS=-std=gnu++14") + #:phases (modify-phases %standard-phases (add-before 'build 'pre-build (lambda _ @@ -532,7 +535,7 @@ has an ease of use unmatched by other C++ callback libraries.") (propagated-inputs `(("libsigc++" ,libsigc++) ("glib" ,glib))) - (home-page "http://gtkmm.org/") + (home-page "https://gtkmm.org/") (synopsis "C++ interface to the GLib library") (description "Glibmm provides a C++ programming interface to the part of GLib that are @@ -544,7 +547,7 @@ useful for C++.") (name "python2-pygobject") ;; This was the last version to declare the 2.0 platform number, i.e. its ;; pkg-config files were named pygobject-2.0.pc - (version "2.28.6") + (version "2.28.7") (source (origin (method url-fetch) @@ -553,7 +556,7 @@ useful for C++.") "/pygobject-" version ".tar.xz")) (sha256 (base32 - "1f5dfxjnil2glfwxnqr14d2cjfbkghsbsn8n04js2c2icr7iv2pv")) + "0nkam61rsn7y3wik3vw46wk5q2cjfh2iph57hl9m39rc8jijb7dv")) (patches (search-patches "python2-pygobject-2-gi-info-type-error-domain.patch")))) (build-system gnu-build-system) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 516a590dc4..60a7925ee5 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1595,7 +1595,7 @@ creating interactive structured graphics.") (native-inputs `(("gtkmm-2" ,gtkmm-2) ("pkg-config" ,pkg-config))) - (home-page "http://gtkmm.org") + (home-page "https://gtkmm.org") (synopsis "C++ bindings to the GNOME Canvas library") (description "C++ bindings to the GNOME Canvas library.") (license license:lgpl2.0+))) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 60f2013614..f1c3d3d010 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1042,7 +1042,7 @@ library.") (native-inputs `(("pkg-config" ,pkg-config))) (propagated-inputs `(("glibmm" ,glibmm) ("atk" ,atk))) - (home-page "http://www.gtkmm.org") + (home-page "https://www.gtkmm.org") (synopsis "C++ interface to the ATK accessibility library") (description "ATKmm provides a C++ programming interface to the ATK accessibility @@ -1052,7 +1052,7 @@ toolkit.") (define-public gtkmm (package (name "gtkmm") - (version "3.22.0") + (version "3.22.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -1060,11 +1060,11 @@ toolkit.") name "-" version ".tar.xz")) (sha256 (base32 - "1x8l0ny6r3ym53z82q9d5fan4m9vi93xy3b3hj1hrclgc95lvnh5")))) + "1400535lhyya462pfx8bp11k3mg3jsbdghlpygskd5ai665dkbwi")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) ("glib" ,glib "bin") ;for 'glib-compile-resources' - ("xorg-server" ,xorg-server))) + ("xorg-server" ,xorg-server-1.19.3))) (propagated-inputs `(("pangomm" ,pangomm) ("cairomm" ,cairomm) @@ -1072,7 +1072,11 @@ toolkit.") ("gtk+" ,gtk+) ("glibmm" ,glibmm))) (arguments - '(#:phases (modify-phases %standard-phases + `(;; XXX: Tests require C++14 or later. Remove this when the default + ;; compiler is >= GCC6. + #:configure-flags '("CXXFLAGS=-std=gnu++14") + #:disallowed-references (,xorg-server-1.19.3) + #:phases (modify-phases %standard-phases (add-before 'check 'run-xvfb (lambda* (#:key inputs #:allow-other-keys) (let ((xorg-server (assoc-ref inputs "xorg-server"))) @@ -1083,7 +1087,7 @@ toolkit.") ;; Don't fail because of the missing /etc/machine-id. (setenv "DBUS_FATAL_WARNINGS" "0") #t)))))) - (home-page "http://gtkmm.org/") + (home-page "https://gtkmm.org/") (synopsis "C++ interface to the GTK+ graphical user interface library") (description @@ -1117,6 +1121,38 @@ extensive documentation, including API reference and a tutorial.") ("gtk+" ,gtk+-2) ("glibmm" ,glibmm))))) +(define-public gtksourceviewmm + (package + (name "gtksourceviewmm") + (version "3.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 "0fgvmhm4h4qmxig87qvangs6ijw53mi40siz7pixlxbrsgiil22i")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (propagated-inputs + ;; In 'Requires' of gtksourceviewmm-3.0.pc. + `(("glibmm" ,glibmm) + ("gtkmm" ,gtkmm) + ("gtksourceview" ,gtksourceview))) + (synopsis "C++ interface to the GTK+ 'GtkTextView' widget") + (description + "gtksourceviewmm is a portable C++ library that extends the standard GTK+ +framework for multiline text editing with support for configurable syntax +highlighting, unlimited undo/redo, search and replace, a completion framework, +printing and other features typical of a source code editor.") + (license license:lgpl2.1+) + (home-page "https://developer.gnome.org/gtksourceview/"))) + +;;; +;;; Python bindings. +;;; + (define-public python-pycairo (package (name "python-pycairo") diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 5dc66c1625..91a440d928 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015, 2017 Christopher Allan Webber <cwebber@dustycloud.org> ;;; Copyright © 2016 Alex Sassmannshausen <alex@pompo.co> @@ -281,6 +281,21 @@ without requiring the source code to be rewritten.") ; when heavily loaded) (replacement #f))) +(define-public guile-2.2.2 + ;; Keep it so that, when 'guix' runs on 2.2.2, 'guix pull' compiles objects + ;; with 2.2.2, thereby avoiding the ABI incompatibility issues described in + ;; <https://bugs.gnu.org/29570>. + (package + (inherit guile-2.2) + (version "2.2.2") + (source (origin + (inherit (package-source guile-2.2)) + (uri (string-append "mirror://gnu/guile/guile-" version + ".tar.xz")) + (sha256 + (base32 + "1azm25zcmxif0skxfrp11d2wc89nrzpjaann9yxdw6pvjxhs948w")))))) + (define-public guile-next (deprecated-package "guile-next" guile-2.2)) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 7a33f6c871..cf612666f1 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") + (version "2.25.1") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -67,7 +67,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "102rwi30n09l8rih6kv6bb7lhv3djklgzill4p2zag0h700yqfq6")))) + "197sm78bm33dvahr5nxqkbmpmdn4b13ahc9mrgn1l7n104bg4phc")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure)) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index cc03f8fc2d..d798833742 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -47,14 +47,14 @@ ;; The 7 release series has an incompatible API, while the 6 series is still ;; maintained. Don't update to 7 until we've made sure that the ImageMagick ;; users are ready for the 7-series API. - (version "6.9.9-36") + (version "6.9.9-37") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "1nhv3cmg4npqibhchp3qgm9pld3n94xwwzv5hgn2s7lqz0zc0vd8")))) + "1hmfw0jcpc3s3gz9zrzjy9amyrfz6gzzjdsyaw3xw994aq9qf4lq")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm new file mode 100644 index 0000000000..81021f6461 --- /dev/null +++ b/gnu/packages/maven.scm @@ -0,0 +1,130 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. + +(define-module (gnu packages maven) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix utils) + #:use-module (guix build-system ant) + #:use-module (gnu packages) + #:use-module (gnu packages java)) + +(define-public maven-resolver-api + (package + (name "maven-resolver-api") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/apache/maven-resolver/" + "archive/maven-resolver-" version ".tar.gz")) + (sha256 + (base32 + "0rpvdg3qr1j88gw0ankf0wnwfyq6238mdlm7s39vf5jrcvhdgwcl")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "maven-resolver-api.jar" + #:source-dir "maven-resolver-api/src/main/java" + #:test-dir "maven-resolver-api/src/test")) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "https://github.com/apache/maven-resolver") + (synopsis "Maven repository system API") + (description "This package contains the API for the maven repository system.") + (license license:asl2.0))) + +(define-public maven-resolver-spi + (package + (inherit maven-resolver-api) + (name "maven-resolver-spi") + (arguments + `(#:jar-name "maven-resolver-spi.jar" + #:source-dir "maven-resolver-spi/src/main/java" + #:test-dir "maven-resolver-spi/src/test" + #:jdk ,icedtea-8)) + (inputs + `(("maven-resolver-api" ,maven-resolver-api))) + (synopsis "Maven repository system SPI") + (description "This package contains the service provider interface (SPI) +for repository system implementations and repository connectors."))) + +(define-public maven-resolver-test-util + (package + (inherit maven-resolver-api) + (name "maven-resolver-test-util") + (arguments + `(#:jar-name "maven-resolver-test-util.jar" + #:source-dir "maven-resolver-test-util/src/main/java" + #:test-dir "maven-resolver-test-util/src/test" + #:jdk ,icedtea-8)) + (inputs + `(("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi))) + (synopsis "Utility classes for testing the maven repository system") + (description "This package contains a collection of utility classes to +ease testing of the repository system."))) + +(define-public maven-resolver-util + (package + (inherit maven-resolver-api) + (name "maven-resolver-util") + (arguments + `(#:jar-name "maven-resolver-util.jar" + #:source-dir "maven-resolver-util/src/main/java" + #:test-dir "maven-resolver-util/src/test" + #:jdk ,icedtea-8)) + (inputs + `(("maven-resolver-api" ,maven-resolver-api))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core) + ("maven-resolver-test-util" ,maven-resolver-test-util))) + (synopsis "Utility classes for the maven repository system") + (description "This package contains a collection of utility classes to +ease usage of the repository system."))) + +(define-public maven-resolver-connector-basic + (package + (inherit maven-resolver-api) + (name "maven-resolver-connector-basic") + (arguments + `(#:jar-name "maven-resolver-connector-basic.jar" + #:source-dir "maven-resolver-connector-basic/src/main/java" + #:test-dir "maven-resolver-connector-basic/src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'build 'generate-sisu + (lambda _ + (mkdir-p "build/classes/META-INF/sisu") + (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named" + (lambda _ + (display "org.eclipse.aether.connector.basic.BasicRepositoryConnectorFactory\n")))))))) + (inputs + `(("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi) + ("maven-resolver-util" ,maven-resolver-util) + ("java-javax-inject" ,java-javax-inject))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core) + ("maven-resolver-test-util" ,maven-resolver-test-util))) + (synopsis "Maven repository connector implementation") + (description "This package contains a repository connector implementation +for repositories using URI-based layouts."))) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 7a4c370c99..b6323c39b2 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -449,14 +449,14 @@ compromised.") (define-public znc (package (name "znc") - (version "1.6.5") + (version "1.6.6") (source (origin (method url-fetch) (uri (string-append "http://znc.in/releases/archive/znc-" version ".tar.gz")) (sha256 (base32 - "1jia6kq6bp8yxfj02d5vj9vqb4pylqcldspyjj6iz82kkka2a0ig")))) + "09cmsnxvi7jg9a0dicf60fxnxdff4aprw7h8vjqlj5ywf6y43f3z")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 65dfa92896..f47749b380 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2609,7 +2609,9 @@ of tools for manipulating and accessing your music.") (("add_subdirectory\\(resources/music\\)") "")))))) (build-system cmake-build-system) (arguments - '(#:tests? #f)) ; no check target + '(#:tests? #f ; no check target + ;; This flag ensures that MilkyTracker links with the JACK library. + #:configure-flags '("-DCMAKE_CXX_FLAGS=-ljack"))) (inputs `(("alsa-lib" ,alsa-lib) ("jack" ,jack-1) diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm index d6bef33695..07c7ed36cb 100644 --- a/gnu/packages/nano.scm +++ b/gnu/packages/nano.scm @@ -30,7 +30,7 @@ (define-public nano (package (name "nano") - (version "2.9.3") + (version "2.9.4") (source (origin (method url-fetch) @@ -38,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "04j05nbnp8vjjwja90d83p4s6ywyl6qhggflcjzw0p9d9gyvr0vp")))) + "0nm3zy4azr5rkxjq7jfybbj3cnddmvxc49rxyqm9cp2zfdp75y9c")))) (build-system gnu-build-system) (inputs `(("gettext" ,gettext-minimal) diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 17423856aa..c110fab086 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -94,7 +94,7 @@ and they are executed on lists of files, hosts, users or other items.") (define-public slurm (package (name "slurm") - (version "17.11.2") + (version "17.11.3") (source (origin (method url-fetch) (uri (string-append @@ -102,7 +102,7 @@ and they are executed on lists of files, hosts, users or other items.") version ".tar.bz2")) (sha256 (base32 - "18yakb8kmhb16n0cv3zhjv8ahvsk9p0max8mmr2flb2c65fawks6")) + "1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 96a51f0dd4..46b6e795ab 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -92,7 +92,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) @@ -101,7 +101,7 @@ human.") version "-src.tar.xz")) (sha256 (base32 - "1v6v59fnbbsssbwy4is6hh2l4qqwy3ddb6dp2jk8clx0xbd5hn7c")))) + "1gdrbpzwbs56anc3k5vklvcackcn214pc8gm5xh5zcymsi8q4zff")))) (build-system cmake-build-system) (arguments '(#:configure-flags '("-DWITH_XC_NETWORKING=YES" @@ -200,7 +200,7 @@ applications, there is xclip