diff options
Diffstat (limited to 'gnu')
58 files changed, 2981 insertions, 738 deletions
diff --git a/gnu/build/linux-boot.scm b/gnu/build/linux-boot.scm index 30d6570b04..0fc90af6a3 100644 --- a/gnu/build/linux-boot.scm +++ b/gnu/build/linux-boot.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -381,7 +381,6 @@ to it are lost." (start-repl)) (display "loading kernel modules...\n") - (current-module-debugging-port (current-output-port)) (for-each (cut load-linux-module* <> #:lookup-module lookup-module) (map lookup-module linux-modules)) diff --git a/gnu/build/linux-modules.scm b/gnu/build/linux-modules.scm index a3bc7d6e33..e6552fdb67 100644 --- a/gnu/build/linux-modules.scm +++ b/gnu/build/linux-modules.scm @@ -144,7 +144,7 @@ true, load its dependencies first (à la 'modprobe'.) The actual files containing modules depended on are obtained by calling LOOKUP-MODULE with the module name." (define (slurp module) - ;; TODO: Use 'mmap' to reduce memory usage. + ;; TODO: Use 'finit_module' to reduce memory usage. (call-with-input-file file get-bytevector-all)) (when recursive? diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 4f335a27d4..6e3024dffd 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com> -;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> +;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com> @@ -402,14 +402,14 @@ connection alive.") bind-release-version))) (package (name "isc-dhcp") - (version "4.3.3") + (version "4.3.3-P1") (source (origin (method url-fetch) (uri (string-append "http://ftp.isc.org/isc/dhcp/" version "/dhcp-" version ".tar.gz")) (sha256 (base32 - "1pjy4lylx7dww1fp2mk5ikya5vxaf97z70279j81n74vn12ljg2m")))) + "08crcsmg4dm2v533aq3883ik8mf4vvvd6r998r4vrgx1zxnqj7n1")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f @@ -700,12 +700,13 @@ system administrator.") version ".tar.gz"))) (sha256 (base32 - "0263gi6i19fyzzc488n0qw3m518i39f6a7qmrfvahk9j10bkh5j3")))) + "0263gi6i19fyzzc488n0qw3m518i39f6a7qmrfvahk9j10bkh5j3")) + (patches (list (search-patch "sudo-CVE-2015-5602.patch"))))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--with-logpath=/var/log/sudo.log" - "--with-rundir=/run/sudo" + "--with-rundir=/var/run/sudo" ;must be cleaned up at boot time "--with-vardir=/var/db/sudo" "--with-iologdir=/var/log/sudo-io" diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 25e1af1750..dd6838140b 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2012, 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2013, 2015 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org> ;;; @@ -157,7 +157,7 @@ PARI is also available as a C library to allow for faster computations.") (define-public gp2c (package (name "gp2c") - (version "0.0.9pl4") + (version "0.0.9pl5") (source (origin (method url-fetch) (uri (string-append @@ -165,7 +165,7 @@ PARI is also available as a C library to allow for faster computations.") version ".tar.gz")) (sha256 (base32 - "079qq4yyxpc53a2kn08gg9pcfgdyffbl14c2hqsic11q8pnsr08z")))) + "1q003mkagc5ib6lqb2xfay7j4ffkwv7xlnznp6wdrq2sbqq4vyak")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (inputs `(("pari-gp" ,pari-gp))) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index df1f67bddd..3cc5cebc2c 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -320,7 +320,8 @@ tools (analyzer, mono/stereo tools, crossovers).") version "/Csound" version ".tar.gz")) (sha256 (base32 - "0a1sni6lr7qpwywpggbkp0ia3h9bwwgf9i87gsag8ra2h30v82hd")))) + "0a1sni6lr7qpwywpggbkp0ia3h9bwwgf9i87gsag8ra2h30v82hd")) + (patches (list (search-patch "csound-header-ordering.patch"))))) (build-system cmake-build-system) (arguments ;; Work around this error on x86_64 with libc 2.22+: @@ -1081,7 +1082,16 @@ software.") #:configure-flags (list (string-append "--boost-includes=" (assoc-ref %build-inputs "boost") - "/include")))) + "/include")) + #:phases (modify-phases %standard-phases + (add-before + 'configure 'set-flags + (lambda* (#:key inputs #:allow-other-keys) + ;; See e.g. https://github.com/lvtk/lvtk/issues/21 + (setenv "LDFLAGS" + (string-append + "-L" (assoc-ref inputs "boost") "/lib " + "-lboost_system"))))))) (inputs `(("boost" ,boost) ("lv2" ,lv2))) @@ -1839,6 +1849,11 @@ result.") "http://kokkinizita.linuxaudio.org" "/linuxaudio/downloads/zita-convolver-" version ".tar.bz2")) + (snippet + ;; Don't optimize for a specific processor architecture. + '(substitute* "libs/Makefile" + (("^CXXFLAGS \\+= -march=native") ""))) + (modules '((guix build utils))) (sha256 (base32 "14qrnczhp5mbwhky64il7kxc4hl1mmh495v60va7i2qnhasr6zmz")))) @@ -1881,6 +1896,11 @@ engine.") "http://kokkinizita.linuxaudio.org" "/linuxaudio/downloads/zita-resampler-" version ".tar.bz2")) + (snippet + ;; Don't optimize for a specific processor architecture. + '(substitute* '("apps/Makefile" "libs/Makefile") + (("^CXXFLAGS \\+= -march=native") ""))) + (modules '((guix build utils))) (sha256 (base32 "0r9ary5sc3y8vba5pad581ha7mgsrlyai83w7w4x2fmhfy64q0wq")))) diff --git a/gnu/packages/bdw-gc.scm b/gnu/packages/bdw-gc.scm index 0a483ef864..992a11bac0 100644 --- a/gnu/packages/bdw-gc.scm +++ b/gnu/packages/bdw-gc.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2012, 2013, 2014, 2016 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org> ;;; ;;; This file is part of GNU Guix. diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 76a1c17737..c6531d669f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com> +;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; @@ -41,12 +41,14 @@ #:use-module (gnu packages cpio) #:use-module (gnu packages file) #:use-module (gnu packages gawk) + #:use-module (gnu packages gcc) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) + #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) @@ -56,6 +58,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages textutils) + #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages vim) #:use-module (gnu packages web) @@ -205,7 +208,7 @@ computational cluster.") (define-public bedtools (package (name "bedtools") - (version "2.24.0") + (version "2.25.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" @@ -213,8 +216,7 @@ computational cluster.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl")) - (patches (list (search-patch "bedtools-32bit-compilation.patch"))))) + "1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) (inputs `(("samtools" ,samtools) @@ -222,25 +224,15 @@ computational cluster.") (arguments '(#:test-target "test" #:phases - (alist-cons-after - 'unpack 'patch-makefile-SHELL-definition - (lambda _ - ;; patch-makefile-SHELL cannot be used here as it does not - ;; yet patch definitions with `:='. Since changes to - ;; patch-makefile-SHELL result in a full rebuild, features - ;; of patch-makefile-SHELL are reimplemented here. - (substitute* "Makefile" - (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n")))) - (alist-delete - 'configure - (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")))) - %standard-phases))))) + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*"))) + #t))))) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") (description @@ -1064,14 +1056,14 @@ data and settings.") (define-public edirect (package (name "edirect") - (version "2.50") + (version "3.50") (source (origin (method url-fetch) ;; Note: older versions are not retained. - (uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip") + (uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz") (sha256 (base32 - "08afhz2ph66h8h381hl1mqyxkdi5nbvzsyj9gfw3jfbdijnpi4qj")))) + "1cr3gzcs3flmgnnbj5iz93vh9w0fca1ilzi2q82cl63ln3mwvpz0")))) (build-system perl-build-system) (arguments `(#:tests? #f ;no "check" target @@ -1111,8 +1103,6 @@ data and settings.") ("perl-uri" ,perl-uri) ("perl-www-robotrules" ,perl-www-robotrules) ("perl" ,perl))) - (native-inputs - `(("unzip" ,unzip))) (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") (description @@ -1436,6 +1426,71 @@ genes in incomplete assemblies or complete genomes.") ;; GPL3+ according to private correspondense with the authors. (license license:gpl3+))) +(define-public fxtract + (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) + (package + (name "fxtract") + (version "2.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/ctSkennerton/fxtract/archive/" + version ".tar.gz")) + (file-name (string-append "ctstennerton-util-" + (string-take util-commit 7) + "-checkout")) + (sha256 + (base32 + "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags (list + (string-append "PREFIX=" (assoc-ref %outputs "out")) + "CC=gcc") + #:test-target "fxtract_test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'copy-util + (lambda* (#:key inputs #:allow-other-keys) + (rmdir "util") + (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") + #t)) + ;; Do not use make install as this requires additional dependencies. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out"/bin"))) + (install-file "fxtract" bin) + #t)))))) + (inputs + `(("pcre" ,pcre) + ("zlib" ,zlib))) + (native-inputs + ;; ctskennerton-util is licensed under GPL2. + `(("ctskennerton-util" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ctSkennerton/util.git") + (commit util-commit))) + (file-name (string-append + "ctstennerton-util-" util-commit "-checkout")) + (sha256 + (base32 + "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) + (home-page "https://github.com/ctSkennerton/fxtract") + (synopsis "Extract sequences from FASTA and FASTQ files") + (description + "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA +or FASTQ) file given a subsequence. It uses a simple substring search for +basic tasks but can change to using POSIX regular expressions, PCRE, hash +lookups or multi-pattern searching as required. By default fxtract looks in +the sequence of each record but can also be told to look in the header, +comment or quality sections.") + (license license:expat)))) + (define-public grit (package (name "grit") @@ -1643,7 +1698,7 @@ from high-throughput sequencing assays.") '(configure install check))))) (native-inputs `(("ant" ,ant) - ("jdk" ,icedtea6 "jdk"))) + ("jdk" ,icedtea "jdk"))) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -1738,6 +1793,55 @@ to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.") (license license:gpl3+))) +(define-public jellyfish + (package + (name "jellyfish") + (version "2.2.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/gmarcais/Jellyfish/" + "releases/download/v" version + "/jellyfish-" version ".tar.gz")) + (sha256 + (base32 + "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk")))) + (build-system gnu-build-system) + (outputs '("out" ;for library + "ruby" ;for Ruby bindings + "python")) ;for Python bindings + (arguments + `(#:configure-flags + (list (string-append "--enable-ruby-binding=" + (assoc-ref %outputs "ruby")) + (string-append "--enable-python-binding=" + (assoc-ref %outputs "python"))) + #:phases + (modify-phases %standard-phases + (add-before 'check 'set-SHELL-variable + (lambda _ + ;; generator_manager.hpp either uses /bin/sh or $SHELL + ;; to run tests. + (setenv "SHELL" (which "bash")) + #t))))) + (native-inputs + `(("bc" ,bc) + ("time" ,time) + ("ruby" ,ruby) + ("python" ,python-2))) + (synopsis "Tool for fast counting of k-mers in DNA") + (description + "Jellyfish is a tool for fast, memory-efficient counting of k-mers in +DNA. A k-mer is a substring of length k, and counting the occurrences of all +such substrings is a central step in many analyses of DNA sequence. Jellyfish +is a command-line program that reads FASTA and multi-FASTA files containing +DNA sequences. It outputs its k-mer counts in a binary format, which can be +translated into a human-readable text format using the @code{jellyfish dump} +command, or queried for specific k-mers with @code{jellyfish query}.") + (home-page "http://www.genome.umd.edu/jellyfish.html") + ;; The combined work is published under the GPLv3 or later. Individual + ;; files such as lib/jsoncpp.cpp are released under the Expat license. + (license (list license:gpl3+ license:expat)))) + (define-public macs (package (name "macs") @@ -2284,7 +2388,7 @@ distribution, coverage uniformity, strand specificity, etc.") (define-public samtools (package (name "samtools") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) @@ -2293,38 +2397,23 @@ distribution, coverage uniformity, strand specificity, etc.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2")))) + "03mnf0mhbfwhqlqfslrhfnw68s3g0fs1as354i9a584mqw1l1smy")))) (build-system gnu-build-system) (arguments - `(;; There are 87 test failures when building on non-64-bit architectures - ;; due to invalid test data. This has since been fixed upstream (see - ;; <https://github.com/samtools/samtools/pull/307>), but as there has - ;; not been a new release we disable the tests for all non-64-bit - ;; systems. - #:tests? ,(string=? (or (%current-system) (%current-target-system)) - "x86_64-linux") - #:modules ((ice-9 ftw) + `(#:modules ((ice-9 ftw) (ice-9 regex) (guix build gnu-build-system) (guix build utils)) - #:make-flags (list "LIBCURSES=-lncurses" - (string-append "prefix=" (assoc-ref %outputs "out"))) + #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) + #:configure-flags (list "--with-ncurses") #:phases (alist-cons-after - 'unpack - 'patch-tests - (lambda* (#:key inputs #:allow-other-keys) - (let ((bash (assoc-ref inputs "bash"))) - (substitute* "test/test.pl" - ;; The test script calls out to /bin/bash - (("/bin/bash") - (string-append bash "/bin/bash")) - ;; There are two failing tests upstream relating to the "stats" - ;; subcommand in test_usage_subcommand ("did not have Usage" - ;; and "usage did not mention samtools stats"), so we disable - ;; them. - (("(test_usage_subcommand\\(.