diff options
| author | Mark H Weaver <mhw@netris.org> | 2017-08-15 03:10:14 -0400 |
|---|---|---|
| committer | Mark H Weaver <mhw@netris.org> | 2017-08-15 03:10:14 -0400 |
| commit | 09ec5a0f0c40afde63975af9e9203884dad86ea7 (patch) | |
| tree | c85530d4a7ed433779d787a0c452ed0d4b7f0f0a /gnu/packages | |
| parent | 3785e42e5219a86d9d8a5208ff18e97e0cbcbe78 (diff) | |
| parent | 2d430f29231d0d817459d86e0fe15089372e9547 (diff) | |
| download | guix-09ec5a0f0c40afde63975af9e9203884dad86ea7.tar.gz | |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages')
32 files changed, 981 insertions, 116 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f0c4e7748a..87cf164c1a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5796,6 +5796,49 @@ differential expression based on a model using the negative binomial distribution.") (license license:lgpl3+))) +(define-public r-dexseq + (package + (name "r-dexseq") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEXSeq" version)) + (sha256 + (base32 + "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg")))) + (properties `((upstream-name . "DEXSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biomart" ,r-biomart) + ("r-deseq2" ,r-deseq2) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-statmod" ,r-statmod) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "http://bioconductor.org/packages/DEXSeq") + (synopsis "Inference of differential exon usage in RNA-Seq") + (description + "This package is focused on finding differential exon usage using RNA-seq +exon counts between samples with different experimental designs. It provides +functions that allows the user to make the necessary statistical tests based +on a model that uses the negative binomial distribution to estimate the +variance between biological replicates and generalized linear models for +testing. The package also provides functions for the visualization and +exploration of the results.") + (license license:gpl3+))) + (define-public r-annotationforge (package (name "r-annotationforge") @@ -9759,3 +9802,66 @@ such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser.") (license license:gpl3+)))) + +(define-public bismark + (package + (name "bismark") + (version "0.16.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/FelixKrueger/Bismark/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq")))) + (build-system perl-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin")) + (docdir (string-append (assoc-ref outputs "out") + "/share/doc/bismark")) + (docs '("Bismark_User_Guide.pdf" + "RELEASE_NOTES.txt")) + (scripts '("bismark" + "bismark_genome_preparation" + "bismark_methylation_extractor" + "bismark2bedGraph" + "bismark2report" + "coverage2cytosine" + "deduplicate_bismark" + "bismark_sitrep.tpl" + "bam2nuc" + "bismark2summary"))) + (mkdir-p docdir) + (mkdir-p bin) + (for-each (lambda (file) (install-file file bin)) + scripts) + (for-each (lambda (file) (install-file file docdir)) + docs) + #t)))))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") + (synopsis "Map bisulfite treated sequence reads and analyze methylation") + (description "Bismark is a program to map bisulfite treated sequencing +reads to a genome of interest and perform methylation calls in a single step. +The output can be easily imported into a genome viewer, such as SeqMonk, and +enables a researcher to analyse the methylation levels of their samples +straight away. Its main features are: + +@itemize +@item Bisulfite mapping and methylation calling in one single step +@item Supports single-end and paired-end read alignments +@item Supports ungapped and gapped alignments +@item Alignment seed length, number of mismatches etc are adjustable +@item Output discriminates between cytosine methylation in CpG, CHG + and CHH context +@end itemize\n") + (license license:gpl3+))) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 6f25b7cd82..fa9e19db7d 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org> +;;; Copyright © 2017 Andy Wingo <wingo@igalia.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -189,6 +190,60 @@ effort, time, and money it would take to develop the software, using the COCOMO model or user-provided parameters.") (license license:gpl2+))) +(define-public cloc + (package + (name "cloc") + (version "1.72") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/AlDanial/cloc/releases/download/v" version + "/cloc-" version ".tar.gz")) + (sha256 + (base32 + "1gl7bxb4bi6pms0zzl133pzpfypvz57hk2cw7yf6rvs8b48kilnz")))) + (build-system gnu-build-system) + (inputs + `(("coreutils" ,coreutils) + ("perl" ,perl) + ("perl-algorithm-diff" ,perl-algorithm-diff) + ("perl-regexp-common" ,perl-regexp-common) + ("perl-digest-md5" ,perl-digest-md5))) + (arguments + `(#:phases (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (zero? + (system* "make" "-C" "Unix" + (string-append "prefix=" out) + (string-append "INSTALL=" + (assoc-ref inputs "coreutils") + "/bin/install") + "install"))))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/cloc") + `("PERL5LIB" ":" = + ,(string-split (getenv "PERL5LIB") #\:))) + #t)))) + #:out-of-source? #t + ;; Tests require some other packages. + #:tests? #f)) + (home-page "https://github.com/AlDanial/cloc") + (synopsis "Count source lines of code (SLOC) and other source code metrics") + (description "cloc counts blank lines, comment lines, and physical lines +of source code in many programming languages. Given two versions of a code +base, cloc can compute differences in blank, comment, and source lines. + +cloc contains code from David Wheeler's SLOCCount. Compared to SLOCCount, +cloc can handle a greater variety of programming langauges.") + (license license:gpl2+))) + (define-public the-silver-searcher (package (name "the-silver-searcher") diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index d02bc20f20..62fe5fe081 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 David Thompson <davet@gnu.org> -;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox> ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr> @@ -52,6 +52,7 @@ #:use-module (guix git-download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system perl) #:use-module (guix build-system python)) (define-public libsodium @@ -437,3 +438,128 @@ PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") (define-public python2-asn1crypto (package-with-python2 python-asn1crypto)) + +(define-public perl-math-random-isaac-xs + (package + (name "perl-math-random-isaac-xs") + (version "1.004") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/J/JA/JAWNSY/" + "Math-Random-ISAAC-XS-" version ".tar.gz")) + (sha256 + (base32 + "0yxqqcqvj51fn7b7j5xqhz65v74arzgainn66c6k7inijbmr1xws")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build) + ("perl-test-nowarnings" ,perl-test-nowarnings))) + (home-page "http://search.cpan.org/dist/Math-Random-ISAAC-XS") + (synopsis "C implementation of the ISAAC PRNG algorithm") + (description "ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a +fast pseudo-random number generator. It is suitable for applications where a +significant amount of random data needs to be produced quickly, such as +solving using the Monte Carlo method or for games. The results are uniformly +distributed, unbiased, and unpredictable unless you know the seed. + +This package implements the same interface as @code{Math::Random::ISAAC}.") + (license license:public-domain))) + +(define-public perl-math-random-isaac + (package + (name "perl-math-random-isaac") + (version "1.004") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/J/JA/JAWNSY/" + "Math-Random-ISAAC-" version ".tar.gz")) + (sha256 + (base32 + "0z1b3xbb3xz71h25fg6jgsccra7migq7s0vawx2rfzi0pwpz0wr7")))) + (build-system perl-build-system) + (native-inputs + `(("perl-test-nowarnings" ,perl-test-nowarnings))) + (propagated-inputs + `(("perl-math-random-isaac-xs" ,perl-math-random-isaac-xs))) + (home-page "http://search.cpan.org/dist/Math-Random-ISAAC") + (synopsis "Perl interface to the ISAAC PRNG algorithm") + (description "ISAAC (Indirection, Shift, Accumulate, Add, and Count) is a +fast pseudo-random number generator. It is suitable for applications where a +significant amount of random data needs to be produced quickly, such as +solving using the Monte Carlo method or for games. The results are uniformly +distributed, unbiased, and unpredictable unless you know the seed. + +This package provides a Perl interface to the ISAAC pseudo random number +generator.") + (license license:public-domain))) + +(define-public perl-crypt-random-source + (package + (name "perl-crypt-random-source") + (version "0.12") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/" + "Crypt-Random-Source-" version ".tar.gz")) + (sha256 + (base32 + "00mw5m52sbz9nqp3f6axyrgcrihqxn7k8gv0vi1kvm1j1nc9g29h")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build-tiny" ,perl-module-build-tiny) + ("perl-test-exception" ,perl-test-exception))) + (propagated-inputs + `(("perl-capture-tiny" ,perl-capture-tiny) + ("perl-module-find" ,perl-module-find) + ("perl-module-runtime" ,perl-module-runtime) + ("perl-moo" ,perl-moo) + ("perl-namespace-clean" ,perl-namespace-clean) + ("perl-sub-exporter" ,perl-sub-exporter) + ("perl-type-tiny" ,perl-type-tiny))) + (home-page "http://search.cpan.org/dist/Crypt-Random-Source") + (synopsis "Get weak or strong random data from pluggable sources") + (description "This module provides implementations for a number of +byte-oriented sources of random data.") + (license (package-license perl)))) + +(define-public perl-math-random-secure + (package + (name "perl-math-random-secure") + (version "0.080001") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/F/FR/FREW/" + "Math-Random-Secure-" version ".tar.gz")) + (sha256 + (base32 + "0dgbf4ncll4kmgkyb9fsaxn0vf2smc9dmwqzgh3259zc2zla995z")))) + (build-system perl-build-system) + (native-inputs + `(("perl-list-moreutils" ,perl-list-moreutils) + ("perl-test-leaktrace" ,perl-test-leaktrace) + ("perl-test-sharedfork" ,perl-test-sharedfork) + ("perl-test-warn" ,perl-test-warn))) + (inputs + `(("perl-crypt-random-source" ,perl-crypt-random-source) + ("perl-math-random-isaac" ,perl-math-random-isaac) + ("perl-math-random-isaac-xs" ,perl-math-random-isaac-xs) + ("perl-moo" ,perl-moo))) + (home-page "http://search.cpan.org/dist/Math-Random-Secure") + (synopsis "Cryptographically secure replacement for rand()") + (description "This module is intended to provide a +cryptographically-secure replacement for Perl's built-in @code{rand} function. +\"Crytographically secure\", in this case, means: + +@enumerate +@item No matter how many numbers you see generated by the random number +generator, you cannot guess the future numbers, and you cannot guess the seed. +@item There are so many possible seeds that it would take decades, centuries, +or millenia for an attacker to try them all. +@item The seed comes from a source that generates relatively strong random +data on your platform, so the seed itself will be as random as possible. +@end enumerate\n") + (license license:artistic2.0))) diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index 492a049a05..23606b4810 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -132,6 +132,7 @@ tunneling, and so on.") (method url-fetch) (uri (string-append "https://curl.haxx.se/download/curl-" version ".tar.xz")) + (patches (search-patches "curl-bounds-check.patch")) (sha256 (base32 "1785vxi0jamiv9d1wr1l45g0fm9ircxdfyfzf7ld8zv0z0i8bmfd")))) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index bb5d2349fd..5a69990c67 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -5226,6 +5226,23 @@ multiplexer.") editing RPM spec files.") (license license:gpl2+))) +(define-public emacs-nix-mode + (package + (inherit nix) + (name "emacs-nix-mode") + (build-system emacs-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir-elisp + ;; Elisp directory is not in root of the source. + (lambda _ + (chdir "misc/emacs")))))) + (synopsis "Emacs major mode for editing Nix expressions") + (description "@code{nixos-mode} provides an Emacs major mode for editing +Nix expressions. It supports syntax highlighting, indenting and refilling of +comments."))) + (define-public emacs-git-messenger (package (name "emacs-git-messenger") diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index b42e631b98..da1a1cf43d 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -59,7 +59,7 @@ (define-public efl (package (name "efl") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (string-append @@ -67,7 +67,7 @@ version ".tar.xz")) (sha256 (base32 - "1d1wmmwgc8pf6lk9g6lflpdxvg85wxxq650d6m30zgr85cb6d27q")))) + "0zll6k4xbbdsxqg53g8jddgv889g5m1xh20i03iz5a52y2bcnh55")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -123,7 +123,7 @@ ("glib" ,glib) ; ecore.pc, ecore-cxx.pc ("harfbuzz" ,harfbuzz) ; evas.pc, evas-cxx.pc ("luajit" ,luajit) ; elua.pc, evas.pc, evas-cxx.pc - ("libinput" ,libinput) ; elput.pc + ("libinput" ,libinput-minimal) ; elput.pc ("libpng" ,libpng) ; evas.pc, evas-cxx.pc ("libsndfile" ,libsndfile) ; ecore-audio.pc, ecore-audio-cxx.pc ("libxkbcommon" ,libxkbcommon) ; ecore-wl2.pc, elementary.pc, elput.pc diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 9f32e9f8e5..436a885d6e 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2016, 2017 Rodger Fox <thylakoid@openmailbox.org> ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com> -;;; Copyright © 2016, 2017 ng0 <ng0@no-reply.pragmatique.xyz> +;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org> ;;; Copyright © 2016 Albin Söderqvist <albin@fripost.org> ;;; Copyright © 2016, 2017 Kei Kebreau <kei@openmailbox.org> ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com> @@ -99,6 +99,7 @@ #:use-module (gnu packages xorg) #:use-module (gnu packages pkg-config) #:use-module (gnu packages databases) + #:use-module (gnu packages shells) #:use-module (gnu packages sdl) #:use-module (gnu packages swig) #:use-module (gnu packages texinfo) @@ -4564,8 +4565,8 @@ at their peak of economic growth and military prowess. ;; There have been no official releases. (define-public open-adventure - (let* ((commit "2483a23690d205f01ecb66165cf4522b541cd991") - (revision "1")) + (let* ((commit "d43854f0f6bb8e9eea7fbce80348150e7e7fc34d") + (revision "2")) (package (name "open-adventure") (version (string-append "2.5-" revision "." (string-take commit 7))) @@ -4577,14 +4578,23 @@ at their peak of economic growth and military prowess. (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1gkvkwbq5cl3llfc7nl41van8awn4myx782pg33bxpbx5l9scwb4")))) + "08bwrvf4axb1rsfd6ia1fddsky9pc1p350vjskhaakg2czc6dsk0")))) (build-system gnu-build-system) (arguments `(#:make-flags (list "CC=gcc") #:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases - (delete 'configure) + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; At this point linenoise is meant to be included, + ;; so we have to really copy it into the working directory + ;; of s. + (let* ((linenoise (assoc-ref inputs "linenoise")) + (noisepath (string-append linenoise "/include/linenoise")) + (out (assoc-ref outputs "out"))) + (copy-recursively noisepath "linenoise")) + #t)) (add-before 'build 'use-echo (lambda _ (substitute* "tests/Makefile" @@ -4594,9 +4604,9 @@ at their peak of economic growth and military prowess. (lambda _ ;; This target is missing a dependency (substitute* "Makefile" - ((".asc.6:" line) - (string-append line " advent.txt"))) - (zero? (system* "make" ".asc.6")))) + ((".adoc.6:" line) + (string-append line " advent.adoc"))) + (zero? (system* "make" ".adoc.6")))) ;; There is no install target (replace 'install (lambda* (#:key outputs #:allow-other-keys) @@ -4607,7 +4617,10 @@ at their peak of economic growth and military prowess. (install-file "advent.6" man)) #t))))) (native-inputs - `(("asciidoc" ,asciidoc))) + `(("asciidoc" ,asciidoc) + ("linenoise" ,linenoise) + ("python" ,python) + ("python-pyyaml" ,python-pyyaml))) (home-page "https://gitlab.com/esr/open-adventure") (synopsis "Colossal Cave Adventure") (description "The original Colossal Cave Adventure from 1976 was the diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index eee91c32bf..da4d66ce36 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -406,14 +406,14 @@ Go. It also includes runtime support libraries for these languages.") (define-public gcc-7 (package (inherit gcc-6) - (version "7.1.0") + (version "7.2.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gcc/gcc-" - version "/gcc-" version ".tar.bz2")) + version "/gcc-" version ".tar.xz")) (sha256 (base32 - "05xwps0ci7wgxh50askpa2r9p8518qxdgh6ad7pnyk7n6p13d0ca")) + "16j7i0888j2f1yp9l0nhji6cq65dy6y4nwy8868a8njbzzwavxqw")) (patches (search-patches "gcc-strmov-store-file-names.patch" "gcc-5.0-libvtv-runpath.patch")))))) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 07a62715de..c2f0a24344 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -54,7 +54,7 @@ (define-public feh (package (name "feh") - (version "2.19.1") + (version "2.19.2") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -62,7 +62,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "1d4ycmai3dpajl0bdr9i56646g4h5j1lb95jjn0nckwcddcj927c")))) + "0v2nwc6sk4vs855a1ncz9vxpzxvs1d5wcjz87rfbypxx7nap2al2")))) (build-system gnu-build-system) (arguments '(#:phases (alist-delete 'configure %standard-phases) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index 6e44175d97..8e17307543 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -45,14 +45,14 @@ ;; 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 "6.9.9-5") + (version "6.9.9-7") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "0mnhwzgap2q2qs899skc41s8gd2g1g6rgs959zxqg6yjx3n48r5a")))) + "1lwsz9b8clygdppgawv2hsry4aykgmawjlwhg3fj70rndv4a8rw4")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm index 03cd033376..25fcb514d0 100644 --- a/gnu/packages/ldc.scm +++ b/gnu/packages/ldc.scm @@ -279,7 +279,7 @@ latest DMD frontend and uses LLVM as backend.") (define-public dub (package (name "dub") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/dlang/dub/archive/" @@ -287,7 +287,7 @@ latest DMD frontend and uses LLVM as backend.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1w3pznyjnmsmasrvv93f82l0sr31fpwg2zcj8hh1b2gvc5761qhi")))) + "0hpl5srbrzwzv8abc96j4cgbmvm1zhr109ljbl7hrphzzc39zyan")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; it would have tested itself by installing some packages (vibe etc) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 5faa8db7e5..c27ddf042a 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2017 Alex Griffin <a@ajgrf.com> ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017 Andy Wingo <wingo@igalia.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -898,17 +899,51 @@ and to return information on pronunciations, meanings and synonyms.") (substitute* "external/libxmlsec/ExternalProject_xmlsec.mk" (("./configure") "$(CONFIG_SHELL) ./configure" )) #t))) - (add-after 'install 'bin-install + (add-after 'install 'bin-and-desktop-install ;; Create 'soffice' and 'libreoffice' symlinks to the executable ;; script. (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (soffice (string-append - out "/lib/libreoffice/program/soffice"))) - (mkdir bin) - (symlink soffice (string-append bin "/soffice")) - (symlink soffice (string-append bin "/libreoffice"))) + (let ((out (assoc-ref outputs "out"))) + (define (symlink-output src dst) + (mkdir-p (dirname (string-append out dst))) + (symlink (string-append out src) (string-append out dst))) + (define (install src dst) + (let ((dst (string-append out dst))) + (mkdir-p (dirname dst)) + (copy-file src dst))) + (define (install-desktop-file app) + (let ((src (string-append "/lib/libreoffice/share/xdg/" + app ".desktop")) + (dst (string-append "/share/applications/libreoffice-" + app ".desktop"))) + (substitute* (string-append out src) + (("Exec=libreoffice[0-9]+\\.