integration." ) (define-public yapet (package (name "yapet") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (string-append "http://www.guengel.ch/myapps/yapet/downloads/yapet-" @@ -208,7 +208,7 @@ applications, there is xclip integration." ) ".tar.bz2")) (sha256 (base32 - "0ydbnqw6icdh07pnv2w6dhvq501bdfvrklv4xmyr8znca9d753if")))) + "1lq46mpxdsbl6qw4cj58hp9q7jckmyvbsi08p5zr77rjgqadxyyy")))) (build-system gnu-build-system) (inputs `(("ncurses" ,ncurses) diff --git a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch index ce18b874c4..c03807323f 100644 --- a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch +++ b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch @@ -1,3 +1,10 @@ +This patch allows libc to be used with the heavily-patched kernel found +on CentOS 6, which identifies itself as 2.6.32. + +See <https://lists.gnu.org/archive/html/guix-devel/2018-02/msg00392.html>. + +Patch taken from Nixpkgs. + diff --git a/sysdeps/unix/sysv/linux/configure b/sysdeps/unix/sysv/linux/configure index cace758c01..38fe7fe0b0 100644 --- a/sysdeps/unix/sysv/linux/configure diff --git a/gnu/packages/patches/thefuck-test-environ.patch b/gnu/packages/patches/thefuck-test-environ.patch index 0c602a38c4..54194d8928 100644 --- a/gnu/packages/patches/thefuck-test-environ.patch +++ b/gnu/packages/patches/thefuck-test-environ.patch @@ -1,14 +1,14 @@ Retain environment setting of "HOME" for tests that need os.path.expanduser() to return a readable directory in the build chroot. ---- thefuck-3.15/tests/test_conf.py -+++ thefuck-3.15/tests/test_conf.py -@@ -12,7 +12,7 @@ - - @pytest.fixture - def environ(monkeypatch): -- data = {} -+ data = {"HOME": os.environ.get("HOME")} - monkeypatch.setattr('thefuck.conf.os.environ', data) - return data +--- thefuck-3.25/tests/conftest.py ++++ thefuck-3.25/tests/conftest.py +@@ -64,6 +64,7 @@ def set_shell(monkeypatch): + @pytest.fixture(autouse=True) + def os_environ(monkeypatch): +- env = {'PATH': os.environ['PATH']} ++ env = {'PATH': os.environ['PATH'], ++ 'HOME': os.environ['HOME']} + monkeypatch.setattr('os.environ', env) + return env diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index d9721f1375..dce651246c 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -22,6 +22,7 @@ ;;; Copyright © 2016 David Craven <david@craven.ch> ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com> ;;; Copyright © 2015, 2016 David Thompson <davet@gnu.org> +;;; Copyright © 2017 Mark Meyer <mark@ofosos.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,11 +46,13 @@ #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages django) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-crypto) + #:use-module (gnu packages tls) #:use-module (gnu packages time) #:use-module (gnu packages xml) #:use-module ((guix licenses) #:prefix license:) @@ -238,6 +241,40 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.") (define-public python2-html5-parser (package-with-python2 python-html5-parser)) +(define-public python-pycurl + (package + (name "python-pycurl") + (version "7.43.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://dl.bintray.com/pycurl/pycurl/pycurl-" + version ".tar.gz")) + (sha256 + (base32 "1ali1gjs9iliwjra7w0y5hwg79a2fd0f4ydvv6k27sgxpbr1n8s3")))) + (build-system python-build-system) + (arguments + ;; The tests attempt to access external web servers, so we cannot run + ;; them. Furthermore, they are skipped altogether when using Python 2. + '(#:tests? #f)) + (native-inputs + `(("python-nose" ,python-nose) + ("python-bottle" ,python-bottle))) + (inputs + `(("curl" ,curl) + ("gnutls" ,gnutls))) + (home-page "http://pycurl.io/") + (synopsis "Lightweight Python wrapper around libcurl") + (description "Pycurl is a lightweight wrapper around libcurl. It provides +high-speed transfers via libcurl and frequently outperforms alternatives.") + + ;; Per 'README.rst', this is dual-licensed: users can redistribute pycurl + ;; under the terms of LGPLv2.1+ or Expat. + (license (list license:lgpl2.1+ license:expat)))) + +(define-public python2-pycurl + (package-with-python2 python-pycurl)) + (define-public python-webencodings (package (name "python-webencodings") diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a0f1f1deab..79ceaa2195 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5875,6 +5875,7 @@ reading and writing MessagePack data.") (define-public python-msgpack-transitional (package (inherit python-msgpack) + (name "python-msgpack-transitional") (arguments (substitute-keyword-arguments (package-arguments python-msgpack) ((#:phases phases) @@ -10408,14 +10409,14 @@ convering text with ANSI color codes to HTML or LaTeX.") (define-public python-ddt (package (name "python-ddt") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (pypi-uri "ddt" version)) (sha256 (base32 - "1c00ikkxr7lha97c81k938bzhgd4pbwamkjn0h4nkhr3xk00zp6n")))) + "1wqkmz0yhanly8sif5vb02p2iik7mwxwph8ywph2kbb8ws8szdpx")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) @@ -10426,8 +10427,9 @@ convering text with ANSI color codes to HTML or LaTeX.") (home-page "https://github.com/txels/ddt") (synopsis "Data-Driven Tests") (description - "DDT (Data-Driven Tests) allows you to multiply one test case by running -it with different test data, and make it appear as multiple test cases.") + "Data-Driven Tests (@dfn{DDT}) allow you to multiply one test case by +running it with different test data, and make it appear as multiple test +cases.") (license license:expat))) (define-public python2-ddt diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8ebdce1376..0ae4dddb64 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5564,6 +5564,38 @@ inferring an appropriate positioning method.") shaped points? Now you can!") (license license:asl2.0)))) +(define-public r-colorout + (package + (name "r-colorout") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/jalvesaq/colorout/archive/" + "v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v")))) + (build-system r-build-system) + (home-page "https://github.com/jalvesaq/colorout") + (synopsis "Colorize output in the R REPL") + (description "@code{colorout} is an R package that colorizes R output when +running in terminal emulator. + +R STDOUT is parsed and numbers, negative numbers, dates in the standard +format, strings, and R constants are identified and wrapped by special ANSI +scape codes that are interpreted by terminal emulators as commands to colorize +the output. R STDERR is also parsed to identify the expressions warning and +error and their translations to many languages. If these expressions are +found, the output is colorized accordingly; otherwise, it is colorized as +STDERROR (blue, by default). + +You can customize the colors according to your taste, guided by the color +table made by the command @code{show256Colors()}. You can also set the colors +to any arbitrary string. In this case, it is up to you to set valid values.") + (license license:gpl3+))) + (define-public java-jdistlib (package (name "java-jdistlib") diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 0207ca36ab..f1ccab9af9 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -239,14 +239,14 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (define-public mg (package (name "mg") - (version "20170401") + (version "20171014") (source (origin (method url-fetch) (uri (string-append "https://homepage.boetes.org/software/mg/mg-" version ".tar.gz")) (sha256 (base32 - "1arasswgdadbb265rahq3867r9s54jva6k4m3p5n0f8mgjqhhdha")) + "0hakfikzsml7z0hja8m8mcahrmfy2piy81bq9nccsjplyfc9clai")) (modules '((guix build utils))) (snippet '(begin @@ -283,7 +283,7 @@ Wordstar-, EMACS-, Pico, Nedit or vi-like key bindings. e3 can be used on (doc (string-append out "/share/doc/mg"))) (install-file "tutorial" doc) #t)))))) - (home-page "http://homepage.boetes.org/software/mg/") + (home-page "https://homepage.boetes.org/software/mg/") (synopsis "Microscopic GNU Emacs clone") (description "Mg (mg) is a GNU Emacs style editor, with which it is \"broadly\" diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 7d546d0b92..baedb2a522 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1344,16 +1344,18 @@ audio, images) from the Web. It can use either mpv or vlc for playback.") (guix build utils) (srfi srfi-26)) #:module-build-flags '("--gtk") - #:phases (modify-phases %standard-phases - (add-after 'install 'wrap-program - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin-dir (string-append (assoc-ref outputs "out") - "/bin/")) - (perl-path (getenv "PERL5LIB"))) - (for-each (cut wrap-program <> - `("PERL5LIB" ":" prefix (,perl-path))) - (find-files