*\\);)" cmd) - (string-append "unless ($subcommand eq 'stats') {" cmd "};"))))) + 'unpack 'patch-tests + (lambda _ + (substitute* "test/test.pl" + ;; The test script calls out to /bin/bash + (("/bin/bash") (which "bash"))) + #t) (alist-cons-after 'install 'install-library (lambda* (#:key outputs #:allow-other-keys) @@ -2339,7 +2428,7 @@ distribution, coverage uniformity, strand specificity, etc.") (install-file file include)) (scandir "." (lambda (name) (string-match "\\.h$" name)))) #t)) - (alist-delete 'configure %standard-phases)))))) + %standard-phases))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("ncurses" ,ncurses) ("perl" ,perl) @@ -2489,7 +2578,7 @@ simultaneously.") `(modify-phases ,phases (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) (inputs - `(("jdk" ,icedtea6 "jdk") + `(("jdk" ,icedtea "jdk") ("ngs-sdk" ,ngs-sdk))) (synopsis "Java bindings for NGS SDK"))) @@ -3418,6 +3507,495 @@ GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome.") (license license:artistic2.0))) +(define-public r-biobase + (package + (name "r-biobase") + (version "2.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biobase" version)) + (sha256 + (base32 + "1qasjpq3kw8h7qw8cin3bjvv1256hqr1mm24fq3v0ymxzlb66szi")))) + (properties + `((upstream-name . "Biobase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "http://bioconductor.org/packages/Biobase") + (synopsis "Base functions for Bioconductor") + (description + "This package provides functions that are needed by many other packages +on Bioconductor or which replace R functions.") + (license license:artistic2.0))) + +(define-public r-annotationdbi + (package + (name "r-annotationdbi") + (version "1.32.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationDbi" version)) + (sha256 + (base32 + "08ncdjvq0l44kqyiv32kn9wnbw1xgfb6qjfzfbjpqrcfp1jygz9j")))) + (properties + `((upstream-name . "AnnotationDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/AnnotationDbi") + (synopsis "Annotation database interface") + (description + "This package provides user interface and database connection code for +annotation data packages using SQLite data storage.") + (license license:artistic2.0))) + +(define-public r-biomart + (package + (name "r-biomart") + (version "2.26.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biomaRt" version)) + (sha256 + (base32 + "1s709055abj2gd35g6nnk5d2ai5ii09iir270l2xika6pi62gj3f")))) + (properties + `((upstream-name . "biomaRt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml))) + (home-page "http://bioconductor.org/packages/biomaRt") + (synopsis "Interface to BioMart databases") + (description + "biomaRt provides an interface to a growing collection of databases +implementing the @url{BioMart software suite, http://www.biomart.org}. The +package enables retrieval of large amounts of data in a uniform way without +the need to know the underlying database schemas or write complex SQL queries. +Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, +Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt +users direct access to a diverse set of data and enable a wide range of +powerful online queries from gene annotation to database mining.") + (license license:artistic2.0))) + +(define-public r-biocparallel + (package + (name "r-biocparallel") + (version "1.4.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocParallel" version)) + (sha256 + (base32 + "1f5mndx66vampcsq0n66afg6x851crl0h3nyv2nyp9bsgzj9cdzq")))) + (properties + `((upstream-name . "BiocParallel"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-logger" ,r-futile-logger) + ("r-snow" ,r-snow))) + (home-page "http://bioconductor.org/packages/BiocParallel") + (synopsis "Bioconductor facilities for parallel evaluation") + (description + "This package provides modified versions and novel implementation of +functions for parallel evaluation, tailored to use with Bioconductor +objects.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-biostrings + (package + (name "r-biostrings") + (version "2.38.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biostrings" version)) + (sha256 + (base32 + "1afp9szc8ci6jn0m3hrrqh6df65cpw3v1dcnl6xir3d3m3lwwmk4")))) + (properties + `((upstream-name . "Biostrings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/Biostrings") + (synopsis "String objects and algorithms for biological sequences") + (description + "This package provides memory efficient string containers, string +matching algorithms, and other utilities, for fast manipulation of large +biological sequences or sets of sequences.") + (license license:artistic2.0))) + +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "1yc3nzzms3igjwr4l9yd3wdac95glcs08b4cfp7disyly0wcskjd")))) + (properties + `((upstream-name . "Rsamtools"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the 'samtools', 'bcftools', and +'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, +binary variant call (BCF) and compressed indexed tab-delimited (tabix) +files.") + (license license:expat))) + +(define-public r-summarizedexperiment + (package + (name "r-summarizedexperiment") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SummarizedExperiment" version)) + (sha256 + (base32 + "0w1dwp99p6i7sc3cn0ir3dr8ksgxwjf16675h5i8n6gbv4rl9lz6")))) + (properties + `((upstream-name . "SummarizedExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "http://bioconductor.org/packages/SummarizedExperiment") + (synopsis "Container for representing genomic ranges by sample") + (description + "The SummarizedExperiment container contains one or more assays, each +represented by a matrix-like object of numeric or other mode. The rows +typically represent genomic ranges of interest and the columns represent +samples.") + (license license:artistic2.0))) + +(define-public r-genomicalignments + (package + (name "r-genomicalignments") + (version "1.6.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicAlignments" version)) + (sha256 + (base32 + "03pxzkmwcpl0d7a09ahan0nllfv7qw2i7w361w6af2s4n3xwrniz")))) + (properties + `((upstream-name . "GenomicAlignments"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "http://bioconductor.org/packages/GenomicAlignments") + (synopsis "Representation and manipulation of short genomic alignments") + (description + "This package provides efficient containers for storing and manipulating +short genomic alignments (typically obtained by aligning short reads to a +reference genome). This includes read counting, computing the coverage, +junction detection, and working with the nucleotide content of the +alignments.") + (license license:artistic2.0))) + +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.30.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "1if31hg56islx5vwydpgs5gkyas26kyvv2ljv1c7jikpm62w14qv")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.22.7") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "1jb4s49ar5j9qslpd3kfdg2wrl4q7ciysd55h9a7zvspymxcngq8")))) + (properties + `((upstream-name . "GenomicFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +transcripts, exons, cds and genes. Flexible methods are provided for +extracting the desired features in a convenient format.") + (license license:artistic2.0))) + +(define-public r-go-db + (package + (name "r-go-db") + (version "3.2.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GO.db" version)) + (sha256 + (base32 + "00gariag9ampz82dh0xllrc26r85d7vdcwc0vca5zdy147rwxr7f")))) + (properties + `((upstream-name . "GO.db"))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/GO.db") + (synopsis "Annotation maps describing the entire Gene Ontology") + (description + "The purpose of this GO.db annotation package is to provide detailed +information about the latest version of the Gene Ontologies.") + (license license:artistic2.0))) + +(define-public r-topgo + (package + (name "r-topgo") + (version "2.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "topGO" version)) + (sha256 + (base32 + "029j9nb39b8l9xlzsp83pmjr8ap247aia387yzaa1yyw8klapdaf")))) + (properties + `((upstream-name . "topGO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) + ("r-sparsem" ,r-sparsem))) + (home-page "http://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") + (description + "The topGO package provides tools for testing @dfn{gene ontology} (GO) +terms while accounting for the topology of the GO graph. Different test +statistics and different methods for eliminating local similarities and +dependencies between GO terms can be implemented and applied.") + ;; Any version of the LGPL applies. + (license license:lgpl2.1+))) + +(define-public r-bsgenome + (package + (name "r-bsgenome") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome" version)) + (sha256 + (base32 + "130w0m6q8kkca7gyz1aqj5jjhalwvwi6rk2yvbjrnj4gpnncyrd2")))) + (properties + `((upstream-name . "BSgenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/BSgenome") + (synopsis "Infrastructure for Biostrings-based genome data packages") + (description + "This package provides infrastructure shared by all Biostrings-based +genome data packages and support for efficient SNP representation.") + (license license:artistic2.0))) + +(define-public r-impute + (package + (name "r-impute") + (version "1.44.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "impute" version)) + (sha256 + (base32 + "0y4x5jk7gsf4xn56jrkdcdnxpcfll4h6ivncd7n4snmzixldvmvw")))) + (inputs + `(("gfortran" ,gfortran))) + (build-system r-build-system) + (home-page "http://bioconductor.org/packages/impute") + (synopsis "Imputation for microarray data") + (description + "This package provides a function to impute missing gene expression +microarray data, using nearest neighbor averaging.") + (license license:gpl2+))) + +(define-public r-seqpattern + (package + (name "r-seqpattern") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "seqPattern" version)) + (sha256 + (base32 + "0p9zj6bic7sa0hb2bjm988kkk5n9r1kvlbqkzvy702f642n0j53i")))) + (properties + `((upstream-name . "seqPattern"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-plotrix" ,r-plotrix))) + (home-page "http://bioconductor.org/packages/seqPattern") + (synopsis "Visualising oligonucleotide patterns and motif occurrences") + (description + "This package provides tools to visualize oligonucleotide patterns and +sequence motif occurrences across a large set of sequences centred at a common +reference point and sorted by a user defined feature.") + (license license:gpl3+))) + +(define-public r-genomation + (package + (name "r-genomation") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomation" version)) + (sha256 + (base32 + "1mzs995snwim13qk9kz4q3nczpnbsy1allwp4whfq0cflg2mndfr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-seqpattern" ,r-seqpattern))) + (home-page "http://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Summary, annotation and visualization of genomic data") + (description + "This package provides a package for summary and annotation of genomic +intervals. Users can visualize and quantify genomic intervals over +pre-defined functional regions, such as promoters, exons, introns, etc. The +genomic intervals represent regions with a defined chromosome position, which +may be associated with a score, such as aligned reads from HT-seq experiments, +TF binding sites, methylation scores, etc. The package can use any tabular +genomic feature data as long as it has minimal information on the locations of +genomic intervals. In addition, it can use BAM or BigWig files as input.") + (license license:artistic2.0))) + (define-public r-qtl (package (name "r-qtl") diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index d3b171245d..0a644e8940 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014 John Darrington <jmd@gnu.org> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. @@ -33,7 +34,7 @@ (define-public boost (package (name "boost") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (string-append @@ -42,8 +43,7 @@ ".tar.bz2")) (sha256 (base32 - "1rfkqxns60171q62cppiyzj8pmsbwp1l8jd7p6crriryqd7j1z7x")) - (patches (list (search-patch "boost-mips-avoid-m32.patch"))))) + "0fzx6dwqbrkd4bcd8pjv0fpapwmrxxwr8yx9g67lihlsk3zzysk8")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) (native-inputs @@ -63,38 +63,38 @@ ;; so we disable that too. ,@(if (string-prefix? "mips64" (or (%current-target-system) (%current-system))) - '("--without-context" "--without-coroutine") + '("--without-context" + "--without-coroutine" "--without-coroutine2") '())))) `(#:tests? #f #:phases - (alist-replace - 'configure - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* '("libs/config/configure" - "libs/spirit/classic/phoenix/test/runtest.sh" - "tools/build/doc/bjam.qbk" - "tools/build/src/engine/execunix.c" - "tools/build/src/engine/Jambase" - "tools/build/src/engine/jambase.c") - (("/bin/sh") (which "sh"))) - - (setenv "SHELL" (which "sh")) - (setenv "CONFIG_SHELL" (which "sh")) + (modify-phases %standard-phases + (replace + 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* '("libs/config/configure" + "libs/spirit/classic/phoenix/test/runtest.sh" + "tools/build/doc/bjam.qbk" + "tools/build/src/engine/execunix.c" + "tools/build/src/engine/Jambase" + "tools/build/src/engine/jambase.c") + (("/bin/sh") (which "sh"))) - (zero? (system* "./bootstrap.sh" - (string-append "--prefix=" out) - "--with-toolset=gcc")))) - (alist-replace - 'build - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "./b2" ,@build-flags))) + (setenv "SHELL" (which "sh")) + (setenv "CONFIG_SHELL" (which "sh")) - (alist-replace + (zero? (system* "./bootstrap.sh" + (string-append "--prefix=" out) + "--with-toolset=gcc"))))) + (replace + 'build + (lambda* (#:key outputs #:allow-other-keys) + (zero? (system* "./b2" ,@build-flags)))) + (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "./b2" "install" ,@build-flags))) - %standard-phases)))))) + (zero? (system* "./b2" "install" ,@build-flags)))))))) (home-page "http://boost.org") (synopsis "Peer-reviewed portable C++ source libraries") diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index e8c936849a..754a435347 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2013, 2015 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -91,14 +92,14 @@ highlighting your own code that seemed comprehensible when you wrote it.") (define-public global ; a global variable (package (name "global") - (version "6.5.1") + (version "6.5.