[0-9]+ ") + (string-append "Exec=" out "/bin/libreoffice ")) + (("Icon=libreoffice[0-9]+\\.[0-9]+") + "Icon=libreoffice") + (("LibreOffice [0-9]+\\.[0-9]+") + "LibreOffice")) + (symlink-output src dst) + (install-file (string-append + "sysui/desktop/appstream-appdata/" + "libreoffice-" app ".appdata.xml") + (string-append out "/share/appdata")))) + (symlink-output "/lib/libreoffice/program/soffice" + "/bin/soffice") + (symlink-output "/lib/libreoffice/program/soffice" + "/bin/libreoffice") + (install "workdir/CustomTarget/sysui/share/libreoffice/openoffice.keys" + "/share/mime-info/libreoffice.keys") + (install "workdir/CustomTarget/sysui/share/libreoffice/openoffice.mime" + "/share/mime-info/libreoffice.mime") + (install + "workdir/CustomTarget/sysui/share/libreoffice/openoffice.org.xml" + "/share/mime/packages/libreoffice.xml") + (for-each install-desktop-file + '("base" "calc" "draw" "impress" "writer")) + (mkdir-p (string-append out "/share/icons")) + (copy-recursively "sysui/desktop/icons/hicolor" + (string-append out "/share/icons/"))) #t))) #:configure-flags (list diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 31572bd7dd..8ae74cbcb7 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -366,8 +366,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) -(define %linux-libre-version "4.12.5") -(define %linux-libre-hash "0kybil1h07fwl9rb0rvmp0w356hi2v1azw603r18vh9x93i8b8xi") +(define %linux-libre-version "4.12.7") +(define %linux-libre-hash "1sjkxkcikdgl2w5h7c5pfyqwi29g69dxp4s2z2yavw7aicc91xfq") (define-public linux-libre (make-linux-libre %linux-libre-version @@ -376,14 +376,14 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.41" - "1mkx7rvcny8b0yjkzd8zc53d15h1w8y75m0x6jx0dz3r9y3k0nql" + (make-linux-libre "4.9.43" + "0fxid4xmnrcq966vz2wsb6spw3i02pvqp2hv8xfrx7dr3hfs9nrr" %intel-compatible-systems #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.80" - "1s0d7lsapghgk6jh6igx2fhzj1f6nwmvhqrl2hdwf3dx14z93mp2" + (make-linux-libre "4.4.82" + "01bn0vn6i22hhwiqfh29m1cir1jrvz643lz13war8k9l6h0dmmwy" %intel-compatible-systems #:configuration-file kernel-config)) @@ -682,16 +682,17 @@ slabtop, and skill.") (define-public e2fsprogs (package (name "e2fsprogs") - (version "1.43.4") + (version "1.43.5") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/kernel/people/tytso/" name "/v" version "/" name "-" version ".tar.xz")) + (patches (search-patches "e2fsprogs-32bit-quota-warnings.patch")) (sha256 (base32 - "092absr4vrlqrkdf9nwh4ykj40ab6hhwrkdr6sjsccd54c8z5csl")))) + "05ssjpmy0fpv2ik6ibm1f47wr6794nf0q50r581vygrqvsd3s7r6")))) (build-system gnu-build-system) (inputs `(("util-linux" ,util-linux))) (native-inputs `(("pkg-config" ,pkg-config) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 9096838d6f..a81f6156ab 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2159,7 +2159,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "17.05.0") + (version "17.05.1") (source (origin (method url-fetch) @@ -2168,7 +2168,7 @@ point numbers.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1bsyd7r12xm2crpizb9iyyki3j0mbazzzwbsh871m06dv2wk97gq")))) + "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) @@ -2182,31 +2182,30 @@ point numbers.") ("gtk+" ,gtk+) ("shared-mime-info" ,shared-mime-info))) (arguments - `(#:phases (modify-phases %standard-phases - (add-before - 'configure 'autoconf - (lambda _ - (zero? (system* "./bootstrap")))) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (wrap-program (string-append (assoc-ref outputs "out") - "/bin/wxmaxima") - `("PATH" ":" prefix - (,(string-append (assoc-ref inputs "maxima") - "/bin"))) - ;; For GtkFileChooserDialog. - `("GSETTINGS_SCHEMA_DIR" = - (,(string-append (assoc-ref inputs "gtk+") - "/share/glib-2.0/schemas"))) - `("XDG_DATA_DIRS" ":" prefix - (;; Needed by gdk-pixbuf to know supported icon formats. - ,(string-append - (assoc-ref inputs "shared-mime-info") "/share") - ;; The default icon theme of GTK+. - ,(string-append - (assoc-ref inputs "adwaita-icon-theme") "/share")))) - #t))))) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autoconf + (lambda _ + (zero? (system* "sh" "bootstrap")))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (wrap-program (string-append (assoc-ref outputs "out") + "/bin/wxmaxima") + `("PATH" ":" prefix + (,(string-append (assoc-ref inputs "maxima") + "/bin"))) + ;; For GtkFileChooserDialog. + `("GSETTINGS_SCHEMA_DIR" = + (,(string-append (assoc-ref inputs "gtk+") + "/share/glib-2.0/schemas"))) + `("XDG_DATA_DIRS" ":" prefix + (;; Needed by gdk-pixbuf to know supported icon formats. + ,(string-append + (assoc-ref inputs "shared-mime-info") "/share") + ;; The default icon theme of GTK+. + ,(string-append + (assoc-ref inputs "adwaita-icon-theme") "/share")))) + #t))))) (home-page "https://andrejv.github.io/wxmaxima/") (synopsis "Graphical user interface for the Maxima computer algebra system") (description diff --git a/gnu/packages/moreutils.scm b/gnu/packages/moreutils.scm index 03ffa8f992..bb6228af7f 100644 --- a/gnu/packages/moreutils.scm +++ b/gnu/packages/moreutils.scm @@ -52,10 +52,18 @@ ("libxml2" ,libxml2) ("libxslt" ,libxslt))) (inputs - `(("perl" ,perl))) + `(("perl" ,perl) + ("perl-timedate" ,perl-timedate) + ("perl-time-duration" ,perl-time-duration))) (arguments `(#:phases (modify-phases %standard-phases + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (wrap-program + (string-append out "/bin/ts") + `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))))))) (delete 'configure)) ; no configure script #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 40996b11be..dcb48fb200 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2264,15 +2264,16 @@ of tools for manipulating and accessing your music.") (define-public milkytracker (package (name "milkytracker") - (version "1.0.0") + (version "1.01.00") (source (origin (method url-fetch) (uri (string-append "https://github.com/milkytracker/" - "MilkyTracker/archive/v" version ".tar.gz")) + "MilkyTracker/archive/v" + version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1p1jd4h274jvcvl05l01v9bj19zhq4sjag92v1zawyi93ib85abz")) + "1dvnddsnn9c83lz4dlm0cfjpc0m524amfkbalxbswdy0qc8cj1wv")) (modules '((guix build utils))) ;; Remove non-FSDG compliant sample songs. (snippet diff --git a/gnu/packages/patches/catdoc-CVE-2017-11110.patch b/gnu/packages/patches/catdoc-CVE-2017-11110.patch new file mode 100644 index 0000000000..71c44f60fb --- /dev/null +++ b/gnu/packages/patches/catdoc-CVE-2017-11110.patch @@ -0,0 +1,45 @@ +Fix CVE-2017-11110: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-11110 +https://bugzilla.redhat.com/show_bug.cgi?id=1468471 +https://security-tracker.debian.org/tracker/CVE-2017-11110 + +Patch copied from openSUSE: + +https://build.opensuse.org/package/view_file/openSUSE:Maintenance:6985/catdoc.openSUSE_Leap_42.2_Update/CVE-2017-11110.patch?expand=1 + +From: Andreas Stieger <astieger@suse.com> +Date: Mon, 10 Jul 2017 15:37:58 +0000 +References: CVE-2017-11110 http://bugzilla.suse.com/show_bug.cgi?id=1047877 + +All .doc I found had sectorSize 0x09 at offset 0x1e. Guarding it against <4. + +--- + src/ole.c | 5 +++++ + 1 file changed, 5 insertions(+) + +Index: catdoc-0.95/src/ole.c +=================================================================== +--- catdoc-0.95.orig/src/ole.c 2016-05-25 06:37:12.000000000 +0200 ++++ catdoc-0.95/src/ole.c 2017-07-10 17:42:33.578308107 +0200 +@@ -106,6 +106,11 @@ FILE* ole_init(FILE *f, void *buffer, si + return NULL; + } + sectorSize = 1<<getshort(oleBuf,0x1e); ++ /* CVE-2017-11110) */ ++ if (sectorSize < 4) { ++ fprintf(stderr,"sectorSize < 4 not supported\n"); ++ return NULL; ++ } + shortSectorSize=1<<getshort(oleBuf,0x20); + + /* Read BBD into memory */ +@@ -147,7 +152,7 @@ FILE* ole_init(FILE *f, void *buffer, si + } + + fseek(newfile, 512+mblock*sectorSize, SEEK_SET); +- if(fread(tmpBuf+MSAT_ORIG_SIZE+(sectorSize-4)*i, ++ if(fread(tmpBuf+MSAT_ORIG_SIZE+(sectorSize-4)*i, /* >= 4 for CVE-2017-11110 */ + 1, sectorSize, newfile) != sectorSize) { + fprintf(stderr, "Error read MSAT!\n"); + ole_finish(); diff --git a/gnu/packages/patches/curl-bounds-check.patch b/gnu/packages/patches/curl-bounds-check.patch new file mode 100644 index 0000000000..4b8ff65304 --- /dev/null +++ b/gnu/packages/patches/curl-bounds-check.patch @@ -0,0 +1,19 @@ +Fix test failure on some 32-bit platforms. + +Patch copied from upstream source repository: + +https://github.com/curl/curl/commit/45a560390c4356bcb81d933bbbb229c8ea2acb63 + +diff --git a/src/tool_paramhlp.c b/src/tool_paramhlp.c +index b9dedc989e..85c5e79a7e 100644 +--- a/src/tool_paramhlp.c ++++ b/src/tool_paramhlp.c +@@ -218,7 +218,7 @@ static ParameterError str2double(double *val, const char *str, long max) + num = strtod(str, &endptr); + if(errno == ERANGE) + return PARAM_NUMBER_TOO_LARGE; +- if((long)num > max) { ++ if(num > max) { + /* too large */ + return PARAM_NUMBER_TOO_LARGE; + } diff --git a/gnu/packages/patches/cvs-2017-12836.patch b/gnu/packages/patches/cvs-2017-12836.patch new file mode 100644 index 0000000000..507ab0f7d0 --- /dev/null +++ b/gnu/packages/patches/cvs-2017-12836.patch @@ -0,0 +1,45 @@ +Fix CVE-2017-12836: + +http://cve.mitre.org/cgi-bin/cvename.cgi?name=2017-12836 +https://security-tracker.debian.org/tracker/CVE-2017-12836 + +Patch adpated from Debian (comments and changelog annotations removed): + +https://anonscm.debian.org/cgit/collab-maint/cvs.git/commit/?h=stretch&id=41e077396e35efb6c879951f44c62dd8a1d0f094 + +From 41e077396e35efb6c879951f44c62dd8a1d0f094 Mon Sep 17 00:00:00 2001 +From: mirabilos <m@mirbsd.org> +Date: Sat, 12 Aug 2017 03:17:18 +0200 +Subject: Fix CVE-2017-12836 (Closes: #871810) for stretch + +--- + debian/changelog | 6 ++++++ + src/rsh-client.c | 10 ++++++++-- + 2 files changed, 14 insertions(+), 2 deletions(-) + +diff --git a/src/rsh-client.c b/src/rsh-client.c +index fe0cfc4..1fc860d 100644 +--- a/src/rsh-client.c ++++ b/src/rsh-client.c +@@ -105,6 +106,9 @@ start_rsh_server (cvsroot_t *root, struct buffer **to_server_p, + rsh_argv[i++] = argvport; + } + ++ /* Only non-option arguments from here. (CVE-2017-12836) */ ++ rsh_argv[i++] = "--"; ++ + rsh_argv[i++] = root->hostname; + rsh_argv[i++] = cvs_server; + if (readonlyfs) +@@ -189,6 +193,8 @@ start_rsh_server (cvsroot_t *root, struct buffer **to_server_p, + *p++ = argvport; + } + ++ *p++ = "--"; ++ + *p++ = root->hostname; + *p++ = command; + *p++ = NULL; +-- +cgit v0.12 + diff --git a/gnu/packages/patches/e2fsprogs-32bit-quota-warnings.patch b/gnu/packages/patches/e2fsprogs-32bit-quota-warnings.patch new file mode 100644 index 0000000000..e7a96a2ac0 --- /dev/null +++ b/gnu/packages/patches/e2fsprogs-32bit-quota-warnings.patch @@ -0,0 +1,46 @@ +Fix a test failure on 32-bit platforms. + +Patch copied from upstream source repository: + +https://git.kernel.org/pub/scm/fs/ext2/e2fsprogs.git/commit/?id=9e31a5696c4b699bf000a07b86601c1fb91c0493 + +diff --git a/lib/support/mkquota.c b/lib/support/mkquota.c +index 00f3a40..931a839 100644 +--- a/lib/support/mkquota.c ++++ b/lib/support/mkquota.c +@@ -50,11 +50,13 @@ static void print_dquot(const char *desc, struct dquot *dq) + { + if (desc) + fprintf(stderr, "%s: ", desc); +- fprintf(stderr, "%u %ld:%ld:%ld %ld:%ld:%ld\n", +- dq->dq_id, dq->dq_dqb.dqb_curspace, +- dq->dq_dqb.dqb_bsoftlimit, dq->dq_dqb.dqb_bhardlimit, +- dq->dq_dqb.dqb_curinodes, +- dq->dq_dqb.dqb_isoftlimit, dq->dq_dqb.dqb_ihardlimit); ++ fprintf(stderr, "%u %lld:%lld:%lld %lld:%lld:%lld\n", ++ dq->dq_id, (long long) dq->dq_dqb.dqb_curspace, ++ (long long) dq->dq_dqb.dqb_bsoftlimit, ++ (long long) dq->dq_dqb.dqb_bhardlimit, ++ (long long) dq->dq_dqb.dqb_curinodes, ++ (long long) dq->dq_dqb.dqb_isoftlimit, ++ (long long) dq->dq_dqb.dqb_ihardlimit); + } + #else + static void print_dquot(const char *desc EXT2FS_ATTR((unused)), +@@ -524,11 +526,11 @@ static int scan_dquots_callback(struct dquot *dquot, void *cb_data) + dq->dq_dqb.dqb_curinodes != dquot->dq_dqb.dqb_curinodes) { + scan_data->usage_is_inconsistent = 1; + fprintf(stderr, "[QUOTA WARNING] Usage inconsistent for ID %u:" +- "actual (%ld, %ld) != expected (%ld, %ld)\n", +- dq->dq_id, dq->dq_dqb.dqb_curspace, +- dq->dq_dqb.dqb_curinodes, +- dquot->dq_dqb.dqb_curspace, +- dquot->dq_dqb.dqb_curinodes); ++ "actual (%lld, %lld) != expected (%lld, %lld)\n", ++ dq->dq_id, (long long) dq->dq_dqb.dqb_curspace, ++ (long long) dq->dq_dqb.dqb_curinodes, ++ (long long) dquot->dq_dqb.dqb_curspace, ++ (long