bin-dir)) - #t)))))) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin-dir (string-append out "/bin/")) + (site-dir (string-append out "/lib/perl5/site_perl/")) + (lib-path (getenv "PERL5LIB"))) + (for-each (cut wrap-program <> + `("PERL5LIB" ":" prefix (,lib-path ,site-dir))) + (find-files bin-dir)) + #t)))))) (synopsis "Lightweight application for searching and streaming videos from YouTube") (description diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 1d83b6f363..478de6a444 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -158,7 +158,7 @@ interpretation of the specifications for these languages.") (define-public vulkan-icd-loader (package (name "vulkan-icd-loader") - (version "1.0.68.0") + (version "1.1.70.0") (source (origin (method url-fetch) @@ -167,7 +167,7 @@ interpretation of the specifications for these languages.") "archive/sdk-" version ".tar.gz")) (sha256 (base32 - "1n5gry5zxpwi7330fmi06snalra8hkbbw68gnwbp531kd5ycyinh")))) + "15qkh77596v3xivnbb3l0q9zbmmsdglnaza2m1g7f8q7bbigyc5x")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;FIXME: 23/39 tests fail. Try "tests/run_all_tests.sh". diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index bd4c34efb6..ef39d71411 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -102,10 +103,10 @@ older or slower computers and embedded systems.") `((setenv "CHOST" ,(%current-target-system))) '()) (setenv "CONFIG_SHELL" (which "bash")) - (zero? - (system* "./configure" - (string-append "--prefix=" out) - "--enable-graphics")))))))) + (invoke "./configure" + (string-append "--prefix=" out) + "--enable-graphics") + #t)))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("zlib" ,zlib) ("openssl" ,openssl) @@ -175,7 +176,8 @@ features including, tables, builtin image display, bookmarks, SSL and more.") #t)) (replace 'install (lambda* (#:key (make-flags '()) #:allow-other-keys) - (zero? (apply system* "make" "install-full" make-flags))))))) + (apply invoke "make" "install-full" make-flags) + #t))))) (synopsis "Text Web Browser") (description "Lynx is a fully-featured World Wide Web (WWW) client for users running @@ -223,7 +225,7 @@ access.") (let* ((out (assoc-ref outputs "out")) (app (string-append out "/share/applications")) (hicolor (string-append out "/share/icons/hicolor"))) - (system* "a2x" "-f" "manpage" "doc/qutebrowser.1.asciidoc") + (invoke "a2x" "-f" "manpage" "doc/qutebrowser.1.asciidoc") (install-file "doc/qutebrowser.1" (string-append out "/share/man/man1")) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index e90794b3c5..2b1f1bdadb 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6371,7 +6371,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.") ;; Required by tests. ("cunit" ,cunit) - ("tzdata" ,tzdata))) + ("tzdata" ,tzdata-for-tests))) (inputs ;; Required to build the tools (i.e. without ‘--enable-lib-only’). `(("c-ares" ,c-ares) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 6fc99de919..1bdb1add07 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -1558,7 +1558,7 @@ input from UTF-8 into the locale's encoding.") (define-public mkfontscale (package (name "mkfontscale") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) @@ -1568,7 +1568,7 @@ input from UTF-8 into the locale's encoding.") ".tar.bz2")) (sha256 (base32 - "081z8lwh9c1gyrx3ad12whnpv3jpfbqsc366mswpfm48mwl54vcc")))) + "0siag28jpm8hj62bgjvw81sjfgrc7vcy2h7127bl4iazxrlxz60y")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) @@ -2276,7 +2276,7 @@ available.") (define-public xdriinfo (package (name "xdriinfo") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) @@ -2286,7 +2286,7 @@ available.") ".tar.bz2")) (sha256 (base32 - "0681d0y8liqakkpz7mmsf689jcxrvs5291r20qi78mc9xxk3gfjc")))) + "0lcx8h3zd11m4w8wf7dyp89826d437iz78cyrix436bqx31x5k6r")))) (build-system gnu-build-system) (inputs `(("mesa" ,mesa) @@ -5421,17 +5421,17 @@ Intrinsics (Xt) Library.") (define-public twm (package (name "twm") - (version "1.0.9") + (version "1.0.10") (source (origin (method url-fetch) (uri (string-append "mirror://xorg/individual/app/" name "-" version - ".tar.gz")) + ".tar.bz2")) (sha256 (base32 - "1s1r00x8add3f27xjqxg6q7mwplwrb72gakbh4y6j052as25wchw")))) + "1ms5cj1w3g26zg6bxdv1j9hl0pxr4300qnv003cz1q3cl7ffljb4")))) (build-system gnu-build-system) (inputs `(("libxt" ,libxt) |