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/global/global-" version ".tar.gz")) (sha256 (base32 - "1y34nbazsw2p6r2jhv27z15qvm9mhy5xjchpz8pwps00shkm578f")))) + "07qx3dbjwkbd1dn42qs7zgj77rxdj2psfrf7bx7yx9al38f87z60")))) (build-system gnu-build-system) (inputs `(("ncurses" ,ncurses) ("libltdl" ,libltdl) @@ -110,18 +111,17 @@ highlighting your own code that seemed comprehensible when you wrote it.") (string-append "--with-sqlite3=" (assoc-ref %build-inputs "sqlite"))) - #:phases (alist-cons-after - 'install 'post-install - (lambda* (#:key outputs #:allow-other-keys) - ;; Install the Emacs Lisp file in the right place. - (let* ((out (assoc-ref outputs "out")) - (data (string-append out "/share/gtags")) - (lisp (string-append out "/share/emacs/site-lisp"))) - (install-file (string-append data "/gtags.el") - lisp) - (delete-file (string-append data "/gtags.el")) - #t)) - %standard-phases))) + #:phases + (modify-phases %standard-phases + (add-after 'install 'post-install + (lambda* (#:key outputs #:allow-other-keys) + ;; Install the Emacs Lisp file in the right place. + (let* ((out (assoc-ref outputs "out")) + (data (string-append out "/share/gtags")) + (lisp (string-append out "/share/emacs/site-lisp"))) + (install-file (string-append data "/gtags.el") lisp) + (delete-file (string-append data "/gtags.el")) + #t)))))) (home-page "http://www.gnu.org/software/global/") (synopsis "Cross-environment source code tag system") (description diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm index d758913859..1928360e2e 100644 --- a/gnu/packages/commencement.scm +++ b/gnu/packages/commencement.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> @@ -462,7 +462,8 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%" (package (inherit (package-with-bootstrap-guile (package-with-explicit-inputs bash inputs - (current-source-location)))) + (current-source-location) + #:guile %bootstrap-guile))) (native-inputs `(("bison" ,bison-boot1)))))) (define gettext-boot0 diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index 258294f6c8..718e8b3e50 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2015, 2016 Andreas Enge <andreas@enge.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -60,7 +60,7 @@ (define-public calibre (package (name "calibre") - (version "2.41.0") + (version "2.48.0") (source (origin (method url-fetch) @@ -69,7 +69,7 @@ version ".tar.xz")) (sha256 (base32 - "069fkcsx7kaazs7f095nkz4jw9jrm0k9zq16ayx41lxjbd1r97ik")) + "0bjzw806czqxkhq9qqkhff8bhfc428pijkidb1h6gr47jqdp4hpg")) ;; Remove non-free or doubtful code, see ;; https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00478.html (modules '((guix build utils))) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 947c7e282c..ba7bd49901 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com> -;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014, 2015 Alex Kost <alezost@gmail.com> ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> @@ -74,14 +74,20 @@ (search-patch "emacs-source-date-epoch.patch"))))) (build-system glib-or-gtk-build-system) (arguments - '(#:phases (alist-cons-before - 'configure 'fix-/bin/pwd - (lambda _ - ;; Use `pwd', not `/bin/pwd'. - (substitute* (find-files "." "^Makefile\\.in$") - (("/bin/pwd") - "pwd"))) - %standard-phases))) + '(#:phases (modify-phases %standard-phases + (add-before 'configure 'fix-/bin/pwd + (lambda _ + ;; Use `pwd', not `/bin/pwd'. + (substitute* (find-files "." "^Makefile\\.in$") + (("/bin/pwd") + "pwd")))) + (add-after 'install 'remove-info.info + (lambda* (#:key outputs #:allow-other-keys) + ;; Remove 'info.info', which is provided by Texinfo. + (let ((out (assoc-ref outputs "out"))) + (delete-file + (string-append out "/share/info/info.info.gz")) + #t)))))) (inputs `(("gnutls" ,gnutls) ("ncurses" ,ncurses) @@ -1008,6 +1014,27 @@ and stored in memory.") (description "This package provides a modern list API library for Emacs.") (license license:gpl3+))) +(define-public emacs-undo-tree + (package + (name "emacs-undo-tree") + (version "0.6.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "http://dr-qubit.org/git/undo-tree.git") + (commit "release/0.6.4"))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0b6hnv6bq1g5np5q2yw9r9aj1cxpp14akm21br7vpb7wp01fv4b3")))) + (build-system emacs-build-system) + (home-page "http://www.dr-qubit.org/emacs.php") + (synopsis "Treat undo history as a tree") + (description "Tree-like interface to Emacs undo system, providing +graphical tree presentation of all previous states of buffer that +allows easily move between them.") + (license license:gpl3+))) + (define-public emacs-s (package (name "emacs-s") diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index aa9fb6fded..e88ee8d904 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -3396,7 +3396,7 @@ work and the interface is well tested.") (define-public epiphany (package (name "epiphany") - (version "3.16.3") + (version "3.18.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -3404,7 +3404,7 @@ work and the interface is well tested.") name "-" version ".tar.xz")) (sha256 (base32 - "1cch4c7gh6lq1i4g0gs39qa2csl4i8a3pcdfapcj5v3r0xvz29ym")))) + "1hm6bpdcc6nf3zamzkvjhpvxnpaxzbnxnacfgl5v8swn643ifdl4")))) (build-system glib-or-gtk-build-system) (arguments ;; FIXME: tests run under Xvfb, but fail with: diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 40a13e7939..6fac8ced40 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -167,7 +167,7 @@ in the Mozilla clients.") (define-public nss (package (name "nss") - (version "3.20.2") + (version "3.21") (source (origin (method url-fetch) (uri (let ((version-with-underscores @@ -178,7 +178,7 @@ in the Mozilla clients.") "nss-" version ".tar.gz"))) (sha256 (base32 - "11pjjcp0mvcyx0ildyz20s9jlqzxsb6a9jlvcq5x1g3zsmckl6hl")) + "0fbjx3xsdm4gjc1gyzy2z315cvyw7yilsm7p9w75rpbwgl15nyiz")) ;; Create nss.pc and nss-config. (patches (list (search-patch "nss-pkgconfig.patch"))))) (build-system gnu-build-system) @@ -205,6 +205,7 @@ in the Mozilla clients.") (alist-replace 'configure (lambda* (#:key system inputs #:allow-other-keys) + (setenv "CC" "gcc") ;; Tells NSS to build for the 64-bit ABI if we are 64-bit system. (when (string-prefix? "x86_64" system) (setenv "USE_64" "1")) @@ -266,7 +267,7 @@ standards.") (define-public icecat (package (name "icecat") - (version "38.5.0-gnu1") + (version "38.5.2-gnu1") (source (origin (method url-fetch) @@ -275,7 +276,7 @@ standards.") name "-" version ".tar.bz2")) (sha256 (base32 - "1bf20mpvx84jsa0dan2hhfc49f30v0wasikv7sh3cg8mwp62faj6")) + "0m18xyb0rd02yaw9xd5z4bab1wr2599iszzqhm86c134jv5vk6cg")) (patches (map search-patch '("icecat-avoid-bundled-includes.patch"))) (modules '((guix build utils))) (snippet diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 4e15b814c8..560febe958 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -143,7 +143,8 @@ storage of the \"EXR\" file format for storing 16-bit floating-point images.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0mn7cz19mn8dcrhkq15h25gl20ammr1wz0j2j3c2vxs6ph7zn8jy")))) + "0mn7cz19mn8dcrhkq15h25gl20ammr1wz0j2j3c2vxs6ph7zn8jy")) + (patches (list (search-patch "openimageio-boost-1.60.patch"))))) (build-system cmake-build-system) ;; FIXME: To run all tests successfully, test image sets from multiple ;; third party sources have to be present. For details see diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index f85ea1970a..916873b356 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -522,7 +522,8 @@ is part of the GNOME accessibility project.") name "-" version ".tar.xz")) (sha256 (base32 - "0mj6xn40py9r9lvzg633fal81xfwfm89d9mvz7jk4lmwk0g49imj")))) + "0mj6xn40py9r9lvzg633fal81xfwfm89d9mvz7jk4lmwk0g49imj")) + (patches (list (search-patch "gtk2-respect-GUIX_GTK2_PATH.patch"))))) (build-system gnu-build-system) (outputs '("out" "doc")) (propagated-inputs @@ -557,7 +558,11 @@ is part of the GNOME accessibility project.") ;; FIXME: re-enable tests requiring an X server (substitute* "gtk/Makefile.in" (("SUBDIRS = theme-bits . tests") "SUBDIRS = theme-bits ."))) - %standard-phases))) + %standard-phases))) + (native-search-paths + (list (search-path-specification + (variable "GUIX_GTK2_PATH") + (files '("lib/gtk-2.0"))))) (synopsis "Cross-platform toolkit for creating graphical user interfaces") (description "GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating @@ -578,7 +583,8 @@ application suites.") name "-" version ".tar.xz")) (sha256 (base32 - "0lp1hn0qydxx03bianzzr0a4maqzsvylrkzr7c3p0050qihwbgjx")))) + "0lp1hn0qydxx03bianzzr0a4maqzsvylrkzr7c3p0050qihwbgjx")) + (patches (list (search-patch "gtk3-respect-GUIX_GTK3_PATH.patch"))))) (propagated-inputs `(("at-spi2-atk" ,at-spi2-atk) ("atk" ,atk) @@ -637,7 +643,11 @@ application suites.") (loaders.cache (find-files librsvg "^loaders\\.cache$"))) (wrap-program prog `("GDK_PIXBUF_MODULE_FILE" = ,loaders.cache)))) - %standard-phases)))))) + %standard-phases)))) + (native-search-paths + (list (search-path-specification + (variable "GUIX_GTK3_PATH") + (files '("lib/gtk-3.0"))))))) ;;; ;;; Guile bindings. diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 60439d1534..3a5b1e1a44 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -81,7 +81,7 @@ 'build (lambda* (#:key inputs outputs #:allow-other-keys) (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) - (setenv "JAVA_HOME" (assoc-ref inputs "icedtea6")) + (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) ;; Build shared libraries. Users of SWT have to set the system ;; property swt.library.path to the "lib" directory of this @@ -115,7 +115,7 @@ (native-inputs `(("pkg-config" ,pkg-config) ("unzip" ,unzip) - ("icedtea6" ,icedtea6 "jdk"))) + ("jdk" ,icedtea "jdk"))) (home-page "https://www.eclipse.org/swt/") (synopsis "Widget toolkit for Java") (description @@ -184,9 +184,9 @@ and is best suited to building Java projects. Ant uses XML to describe the build process and its dependencies, whereas Make uses Makefile format.") (license license:asl2.0))) -(define-public icedtea6 +(define-public icedtea-6 (package - (name "icedtea6") + (name "icedtea") (version "1.13.9") (source (origin (method url-fetch) @@ -265,7 +265,7 @@ build process and its dependencies, whereas Make uses Makefile format.") "--without-rhino" "--disable-downloading" "--disable-tests" ;they are run in the check phase instead - ,(string-append "--with-openjdk-src-dir=" "./openjdk") + "--with-openjdk-src-dir=./openjdk.src" ,(string-append "--with-javac=" jdk "/bin/javac") ,(string-append "--with-ecj-jar=" ecj) ,(string-append "--with-gcj=" gcj) @@ -277,9 +277,9 @@ build process and its dependencies, whereas Make uses Makefile format.") (lambda* (#:key source inputs #:allow-other-keys) (and (zero? (system* "tar" "xvf" source)) (begin - (chdir (string-append ,name "-" ,version)) - (mkdir "openjdk") - (with-directory-excursion "openjdk" + (chdir (string-append "icedtea6-" ,version)) + (mkdir "openjdk.src") + (with-directory-excursion "openjdk.src" (copy-file (assoc-ref inputs "openjdk6-src") "openjdk6-src.tar.xz") (zero? (system* "tar" "xvf" "openjdk6-src.tar.xz")))))) @@ -302,7 +302,7 @@ build process and its dependencies, whereas Make uses Makefile format.") (lambda _ ;; buildtree.make generates shell scripts, so we need to replace ;; the generated shebang - (substitute* '("openjdk/hotspot/make/linux/makefiles/buildtree.make") + (substitute* '("openjdk.src/hotspot/make/linux/makefiles/buildtree.make") (("/bin/sh") (which "bash"))) (let ((corebin (string-append @@ -311,8 +311,8 @@ build process and its dependencies, whereas Make uses Makefile format.") (assoc-ref %build-inputs "binutils") "/bin/")) (grepbin (string-append (assoc-ref %build-inputs "grep") "/bin/"))) - (substitute* '("openjdk/jdk/make/common/shared/Defs-linux.gmk" - "openjdk/corba/make/common/shared/Defs-linux.gmk") + (substitute* '("openjdk.src/jdk/make/common/shared/Defs-linux.gmk" + "openjdk.src/corba/make/common/shared/Defs-linux.gmk") (("UNIXCOMMAND_PATH = /bin/") (string-append "UNIXCOMMAND_PATH = " corebin)) (("USRBIN_PATH = /usr/bin/") @@ -326,8 +326,8 @@ build process and its dependencies, whereas Make uses Makefile format.") (string-append "DEF_OBJCOPY = " (which "objcopy")))) ;; fix hard-coded utility paths - (substitute* '("openjdk/jdk/make/common/shared/Defs-utils.gmk" - "openjdk/corba/make/common/shared/Defs-utils.gmk") + (substitute* '("openjdk.src/jdk/make/common/shared/Defs-utils.gmk" + "openjdk.src/corba/make/common/shared/Defs-utils.gmk") (("ECHO *=.*echo") (string-append "ECHO = " (which "echo"))) (("^GREP *=.