long) dquot->dq_dqb.dqb_curinodes); + } + + if (scan_data->update_limits) { diff --git a/gnu/packages/patches/qemu-CVE-2017-10664.patch b/gnu/packages/patches/qemu-CVE-2017-10664.patch new file mode 100644 index 0000000000..2b60de3dca --- /dev/null +++ b/gnu/packages/patches/qemu-CVE-2017-10664.patch @@ -0,0 +1,27 @@ +Fix CVE-2017-10664: + +https://lists.gnu.org/archive/html/qemu-devel/2017-06/msg02693.html +https://bugzilla.redhat.com/show_bug.cgi?id=1466190 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-10664 +https://security-tracker.debian.org/tracker/CVE-2017-10664 + +Patch copied from upstream source repository: + +https://git.qemu.org/gitweb.cgi?p=qemu.git;a=commitdiff;h=041e32b8d9d076980b4e35317c0339e57ab888f1 + +diff --git a/qemu-nbd.c b/qemu-nbd.c +index 9464a0461c..4dd3fd4732 100644 +--- a/qemu-nbd.c ++++ b/qemu-nbd.c +@@ -581,6 +581,10 @@ int main(int argc, char **argv) + sa_sigterm.sa_handler = termsig_handler; + sigaction(SIGTERM, &sa_sigterm, NULL); + ++#ifdef CONFIG_POSIX ++ signal(SIGPIPE, SIG_IGN); ++#endif ++ + module_call_init(MODULE_INIT_TRACE); + qcrypto_init(&error_fatal); + + diff --git a/gnu/packages/patches/qemu-CVE-2017-10806.patch b/gnu/packages/patches/qemu-CVE-2017-10806.patch new file mode 100644 index 0000000000..ebf782fe7b --- /dev/null +++ b/gnu/packages/patches/qemu-CVE-2017-10806.patch @@ -0,0 +1,38 @@ +Fix CVE-2017-10806: + +https://lists.nongnu.org/archive/html/qemu-devel/2017-05/msg03087.html +https://bugzilla.redhat.com/show_bug.cgi?id=1468496 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-10806 +https://security-tracker.debian.org/tracker/CVE-2017-10806 + +Patch copied from upstream source repository: + +https://git.qemu.org/gitweb.cgi?p=qemu.git;a=commit;h=bd4a683505b27adc1ac809f71e918e58573d851d + +diff --git a/hw/usb/redirect.c b/hw/usb/redirect.c +index b001a27f05..ad5ef783a6 100644 +--- a/hw/usb/redirect.c ++++ b/hw/usb/redirect.c +@@ -229,21 +229,10 @@ static void usbredir_log(void *priv, int level, const char *msg) + static void usbredir_log_data(USBRedirDevice *dev, const char *desc, + const uint8_t *data, int len) + { +- int i, j, n; +- + if (dev->debug < usbredirparser_debug_data) { + return; + } +- +- for (i = 0; i < len; i += j) { +- char buf[128]; +- +- n = sprintf(buf, "%s", desc); +- for (j = 0; j < 8 && i + j < len; j++) { +- n += sprintf(buf + n, " %02X", data[i + j]); +- } +- error_report("%s", buf); +- } ++ qemu_hexdump((char *)data, stderr, desc, len); + } + + /* diff --git a/gnu/packages/patches/qemu-CVE-2017-10911.patch b/gnu/packages/patches/qemu-CVE-2017-10911.patch new file mode 100644 index 0000000000..1dcb860a2d --- /dev/null +++ b/gnu/packages/patches/qemu-CVE-2017-10911.patch @@ -0,0 +1,106 @@ +Fix CVE-2017-10911: + +https://xenbits.xen.org/xsa/advisory-216.html +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-10911 +https://security-tracker.debian.org/tracker/CVE-2017-10911 + +Patch copied from Xen Security Advisory: + +https://xenbits.xen.org/xsa/xsa216-qemuu.patch + +--- a/hw/block/xen_blkif.h ++++ b/hw/block/xen_blkif.h +@@ -14,9 +14,6 @@ + struct blkif_common_request { + char dummy; + }; +-struct blkif_common_response { +- char dummy; +-}; + + /* i386 protocol version */ + #pragma pack(push, 4) +@@ -36,13 +33,7 @@ struct blkif_x86_32_request_discard { + blkif_sector_t sector_number; /* start sector idx on disk (r/w only) */ + uint64_t nr_sectors; /* # of contiguous sectors to discard */ + }; +-struct blkif_x86_32_response { +- uint64_t id; /* copied from request */ +- uint8_t operation; /* copied from request */ +- int16_t status; /* BLKIF_RSP_??? */ +-}; + typedef struct blkif_x86_32_request blkif_x86_32_request_t; +-typedef struct blkif_x86_32_response blkif_x86_32_response_t; + #pragma pack(pop) + + /* x86_64 protocol version */ +@@ -62,20 +53,14 @@ struct blkif_x86_64_request_discard { + blkif_sector_t sector_number; /* start sector idx on disk (r/w only) */ + uint64_t nr_sectors; /* # of contiguous sectors to discard */ + }; +-struct blkif_x86_64_response { +- uint64_t __attribute__((__aligned__(8))) id; +- uint8_t operation; /* copied from request */ +- int16_t status; /* BLKIF_RSP_??? */ +-}; + typedef struct blkif_x86_64_request blkif_x86_64_request_t; +-typedef struct blkif_x86_64_response blkif_x86_64_response_t; + + DEFINE_RING_TYPES(blkif_common, struct blkif_common_request, +- struct blkif_common_response); ++ struct blkif_response); + DEFINE_RING_TYPES(blkif_x86_32, struct blkif_x86_32_request, +- struct blkif_x86_32_response); ++ struct blkif_response QEMU_PACKED); + DEFINE_RING_TYPES(blkif_x86_64, struct blkif_x86_64_request, +- struct blkif_x86_64_response); ++ struct blkif_response); + + union blkif_back_rings { + blkif_back_ring_t native; +--- a/hw/block/xen_disk.c ++++ b/hw/block/xen_disk.c +@@ -769,31 +769,30 @@ static int blk_send_response_one(struct + struct XenBlkDev *blkdev = ioreq->blkdev; + int send_notify = 0; + int have_requests = 0; +- blkif_response_t resp; +- void *dst; +- +- resp.id = ioreq->req.id; +- resp.operation = ioreq->req.operation; +- resp.status = ioreq->status; ++ blkif_response_t *resp; + + /* Place on the response ring for the relevant domain. */ + switch (blkdev->protocol) { + case BLKIF_PROTOCOL_NATIVE: +- dst = RING_GET_RESPONSE(&blkdev->rings.native, blkdev->rings.native.rsp_prod_pvt); ++ resp = RING_GET_RESPONSE(&blkdev->rings.native, ++ blkdev->rings.native.rsp_prod_pvt); + break; + case BLKIF_PROTOCOL_X86_32: +- dst = RING_GET_RESPONSE(&blkdev->rings.x86_32_part, +- blkdev->rings.x86_32_part.rsp_prod_pvt); ++ resp = RING_GET_RESPONSE(&blkdev->rings.x86_32_part, ++ blkdev->rings.x86_32_part.rsp_prod_pvt); + break; + case BLKIF_PROTOCOL_X86_64: +- dst = RING_GET_RESPONSE(&blkdev->rings.x86_64_part, +- blkdev->rings.x86_64_part.rsp_prod_pvt); ++ resp = RING_GET_RESPONSE(&blkdev->rings.x86_64_part, ++ blkdev->rings.x86_64_part.rsp_prod_pvt); + break; + default: +- dst = NULL; + return 0; + } +- memcpy(dst, &resp, sizeof(resp)); ++ ++ resp->id = ioreq->req.id; ++ resp->operation = ioreq->req.operation; ++ resp->status = ioreq->status; ++ + blkdev->rings.common.rsp_prod_pvt++; + + RING_PUSH_RESPONSES_AND_CHECK_NOTIFY(&blkdev->rings.common, send_notify); diff --git a/gnu/packages/patches/qemu-CVE-2017-11434.patch b/gnu/packages/patches/qemu-CVE-2017-11434.patch new file mode 100644 index 0000000000..4da701a73d --- /dev/null +++ b/gnu/packages/patches/qemu-CVE-2017-11434.patch @@ -0,0 +1,25 @@ +Fix CVE-2017-11434: + +https://lists.gnu.org/archive/html/qemu-devel/2017-07/msg05001.html +https://bugzilla.redhat.com/show_bug.cgi?id=1472611 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-11434 +https://security-tracker.debian.org/tracker/CVE-2017-11434 + +Patch copied from upstream source repository: + +https://git.qemu.org/gitweb.cgi?p=qemu.git;a=commit;h=413d463f43fbc4dd3a601e80a5724aa384a265a0 + +diff --git a/slirp/bootp.c b/slirp/bootp.c +index 5a4646c182..5dd1a415b5 100644 +--- a/slirp/bootp.c ++++ b/slirp/bootp.c +@@ -123,6 +123,9 @@ static void dhcp_decode(const struct bootp_t *bp, int *pmsg_type, + if (p >= p_end) + break; + len = *p++; ++ if (p + len > p_end) { ++ break; ++ } + DPRINTF("dhcp: tag=%d len=%d\n", tag, len); + + switch(tag) { diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 4a87d0ae63..2b2b2ea1fe 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr> -;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr> ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org> @@ -3419,6 +3419,30 @@ objects, which execute a given code block when destroyed, and scoped guards, which are tied to the scope exit.") (license (package-license perl)))) +(define-public perl-hash-fieldhash + (package + (name "perl-hash-fieldhash") + (version "0.15") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/G/GF/GFUJI/" + "Hash-FieldHash-" version ".tar.gz")) + (sha256 + (base32 + "1wg8nzczfxif55j2nbymbhyd25pjy7dqs4bvd6jrcds3ll3mflaw")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build) + ("perl-test-leaktrace" ,perl-test-leaktrace))) + (home-page "http://search.cpan.org/dist/Hash-FieldHash") + (synopsis "Lightweight field hash for inside-out objects") + (description "@code{Hash::FieldHash} provides the field hash mechanism +which supports the inside-out technique. It is an alternative to +@code{Hash::Util::FieldHash} with a simpler interface, higher performance, and +relic support.") + (license (package-license perl)))) + (define-public perl-hash-merge (package (name "perl-hash-merge") @@ -5742,6 +5766,27 @@ can also be useful as a development and debugging tool for catching updates to variables that should not be changed.") (license (package-license perl)))) +(define-public perl-ref-util-xs + (package + (name "perl-ref-util-xs") + (version "0.116") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/X/XS/XSAWYERX/" + "Ref-Util-XS-" version ".tar.gz")) + (sha256 + (base32 + "0l5dzbd71iclv8fdjk7685rq6pbfiiydh0n70br6g9l9iy2smr6f")))) + (build-system perl-build-system) + (home-page "http://search.cpan.org/dist/Ref-Util-XS") + (synopsis "XS implementation for Ref::Util") + (description "@code{Ref::Util::XS} is the XS implementation of +@code{Ref::Util}, which provides several functions to help identify references +in a more convenient way than the usual approach of examining the return value +of @code{ref}.") + (license x11))) + (define-public perl-regexp-common (package (name "perl-regexp-common") @@ -5767,6 +5812,27 @@ codes.") ;; Quad-licensed: Perl Artistic, Perl Artistic 2.0, X11, and BSD. (license (list (package-license perl) x11 bsd-3)))) +(define-public perl-regexp-util + (package + (name "perl-regexp-util") + (version "0.003") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/T/TO/TOBYINK/" + "Regexp-Util-" version ".tar.gz")) + (sha256 + (base32 + "01n1cggiflsnp9f6adkcxzkc0qpgssz60cwnyyd8mzavh2ximr5a")))) + (build-system perl-build-system) + (home-page "http://search.cpan.org/dist/Regexp-Util") + (synopsis "Selection of general-utility regexp subroutines") + (description "This package provides a selection of regular expression +subroutines including @code{is_regexp}, @code{regexp_seen_evals}, +@code{regexp_is_foreign}, @code{regexp_is_anchored}, @code{serialize_regexp}, +and @code{deserialize_regexp}.") + (license (package-license perl)))) + (define-public perl-role-tiny (package (name "perl-role-tiny") @@ -7955,6 +8021,68 @@ that are designed to minimize common mistakes with eval blocks, and nothing else.") (license x11))) +(define-public perl-type-tie + (package + (name "perl-type-tie") + (version "0.009") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/T/TO/TOBYINK/" + "Type-Tie-" version ".tar.gz")) + (sha256 + (base32 + "1wv32kd7gx4kfyvzs13y029f49qbbji991wawvarac7rlz09wpan")))) + (build-system perl-build-system) + (native-inputs + `(("perl-test-fatal" ,perl-test-fatal) + ("perl-test-requires" ,perl-test-requires))) + (propagated-inputs + `(("perl-exporter-tiny" ,perl-exporter-tiny) + ("perl-hash-fieldhash" ,perl-hash-fieldhash))) + (home-page "http://search.cpan.org/dist/Type-Tie") + (synopsis "Tie a variable to a type constraint") + (description "This module exports a single function: @code{ttie}. It ties +a variable to a type constraint, ensuring that whatever values stored in the +variable will conform to the type constraint. If the type constraint has +coercions, these will be used if necessary to ensure values assigned to the +variable conform.") + (license (package-license perl)))) + +(define-public perl-type-tiny + (package + (name "perl-type-tiny") + (version "1.002001") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/T/TO/TOBYINK/" + "Type-Tiny-" version ".tar.gz")) + (sha256 + (base32 + "1p8krim8kvw123nady96fagi8sk2pj1z8jkr4r8n45ihyamfxjck")))) + (build-system perl-build-system) + (native-inputs + `(("perl-test-warnings" ,perl-test-warnings))) + (propagated-inputs + `(("perl-devel-lexalias" ,perl-devel-lexalias) + ("perl-devel-stacktrace" ,perl-devel-stacktrace) + ("perl-exporter-tiny" ,perl-exporter-tiny) + ("perl-moo" ,perl-moo) + ("perl-moose" ,perl-moose) + ("perl-mouse" ,perl-mouse) + ("perl-ref-util-xs" ,perl-ref-util-xs) + ("perl-regexp-util" ,perl-regexp-util) + ("perl-type-tie" ,perl-type-tie))) + (home-page "http://search.cpan.org/dist/Type-Tiny") + (synopsis "Tiny, yet Moo(se)-compatible type constraint") + (description "@code{Type::Tiny} is a small class for writing type +constraints, inspired by Moose's type constraint API. It has only one +non-core dependency (and even that is simply a module that was previously +distributed as part of @code{Type::Tiny} but has since been spun off), and can +be used with Moose, Mouse and Moo (or none of the above).") + (license (package-license perl)))) + (define-public perl-types-serialiser (package (name "perl-types-serialiser") diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f5f89c9e06..5557b6042b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -14324,10 +14324,12 @@ Pylint has many rules enabled by default, way too much to silence them all on a minimally sized program. It's highly configurable and handle pragmas to control it from within your code. Additionally, it is possible to write plugins to add your own checks.") + (properties `((python2-variant . ,(delay python2-pylint)))) (license license:gpl2+))) (define-public python2-pylint - (let ((pylint (package-with-python2 python-pylint))) + (let ((pylint (package-with-python2 + (strip-python2-variant python-pylint)))) (package (inherit pylint) (propagated-inputs `(("python2-backports-functools-lru-cache" diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 89db28ff06..37307c807b 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -449,38 +449,41 @@ operating system.") (license bsd-3)))) (define-public linenoise - (package - (name "linenoise") - (version "1.