*grep") @@ -370,7 +370,7 @@ build process and its dependencies, whereas Make uses Makefile format.") ;; Some of these timestamps cause problems as they are more than ;; 10 years ago, failing the build process. (substitute* - "openjdk/jdk/src/share/classes/java/util/CurrencyData.properties" + "openjdk.src/jdk/src/share/classes/java/util/CurrencyData.properties" (("AZ=AZM;2005-12-31-20-00-00;AZN") "AZ=AZN") (("MZ=MZM;2006-06-30-22-00-00;MZN") "MZ=MZN") (("RO=ROL;2005-06-30-21-00-00;RON") "RO=RON") @@ -417,7 +417,7 @@ build process and its dependencies, whereas Make uses Makefile format.") (alist-cons-before 'check 'fix-hotspot-tests (lambda _ - (with-directory-excursion "openjdk/hotspot/test/" + (with-directory-excursion "openjdk.src/hotspot/test/" (substitute* "jprt.config" (("PATH=\"\\$\\{path4sdk\\}\"") (string-append "PATH=" (getenv "PATH"))) @@ -432,7 +432,7 @@ build process and its dependencies, whereas Make uses Makefile format.") (alist-cons-before 'check 'fix-jdk-tests (lambda _ - (with-directory-excursion "openjdk/jdk/test/" + (with-directory-excursion "openjdk.src/jdk/test/" (substitute* "com/sun/jdi/JdbReadTwiceTest.sh" (("/bin/pwd") (which "pwd"))) (substitute* "com/sun/jdi/ShellScaffold.sh" @@ -514,7 +514,8 @@ build process and its dependencies, whereas Make uses Makefile format.") (alist-replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((doc (string-append (assoc-ref outputs "doc") "/share/doc/" ,name)) + (let ((doc (string-append (assoc-ref outputs "doc") + "/share/doc/icedtea")) (jre (assoc-ref outputs "out")) (jdk (assoc-ref outputs "jdk"))) (copy-recursively "openjdk.build/docs" doc) @@ -575,7 +576,7 @@ build process and its dependencies, whereas Make uses Makefile format.") ;; same license as both GNU Classpath and OpenJDK. (license license:gpl2+))) -(define-public icedtea7 +(define-public icedtea-7 (let* ((version "2.6.3") (drop (lambda (name hash) (origin @@ -584,8 +585,7 @@ build process and its dependencies, whereas Make uses Makefile format.") "http://icedtea.classpath.org/download/drops/" "/icedtea7/" version "/" name ".tar.bz2")) (sha256 (base32 hash)))))) - (package (inherit icedtea6) - (name "icedtea7") + (package (inherit icedtea-6) (version version) (source (origin (method url-fetch) @@ -616,51 +616,42 @@ build process and its dependencies, whereas Make uses Makefile format.") #:tests? #f ;; Apparently, the C locale is needed for some of the tests. #:locale "C" - ,@(substitute-keyword-arguments (package-arguments icedtea6) + ,@(substitute-keyword-arguments (package-arguments icedtea-6) + ((#:modules modules) + `((ice-9 match) + (srfi srfi-26) + ,@modules)) ((#:configure-flags flags) - `(delete "--with-openjdk-src-dir=./openjdk" - ;; TODO: package pcsc and sctp, and add to inputs - (append '("--disable-system-pcsc" - "--disable-system-sctp") - ,flags))) + ;; TODO: package pcsc and sctp, and add to inputs + `(append '("--disable-system-pcsc" + "--disable-system-sctp") + ,flags)) ((#:phases phases) `(modify-phases ,phases - (replace - 'unpack - (lambda* (#:key source inputs #:allow-other-keys) - (let ((target (string-append "icedtea-" ,version)) - (unpack (lambda (drop dir) - (mkdir dir) - (zero? (system* "tar" "xvjf" - (assoc-ref inputs drop) - "-C" dir - "--strip-components=1"))))) - (and (zero? (system* "tar" "xvf" source)) - (chdir target) - (unpack "openjdk-drop" "openjdk") - (unpack "corba-drop" "openjdk/corba") - (unpack "jdk-drop" "openjdk/jdk") - (unpack "hotspot-drop" "openjdk/hotspot") - - ;; The build framework checks the tarballs, so we - ;; need to keep them around even though we have - ;; already unpacked some of them for patching. - (begin - (copy-file (assoc-ref inputs "openjdk-drop") - "openjdk.tar.bz2") - (copy-file (assoc-ref inputs "corba-drop") - "corba.tar.bz2") - (copy-file (assoc-ref inputs "hotspot-drop") - "hotspot.tar.bz2") - (copy-file (assoc-ref inputs "jaxp-drop") - "jaxp.tar.bz2") - (copy-file (assoc-ref inputs "jaxws-drop") - "jaxws.tar.bz2") - (copy-file (assoc-ref inputs "jdk-drop") - "jdk.tar.bz2") - (copy-file (assoc-ref inputs "langtools-drop") - "langtools.tar.bz2") - #t))))) + (replace 'unpack + (lambda* (#:key source inputs #:allow-other-keys) + (let ((target (string-append "icedtea-" ,version)) + (unpack (lambda* (name #:optional dir) + (let ((dir (or dir + (string-drop-right name 5)))) + (mkdir dir) + (zero? (system* "tar" "xvf" + (assoc-ref inputs name) + "-C" dir + "--strip-components=1")))))) + (mkdir target) + (and + (zero? (system* "tar" "xvf" source + "-C" target "--strip-components=1")) + (chdir target) + (unpack "openjdk-src" "openjdk.src") + (with-directory-excursion "openjdk.src" + (for-each unpack + (filter (cut string-suffix? "-drop" <>) + (map (match-lambda + ((name . _) name)) + inputs)))) + #t)))) (replace 'set-additional-paths (lambda* (#:key inputs #:allow-other-keys) @@ -670,7 +661,7 @@ build process and its dependencies, whereas Make uses Makefile format.") (str (read-line port))) (close-pipe port) str))) - (substitute* "openjdk/jdk/make/common/shared/Sanity.gmk" + (substitute* "openjdk.src/jdk/make/common/shared/Sanity.gmk" (("ALSA_INCLUDE=/usr/include/alsa/version.h") (string-append "ALSA_INCLUDE=" (assoc-ref inputs "alsa-lib") @@ -698,7 +689,7 @@ build process and its dependencies, whereas Make uses Makefile format.") (add-after 'unpack 'fix-x11-extension-include-path (lambda* (#:key inputs #:allow-other-keys) - (substitute* "openjdk/jdk/make/sun/awt/mawt.gmk" + (substitute* "openjdk.src/jdk/make/sun/awt/mawt.gmk" (((string-append "\\$\\(firstword \\$\\(wildcard " "\\$\\(OPENWIN_HOME\\)" "/include/X11/extensions\\).*$")) @@ -719,14 +710,14 @@ build process and its dependencies, whereas Make uses Makefile format.") (string-append "PATH=" (getenv "PATH")))) (substitute* "test/jtreg/com/sun/javatest/util/SysEnv.java" (("/usr/bin/env") (which "env"))) - (substitute* "openjdk/hotspot/test/test_env.sh" + (substitute* "openjdk.src/hotspot/test/test_env.sh" (("/bin/rm") (which "rm")) (("/bin/cp") (which "cp")) (("/bin/mv") (which "mv"))) #t)) (delete 'patch-patches)))))) (native-inputs - `(("openjdk-drop" + `(("openjdk-src" ,(drop "openjdk" "0vflz0hhq4arykvvmsv3yas4yk9i0jm57287iqvs3a4832xjcpcy")) ("corba-drop" @@ -747,5 +738,7 @@ build process and its dependencies, whereas Make uses Makefile format.") ("hotspot-drop" ,(drop "hotspot" "03pggsrhkzpjnj939vhr3b7mcrhfp22b7yg3hkx52kcv8dqkg3yx")) - ,@(fold alist-delete (package-native-inputs icedtea6) + ,@(fold alist-delete (package-native-inputs icedtea-6) '("openjdk6-src"))))))) + +(define-public icedtea icedtea-7) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index fc152c8720..4e6b87116a 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -20,6 +20,8 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix utils) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages algebra) @@ -27,6 +29,7 @@ #:use-module (gnu packages elf) #:use-module (gnu packages gcc) #:use-module (gnu packages llvm) + #:use-module (gnu packages libevent) #:use-module (gnu packages libunwind) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) ; mpfr @@ -36,21 +39,44 @@ #:use-module (gnu packages python) #:use-module (gnu packages textutils) #:use-module (gnu packages version-control) + #:use-module (gnu packages wget) #:use-module (ice-9 match)) +(define libuv-julia + (let ((commit "07730c4bd595b4d45a498a8ee0bcd53878ff7c10") + (revision "2")) + (package (inherit libuv) + (name "libuv-julia") + (version (string-append "0.11.26." revision "-" (string-take commit 8))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLang/libuv.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1r0d4wb41w8k3bi9sjr7kapk1ag131ss2fbqa4jz4gnrzvw94sqx")))) + (build-system gnu-build-system) + (arguments + (substitute-keyword-arguments (package-arguments libuv) + ((#:phases phases) + `(modify-phases ,phases + (delete 'autogen))))) + (home-page "https://github.com/JuliaLang/libuv")))) + (define-public julia (package (name "julia") - (version "0.3.10") + (version "0.4.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/JuliaLang/julia/releases/download/v" - version "/julia-" version "_c8ceeefcc1.tar.gz")) + version "/julia-" version "-full.tar.gz")) (sha256 (base32 - "0j6mw6wr35lxid10nh9gz7k6wck3a90ic92w99n1r052325gl9r7")) - (patches (list (search-patch "julia-0.3.10-fix-empty-array.patch"))))) + "1i8k847d8n9v37xg69grpl51dysx36p0phwf0d1qxpsqixdg579b")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -66,8 +92,7 @@ #:phases (modify-phases %standard-phases (delete 'configure) - (add-after - 'unpack 'hardcode-soname-map + (add-after 'unpack 'hardcode-soname-map ;; ./src/ccall.cpp creates a map from library names to paths using the ;; output of "/sbin/ldconfig -p". Since ldconfig is not used in Guix, ;; we patch ccall.cpp to contain a static map. @@ -82,46 +107,70 @@ "sonameMap[\"" libname "\"] = " "\"" (assoc-ref inputs input) "/lib/" soname "\";"))) '(("libc" "libc" "libc.so.6") - ("pcre" "libpcre" "libpcre.so") + ("pcre2" "libpcre2-8" "libpcre2-8.so") ("mpfr" "libmpfr" "libmpfr.so") ("openblas" "libblas" "libopenblas.so") ("arpack-ng" "libarpack" "libarpack.so") ("lapack" "liblapack" "liblapack.so") + ("libgit2" "libgit2" "libgit2.so") ("gmp" "libgmp" "libgmp.so") ("openlibm" "libopenlibm" "libopenlibm.so") ("openspecfun" "libopenspecfun" "libopenspecfun.so") ("fftw" "libfftw3" "libfftw3.so") ("fftwf" "libfftw3f" "libfftw3f.so")))))) #t)) - ;; This phase will no longer be necessary in 0.3.11; see - ;; https://github.com/JuliaLang/julia/issues/12028 - (add-before - 'build 'fix-building-with-mcjit-llvm - (lambda _ - (substitute* "src/cgutils.cpp" - (("addComdat\\(gv\\);") "")) - #t)) - (add-before - 'build 'patch-include-path - (lambda _ + (add-before 'build 'fix-include-and-link-paths + (lambda* (#:key inputs #:allow-other-keys) + ;; LIBUTF8PROC is a linker flag, not a build target. It is + ;; included in the LIBFILES_* variable which is used as a + ;; collection of build targets and a list of libraries to link + ;; against. + (substitute* "src/flisp/Makefile" + (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)") + "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)") + (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)") + "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)")) + + ;; The REPL must be linked with libuv. + (substitute* "ui/Makefile" + (("JLDFLAGS \\+= ") + (string-append "JLDFLAGS += " + (assoc-ref %build-inputs "libuv") + "/lib/libuv.so "))) + (substitute* "deps/Makefile" (("/usr/include/double-conversion") (string-append (assoc-ref %build-inputs "double-conversion") "/include/double-conversion"))) + (substitute* "base/Makefile" + (("\\$\\(build_includedir\\)/uv-errno.h") + (string-append (assoc-ref inputs "libuv") + "/include/uv-errno.h"))) #t)) - (add-before - 'build 'replace-default-shell + (add-before 'build 'replace-default-shell (lambda _ (substitute* "base/client.jl" (("/bin/sh") (which "sh"))) #t)) - (add-before - 'check 'disable-broken-test - ;; One test fails because it produces slightly different output. - (lambda _ - (substitute* "test/repl.jl" - (("@test output") "# @test output")) - #t))) + (add-after 'unpack 'hardcode-paths + (lambda _ + (substitute* "base/interactiveutil.jl" + (("`which") (string-append "`" (which "which"))) + (("`wget") (string-append "`" (which "wget")))) + #t)) + (add-before 'check 'disable-broken-tests + (lambda _ + (substitute* "test/choosetests.jl" + ;; These tests time out. See + ;; https://github.com/JuliaLang/julia/issues/14374 for ongoing + ;; discussion. + (("\"replcompletions\",") "") + (("\"repl\",") "")) + (substitute* "test/repl.jl" + ;; This test fails because we cannot escape the build + ;; directory. + (("@test pwd\\(\\) == homedir\\(\\)") "#")) + #t))) #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")) @@ -137,7 +186,6 @@ (_ "MARCH=UNSUPPORTED")) "CONFIG_SHELL=bash" ;needed to build bundled libraries - "USE_SYSTEM_LIBUV=0" ;Julia expects a modified libuv "USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no ;build system for a shared library. "USE_SYSTEM_RMATH=0" ;Julia uses a bundled version of R's math @@ -158,10 +206,22 @@ ;; (assoc-ref %build-inputs "suitesparse") ;; "/include") + "USE_GPL_LIBS=1" ;proudly "USE_SYSTEM_GRISU=1" ;for double-conversion "USE_SYSTEM_UTF8PROC=1" + (string-append "UTF8PROC_INC=" + (assoc-ref %build-inputs "utf8proc") + "/include") "USE_SYSTEM_LLVM=1" "USE_SYSTEM_LIBUNWIND=1" + "USE_SYSTEM_LIBUV=1" + (string-append "LIBUV=" + (assoc-ref %build-inputs "libuv") + "/lib/libuv.so") + (string-append "LIBUV_INC=" + (assoc-ref %build-inputs "libuv") + "/include") + "USE_SYSTEM_PATCHELF=1" "USE_SYSTEM_PCRE=1" "USE_SYSTEM_OPENLIBM=1" "USE_SYSTEM_GMP=1" @@ -172,26 +232,29 @@ (inputs `(("llvm" ,llvm-3.5) ("arpack-ng" ,arpack-ng) + ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like ("lapack" ,lapack) ("openblas" ,openblas) ;Julia does not build with Atlas ("libunwind" ,libunwind) ("openlibm" ,openlibm) ("openspecfun" ,openspecfun) ("double-conversion" ,double-conversion) + ("libgit2" ,libgit2) ("fftw" ,fftw) ("fftwf" ,fftwf) ("fortran" ,gfortran) - ("pcre" ,pcre) + ("libuv" ,libuv-julia) + ("pcre2" ,pcre2) ("utf8proc" ,utf8proc) - ("git" ,git) ("mpfr" ,mpfr) + ("wget" ,wget) + ("which" ,which) ("gmp" ,gmp))) (native-inputs `(("perl" ,perl) ("patchelf" ,patchelf) ("pkg-config" ,pkg-config) - ("python" ,python-2) - ("which" ,which))) + ("python" ,python-2))) ;; Julia is not officially released for ARM and MIPS. ;; See https://github.com/JuliaLang/julia/issues/10639 (supported-systems '("i686-linux" "x86_64-linux")) diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm index f0c372bc29..4a9cebde01 100644 --- a/gnu/packages/kodi.scm +++ b/gnu/packages/kodi.scm @@ -149,7 +149,7 @@ ("doxygen" ,doxygen) ("gawk" ,gawk) ("gettext" ,gnu-gettext) - ("icedtea7" ,icedtea7) ; needed at build-time only, mandatory + ("icedtea" ,icedtea) ; needed at build-time only, mandatory ("libtool" ,libtool) ("pkg-config" ,pkg-config) ("swig" ,swig) diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm new file mode 100644 index 0000000000..1981bc115d --- /dev/null +++ b/gnu/packages/ldc.scm @@ -0,0 +1,118 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2015 Roel Janssen <roel@gnu.org> +;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl> +;;; +;;; 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 ldc) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system cmake) + #:use-module (gnu packages) + #:use-module (gnu packages base) + #:use-module (gnu packages libedit) + #:use-module (gnu packages llvm) + #:use-module (gnu packages textutils) + #:use-module (gnu packages zip)) + +(define-public ldc + (package + (name "ldc") + (version "0.16.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/ldc-developers/ldc/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jvilxx0rpqmkbja4m69fhd5g09697xq7vyqp2hz4hvxmmmv4j40")))) + (build-system cmake-build-system) + ;; LDC currently only supports the x86_64 and i686 architectures. + (supported-systems '("x86_64-linux" "i686-linux")) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (zero? (system* "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and (unpack "phobos-src" "runtime/phobos") + (unpack "druntime-src" "runtime/druntime") + (unpack "dmd-testsuite-src" "tests/d2/dmd-testsuite"))))) + (add-after 'unpack-submodule-sources 'patch-phobos + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "runtime/phobos/std/process.d" + (("/bin/sh") (which "sh")) + (("echo") (which "echo"))) + (substitute* "runtime/phobos/std/datetime.d" + (("/usr/share/zoneinfo/") + (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo"))) + (substitute* "tests/d2/dmd-testsuite/Makefile" + (("/bin/bash") (which "bash"))) + #t))))) + (inputs + `(("libconfig" ,libconfig) + ("libedit" ,libedit) + ("tzdata" ,tzdata))) + (native-inputs + `(("llvm" ,llvm) + ("clang" ,clang) + ("unzip" ,unzip) + ("phobos-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ldc-developers/phobos/archive/ldc-v" + version ".tar.gz")) + (sha256 + (base32 + "0sgdj0536c4nb118yiw1f8lqy5d3g3lpg9l99l165lk9xy45l9z4")) + (patches (list (search-patch "ldc-disable-tests.patch"))))) + ("druntime-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ldc-developers/druntime/archive/ldc-v" + version ".tar.gz")) + (sha256 + (base32 + "0z4mkyddx6c4sy1vqgqvavz55083dsxws681qkh93jh1rpby9yg6")))) + ("dmd-testsuite-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ldc-developers/dmd-testsuite/archive/ldc-v" + version ".tar.gz")) + (sha256 + (base32 + "0yc6miidzgl9k33ygk7xcppmfd6kivqj02cvv4fmkbs3qz4yy3z1")))))) + (home-page "http://wiki.dlang.org/LDC") + (synopsis "LLVM compiler for the D programming language") + (description + "LDC is a compiler for the D programming language. It is based on the +latest DMD frontend and uses LLVM as backend.") + ;; Most of the code is released under BSD-3, except for code originally + ;; written for GDC, which is released under GPLv2+, and the DMD frontend, + ;; which is released under the "Boost Software License version 1.0". + (license (list license:bsd-3 + license:gpl2+ + license:boost1.0)))) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 7496a6c8b9..a82cde7d0a 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -25,6 +25,7 @@ non-copyleft x11-style)) #:use-module (guix packages) #:use-module (guix utils) + #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bison) @@ -130,15 +131,18 @@ CSV, CSS and XML.") "03ygxyb0vfjv8raif5q62sl33b54wkr5rzgadb8slijm6k281wpn")))) (build-system gnu-build-system) (native-inputs - `(("boost" ,boost) - ("cppunit" ,cppunit) + `(("cppunit" ,cppunit) ("doxygen" ,doxygen) ("pkg-config" ,pkg-config))) (inputs `(("zlib" ,zlib))) + (propagated-inputs ; Referenced by .la files + `(("boost" ,boost))) (arguments ;; avoid triggering configure errors by simple inclusion of boost headers - `(#:configure-flags '("--disable-werror"))) + `(#:configure-flags '("--disable-werror" + ;; Avoid undefined library references + "LDFLAGS=-lboost_system"))) (home-page "http://sourceforge.net/p/libwpd/wiki/librevenge/") (synopsis "Document importer for office suites") (description "Librevenge is a base library for writing document import @@ -244,7 +248,8 @@ working with graphics in the WPG (WordPerfect Graphics) format.") (uri (string-append "mirror://sourceforge/" name "/" name "-" version ".tar.gz")) (sha256 (base32 - "1dprvk4fibylv24l7gr49gfqbkfgmxynvgssvdcycgpf7n8h4zm8")))) + "1dprvk4fibylv24l7gr49gfqbkfgmxynvgssvdcycgpf7n8h4zm8")) + (patches (list (search-patch "libcmis-fix-test-onedrive.patch"))))) (build-system gnu-build-system) (native-inputs `(("cppunit" ,cppunit) @@ -805,6 +810,8 @@ and to return information on pronunciations, meanings and synonyms.") "--with-system-libs" ; enable all --with-system-* flags (string-append "--with-boost-libdir=" (assoc-ref %build-inputs "boost") "/lib") + ;; Avoid undefined symbols required by boost::spirit + "LDFLAGS=-lboost_system" ;; Avoid a dependency on ucpp. "--with-idlc-cpp=cpp" ;; The fonts require an external tarball (crosextrafonts). diff --git a/gnu/packages/linux-libre-i686.conf b/gnu/packages/linux-libre-i686.conf index aae4dfe61c..e877f195af 100644 --- a/gnu/packages/linux-libre-i686.conf +++ b/gnu/packages/linux-libre-i686.conf @@ -1,6 +1,6 @@ # # Automatically generated file; DO NOT EDIT. -# Linux/x86 4.3.0-gnu Kernel Configuration +# Linux/x86 4.4.0-gnu Kernel Configuration # # CONFIG_64BIT is not set CONFIG_X86_32=y @@ -274,8 +274,8 @@ CONFIG_SECCOMP_FILTER=y CONFIG_HAVE_CC_STACKPROTECTOR=y CONFIG_CC_STACKPROTECTOR=y # CONFIG_CC_STACKPROTECTOR_NONE is not set -CONFIG_CC_STACKPROTECTOR_REGULAR=y -# CONFIG_CC_STACKPROTECTOR_STRONG is not set +# CONFIG_CC_STACKPROTECTOR_REGULAR is not set +CONFIG_CC_STACKPROTECTOR_STRONG=y CONFIG_HAVE_IRQ_TIME_ACCOUNTING=y CONFIG_HAVE_ARCH_TRANSPARENT_HUGEPAGE=y CONFIG_HAVE_ARCH_HUGE_VMAP=y @@ -309,7 +309,6 @@ CONFIG_MODULE_SRCVERSION_ALL=y # CONFIG_MODULE_SIG_SHA512 is not set # CONFIG_MODULE_COMPRESS is not set CONFIG_MODULES_TREE_LOOKUP=y -CONFIG_STOP_MACHINE=y CONFIG_BLOCK=y CONFIG_LBDAF=y CONFIG_BLK_DEV_BSG=y @@ -386,7 +385,7 @@ CONFIG_X86_INTEL_MID=y # CONFIG_X86_INTEL_QUARK is not set CONFIG_X86_INTEL_LPSS=y CONFIG_X86_AMD_PLATFORM_DEVICE=y -CONFIG_IOSF_MBI=m +CONFIG_IOSF_MBI=y CONFIG_IOSF_MBI_DEBUG=y # CONFIG_X86_RDC321X is not set # CONFIG_X86_32_NON_STANDARD is not set @@ -482,9 +481,6 @@ CONFIG_MICROCODE=y CONFIG_MICROCODE_INTEL=y CONFIG_MICROCODE_AMD=y CONFIG_MICROCODE_OLD_INTERFACE=y -CONFIG_MICROCODE_INTEL_EARLY=y -CONFIG_MICROCODE_AMD_EARLY=y -CONFIG_MICROCODE_EARLY=y CONFIG_X86_MSR=m CONFIG_X86_CPUID=m # CONFIG_NOHIGHMEM is not set @@ -622,6 +618,7 @@ CONFIG_ACPI=y CONFIG_ACPI_LEGACY_TABLES_LOOKUP=y CONFIG_ARCH_MIGHT_HAVE_ACPI_PDC=y CONFIG_ACPI_SYSTEM_POWER_STATES_SUPPORT=y +# CONFIG_ACPI_DEBUGGER is not set CONFIG_ACPI_SLEEP=y # CONFIG_ACPI_PROCFS_POWER is not set CONFIG_ACPI_REV_OVERRIDE_POSSIBLE=y @@ -991,7 +988,7 @@ CONFIG_NF_CONNTRACK_TFTP=m CONFIG_NF_CT_NETLINK=m CONFIG_NF_CT_NETLINK_TIMEOUT=m CONFIG_NF_CT_NETLINK_HELPER=m -CONFIG_NETFILTER_NETLINK_QUEUE_CT=y +CONFIG_NETFILTER_NETLINK_GLUE_CT=y CONFIG_NF_NAT=m CONFIG_NF_NAT_NEEDED=y CONFIG_NF_NAT_PROTO_DCCP=m @@ -1360,6 +1357,7 @@ CONFIG_6LOWPAN_NHC_MOBILITY=m CONFIG_6LOWPAN_NHC_ROUTING=m CONFIG_6LOWPAN_NHC_UDP=m CONFIG_IEEE802154=m +CONFIG_IEEE802154_NL802154_EXPERIMENTAL=y CONFIG_IEEE802154_SOCKET=m CONFIG_IEEE802154_6LOWPAN=m CONFIG_MAC802154=m @@ -1458,6 +1456,7 @@ CONFIG_MPLS_ROUTING=m CONFIG_MPLS_IPTUNNEL=m CONFIG_HSR=m # CONFIG_NET_SWITCHDEV is not set +CONFIG_NET_L3_MASTER_DEV=y CONFIG_RPS=y CONFIG_RFS_ACCEL=y CONFIG_XPS=y @@ -1670,6 +1669,7 @@ CONFIG_CFG80211=m CONFIG_CFG80211_DEFAULT_PS=y CONFIG_CFG80211_DEBUGFS=y # CONFIG_CFG80211_INTERNAL_REGDB is not set +CONFIG_CFG80211_CRDA_SUPPORT=y CONFIG_CFG80211_WEXT=y CONFIG_CFG80211_WEXT_EXPORT=y CONFIG_LIB80211=m @@ -1711,7 +1711,7 @@ CONFIG_CEPH_LIB_USE_DNS_RESOLVER=y CONFIG_NFC=m CONFIG_NFC_DIGITAL=m CONFIG_NFC_NCI=m -CONFIG_NFC_NCI_SPI=y +CONFIG_NFC_NCI_SPI=m CONFIG_NFC_NCI_UART=m CONFIG_NFC_HCI=m CONFIG_NFC_SHDLC=y @@ -1725,6 +1725,8 @@ CONFIG_NFC_TRF7970A=m CONFIG_NFC_MEI_PHY=m CONFIG_NFC_SIM=m CONFIG_NFC_PORT100=m +CONFIG_NFC_FDP=m +CONFIG_NFC_FDP_I2C=m CONFIG_NFC_PN544=m CONFIG_NFC_PN544_I2C=m CONFIG_NFC_PN544_MEI=m @@ -1734,6 +1736,8 @@ CONFIG_NFC_MICROREAD_MEI=m CONFIG_NFC_MRVL=m CONFIG_NFC_MRVL_USB=m CONFIG_NFC_MRVL_UART=m +CONFIG_NFC_MRVL_I2C=m +CONFIG_NFC_MRVL_SPI=m CONFIG_NFC_ST21NFCA=m CONFIG_NFC_ST21NFCA_I2C=m CONFIG_NFC_ST_NCI=m @@ -1996,7 +2000,6 @@ CONFIG_BLK_DEV_CRYPTOLOOP=m CONFIG_BLK_DEV_DRBD=m # CONFIG_DRBD_FAULT_INJECTION is not set CONFIG_BLK_DEV_NBD=m -CONFIG_BLK_DEV_NVME=m CONFIG_BLK_DEV_OSD=m CONFIG_BLK_DEV_SX8=m CONFIG_BLK_DEV_RAM=y @@ -2013,6 +2016,7 @@ CONFIG_VIRTIO_BLK=y # CONFIG_BLK_DEV_HD is not set CONFIG_BLK_DEV_RBD=m CONFIG_BLK_DEV_RSXX=m +CONFIG_BLK_DEV_NVME=m # # Misc devices @@ -2100,6 +2104,10 @@ CONFIG_VMWARE_VMCI=m # # SCIF Driver # + +# +# Intel MIC Coprocessor State Management (COSM) Drivers +# CONFIG_ECHO=m # CONFIG_CXL_BASE is not set # CONFIG_CXL_KERNEL_API is not set @@ -2190,12 +2198,10 @@ CONFIG_MEGARAID_MM=m CONFIG_MEGARAID_MAILBOX=m CONFIG_MEGARAID_LEGACY=m CONFIG_MEGARAID_SAS=m -CONFIG_SCSI_MPT2SAS=m -CONFIG_SCSI_MPT2SAS_MAX_SGE=128 -# CONFIG_SCSI_MPT2SAS_LOGGING is not set CONFIG_SCSI_MPT3SAS=m +CONFIG_SCSI_MPT2SAS_MAX_SGE=128 CONFIG_SCSI_MPT3SAS_MAX_SGE=128 -# CONFIG_SCSI_MPT3SAS_LOGGING is not set +CONFIG_SCSI_MPT2SAS=m CONFIG_SCSI_UFSHCD=m CONFIG_SCSI_UFSHCD_PCI=m CONFIG_SCSI_UFSHCD_PLATFORM=m @@ -2580,6 +2586,8 @@ CONFIG_ATL1=m CONFIG_ATL1E=m CONFIG_ATL1C=m CONFIG_ALX=m +CONFIG_NET_VENDOR_AURORA=y +CONFIG_AURORA_NB8800=m CONFIG_NET_CADENCE=y CONFIG_MACB=m CONFIG_NET_VENDOR_BROADCOM=y @@ -2594,6 +2602,8 @@ CONFIG_TIGON3=m CONFIG_BNX2X=m CONFIG_BNX2X_SRIOV=y CONFIG_BNX2X_VXLAN=y +CONFIG_BNXT=m +CONFIG_BNXT_SRIOV=y CONFIG_NET_VENDOR_BROCADE=y CONFIG_BNA=m CONFIG_NET_VENDOR_CAVIUM=y @@ -2663,7 +2673,6 @@ CONFIG_I40EVF=m CONFIG_FM10K=m CONFIG_FM10K_VXLAN=y CONFIG_NET_VENDOR_I825XX=y -CONFIG_IP1000=m CONFIG_JME=m CONFIG_NET_VENDOR_MARVELL=y CONFIG_MVMDIO=m @@ -2690,6 +2699,7 @@ CONFIG_KSZ884X_PCI=m CONFIG_NET_VENDOR_MICROCHIP=y CONFIG_ENC28J60=m # CONFIG_ENC28J60_WRITEVERIFY is not set +CONFIG_ENCX24J600=m CONFIG_NET_VENDOR_MYRI=y CONFIG_MYRI10GE=m CONFIG_FEALNX=m @@ -2720,6 +2730,8 @@ CONFIG_QLCNIC_VXLAN=y CONFIG_QLCNIC_HWMON=y CONFIG_QLGE=m CONFIG_NETXEN_NIC=m +CONFIG_QED=m +CONFIG_QEDE=m CONFIG_NET_VENDOR_QUALCOMM=y CONFIG_NET_VENDOR_REALTEK=y CONFIG_ATP=m @@ -2804,6 +2816,7 @@ CONFIG_CICADA_PHY=m CONFIG_VITESSE_PHY=m CONFIG_TERANETICS_PHY=m CONFIG_SMSC_PHY=m +CONFIG_BCM_NET_PHYLIB=m CONFIG_BROADCOM_PHY=m CONFIG_BCM7XXX_PHY=m CONFIG_BCM87XX_PHY=m @@ -2813,7 +2826,7 @@ CONFIG_NATIONAL_PHY=m CONFIG_STE10XP=m CONFIG_LSI_ET1011C_PHY=m CONFIG_MICREL_PHY=m -# CONFIG_DP83848_PHY is not set +CONFIG_DP83848_PHY=m CONFIG_DP83867_PHY=m CONFIG_MICROCHIP_PHY=m CONFIG_FIXED_PHY=y @@ -2897,10 +2910,10 @@ CONFIG_PCMCIA_WL3501=m # CONFIG_PRISM54 is not set CONFIG_USB_ZD1201=m CONFIG_USB_NET_RNDIS_WLAN=m +CONFIG_ADM8211=m CONFIG_RTL8180=m CONFIG_RTL8187=m CONFIG_RTL8187_LEDS=y -CONFIG_ADM8211=m CONFIG_MAC80211_HWSIM=m CONFIG_MWL8K=m CONFIG_ATH_COMMON=m @@ -2954,7 +2967,6 @@ CONFIG_B43_BUSES_BCMA_AND_SSB=y # CONFIG_B43_BUSES_SSB is not set CONFIG_B43_PCI_AUTOSELECT=y CONFIG_B43_PCICORE_AUTOSELECT=y -# CONFIG_B43_PCMCIA is not set # CONFIG_B43_SDIO is not set CONFIG_B43_BCMA_PIO=y CONFIG_B43_PIO=y @@ -3096,6 +3108,8 @@ CONFIG_RTLWIFI_USB=m CONFIG_RTL8192C_COMMON=m CONFIG_RTL8723_COMMON=m CONFIG_RTLBTCOEXIST=m +CONFIG_RTL8XXXU=m +CONFIG_RTL8XXXU_UNTESTED=y CONFIG_WL_TI=y CONFIG_WL1251=m CONFIG_WL1251_SPI=m @@ -3157,6 +3171,7 @@ CONFIG_SBNI=m CONFIG_IEEE802154_DRIVERS=m CONFIG_IEEE802154_FAKELB=m CONFIG_IEEE802154_AT86RF230=m +CONFIG_IEEE802154_AT86RF230_DEBUGFS=y CONFIG_IEEE802154_MRF24J40=m CONFIG_IEEE802154_CC2520=m CONFIG_IEEE802154_ATUSB=m @@ -3312,6 +3327,10 @@ CONFIG_MISDN_NETJET=m CONFIG_MISDN_IPAC=m CONFIG_MISDN_ISAR=m CONFIG_ISDN_HDLC=m +CONFIG_NVM=y +# CONFIG_NVM_DEBUG is not set +CONFIG_NVM_GENNVM=m +CONFIG_NVM_RRPC=m # # Input device support @@ -3451,6 +3470,7 @@ CONFIG_TOUCHSCREEN_DA9052=m CONFIG_TOUCHSCREEN_DYNAPRO=m CONFIG_TOUCHSCREEN_HAMPSHIRE=m CONFIG_TOUCHSCREEN_EETI=m +CONFIG_TOUCHSCREEN_FT6236=m CONFIG_TOUCHSCREEN_FUJITSU=m CONFIG_TOUCHSCREEN_GOODIX=m CONFIG_TOUCHSCREEN_ILI210X=m @@ -3502,6 +3522,8 @@ CONFIG_TOUCHSCREEN_USB_NEXIO=y CONFIG_TOUCHSCREEN_USB_EASYTOUCH=y CONFIG_TOUCHSCREEN_TOUCHIT213=m CONFIG_TOUCHSCREEN_TSC_SERIO=m +CONFIG_TOUCHSCREEN_TSC200X_CORE=m +CONFIG_TOUCHSCREEN_TSC2004=m CONFIG_TOUCHSCREEN_TSC2005=m CONFIG_TOUCHSCREEN_TSC2007=m CONFIG_TOUCHSCREEN_PCAP=m @@ -3510,6 +3532,7 @@ CONFIG_TOUCHSCREEN_SUR40=m CONFIG_TOUCHSCREEN_SX8654=m CONFIG_TOUCHSCREEN_TPS6507X=m CONFIG_TOUCHSCREEN_ZFORCE=m +CONFIG_TOUCHSCREEN_ROHM_BU21023=m CONFIG_INPUT_MISC=y CONFIG_INPUT_88PM860X_ONKEY=m CONFIG_INPUT_88PM80X_ONKEY=m @@ -3586,6 +3609,7 @@ CONFIG_SERIO_ALTERA_PS2=m CONFIG_SERIO_PS2MULT=m CONFIG_SERIO_ARC_PS2=m CONFIG_HYPERV_KEYBOARD=m +CONFIG_USERIO=m CONFIG_GAMEPORT=m CONFIG_GAMEPORT_NS558=m CONFIG_GAMEPORT_L4=m @@ -3647,8 +3671,11 @@ CONFIG_SERIAL_8250_HUB6=m CONFIG_SERIAL_8250_SHARE_IRQ=y # CONFIG_SERIAL_8250_DETECT_IRQ is not set CONFIG_SERIAL_8250_RSA=y +# CONFIG_SERIAL_8250_FSL is not set CONFIG_SERIAL_8250_DW=m +CONFIG_SERIAL_8250_RT288X=y CONFIG_SERIAL_8250_FINTEK=m +CONFIG_SERIAL_8250_MID=m # # Non-8250 serial port support @@ -3806,6 +3833,7 @@ CONFIG_I2C_CBUS_GPIO=m CONFIG_I2C_DESIGNWARE_CORE=m CONFIG_I2C_DESIGNWARE_PLATFORM=m CONFIG_I2C_DESIGNWARE_PCI=m +CONFIG_I2C_DESIGNWARE_BAYTRAIL=y CONFIG_I2C_EG20T=m CONFIG_I2C_EMEV2=m CONFIG_I2C_GPIO=m @@ -3925,6 +3953,7 @@ CONFIG_PINCTRL_AMD=y CONFIG_PINCTRL_BAYTRAIL=y CONFIG_PINCTRL_CHERRYVIEW=m CONFIG_PINCTRL_INTEL=m +CONFIG_PINCTRL_BROXTON=m CONFIG_PINCTRL_SUNRISEPOINT=m CONFIG_ARCH_WANT_OPTIONAL_GPIOLIB=y CONFIG_GPIOLIB=y @@ -3939,15 +3968,22 @@ CONFIG_GPIO_MAX730X=m # # Memory mapped GPIO drivers # +CONFIG_GPIO_AMDPT=m CONFIG_GPIO_DWAPB=m -CONFIG_GPIO_F7188X=m CONFIG_GPIO_GENERIC_PLATFORM=m CONFIG_GPIO_ICH=m -CONFIG_GPIO_IT8761E=m CONFIG_GPIO_LYNXPOINT=y +CONFIG_GPIO_VX855=m +CONFIG_GPIO_ZX=y + +# +# Port-mapped I/O GPIO drivers +# +CONFIG_GPIO_104_IDIO_16=m +CONFIG_GPIO_F7188X=m +CONFIG_GPIO_IT87=m CONFIG_GPIO_SCH=m CONFIG_GPIO_SCH311X=m -CONFIG_GPIO_VX855=m # # I2C GPIO expanders @@ -3999,9 +4035,12 @@ CONFIG_GPIO_RDC321X=m # SPI GPIO expanders # CONFIG_GPIO_MAX7301=m -CONFIG_GPIO_MCP23S08=m CONFIG_GPIO_MC33880=m -CONFIG_GPIO_ZX=y + +# +# SPI or I2C GPIO expanders +# +CONFIG_GPIO_MCP23S08=m # # USB GPIO expanders @@ -4052,12 +4091,13 @@ CONFIG_BATTERY_DS2780=m CONFIG_BATTERY_DS2781=m CONFIG_BATTERY_DS2782=m CONFIG_BATTERY_SBS=m -CONFIG_BATTERY_BQ27x00=m -CONFIG_BATTERY_BQ27X00_I2C=y -CONFIG_BATTERY_BQ27X00_PLATFORM=y +CONFIG_BATTERY_BQ27XXX=m +CONFIG_BATTERY_BQ27XXX_I2C=y +CONFIG_BATTERY_BQ27XXX_PLATFORM=y CONFIG_BATTERY_DA9030=m CONFIG_BATTERY_DA9052=m CONFIG_CHARGER_DA9150=m +CONFIG_BATTERY_DA9150=m