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/antirez/linenoise/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "05006hd56xcvxjdpll4x720bpfan7vwqmxbw8a2kvm10w57ll1gm")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ;No tests are included - #:make-flags (list "CC=gcc") - #:phases - (modify-phases %standard-phases - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - ;; At the moment there is no 'make install' in upstream. - (let* ((out (assoc-ref outputs "out"))) - (install-file "linenoise.h" - (string-append out "/include/linenoise")) - (install-file "linenoise.c" - (string-append out "/include/linenoise")) - #t)))))) - (home-page "https://github.com/antirez/linenoise") - (synopsis "Minimal zero-config readline replacement") - (description - "Linenoise is a minimal, zero-config, readline replacement. + (let ((commit "2105ce445821381cf1bca87b6d386d4ea88ee20d") + (revision "1")) + (package + (name "linenoise") + (version (string-append "1.0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/antirez/linenoise") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1z16qwix8z6a40fskdgxsibkqgdrp4q6ncp4n6hnv4r9iihy2d8r")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;No tests are included + #:make-flags (list "CC=gcc") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + ;; At the moment there is no 'make install' in upstream. + (let* ((out (assoc-ref outputs "out"))) + (install-file "linenoise.h" + (string-append out "/include/linenoise")) + (install-file "linenoise.c" + (string-append out "/include/linenoise")) + #t)))))) + (home-page "https://github.com/antirez/linenoise") + (synopsis "Minimal zero-config readline replacement") + (description + "Linenoise is a minimal, zero-config, readline replacement. Its features include: @enumerate @@ -490,7 +493,7 @@ Its features include: @item Hints (suggestions at the right of the prompt as you type) @item A subset of VT100 escapes, ANSI.SYS compatible @end enumerate\n") - (license bsd-2))) + (license bsd-2)))) (define-public s-shell (let ((commit "6604341edb3a775ff94415762af3ee9bd86bfb3c") diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index e8ae30cd6d..537d013345 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2017 Rene Saavedra <rennes@openmailbox.org> ;;; Copyright © 2017 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2017 Kei Kebreau <kei@openmailbox.org> +;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -409,6 +410,7 @@ runs Word\".") (method url-fetch) (uri (string-append "http://ftp.wagner.pp.ru/pub/catdoc/" "catdoc-" version ".tar.gz")) + (patches (search-patches "catdoc-CVE-2017-11110.patch")) (sha256 (base32 "15h7v3bmwfk4z8r78xs5ih6vd0pskn0rj90xghvbzdjj0cc88jji")))) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index bff6471559..7c1f02d5ad 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -350,18 +350,21 @@ everything from small to very large projects with speed and efficiency.") (home-page "https://git-scm.com/"))) ;; Some dependent packages directly access internal interfaces which -;; have changed in 2.12 +;; have changed in 2.12. TODO: Remove this for cgit > 1.1. (define-public git@2.10 (package (inherit git) - (version "2.10.3") - (source (origin - (method url-fetch) - (uri (string-append "mirror://kernel.org/software/scm/git/git-" - version ".tar.xz")) - (sha256 - (base32 - "02mb7yi49algsya3hnkcxdslwb6p1bi7c732z1g8kzq4hs838m7z")))))) + (version "2.10.4") + (source (origin + (method url-fetch) + (uri (string-append "mirror://kernel.org/software/scm/git/git-" + version ".tar.xz")) + (sha256 + (base32 + "1pni4mgih5w42813dxljl61s7xmcpdnar34d9m4548hzpljjyd4l")))) + (arguments + `(#:tests? #f + ,@(package-arguments git))))) (define-public libgit2 (package @@ -921,6 +924,7 @@ machine.") (uri (string-append "https://ftp.gnu.org/non-gnu/cvs/source/feature/" version "/cvs-" version ".tar.bz2")) + (patches (search-patches "cvs-2017-12836.patch")) (sha256 (base32 "0pjir8cwn0087mxszzbsi1gyfc6373vif96cw4q3m1x6p49kd1bq")))) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index fdb7d48aec..610b258dfc 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1121,7 +1121,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.08.06") + (version "2017.08.13") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -1129,7 +1129,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "1vdfda2w1ckhqna8xcpphr5l0rp9zhs368lic4f7144rxvbydiwm")))) + "1parn0xda7mp1phcj19axldifgh6mcwia6wdi3m20kidc9m4wb11")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 49998120d2..ab364cd1fb 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2015, 2016, 2017 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -82,7 +83,11 @@ "qemu-CVE-2017-8379.patch" "qemu-CVE-2017-8380.patch" "qemu-CVE-2017-9524.patch" - "qemu-CVE-2017-11334.patch")) + "qemu-CVE-2017-10664.patch" + "qemu-CVE-2017-10806.patch" + "qemu-CVE-2017-10911.patch" + "qemu-CVE-2017-11334.patch" + "qemu-CVE-2017-11434.patch")) (sha256 (base32 "08mhfs0ndbkyqgw7fjaa9vjxf4dinrly656f6hjzvmaz7hzc677h")))) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 7150fb28da..565e6e8927 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -93,6 +93,14 @@ (build-system python-build-system) (arguments `(#:python ,python-2 ;incompatible with python 3 + #:phases + (modify-phases %standard-phases + (add-before 'build 'configure + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "screenlayout/xrandr.py" + (("\"xrandr\"") (string-append "\"" (assoc-ref inputs "xrandr") + "/bin/xrandr\""))) + #t))) #:tests? #f)) ;no tests (inputs `(("pygtk" ,python2-pygtk) ("xrandr" ,xrandr))) |