CONFIG_AXP288_CHARGER=m CONFIG_AXP288_FUEL_GAUGE=m CONFIG_BATTERY_MAX17040=m @@ -4085,9 +4125,11 @@ CONFIG_CHARGER_BQ24735=m CONFIG_CHARGER_BQ25890=m CONFIG_CHARGER_SMB347=m CONFIG_CHARGER_TPS65090=m +CONFIG_CHARGER_TPS65217=m CONFIG_BATTERY_GAUGE_LTC2941=m CONFIG_BATTERY_RT5033=m CONFIG_CHARGER_RT9455=m +CONFIG_AXP20X_POWER=m CONFIG_POWER_RESET=y CONFIG_POWER_RESET_RESTART=y CONFIG_POWER_AVS=y @@ -4165,6 +4207,7 @@ CONFIG_SENSORS_MAX6639=m CONFIG_SENSORS_MAX6642=m CONFIG_SENSORS_MAX6650=m CONFIG_SENSORS_MAX6697=m +CONFIG_SENSORS_MAX31790=m CONFIG_SENSORS_HTU21=m CONFIG_SENSORS_MCP3021=m CONFIG_SENSORS_MENF21BMC_HWMON=m @@ -4338,6 +4381,7 @@ CONFIG_W83877F_WDT=m CONFIG_W83977F_WDT=m CONFIG_MACHZ_WDT=m CONFIG_SBC_EPX_C3_WATCHDOG=m +CONFIG_BCM7038_WDT=m CONFIG_MEN_A21_WDT=m CONFIG_XEN_WDT=m @@ -4373,6 +4417,7 @@ CONFIG_SSB_PCMCIAHOST_POSSIBLE=y # CONFIG_SSB_PCMCIAHOST is not set CONFIG_SSB_SDIOHOST_POSSIBLE=y CONFIG_SSB_SDIOHOST=y +CONFIG_SSB_HOST_SOC=y # CONFIG_SSB_SILENT is not set # CONFIG_SSB_DEBUG is not set CONFIG_SSB_DRIVER_PCICORE_POSSIBLE=y @@ -4904,6 +4949,7 @@ CONFIG_VIDEO_MEM2MEM_DEINTERLACE=m CONFIG_VIDEO_SH_VEU=m CONFIG_V4L_TEST_DRIVERS=y CONFIG_VIDEO_VIVID=m +CONFIG_VIDEO_VIVID_MAX_DEVS=64 CONFIG_VIDEO_VIM2M=m CONFIG_DVB_PLATFORM_DRIVERS=y @@ -5306,7 +5352,7 @@ CONFIG_DRM_RADEON=m # CONFIG_DRM_RADEON_USERPTR is not set # CONFIG_DRM_RADEON_UMS is not set CONFIG_DRM_AMDGPU=m -CONFIG_DRM_AMDGPU_CIK=y +# CONFIG_DRM_AMDGPU_CIK is not set CONFIG_DRM_AMDGPU_USERPTR=y CONFIG_DRM_NOUVEAU=m CONFIG_NOUVEAU_DEBUG=5 @@ -5449,6 +5495,7 @@ CONFIG_FB_GEODE_GX1=m CONFIG_FB_SM501=m CONFIG_FB_SMSCUFX=m CONFIG_FB_UDL=m +CONFIG_FB_IBM_GXT4500=m # CONFIG_FB_VIRTUAL is not set CONFIG_XEN_FBDEV_FRONTEND=m CONFIG_FB_METRONOME=m @@ -5541,7 +5588,9 @@ CONFIG_SND_SEQUENCER=m CONFIG_SND_SEQ_DUMMY=m CONFIG_SND_OSSEMUL=y CONFIG_SND_MIXER_OSS=m -# CONFIG_SND_PCM_OSS is not set +CONFIG_SND_PCM_OSS=m +CONFIG_SND_PCM_OSS_PLUGINS=y +CONFIG_SND_PCM_TIMER=y # CONFIG_SND_SEQUENCER_OSS is not set CONFIG_SND_HRTIMER=m CONFIG_SND_SEQ_HRTIMER_DEFAULT=y @@ -5717,6 +5766,7 @@ CONFIG_SND_HDA_POWER_SAVE_DEFAULT=0 CONFIG_SND_HDA_CORE=m CONFIG_SND_HDA_DSP_LOADER=y CONFIG_SND_HDA_I915=y +CONFIG_SND_HDA_EXT_CORE=m CONFIG_SND_HDA_PREALLOC_SIZE=64 CONFIG_SND_SPI=y CONFIG_SND_USB=y @@ -5742,12 +5792,16 @@ CONFIG_SND_ISIGHT=m CONFIG_SND_SCS1X=m CONFIG_SND_FIREWORKS=m CONFIG_SND_BEBOB=m +CONFIG_SND_FIREWIRE_DIGI00X=m +CONFIG_SND_FIREWIRE_TASCAM=m CONFIG_SND_PCMCIA=y CONFIG_SND_VXPOCKET=m CONFIG_SND_PDAUDIOCF=m CONFIG_SND_SOC=m CONFIG_SND_SOC_AC97_BUS=y CONFIG_SND_SOC_GENERIC_DMAENGINE_PCM=y +CONFIG_SND_SOC_COMPRESS=y +CONFIG_SND_SOC_TOPOLOGY=y CONFIG_SND_ATMEL_SOC=m CONFIG_SND_DESIGNWARE_I2S=m @@ -5781,6 +5835,13 @@ CONFIG_SND_SOC_INTEL_BYTCR_RT5640_MACH=m CONFIG_SND_SOC_INTEL_CHT_BSW_RT5672_MACH=m CONFIG_SND_SOC_INTEL_CHT_BSW_RT5645_MACH=m CONFIG_SND_SOC_INTEL_CHT_BSW_MAX98090_TI_MACH=m +CONFIG_SND_SOC_INTEL_SKYLAKE=m +CONFIG_SND_SOC_INTEL_SKL_RT286_MACH=m + +# +# Allwinner SoC Audio support +# +CONFIG_SND_SUN4I_CODEC=m CONFIG_SND_SOC_XTFPGA_I2S=m CONFIG_SND_SOC_I2C_AND_SPI=m @@ -5791,6 +5852,7 @@ CONFIG_SND_SOC_AC97_CODEC=m CONFIG_SND_SOC_ADAU1701=m CONFIG_SND_SOC_AK4104=m CONFIG_SND_SOC_AK4554=m +CONFIG_SND_SOC_AK4613=m CONFIG_SND_SOC_AK4642=m CONFIG_SND_SOC_AK5386=m CONFIG_SND_SOC_ALC5623=m @@ -5808,7 +5870,7 @@ CONFIG_SND_SOC_CS4271_SPI=m CONFIG_SND_SOC_CS42XX8=m CONFIG_SND_SOC_CS42XX8_I2C=m CONFIG_SND_SOC_CS4349=m -CONFIG_SND_SOC_HDMI_CODEC=m +CONFIG_SND_SOC_DMIC=m CONFIG_SND_SOC_ES8328=m CONFIG_SND_SOC_GTM601=m CONFIG_SND_SOC_MAX98090=m @@ -5894,6 +5956,7 @@ CONFIG_HID_BELKIN=m CONFIG_HID_BETOP_FF=m CONFIG_HID_CHERRY=m CONFIG_HID_CHICONY=m +CONFIG_HID_CORSAIR=m CONFIG_HID_PRODIKEYS=m CONFIG_HID_CP2112=m CONFIG_HID_CYPRESS=m @@ -5904,6 +5967,7 @@ CONFIG_HID_ELECOM=m CONFIG_HID_ELO=m CONFIG_HID_EZKEY=m CONFIG_HID_GEMBIRD=m +CONFIG_HID_GFRM=m CONFIG_HID_HOLTEK=m CONFIG_HOLTEK_FF=y CONFIG_HID_GT683R=m @@ -6002,7 +6066,6 @@ CONFIG_USB_DYNAMIC_MINORS=y # CONFIG_USB_OTG is not set # CONFIG_USB_OTG_WHITELIST is not set # CONFIG_USB_OTG_BLACKLIST_HUB is not set -# CONFIG_USB_OTG_FSM is not set CONFIG_USB_ULPI_BUS=m CONFIG_USB_MON=m CONFIG_USB_WUSB=m @@ -6024,7 +6087,6 @@ CONFIG_USB_EHCI_HCD_PLATFORM=y CONFIG_USB_OXU210HP_HCD=m CONFIG_USB_ISP116X_HCD=m CONFIG_USB_ISP1362_HCD=m -CONFIG_USB_FUSBH200_HCD=m CONFIG_USB_FOTG210_HCD=m CONFIG_USB_MAX3421_HCD=m CONFIG_USB_OHCI_HCD=y @@ -6346,7 +6408,6 @@ CONFIG_UWB_WHCI=m CONFIG_UWB_I1480U=m CONFIG_MMC=y # CONFIG_MMC_DEBUG is not set -# CONFIG_MMC_CLKGATE is not set # # MMC/SD/SDIO Card Drivers @@ -6412,10 +6473,11 @@ CONFIG_LEDS_PCA9532=m CONFIG_LEDS_PCA9532_GPIO=y CONFIG_LEDS_GPIO=m CONFIG_LEDS_LP3944=m -# CONFIG_LEDS_LP5521 is not set -# CONFIG_LEDS_LP5523 is not set -# CONFIG_LEDS_LP5562 is not set -# CONFIG_LEDS_LP8501 is not set +CONFIG_LEDS_LP55XX_COMMON=m +CONFIG_LEDS_LP5521=m +CONFIG_LEDS_LP5523=m +CONFIG_LEDS_LP5562=m +CONFIG_LEDS_LP8501=m CONFIG_LEDS_LP8788=m CONFIG_LEDS_LP8860=m CONFIG_LEDS_CLEVO_MAIL=m @@ -6573,6 +6635,7 @@ CONFIG_RTC_DRV_RX8581=m CONFIG_RTC_DRV_RX8025=m CONFIG_RTC_DRV_EM3027=m CONFIG_RTC_DRV_RV3029C2=m +CONFIG_RTC_DRV_RV8803=m CONFIG_RTC_DRV_S5M=m # @@ -6646,7 +6709,7 @@ CONFIG_DMADEVICES=y CONFIG_DMA_ENGINE=y CONFIG_DMA_VIRTUAL_CHANNELS=m CONFIG_DMA_ACPI=y -CONFIG_IDMA64=m +CONFIG_INTEL_IDMA64=m CONFIG_PCH_DMA=m CONFIG_TIMB_DMA=m CONFIG_DW_DMAC_CORE=m @@ -6683,6 +6746,7 @@ CONFIG_VFIO_PCI=m CONFIG_VFIO_PCI_VGA=y CONFIG_VFIO_PCI_MMAP=y CONFIG_VFIO_PCI_INTX=y +CONFIG_IRQ_BYPASS_MANAGER=m CONFIG_VIRT_DRIVERS=y CONFIG_VIRTIO=y @@ -6771,7 +6835,6 @@ CONFIG_COMEDI_DT2815=m CONFIG_COMEDI_DT2817=m CONFIG_COMEDI_DT282X=m CONFIG_COMEDI_DMM32AT=m -CONFIG_COMEDI_UNIOXX5=m CONFIG_COMEDI_FL512=m CONFIG_COMEDI_AIO_AIO12_8=m CONFIG_COMEDI_AIO_IIRO_16=m @@ -6990,9 +7053,6 @@ CONFIG_IIO_SIMPLE_DUMMY=m # CONFIG_IIO_SIMPLE_DUMMY_BUFFER is not set CONFIG_FB_SM750=m CONFIG_FB_XGI=m -CONFIG_FT1000=m -CONFIG_FT1000_USB=m -CONFIG_FT1000_PCMCIA=m # # Speakup console speech @@ -7028,7 +7088,7 @@ CONFIG_LIRC_SERIAL=m CONFIG_LIRC_SERIAL_TRANSMITTER=y CONFIG_LIRC_SIR=m CONFIG_LIRC_ZILOG=m -CONFIG_STAGING_RDMA=y +CONFIG_STAGING_RDMA=m CONFIG_INFINIBAND_AMSO1100=m # CONFIG_INFINIBAND_AMSO1100_DEBUG is not set @@ -7048,14 +7108,7 @@ CONFIG_FWTTY_MAX_TOTAL_PORTS=64 CONFIG_FWTTY_MAX_CARD_PORTS=32 CONFIG_MTD_SPINAND_MT29F=m CONFIG_MTD_SPINAND_ONDIEECC=y -CONFIG_LUSTRE_FS=m -CONFIG_LUSTRE_OBD_MAX_IOCTL_BUFFER=8192 -# CONFIG_LUSTRE_DEBUG_EXPENSIVE_CHECK is not set -CONFIG_LUSTRE_LLITE_LLOOP=m -CONFIG_LNET=m -CONFIG_LNET_MAX_PAYLOAD=1048576 -CONFIG_LNET_SELFTEST=m -CONFIG_LNET_XPRT_IB=m +# CONFIG_LUSTRE_FS is not set CONFIG_DGNC=m CONFIG_DGAP=m CONFIG_GS_FPGABOOT=m @@ -7082,6 +7135,7 @@ CONFIG_FB_TFT_SSD1306=m CONFIG_FB_TFT_SSD1331=m CONFIG_FB_TFT_SSD1351=m CONFIG_FB_TFT_ST7735R=m +CONFIG_FB_TFT_ST7789V=m CONFIG_FB_TFT_TINYLCD=m CONFIG_FB_TFT_TLS8204=m CONFIG_FB_TFT_UC1611=m @@ -7090,6 +7144,7 @@ CONFIG_FB_TFT_UPD161704=m CONFIG_FB_TFT_WATTEROTT=m CONFIG_FB_FLEX=m CONFIG_FB_TFT_FBTFT_DEVICE=m +# CONFIG_WILC1000_DRIVER is not set CONFIG_MOST=m CONFIG_MOSTCORE=m CONFIG_AIM_CDEV=m @@ -7142,6 +7197,7 @@ CONFIG_TOPSTAR_LAPTOP=m CONFIG_ACPI_TOSHIBA=m CONFIG_TOSHIBA_BT_RFKILL=m CONFIG_TOSHIBA_HAPS=m +CONFIG_TOSHIBA_WMI=m CONFIG_ACPI_CMPC=m CONFIG_INTEL_SCU_IPC=y CONFIG_INTEL_SCU_IPC_UTIL=m @@ -7211,6 +7267,7 @@ CONFIG_IOMMU_SUPPORT=y CONFIG_IOMMU_IOVA=y CONFIG_DMAR_TABLE=y CONFIG_INTEL_IOMMU=y +CONFIG_INTEL_IOMMU_SVM=y # CONFIG_INTEL_IOMMU_DEFAULT_ON is not set CONFIG_INTEL_IOMMU_FLOPPY_WA=y @@ -7263,17 +7320,20 @@ CONFIG_EXTCON_USB_GPIO=m CONFIG_MEMORY=y CONFIG_IIO=m CONFIG_IIO_BUFFER=y -CONFIG_IIO_BUFFER_CB=y +CONFIG_IIO_BUFFER_CB=m CONFIG_IIO_KFIFO_BUF=m CONFIG_IIO_TRIGGERED_BUFFER=m CONFIG_IIO_TRIGGER=y CONFIG_IIO_CONSUMERS_PER_TRIGGER=2 +CONFIG_IIO_TRIGGERED_EVENT=m # # Accelerometers # CONFIG_BMA180=m CONFIG_BMC150_ACCEL=m +CONFIG_BMC150_ACCEL_I2C=m +CONFIG_BMC150_ACCEL_SPI=m CONFIG_HID_SENSOR_ACCEL_3D=m CONFIG_IIO_ST_ACCEL_3AXIS=m CONFIG_IIO_ST_ACCEL_I2C_3AXIS=m @@ -7284,6 +7344,7 @@ CONFIG_MMA8452=m CONFIG_MMA9551_CORE=m CONFIG_MMA9551=m CONFIG_MMA9553=m +CONFIG_MXC4005=m CONFIG_STK8312=m CONFIG_STK8BA50=m @@ -7301,8 +7362,9 @@ CONFIG_AD7887=m CONFIG_AD7923=m CONFIG_AD799X=m CONFIG_AXP288_ADC=m -CONFIG_DA9150_GPADC=m CONFIG_CC10001_ADC=m +CONFIG_DA9150_GPADC=m +CONFIG_HI8435=m CONFIG_LP8788_ADC=m CONFIG_MAX1027=m CONFIG_MAX1363=m @@ -7325,10 +7387,16 @@ CONFIG_VIPERBOARD_ADC=m CONFIG_AD8366=m # +# Chemical Sensors +# +CONFIG_VZ89X=m + +# # Hid Sensor IIO Common # CONFIG_HID_SENSOR_IIO_COMMON=m CONFIG_HID_SENSOR_IIO_TRIGGER=m +CONFIG_IIO_MS_SENSORS_I2C=m # # SSP Sensor Common @@ -7383,6 +7451,8 @@ CONFIG_ADIS16136=m CONFIG_ADIS16260=m CONFIG_ADXRS450=m CONFIG_BMG160=m +CONFIG_BMG160_I2C=m +CONFIG_BMG160_SPI=m CONFIG_HID_SENSOR_GYRO_3D=m CONFIG_IIO_ST_GYRO_3AXIS=m CONFIG_IIO_ST_GYRO_I2C_3AXIS=m @@ -7393,6 +7463,8 @@ CONFIG_ITG3200=m # Humidity sensors # CONFIG_DHT11=m +CONFIG_HDC100X=m +CONFIG_HTU21=m CONFIG_SI7005=m CONFIG_SI7020=m @@ -7413,6 +7485,7 @@ CONFIG_ACPI_ALS=m CONFIG_ADJD_S311=m CONFIG_AL3320A=m CONFIG_APDS9300=m +CONFIG_APDS9960=m CONFIG_BH1750=m CONFIG_CM32181=m CONFIG_CM3232=m @@ -7433,6 +7506,7 @@ CONFIG_TCS3414=m CONFIG_TCS3472=m CONFIG_SENSORS_TSL2563=m CONFIG_TSL4531=m +CONFIG_US5182D=m CONFIG_VCNL4000=m # @@ -7440,13 +7514,13 @@ CONFIG_VCNL4000=m # CONFIG_AK8975=m CONFIG_AK09911=m +CONFIG_BMC150_MAGN=m CONFIG_MAG3110=m CONFIG_HID_SENSOR_MAGNETOMETER_3D=m CONFIG_MMC35240=m CONFIG_IIO_ST_MAGN_3AXIS=m CONFIG_IIO_ST_MAGN_I2C_3AXIS=m CONFIG_IIO_ST_MAGN_SPI_3AXIS=m -CONFIG_BMC150_MAGN=m # # Inclinometer sensors @@ -7461,6 +7535,11 @@ CONFIG_IIO_INTERRUPT_TRIGGER=m CONFIG_IIO_SYSFS_TRIGGER=m # +# Digital potentiometers +# +CONFIG_MCP4531=m + +# # Pressure sensors # CONFIG_BMP280=m @@ -7470,6 +7549,7 @@ CONFIG_MPL3115=m CONFIG_MS5611=m CONFIG_MS5611_I2C=m CONFIG_MS5611_SPI=m +CONFIG_MS5637=m CONFIG_IIO_ST_PRESS=m CONFIG_IIO_ST_PRESS_I2C=m CONFIG_IIO_ST_PRESS_SPI=m @@ -7483,6 +7563,7 @@ CONFIG_AS3935=m # # Proximity sensors # +CONFIG_LIDAR_LITE_V2=m CONFIG_SX9500=m # @@ -7490,6 +7571,8 @@ CONFIG_SX9500=m # CONFIG_MLX90614=m CONFIG_TMP006=m +CONFIG_TSYS01=m +CONFIG_TSYS02D=m CONFIG_NTB=m CONFIG_NTB_PINGPONG=m CONFIG_NTB_TOOL=m @@ -7519,6 +7602,7 @@ CONFIG_PWM_LP3943=m CONFIG_PWM_LPSS=m CONFIG_PWM_LPSS_PCI=m CONFIG_PWM_LPSS_PLATFORM=m +CONFIG_PWM_PCA9685=m CONFIG_PWM_TWL=m CONFIG_PWM_TWL_LED=m CONFIG_IPACK_BUS=m @@ -7566,6 +7650,22 @@ CONFIG_ND_CLAIM=y CONFIG_ND_BTT=m CONFIG_BTT=y CONFIG_NVMEM=m +CONFIG_STM=m +CONFIG_STM_DUMMY=m +CONFIG_STM_SOURCE_CONSOLE=m +CONFIG_INTEL_TH=m +CONFIG_INTEL_TH_PCI=m +CONFIG_INTEL_TH_GTH=m +CONFIG_INTEL_TH_STH=m +CONFIG_INTEL_TH_MSU=m +CONFIG_INTEL_TH_PTI=m +# CONFIG_INTEL_TH_DEBUG is not set + +# +# FPGA Configuration Support +# +CONFIG_FPGA=m +CONFIG_FPGA_MGR_ZYNQ_FPGA=m # # Firmware Drivers @@ -7590,6 +7690,7 @@ CONFIG_EFI_ESRT=y CONFIG_EFI_VARS_PSTORE=m # CONFIG_EFI_VARS_PSTORE_DEFAULT_DISABLE is not set CONFIG_EFI_RUNTIME_MAP=y +# CONFIG_EFI_FAKE_MEMMAP is not set CONFIG_EFI_RUNTIME_WRAPPERS=y CONFIG_UEFI_CPER=y @@ -7756,6 +7857,7 @@ CONFIG_UBIFS_FS=m # CONFIG_UBIFS_FS_ADVANCED_COMPR is not set CONFIG_UBIFS_FS_LZO=y CONFIG_UBIFS_FS_ZLIB=y +CONFIG_UBIFS_ATIME_SUPPORT=y # CONFIG_LOGFS is not set CONFIG_CRAMFS=m CONFIG_SQUASHFS=m @@ -7766,7 +7868,7 @@ CONFIG_SQUASHFS_FILE_DIRECT=y CONFIG_SQUASHFS_DECOMP_MULTI_PERCPU=y CONFIG_SQUASHFS_XATTR=y CONFIG_SQUASHFS_ZLIB=y -# CONFIG_SQUASHFS_LZ4 is not set +CONFIG_SQUASHFS_LZ4=y CONFIG_SQUASHFS_LZO=y CONFIG_SQUASHFS_XZ=y # CONFIG_SQUASHFS_4K_DEVBLK_SIZE is not set @@ -7951,6 +8053,7 @@ CONFIG_UNUSED_SYMBOLS=y CONFIG_DEBUG_FS=y # CONFIG_HEADERS_CHECK is not set # CONFIG_DEBUG_SECTION_MISMATCH is not set +CONFIG_SECTION_MISMATCH_WARN_ONLY=y CONFIG_ARCH_WANT_FRAME_POINTERS=y CONFIG_FRAME_POINTER=y # CONFIG_DEBUG_FORCE_WEAK_PER_CPU is not set @@ -8090,6 +8193,7 @@ CONFIG_MMIOTRACE=y # CONFIG_RING_BUFFER_BENCHMARK is not set # CONFIG_RING_BUFFER_STARTUP_TEST is not set # CONFIG_TRACE_ENUM_MAP_FILE is not set +CONFIG_TRACING_EVENTS_GPIO=y # # Runtime Testing @@ -8106,6 +8210,7 @@ CONFIG_ASYNC_RAID6_TEST=m CONFIG_TEST_HEXDUMP=m CONFIG_TEST_STRING_HELPERS=m CONFIG_TEST_KSTRTOX=m +CONFIG_TEST_PRINTF=m # CONFIG_TEST_RHASHTABLE is not set # CONFIG_PROVIDE_OHCI1394_DMA_INIT is not set # CONFIG_DMA_API_DEBUG is not set @@ -8131,9 +8236,12 @@ CONFIG_STRICT_DEVMEM=y CONFIG_EARLY_PRINTK=y CONFIG_EARLY_PRINTK_DBGP=y CONFIG_EARLY_PRINTK_EFI=y +# CONFIG_X86_PTDUMP_CORE is not set # CONFIG_X86_PTDUMP is not set +# CONFIG_EFI_PGT_DUMP is not set CONFIG_DEBUG_RODATA=y # CONFIG_DEBUG_RODATA_TEST is not set +# CONFIG_DEBUG_WX is not set CONFIG_DEBUG_SET_MODULE_RONX=y # CONFIG_DEBUG_NX_TEST is not set CONFIG_DOUBLEFAULT=y @@ -8286,6 +8394,7 @@ CONFIG_CRYPTO_ECB=y CONFIG_CRYPTO_LRW=m CONFIG_CRYPTO_PCBC=m CONFIG_CRYPTO_XTS=m +CONFIG_CRYPTO_KEYWRAP=m # # Hash modes @@ -8408,6 +8517,7 @@ CONFIG_HAVE_KVM_MSI=y CONFIG_HAVE_KVM_CPU_RELAX_INTERCEPT=y CONFIG_KVM_VFIO=y CONFIG_KVM_GENERIC_DIRTYLOG_READ_PROTECT=y +CONFIG_HAVE_KVM_IRQ_BYPASS=y CONFIG_VIRTUALIZATION=y CONFIG_KVM=m CONFIG_KVM_INTEL=m diff --git a/gnu/packages/linux-libre-x86_64.conf b/gnu/packages/linux-libre-x86_64.conf index 6c233c079a..406053ab7a 100644 --- a/gnu/packages/linux-libre-x86_64.conf +++ b/gnu/packages/linux-libre-x86_64.conf @@ -1,6 +1,6 @@ # # Automatically generated file; DO NOT EDIT. -# Linux/x86 4.3.0-gnu Kernel Configuration +# Linux/x86 4.4.0-gnu Kernel Configuration # CONFIG_64BIT=y CONFIG_X86_64=y @@ -284,8 +284,8 @@ CONFIG_SECCOMP_FILTER=y CONFIG_HAVE_CC_STACKPROTECTOR=y CONFIG_CC_STACKPROTECTOR=y # CONFIG_CC_STACKPROTECTOR_NONE is not set -CONFIG_CC_STACKPROTECTOR_REGULAR=y -# CONFIG_CC_STACKPROTECTOR_STRONG is not set +# CONFIG_CC_STACKPROTECTOR_REGULAR is not set +CONFIG_CC_STACKPROTECTOR_STRONG=y CONFIG_HAVE_CONTEXT_TRACKING=y CONFIG_HAVE_VIRT_CPU_ACCOUNTING_GEN=y CONFIG_HAVE_IRQ_TIME_ACCOUNTING=y @@ -322,7 +322,6 @@ CONFIG_MODULE_SRCVERSION_ALL=y # CONFIG_MODULE_SIG_SHA512 is not set # CONFIG_MODULE_COMPRESS is not set CONFIG_MODULES_TREE_LOOKUP=y -CONFIG_STOP_MACHINE=y CONFIG_BLOCK=y CONFIG_BLK_DEV_BSG=y CONFIG_BLK_DEV_BSGLIB=y @@ -388,7 +387,7 @@ CONFIG_FREEZER=y # # Processor type and features # -CONFIG_ZONE_DMA=y +# CONFIG_ZONE_DMA is not set CONFIG_SMP=y CONFIG_X86_FEATURE_NAMES=y CONFIG_X86_X2APIC=y @@ -400,7 +399,7 @@ CONFIG_X86_NUMACHIP=y # CONFIG_X86_GOLDFISH is not set CONFIG_X86_INTEL_LPSS=y CONFIG_X86_AMD_PLATFORM_DEVICE=y -CONFIG_IOSF_MBI=m +CONFIG_IOSF_MBI=y CONFIG_IOSF_MBI_DEBUG=y CONFIG_X86_SUPPORTS_MEMORY_FAILURE=y CONFIG_SCHED_OMIT_FRAME_POINTER=y @@ -469,9 +468,6 @@ CONFIG_MICROCODE=y CONFIG_MICROCODE_INTEL=y CONFIG_MICROCODE_AMD=y CONFIG_MICROCODE_OLD_INTERFACE=y -CONFIG_MICROCODE_INTEL_EARLY=y -CONFIG_MICROCODE_AMD_EARLY=y -CONFIG_MICROCODE_EARLY=y CONFIG_X86_MSR=m CONFIG_X86_CPUID=m CONFIG_ARCH_PHYS_ADDR_T_64BIT=y @@ -507,7 +503,6 @@ CONFIG_HAVE_BOOTMEM_INFO_NODE=y CONFIG_MEMORY_HOTPLUG=y CONFIG_MEMORY_HOTPLUG_SPARSE=y CONFIG_MEMORY_HOTREMOVE=y -CONFIG_PAGEFLAGS_EXTENDED=y CONFIG_SPLIT_PTLOCK_CPUS=4 CONFIG_ARCH_ENABLE_SPLIT_PMD_PTLOCK=y CONFIG_MEMORY_BALLOON=y @@ -516,8 +511,7 @@ CONFIG_COMPACTION=y CONFIG_MIGRATION=y CONFIG_ARCH_ENABLE_HUGEPAGE_MIGRATION=y CONFIG_PHYS_ADDR_T_64BIT=y -CONFIG_ZONE_DMA_FLAG=1 -CONFIG_BOUNCE=y +CONFIG_ZONE_DMA_FLAG=0 CONFIG_VIRT_TO_BUS=y CONFIG_MMU_NOTIFIER=y CONFIG_KSM=y @@ -545,6 +539,7 @@ CONFIG_GENERIC_EARLY_IOREMAP=y CONFIG_ARCH_SUPPORTS_DEFERRED_STRUCT_PAGE_INIT=y # CONFIG_DEFERRED_STRUCT_PAGE_INIT is not set CONFIG_IDLE_PAGE_TRACKING=y +CONFIG_ZONE_DEVICE=y CONFIG_FRAME_VECTOR=y CONFIG_X86_PMEM_LEGACY_DEVICE=y CONFIG_X86_PMEM_LEGACY=y @@ -586,6 +581,9 @@ CONFIG_HOTPLUG_CPU=y # CONFIG_BOOTPARAM_HOTPLUG_CPU0 is not set # CONFIG_DEBUG_HOTPLUG_CPU0 is not set # CONFIG_COMPAT_VDSO is not set +# CONFIG_LEGACY_VSYSCALL_NATIVE is not set +CONFIG_LEGACY_VSYSCALL_EMULATE=y +# CONFIG_LEGACY_VSYSCALL_NONE is not set # CONFIG_CMDLINE_BOOL is not set CONFIG_MODIFY_LDT_SYSCALL=y CONFIG_HAVE_LIVEPATCH=y @@ -624,6 +622,7 @@ CONFIG_ACPI=y CONFIG_ACPI_LEGACY_TABLES_LOOKUP=y CONFIG_ARCH_MIGHT_HAVE_ACPI_PDC=y CONFIG_ACPI_SYSTEM_POWER_STATES_SUPPORT=y +# CONFIG_ACPI_DEBUGGER is not set CONFIG_ACPI_SLEEP=y # CONFIG_ACPI_PROCFS_POWER is not set CONFIG_ACPI_REV_OVERRIDE_POSSIBLE=y @@ -967,7 +966,7 @@ CONFIG_NF_CONNTRACK_TFTP=m CONFIG_NF_CT_NETLINK=m CONFIG_NF_CT_NETLINK_TIMEOUT=m CONFIG_NF_CT_NETLINK_HELPER=m -CONFIG_NETFILTER_NETLINK_QUEUE_CT=y +CONFIG_NETFILTER_NETLINK_GLUE_CT=y CONFIG_NF_NAT=m CONFIG_NF_NAT_NEEDED=y CONFIG_NF_NAT_PROTO_DCCP=m @@ -1332,6 +1331,7 @@ CONFIG_6LOWPAN_NHC_MOBILITY=m CONFIG_6LOWPAN_NHC_ROUTING=m CONFIG_6LOWPAN_NHC_UDP=m CONFIG_IEEE802154=m +CONFIG_IEEE802154_NL802154_EXPERIMENTAL=y CONFIG_IEEE802154_SOCKET=m CONFIG_IEEE802154_6LOWPAN=m CONFIG_MAC802154=m @@ -1430,6 +1430,7 @@ CONFIG_MPLS_ROUTING=m CONFIG_MPLS_IPTUNNEL=m CONFIG_HSR=m # CONFIG_NET_SWITCHDEV is not set +CONFIG_NET_L3_MASTER_DEV=y CONFIG_RPS=y CONFIG_RFS_ACCEL=y CONFIG_XPS=y @@ -1636,6 +1637,7 @@ CONFIG_CFG80211=m CONFIG_CFG80211_DEFAULT_PS=y CONFIG_CFG80211_DEBUGFS=y # CONFIG_CFG80211_INTERNAL_REGDB is not set +CONFIG_CFG80211_CRDA_SUPPORT=y CONFIG_CFG80211_WEXT=y CONFIG_CFG80211_WEXT_EXPORT=y CONFIG_LIB80211=m @@ -1677,7 +1679,7 @@ CONFIG_CEPH_LIB_USE_DNS_RESOLVER=y CONFIG_NFC=m CONFIG_NFC_DIGITAL=m CONFIG_NFC_NCI=m -CONFIG_NFC_NCI_SPI=y +CONFIG_NFC_NCI_SPI=m CONFIG_NFC_NCI_UART=m CONFIG_NFC_HCI=m CONFIG_NFC_SHDLC=y @@ -1691,6 +1693,8 @@ CONFIG_NFC_TRF7970A=m CONFIG_NFC_MEI_PHY=m CONFIG_NFC_SIM=m CONFIG_NFC_PORT100=m +CONFIG_NFC_FDP=m +CONFIG_NFC_FDP_I2C=m CONFIG_NFC_PN544=m CONFIG_NFC_PN544_I2C=m CONFIG_NFC_PN544_MEI=m @@ -1700,6 +1704,8 @@ CONFIG_NFC_MICROREAD_MEI=m CONFIG_NFC_MRVL=m CONFIG_NFC_MRVL_USB=m CONFIG_NFC_MRVL_UART=m +CONFIG_NFC_MRVL_I2C=m +CONFIG_NFC_MRVL_SPI=m CONFIG_NFC_ST21NFCA=m CONFIG_NFC_ST21NFCA_I2C=m CONFIG_NFC_ST_NCI=m @@ -1957,7 +1963,6 @@ CONFIG_BLK_DEV_CRYPTOLOOP=m CONFIG_BLK_DEV_DRBD=m # CONFIG_DRBD_FAULT_INJECTION is not set CONFIG_BLK_DEV_NBD=m -CONFIG_BLK_DEV_NVME=m CONFIG_BLK_DEV_SKD=m CONFIG_BLK_DEV_OSD=m CONFIG_BLK_DEV_SX8=m @@ -1975,6 +1980,7 @@ CONFIG_VIRTIO_BLK=y # CONFIG_BLK_DEV_HD is not set CONFIG_BLK_DEV_RBD=m CONFIG_BLK_DEV_RSXX=m +CONFIG_BLK_DEV_NVME=m # # Misc devices @@ -2064,6 +2070,11 @@ CONFIG_INTEL_MIC_CARD=m # SCIF Driver # CONFIG_SCIF=m + +# +# Intel MIC Coprocessor State Management (COSM) Drivers +# +CONFIG_MIC_COSM=m CONFIG_GENWQE=m CONFIG_GENWQE_PLATFORM_ERROR_RECOVERY=0 CONFIG_ECHO=m @@ -2151,12 +2162,10 @@ CONFIG_MEGARAID_MM=m CONFIG_MEGARAID_MAILBOX=m CONFIG_MEGARAID_LEGACY=m CONFIG_MEGARAID_SAS=m -CONFIG_SCSI_MPT2SAS=m -CONFIG_SCSI_MPT2SAS_MAX_SGE=128 -# CONFIG_SCSI_MPT2SAS_LOGGING is not set CONFIG_SCSI_MPT3SAS=m +CONFIG_SCSI_MPT2SAS_MAX_SGE=128 CONFIG_SCSI_MPT3SAS_MAX_SGE=128 -# CONFIG_SCSI_MPT3SAS_LOGGING is not set +CONFIG_SCSI_MPT2SAS=m CONFIG_SCSI_UFSHCD=m CONFIG_SCSI_UFSHCD_PCI=m CONFIG_SCSI_UFSHCD_PLATFORM=m @@ -2511,6 +2520,8 @@ CONFIG_ATL1=m CONFIG_ATL1E=m CONFIG_ATL1C=m CONFIG_ALX=m +CONFIG_NET_VENDOR_AURORA=y +CONFIG_AURORA_NB8800=m CONFIG_NET_CADENCE=y CONFIG_MACB=m CONFIG_NET_VENDOR_BROADCOM=y @@ -2525,6 +2536,8 @@ CONFIG_TIGON3=m CONFIG_BNX2X=m CONFIG_BNX2X_SRIOV=y CONFIG_BNX2X_VXLAN=y +CONFIG_BNXT=m +CONFIG_BNXT_SRIOV=y CONFIG_NET_VENDOR_BROCADE=y CONFIG_BNA=m CONFIG_NET_VENDOR_CAVIUM=y @@ -2597,7 +2610,6 @@ CONFIG_I40EVF=m CONFIG_FM10K=m CONFIG_FM10K_VXLAN=y CONFIG_NET_VENDOR_I825XX=y -CONFIG_IP1000=m CONFIG_JME=m CONFIG_NET_VENDOR_MARVELL=y CONFIG_MVMDIO=m @@ -2624,6 +2636,7 @@ CONFIG_KSZ884X_PCI=m CONFIG_NET_VENDOR_MICROCHIP=y CONFIG_ENC28J60=m # CONFIG_ENC28J60_WRITEVERIFY is not set +CONFIG_ENCX24J600=m CONFIG_NET_VENDOR_MYRI=y CONFIG_MYRI10GE=m CONFIG_MYRI10GE_DCA=y @@ -2651,6 +2664,8 @@ CONFIG_QLCNIC_VXLAN=y CONFIG_QLCNIC_HWMON=y CONFIG_QLGE=m CONFIG_NETXEN_NIC=m +CONFIG_QED=m +CONFIG_QEDE=m CONFIG_NET_VENDOR_QUALCOMM=y CONFIG_NET_VENDOR_REALTEK=y CONFIG_ATP=m @@ -2734,6 +2749,7 @@ CONFIG_CICADA_PHY=m CONFIG_VITESSE_PHY=m CONFIG_TERANETICS_PHY=m CONFIG_SMSC_PHY=m +CONFIG_BCM_NET_PHYLIB=m CONFIG_BROADCOM_PHY=m CONFIG_BCM7XXX_PHY=m CONFIG_BCM87XX_PHY=m @@ -2743,7 +2759,7 @@ CONFIG_NATIONAL_PHY=m CONFIG_STE10XP=m CONFIG_LSI_ET1011C_PHY=m CONFIG_MICREL_PHY=m -# CONFIG_DP83848_PHY is not set +CONFIG_DP83848_PHY=m CONFIG_DP83867_PHY=m CONFIG_MICROCHIP_PHY=m CONFIG_FIXED_PHY=y @@ -2828,10 +2844,10 @@ CONFIG_PCMCIA_WL3501=m # CONFIG_PRISM54 is not set CONFIG_USB_ZD1201=m CONFIG_USB_NET_RNDIS_WLAN=m +CONFIG_ADM8211=m CONFIG_RTL8180=m CONFIG_RTL8187=m CONFIG_RTL8187_LEDS=y -CONFIG_ADM8211=m CONFIG_MAC80211_HWSIM=m CONFIG_MWL8K=m CONFIG_ATH_COMMON=m @@ -2885,7 +2901,6 @@ CONFIG_B43_BUSES_BCMA_AND_SSB=y # CONFIG_B43_BUSES_SSB is not set CONFIG_B43_PCI_AUTOSELECT=y CONFIG_B43_PCICORE_AUTOSELECT=y -# CONFIG_B43_PCMCIA is not set # CONFIG_B43_SDIO is not set CONFIG_B43_BCMA_PIO=y CONFIG_B43_PIO=y @@ -3027,6 +3042,8 @@ CONFIG_RTLWIFI_USB=m CONFIG_RTL8192C_COMMON=m CONFIG_RTL8723_COMMON=m CONFIG_RTLBTCOEXIST=m +CONFIG_RTL8XXXU=m +CONFIG_RTL8XXXU_UNTESTED=y CONFIG_WL_TI=y CONFIG_WL1251=m CONFIG_WL1251_SPI=m @@ -3082,6 +3099,7 @@ CONFIG_SBNI=m CONFIG_IEEE802154_DRIVERS=m CONFIG_IEEE802154_FAKELB=m CONFIG_IEEE802154_AT86RF230=m +CONFIG_IEEE802154_AT86RF230_DEBUGFS=y CONFIG_IEEE802154_MRF24J40=m CONFIG_IEEE802154_CC2520=m CONFIG_IEEE802154_ATUSB=m @@ -3221,6 +3239,10 @@ CONFIG_MISDN_NETJET=m CONFIG_MISDN_IPAC=m CONFIG_MISDN_ISAR=m CONFIG_ISDN_HDLC=m +CONFIG_NVM=y +# CONFIG_NVM_DEBUG is not set +CONFIG_NVM_GENNVM=m +CONFIG_NVM_RRPC=m # # Input device support @@ -3357,6 +3379,7 @@ CONFIG_TOUCHSCREEN_DA9052=m CONFIG_TOUCHSCREEN_DYNAPRO=m CONFIG_TOUCHSCREEN_HAMPSHIRE=m CONFIG_TOUCHSCREEN_EETI=m +CONFIG_TOUCHSCREEN_FT6236=m CONFIG_TOUCHSCREEN_FUJITSU=m CONFIG_TOUCHSCREEN_GOODIX=m CONFIG_TOUCHSCREEN_ILI210X=m @@ -3406,6 +3429,8 @@ CONFIG_TOUCHSCREEN_USB_NEXIO=y CONFIG_TOUCHSCREEN_USB_EASYTOUCH=y CONFIG_TOUCHSCREEN_TOUCHIT213=m CONFIG_TOUCHSCREEN_TSC_SERIO=m +CONFIG_TOUCHSCREEN_TSC200X_CORE=m +CONFIG_TOUCHSCREEN_TSC2004=m CONFIG_TOUCHSCREEN_TSC2005=m CONFIG_TOUCHSCREEN_TSC2007=m CONFIG_TOUCHSCREEN_PCAP=m @@ -3414,6 +3439,7 @@ CONFIG_TOUCHSCREEN_SUR40=m CONFIG_TOUCHSCREEN_SX8654=m CONFIG_TOUCHSCREEN_TPS6507X=m CONFIG_TOUCHSCREEN_ZFORCE=m +CONFIG_TOUCHSCREEN_ROHM_BU21023=m CONFIG_INPUT_MISC=y CONFIG_INPUT_88PM860X_ONKEY=m CONFIG_INPUT_88PM80X_ONKEY=m @@ -3489,6 +3515,7 @@ CONFIG_SERIO_ALTERA_PS2=m CONFIG_SERIO_PS2MULT=m CONFIG_SERIO_ARC_PS2=m CONFIG_HYPERV_KEYBOARD=m +CONFIG_USERIO=m CONFIG_GAMEPORT=m CONFIG_GAMEPORT_NS558=m CONFIG_GAMEPORT_L4=m @@ -3545,8 +3572,11 @@ CONFIG_SERIAL_8250_MANY_PORTS=y CONFIG_SERIAL_8250_SHARE_IRQ=y # CONFIG_SERIAL_8250_DETECT_IRQ is not set CONFIG_SERIAL_8250_RSA=y +# CONFIG_SERIAL_8250_FSL is not set CONFIG_SERIAL_8250_DW=m +CONFIG_SERIAL_8250_RT288X=y CONFIG_SERIAL_8250_FINTEK=m +CONFIG_SERIAL_8250_MID=m # # Non-8250 serial port support @@ -3696,6 +3726,7 @@ CONFIG_I2C_CBUS_GPIO=m CONFIG_I2C_DESIGNWARE_CORE=m CONFIG_I2C_DESIGNWARE_PLATFORM=m CONFIG_I2C_DESIGNWARE_PCI=m +CONFIG_I2C_DESIGNWARE_BAYTRAIL=y CONFIG_I2C_EMEV2=m CONFIG_I2C_GPIO=m CONFIG_I2C_KEMPLD=m @@ -3810,6 +3841,7 @@ CONFIG_PINCTRL_AMD=y CONFIG_PINCTRL_BAYTRAIL=y CONFIG_PINCTRL_CHERRYVIEW=m CONFIG_PINCTRL_INTEL=m +CONFIG_PINCTRL_BROXTON=m CONFIG_PINCTRL_SUNRISEPOINT=m CONFIG_ARCH_WANT_OPTIONAL_GPIOLIB=y CONFIG_GPIOLIB=y @@ -3824,15 +3856,22 @@ CONFIG_GPIO_MAX730X=m # # Memory mapped GPIO drivers # +CONFIG_GPIO_AMDPT=m CONFIG_GPIO_DWAPB=m -CONFIG_GPIO_F7188X=m CONFIG_GPIO_GENERIC_PLATFORM=m CONFIG_GPIO_ICH=m -CONFIG_GPIO_IT8761E=m CONFIG_GPIO_LYNXPOINT=y +CONFIG_GPIO_VX855=m +CONFIG_GPIO_ZX=y + +# +# Port-mapped I/O GPIO drivers +# +CONFIG_GPIO_104_IDIO_16=m +CONFIG_GPIO_F7188X=m +CONFIG_GPIO_IT87=m CONFIG_GPIO_SCH=m CONFIG_GPIO_SCH311X=m -CONFIG_GPIO_VX855=m # # I2C GPIO expanders @@ -3880,9 +3919,12 @@ CONFIG_GPIO_RDC321X=m # SPI GPIO expanders # CONFIG_GPIO_MAX7301=m -CONFIG_GPIO_MCP23S08=m CONFIG_GPIO_MC33880=m -CONFIG_GPIO_ZX=y + +# +# SPI or I2C GPIO expanders +# +CONFIG_GPIO_MCP23S08=m # # USB GPIO expanders @@ -3933,12 +3975,13 @@ CONFIG_BATTERY_DS2780=m CONFIG_BATTERY_DS2781=m CONFIG_BATTERY_DS2782=m CONFIG_BATTERY_SBS=m -CONFIG_BATTERY_BQ27x00=m -CONFIG_BATTERY_BQ27X00_I2C=y -CONFIG_BATTERY_BQ27X00_PLATFORM=y +CONFIG_BATTERY_BQ27XXX=m +CONFIG_BATTERY_BQ27XXX_I2C=y +CONFIG_BATTERY_BQ27XXX_PLATFORM=y CONFIG_BATTERY_DA9030=m CONFIG_BATTERY_DA9052=m CONFIG_CHARGER_DA9150=m +CONFIG_BATTERY_DA9150=m CONFIG_AXP288_CHARGER=m CONFIG_AXP288_FUEL_GAUGE=m CONFIG_BATTERY_MAX17040=m @@ -3965,9 +4008,11 @@ CONFIG_CHARGER_BQ24735=m CONFIG_CHARGER_BQ25890=m CONFIG_CHARGER_SMB347=m CONFIG_CHARGER_TPS65090=m +CONFIG_CHARGER_TPS65217=m CONFIG_BATTERY_GAUGE_LTC2941=m CONFIG_BATTERY_RT5033=m CONFIG_CHARGER_RT9455=m +CONFIG_AXP20X_POWER=m CONFIG_POWER_RESET=y CONFIG_POWER_RESET_RESTART=y CONFIG_POWER_AVS=y @@ -4045,6 +4090,7 @@ CONFIG_SENSORS_MAX6639=m CONFIG_SENSORS_MAX6642=m CONFIG_SENSORS_MAX6650=m CONFIG_SENSORS_MAX6697=m +CONFIG_SENSORS_MAX31790=m CONFIG_SENSORS_HTU21=m CONFIG_SENSORS_MCP3021=m CONFIG_SENSORS_MENF21BMC_HWMON=m @@ -4213,6 +4259,7 @@ CONFIG_W83877F_WDT=m CONFIG_W83977F_WDT=m CONFIG_MACHZ_WDT=m CONFIG_SBC_EPX_C3_WATCHDOG=m +CONFIG_BCM7038_WDT=m CONFIG_MEN_A21_WDT=m CONFIG_XEN_WDT=m @@ -4241,6 +4288,7 @@ CONFIG_SSB_PCMCIAHOST_POSSIBLE=y # CONFIG_SSB_PCMCIAHOST is not set CONFIG_SSB_SDIOHOST_POSSIBLE=y CONFIG_SSB_SDIOHOST=y +CONFIG_SSB_HOST_SOC=y # CONFIG_SSB_SILENT is not set # CONFIG_SSB_DEBUG is not set CONFIG_SSB_DRIVER_PCICORE_POSSIBLE=y @@ -4767,6 +4815,7 @@ CONFIG_VIDEO_MEM2MEM_DEINTERLACE=m CONFIG_VIDEO_SH_VEU=m CONFIG_V4L_TEST_DRIVERS=y CONFIG_VIDEO_VIVID=m +CONFIG_VIDEO_VIVID_MAX_DEVS=64 CONFIG_VIDEO_VIM2M=m CONFIG_DVB_PLATFORM_DRIVERS=y @@ -5147,7 +5196,7 @@ CONFIG_DRM_RADEON=m # CONFIG_DRM_RADEON_USERPTR is not set # CONFIG_DRM_RADEON_UMS is not set CONFIG_DRM_AMDGPU=m -CONFIG_DRM_AMDGPU_CIK=y +# CONFIG_DRM_AMDGPU_CIK is not set CONFIG_DRM_AMDGPU_USERPTR=y CONFIG_DRM_NOUVEAU=m CONFIG_NOUVEAU_DEBUG=5 @@ -5284,6 +5333,7 @@ CONFIG_FB_CARMINE_DRAM_EVAL=y CONFIG_FB_SM501=m CONFIG_FB_SMSCUFX=m CONFIG_FB_UDL=m +CONFIG_FB_IBM_GXT4500=m # CONFIG_FB_VIRTUAL is not set CONFIG_XEN_FBDEV_FRONTEND=m CONFIG_FB_METRONOME=m @@ -5375,7 +5425,9 @@ CONFIG_SND_SEQUENCER=m CONFIG_SND_SEQ_DUMMY=m CONFIG_SND_OSSEMUL=y CONFIG_SND_MIXER_OSS=m -# CONFIG_SND_PCM_OSS is not set +CONFIG_SND_PCM_OSS=m +CONFIG_SND_PCM_OSS_PLUGINS=y +CONFIG_SND_PCM_TIMER=y # CONFIG_SND_SEQUENCER_OSS is not set CONFIG_SND_HRTIMER=m CONFIG_SND_SEQ_HRTIMER_DEFAULT=y @@ -5392,7 +5444,7 @@ CONFIG_SND_RAWMIDI_SEQ=m CONFIG_SND_OPL3_LIB_SEQ=m # CONFIG_SND_OPL4_LIB_SEQ is not set # CONFIG_SND_SBAWE_SEQ is not set -CONFIG_SND_EMU10K1_SEQ=m +# CONFIG_SND_EMU10K1_SEQ is not set CONFIG_SND_MPU401_UART=m CONFIG_SND_OPL3_LIB=m CONFIG_SND_VX_LIB=m @@ -5412,9 +5464,7 @@ CONFIG_SND_AC97_POWER_SAVE_DEFAULT=0 CONFIG_SND_SB_COMMON=m CONFIG_SND_PCI=y CONFIG_SND_AD1889=m -CONFIG_SND_ALS300=m CONFIG_SND_ALS4000=m -CONFIG_SND_ALI5451=m CONFIG_SND_ASIHPI=m CONFIG_SND_ATIIXP=m CONFIG_SND_ATIIXP_MODEM=m @@ -5422,7 +5472,6 @@ CONFIG_SND_AU8810=m CONFIG_SND_AU8820=m CONFIG_SND_AU8830=m CONFIG_SND_AW2=m -CONFIG_SND_AZT3328=m CONFIG_SND_BT87X=m # CONFIG_SND_BT87X_OVERCLOCK is not set CONFIG_SND_CA0106=m @@ -5447,27 +5496,18 @@ CONFIG_SND_INDIGOIO=m CONFIG_SND_INDIGODJ=m CONFIG_SND_INDIGOIOX=m CONFIG_SND_INDIGODJX=m -CONFIG_SND_EMU10K1=m -CONFIG_SND_EMU10K1X=m CONFIG_SND_ENS1370=m CONFIG_SND_ENS1371=m -CONFIG_SND_ES1938=m -CONFIG_SND_ES1968=m -CONFIG_SND_ES1968_INPUT=y -CONFIG_SND_ES1968_RADIO=y CONFIG_SND_FM801=m CONFIG_SND_FM801_TEA575X_BOOL=y CONFIG_SND_HDSP=m CONFIG_SND_HDSPM=m -CONFIG_SND_ICE1712=m CONFIG_SND_ICE1724=m CONFIG_SND_INTEL8X0=m CONFIG_SND_INTEL8X0M=m CONFIG_SND_KORG1212=m CONFIG_SND_LOLA=m CONFIG_SND_LX6464ES=m -CONFIG_SND_MAESTRO3=m -CONFIG_SND_MAESTRO3_INPUT=y CONFIG_SND_MIXART=m CONFIG_SND_NM256=m CONFIG_SND_PCXHR=m @@ -5475,8 +5515,6 @@ CONFIG_SND_RIPTIDE=m CONFIG_SND_RME32=m CONFIG_SND_RME96=m CONFIG_SND_RME9652=m -CONFIG_SND_SONICVIBES=m -CONFIG_SND_TRIDENT=m CONFIG_SND_VIA82XX=m CONFIG_SND_VIA82XX_MODEM=m CONFIG_SND_VIRTUOSO=m @@ -5510,6 +5548,7 @@ CONFIG_SND_HDA_POWER_SAVE_DEFAULT=0 CONFIG_SND_HDA_CORE=m CONFIG_SND_HDA_DSP_LOADER=y CONFIG_SND_HDA_I915=y +CONFIG_SND_HDA_EXT_CORE=m CONFIG_SND_HDA_PREALLOC_SIZE=64 CONFIG_SND_SPI=y CONFIG_SND_USB=y @@ -5535,12 +5574,16 @@ CONFIG_SND_ISIGHT=m CONFIG_SND_SCS1X=m CONFIG_SND_FIREWORKS=m CONFIG_SND_BEBOB=m +CONFIG_SND_FIREWIRE_DIGI00X=m +CONFIG_SND_FIREWIRE_TASCAM=m CONFIG_SND_PCMCIA=y CONFIG_SND_VXPOCKET=m CONFIG_SND_PDAUDIOCF=m CONFIG_SND_SOC=m CONFIG_SND_SOC_AC97_BUS=y CONFIG_SND_SOC_GENERIC_DMAENGINE_PCM=y +CONFIG_SND_SOC_COMPRESS=y +CONFIG_SND_SOC_TOPOLOGY=y CONFIG_SND_ATMEL_SOC=m CONFIG_SND_DESIGNWARE_I2S=m @@ -5572,6 +5615,13 @@ CONFIG_SND_SOC_INTEL_BYTCR_RT5640_MACH=m CONFIG_SND_SOC_INTEL_CHT_BSW_RT5672_MACH=m CONFIG_SND_SOC_INTEL_CHT_BSW_RT5645_MACH=m CONFIG_SND_SOC_INTEL_CHT_BSW_MAX98090_TI_MACH=m +CONFIG_SND_SOC_INTEL_SKYLAKE=m +CONFIG_SND_SOC_INTEL_SKL_RT286_MACH=m + +# +# Allwinner SoC Audio support +# +CONFIG_SND_SUN4I_CODEC=m CONFIG_SND_SOC_XTFPGA_I2S=m CONFIG_SND_SOC_I2C_AND_SPI=m @@ -5582,6 +5632,7 @@ CONFIG_SND_SOC_AC97_CODEC=m CONFIG_SND_SOC_ADAU1701=m CONFIG_SND_SOC_AK4104=m CONFIG_SND_SOC_AK4554=m +CONFIG_SND_SOC_AK4613=m CONFIG_SND_SOC_AK4642=m CONFIG_SND_SOC_AK5386=m CONFIG_SND_SOC_ALC5623=m @@ -5599,7 +5650,7 @@ CONFIG_SND_SOC_CS4271_SPI=m CONFIG_SND_SOC_CS42XX8=m CONFIG_SND_SOC_CS42XX8_I2C=m CONFIG_SND_SOC_CS4349=m -CONFIG_SND_SOC_HDMI_CODEC=m +CONFIG_SND_SOC_DMIC=m CONFIG_SND_SOC_ES8328=m CONFIG_SND_SOC_GTM601=m CONFIG_SND_SOC_MAX98090=m @@ -5684,6 +5735,7 @@ CONFIG_HID_BELKIN=m CONFIG_HID_BETOP_FF=m CONFIG_HID_CHERRY=m CONFIG_HID_CHICONY=m +CONFIG_HID_CORSAIR=m CONFIG_HID_PRODIKEYS=m CONFIG_HID_CP2112=m CONFIG_HID_CYPRESS=m @@ -5694,6 +5746,7 @@ CONFIG_HID_ELECOM=m CONFIG_HID_ELO=m CONFIG_HID_EZKEY=m CONFIG_HID_GEMBIRD=m +CONFIG_HID_GFRM=m CONFIG_HID_HOLTEK=m CONFIG_HOLTEK_FF=y CONFIG_HID_GT683R=m @@ -5792,7 +5845,6 @@ CONFIG_USB_DYNAMIC_MINORS=y # CONFIG_USB_OTG is not set # CONFIG_USB_OTG_WHITELIST is not set # CONFIG_USB_OTG_BLACKLIST_HUB is not set -# CONFIG_USB_OTG_FSM is not set CONFIG_USB_ULPI_BUS=m CONFIG_USB_MON=m CONFIG_USB_WUSB=m @@ -5814,7 +5866,6 @@ CONFIG_USB_EHCI_HCD_PLATFORM=y CONFIG_USB_OXU210HP_HCD=m CONFIG_USB_ISP116X_HCD=m CONFIG_USB_ISP1362_HCD=m -CONFIG_USB_FUSBH200_HCD=m CONFIG_USB_FOTG210_HCD=m CONFIG_USB_MAX3421_HCD=m CONFIG_USB_OHCI_HCD=y @@ -6136,7 +6187,6 @@ CONFIG_UWB_WHCI=m CONFIG_UWB_I1480U=m CONFIG_MMC=y # CONFIG_MMC_DEBUG is not set -# CONFIG_MMC_CLKGATE is not set # # MMC/SD/SDIO Card Drivers @@ -6201,10 +6251,11 @@ CONFIG_LEDS_PCA9532=m CONFIG_LEDS_PCA9532_GPIO=y CONFIG_LEDS_GPIO=m CONFIG_LEDS_LP3944=m -# CONFIG_LEDS_LP5521 is not set -# CONFIG_LEDS_LP5523 is not set -# CONFIG_LEDS_LP5562 is not set -# CONFIG_LEDS_LP8501 is not set +CONFIG_LEDS_LP55XX_COMMON=m +CONFIG_LEDS_LP5521=m +CONFIG_LEDS_LP5523=m +CONFIG_LEDS_LP5562=m +CONFIG_LEDS_LP8501=m CONFIG_LEDS_LP8788=m CONFIG_LEDS_LP8860=m CONFIG_LEDS_CLEVO_MAIL=m @@ -6359,6 +6410,7 @@ CONFIG_RTC_DRV_RX8581=m CONFIG_RTC_DRV_RX8025=m CONFIG_RTC_DRV_EM3027=m CONFIG_RTC_DRV_RV3029C2=m +CONFIG_RTC_DRV_RV8803=m CONFIG_RTC_DRV_S5M=m # @@ -6431,14 +6483,13 @@ CONFIG_DMADEVICES=y CONFIG_DMA_ENGINE=y CONFIG_DMA_VIRTUAL_CHANNELS=m CONFIG_DMA_ACPI=y -CONFIG_IDMA64=m +CONFIG_INTEL_IDMA64=m CONFIG_INTEL_IOATDMA=m CONFIG_INTEL_MIC_X100_DMA=m CONFIG_DW_DMAC_CORE=m CONFIG_DW_DMAC=m CONFIG_DW_DMAC_PCI=m CONFIG_HSU_DMA=m -CONFIG_HSU_DMA_PCI=m # # DMA Clients @@ -6470,6 +6521,7 @@ CONFIG_VFIO_PCI=m CONFIG_VFIO_PCI_VGA=y CONFIG_VFIO_PCI_MMAP=y CONFIG_VFIO_PCI_INTX=y +CONFIG_IRQ_BYPASS_MANAGER=m CONFIG_VIRT_DRIVERS=y CONFIG_VIRTIO=y @@ -6559,7 +6611,6 @@ CONFIG_COMEDI_DT2815=m CONFIG_COMEDI_DT2817=m CONFIG_COMEDI_DT282X=m CONFIG_COMEDI_DMM32AT=m -CONFIG_COMEDI_UNIOXX5=m CONFIG_COMEDI_FL512=m CONFIG_COMEDI_AIO_AIO12_8=m CONFIG_COMEDI_AIO_IIRO_16=m @@ -6778,9 +6829,6 @@ CONFIG_IIO_SIMPLE_DUMMY=m # CONFIG_IIO_SIMPLE_DUMMY_BUFFER is not set CONFIG_FB_SM750=m CONFIG_FB_XGI=m -CONFIG_FT1000=m -CONFIG_FT1000_USB=m -CONFIG_FT1000_PCMCIA=m # # Speakup console speech @@ -6812,7 +6860,7 @@ CONFIG_LIRC_SERIAL=m CONFIG_LIRC_SERIAL_TRANSMITTER=y CONFIG_LIRC_SIR=m CONFIG_LIRC_ZILOG=m -CONFIG_STAGING_RDMA=y +CONFIG_STAGING_RDMA=m CONFIG_INFINIBAND_AMSO1100=m # CONFIG_INFINIBAND_AMSO1100_DEBUG is not set CONFIG_INFINIBAND_HFI1=m @@ -6838,14 +6886,7 @@ CONFIG_FWTTY_MAX_TOTAL_PORTS=64 CONFIG_FWTTY_MAX_CARD_PORTS=32 CONFIG_MTD_SPINAND_MT29F=m CONFIG_MTD_SPINAND_ONDIEECC=y -CONFIG_LUSTRE_FS=m -CONFIG_LUSTRE_OBD_MAX_IOCTL_BUFFER=8192 -# CONFIG_LUSTRE_DEBUG_EXPENSIVE_CHECK is not set -CONFIG_LUSTRE_LLITE_LLOOP=m -CONFIG_LNET=m -CONFIG_LNET_MAX_PAYLOAD=1048576 -CONFIG_LNET_SELFTEST=m -CONFIG_LNET_XPRT_IB=m +# CONFIG_LUSTRE_FS is not set CONFIG_DGNC=m CONFIG_DGAP=m CONFIG_GS_FPGABOOT=m @@ -6853,6 +6894,8 @@ CONFIG_CRYPTO_SKEIN=y CONFIG_UNISYSSPAR=y CONFIG_UNISYS_VISORBUS=m CONFIG_UNISYS_VISORNIC=m +CONFIG_UNISYS_VISORINPUT=m +CONFIG_UNISYS_VISORHBA=m CONFIG_FB_TFT=m CONFIG_FB_TFT_AGM1264K_FL=m CONFIG_FB_TFT_BD663474=m @@ -6876,6 +6919,7 @@ CONFIG_FB_TFT_SSD1306=m CONFIG_FB_TFT_SSD1331=m CONFIG_FB_TFT_SSD1351=m CONFIG_FB_TFT_ST7735R=m +CONFIG_FB_TFT_ST7789V=m CONFIG_FB_TFT_TINYLCD=m CONFIG_FB_TFT_TLS8204=m CONFIG_FB_TFT_UC1611=m @@ -6884,6 +6928,7 @@ CONFIG_FB_TFT_UPD161704=m CONFIG_FB_TFT_WATTEROTT=m CONFIG_FB_FLEX=m CONFIG_FB_TFT_FBTFT_DEVICE=m +# CONFIG_WILC1000_DRIVER is not set CONFIG_MOST=m CONFIG_MOSTCORE=m CONFIG_AIM_CDEV=m @@ -6935,6 +6980,7 @@ CONFIG_TOPSTAR_LAPTOP=m CONFIG_ACPI_TOSHIBA=m CONFIG_TOSHIBA_BT_RFKILL=m CONFIG_TOSHIBA_HAPS=m +CONFIG_TOSHIBA_WMI=m CONFIG_ACPI_CMPC=m CONFIG_INTEL_IPS=m CONFIG_IBM_RTL=m @@ -7000,6 +7046,7 @@ CONFIG_AMD_IOMMU_STATS=y CONFIG_AMD_IOMMU_V2=m CONFIG_DMAR_TABLE=y CONFIG_INTEL_IOMMU=y +CONFIG_INTEL_IOMMU_SVM=y # CONFIG_INTEL_IOMMU_DEFAULT_ON is not set CONFIG_INTEL_IOMMU_FLOPPY_WA=y CONFIG_IRQ_REMAP=y @@ -7053,17 +7100,20 @@ CONFIG_EXTCON_USB_GPIO=m CONFIG_MEMORY=y CONFIG_IIO=m CONFIG_IIO_BUFFER=y -CONFIG_IIO_BUFFER_CB=y +CONFIG_IIO_BUFFER_CB=m CONFIG_IIO_KFIFO_BUF=m CONFIG_IIO_TRIGGERED_BUFFER=m CONFIG_IIO_TRIGGER=y CONFIG_IIO_CONSUMERS_PER_TRIGGER=2 +CONFIG_IIO_TRIGGERED_EVENT=m # # Accelerometers # CONFIG_BMA180=m CONFIG_BMC150_ACCEL=m +CONFIG_BMC150_ACCEL_I2C=m +CONFIG_BMC150_ACCEL_SPI=m CONFIG_HID_SENSOR_ACCEL_3D=m CONFIG_IIO_ST_ACCEL_3AXIS=m CONFIG_IIO_ST_ACCEL_I2C_3AXIS=m @@ -7074,6 +7124,7 @@ CONFIG_MMA8452=m CONFIG_MMA9551_CORE=m CONFIG_MMA9551=m CONFIG_MMA9553=m +CONFIG_MXC4005=m CONFIG_STK8312=m CONFIG_STK8BA50=m @@ -7091,8 +7142,9 @@ CONFIG_AD7887=m CONFIG_AD7923=m CONFIG_AD799X=m CONFIG_AXP288_ADC=m -CONFIG_DA9150_GPADC=m CONFIG_CC10001_ADC=m +CONFIG_DA9150_GPADC=m +CONFIG_HI8435=m CONFIG_LP8788_ADC=m CONFIG_MAX1027=m CONFIG_MAX1363=m @@ -7115,10 +7167,16 @@ CONFIG_VIPERBOARD_ADC=m CONFIG_AD8366=m # +# Chemical Sensors +# +CONFIG_VZ89X=m + +# # Hid Sensor IIO Common # CONFIG_HID_SENSOR_IIO_COMMON=m CONFIG_HID_SENSOR_IIO_TRIGGER=m +CONFIG_IIO_MS_SENSORS_I2C=m # # SSP Sensor Common @@ -7173,6 +7231,8 @@ CONFIG_ADIS16136=m CONFIG_ADIS16260=m CONFIG_ADXRS450=m CONFIG_BMG160=m +CONFIG_BMG160_I2C=m +CONFIG_BMG160_SPI=m CONFIG_HID_SENSOR_GYRO_3D=m CONFIG_IIO_ST_GYRO_3AXIS=m CONFIG_IIO_ST_GYRO_I2C_3AXIS=m @@ -7183,6 +7243,8 @@ CONFIG_ITG3200=m # Humidity sensors # CONFIG_DHT11=m +CONFIG_HDC100X=m +CONFIG_HTU21=m CONFIG_SI7005=m CONFIG_SI7020=m @@ -7203,6 +7265,7 @@ CONFIG_ACPI_ALS=m CONFIG_ADJD_S311=m CONFIG_AL3320A=m CONFIG_APDS9300=m +CONFIG_APDS9960=m CONFIG_BH1750=m CONFIG_CM32181=m CONFIG_CM3232=m @@ -7223,6 +7286,7 @@ CONFIG_TCS3414=m CONFIG_TCS3472=m CONFIG_SENSORS_TSL2563=m CONFIG_TSL4531=m +CONFIG_US5182D=m CONFIG_VCNL4000=m # @@ -7230,13 +7294,13 @@ CONFIG_VCNL4000=m # CONFIG_AK8975=m CONFIG_AK09911=m +CONFIG_BMC150_MAGN=m CONFIG_MAG3110=m CONFIG_HID_SENSOR_MAGNETOMETER_3D=m CONFIG_MMC35240=m CONFIG_IIO_ST_MAGN_3AXIS=m CONFIG_IIO_ST_MAGN_I2C_3AXIS=m CONFIG_IIO_ST_MAGN_SPI_3AXIS=m -CONFIG_BMC150_MAGN=m # # Inclinometer sensors @@ -7251,6 +7315,11 @@ CONFIG_IIO_INTERRUPT_TRIGGER=m CONFIG_IIO_SYSFS_TRIGGER=m # +# Digital potentiometers +# +CONFIG_MCP4531=m + +# # Pressure sensors # CONFIG_BMP280=m @@ -7260,6 +7329,7 @@ CONFIG_MPL3115=m CONFIG_MS5611=m CONFIG_MS5611_I2C=m CONFIG_MS5611_SPI=m +CONFIG_MS5637=m CONFIG_IIO_ST_PRESS=m CONFIG_IIO_ST_PRESS_I2C=m CONFIG_IIO_ST_PRESS_SPI=m @@ -7273,6 +7343,7 @@ CONFIG_AS3935=m # # Proximity sensors # +CONFIG_LIDAR_LITE_V2=m CONFIG_SX9500=m # @@ -7280,6 +7351,8 @@ CONFIG_SX9500=m # CONFIG_MLX90614=m CONFIG_TMP006=m +CONFIG_TSYS01=m +CONFIG_TSYS02D=m CONFIG_NTB=m CONFIG_NTB_INTEL=m CONFIG_NTB_PINGPONG=m @@ -7310,6 +7383,7 @@ CONFIG_PWM_LP3943=m CONFIG_PWM_LPSS=m CONFIG_PWM_LPSS_PCI=m CONFIG_PWM_LPSS_PLATFORM=m +CONFIG_PWM_PCA9685=m CONFIG_PWM_TWL=m CONFIG_PWM_TWL_LED=m CONFIG_IPACK_BUS=m @@ -7356,7 +7430,25 @@ CONFIG_ND_BLK=m CONFIG_ND_CLAIM=y CONFIG_ND_BTT=m CONFIG_BTT=y +CONFIG_ND_PFN=m +CONFIG_NVDIMM_PFN=y CONFIG_NVMEM=m +CONFIG_STM=m +CONFIG_STM_DUMMY=m +CONFIG_STM_SOURCE_CONSOLE=m +CONFIG_INTEL_TH=m +CONFIG_INTEL_TH_PCI=m +CONFIG_INTEL_TH_GTH=m +CONFIG_INTEL_TH_STH=m +CONFIG_INTEL_TH_MSU=m +CONFIG_INTEL_TH_PTI=m +# CONFIG_INTEL_TH_DEBUG is not set + +# +# FPGA Configuration Support +# +CONFIG_FPGA=m +CONFIG_FPGA_MGR_ZYNQ_FPGA=m # # Firmware Drivers @@ -7381,6 +7473,7 @@ CONFIG_EFI_ESRT=y CONFIG_EFI_VARS_PSTORE=m # CONFIG_EFI_VARS_PSTORE_DEFAULT_DISABLE is not set CONFIG_EFI_RUNTIME_MAP=y +# CONFIG_EFI_FAKE_MEMMAP is not set CONFIG_EFI_RUNTIME_WRAPPERS=y CONFIG_UEFI_CPER=y @@ -7548,6 +7641,7 @@ CONFIG_UBIFS_FS=m # CONFIG_UBIFS_FS_ADVANCED_COMPR is not set CONFIG_UBIFS_FS_LZO=y CONFIG_UBIFS_FS_ZLIB=y +CONFIG_UBIFS_ATIME_SUPPORT=y # CONFIG_LOGFS is not set CONFIG_CRAMFS=m CONFIG_SQUASHFS=m @@ -7558,7 +7652,7 @@ CONFIG_SQUASHFS_FILE_DIRECT=y CONFIG_SQUASHFS_DECOMP_MULTI_PERCPU=y CONFIG_SQUASHFS_XATTR=y CONFIG_SQUASHFS_ZLIB=y -# CONFIG_SQUASHFS_LZ4 is not set +CONFIG_SQUASHFS_LZ4=y CONFIG_SQUASHFS_LZO=y CONFIG_SQUASHFS_XZ=y # CONFIG_SQUASHFS_4K_DEVBLK_SIZE is not set @@ -7743,6 +7837,7 @@ CONFIG_UNUSED_SYMBOLS=y CONFIG_DEBUG_FS=y # CONFIG_HEADERS_CHECK is not set # CONFIG_DEBUG_SECTION_MISMATCH is not set +CONFIG_SECTION_MISMATCH_WARN_ONLY=y CONFIG_ARCH_WANT_FRAME_POINTERS=y CONFIG_FRAME_POINTER=y # CONFIG_DEBUG_FORCE_WEAK_PER_CPU is not set @@ -7884,6 +7979,7 @@ CONFIG_MMIOTRACE=y # CONFIG_RING_BUFFER_BENCHMARK is not set # CONFIG_RING_BUFFER_STARTUP_TEST is not set # CONFIG_TRACE_ENUM_MAP_FILE is not set +CONFIG_TRACING_EVENTS_GPIO=y # # Runtime Testing @@ -7900,6 +7996,7 @@ CONFIG_ASYNC_RAID6_TEST=m CONFIG_TEST_HEXDUMP=m CONFIG_TEST_STRING_HELPERS=m CONFIG_TEST_KSTRTOX=m +CONFIG_TEST_PRINTF=m # CONFIG_TEST_RHASHTABLE is not set # CONFIG_PROVIDE_OHCI1394_DMA_INIT is not set # CONFIG_DMA_API_DEBUG is not set @@ -7925,9 +8022,12 @@ CONFIG_STRICT_DEVMEM=y CONFIG_EARLY_PRINTK=y CONFIG_EARLY_PRINTK_DBGP=y CONFIG_EARLY_PRINTK_EFI=y +# CONFIG_X86_PTDUMP_CORE is not set # CONFIG_X86_PTDUMP is not set +# CONFIG_EFI_PGT_DUMP is not set CONFIG_DEBUG_RODATA=y # CONFIG_DEBUG_RODATA_TEST is not set +# CONFIG_DEBUG_WX is not set CONFIG_DEBUG_SET_MODULE_RONX=y # CONFIG_DEBUG_NX_TEST is not set CONFIG_DOUBLEFAULT=y @@ -8081,6 +8181,7 @@ CONFIG_CRYPTO_ECB=y CONFIG_CRYPTO_LRW=m CONFIG_CRYPTO_PCBC=m CONFIG_CRYPTO_XTS=m +CONFIG_CRYPTO_KEYWRAP=m # # Hash modes @@ -8222,6 +8323,7 @@ CONFIG_HAVE_KVM_CPU_RELAX_INTERCEPT=y CONFIG_KVM_VFIO=y CONFIG_KVM_GENERIC_DIRTYLOG_READ_PROTECT=y CONFIG_KVM_COMPAT=y +CONFIG_HAVE_KVM_IRQ_BYPASS=y CONFIG_VIRTUALIZATION=y CONFIG_KVM=m CONFIG_KVM_INTEL=m diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 798b1e26d8..7250cd5002 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -211,7 +211,7 @@ for SYSTEM, or #f if there is no configuration for SYSTEM." #f))) (define-public linux-libre - (let* ((version "4.3.3") + (let* ((version "4.4") (build-phase '(lambda* (#:key system inputs #:allow-other-keys #:rest args) ;; Apply the neat patch. @@ -285,7 +285,7 @@ for SYSTEM, or #f if there is no configuration for SYSTEM." (uri (linux-libre-urls version)) (sha256 (base32 - "1z43kzs1pzwq5mkyh7zk8nq38sxlswp65824v54dzwngyc252a18")))) + "1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm")))) (build-system gnu-build-system) (supported-systems '("x86_64-linux" "i686-linux")) (native-inputs `(("perl" ,perl) @@ -1784,7 +1784,7 @@ country-specific regulations for the wireless spectrum.") (source (origin (method url-fetch) (uri (string-append - "http://dl.lm-sensors.org/lm-sensors/releases/lm_sensors-" + "ftp://ftp.netroedge.com/pub/lm-sensors/lm_sensors-" version ".tar.bz2")) (sha256 (base32 @@ -1842,7 +1842,7 @@ country-specific regulations for the wireless spectrum.") (string-append (assoc-ref inputs "coreutils") "/bin/readlink -f")))) %standard-phases)))) - (home-page "http://www.lm-sensors.org/") + (home-page "http://jdelvare.nerim.net/devel.html#lmsensors") (synopsis "Utilities to read temperature/voltage/fan sensors") (description "Lm-sensors is a hardware health monitoring package for Linux. It allows @@ -1857,7 +1857,7 @@ It works with most newer systems.") (source (origin (method url-fetch) (uri (string-append - "http://dl.lm-sensors.org/i2c-tools/releases/i2c-tools-" + "http://jdelvare.nerim.net/mirror/i2c-tools/i2c-tools-" version ".tar.bz2")) (sha256 (base32 @@ -1871,7 +1871,7 @@ It works with most newer systems.") #:phases (alist-delete 'configure %standard-phases))) (inputs `(("perl" ,perl))) - (home-page "http://www.lm-sensors.org/wiki/I2CTools") + (home-page "http://jdelvare.nerim.net/devel.html#i2ctools") (synopsis "I2C tools for Linux") (description "The i2c-tools package contains a heterogeneous set of I2C tools for diff --git a/gnu/packages/man.scm b/gnu/packages/man.scm index b11c0d149c..ab5e770b52 100644 --- a/gnu/packages/man.scm +++ b/gnu/packages/man.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014 David Thompson <dthompson2@worcester.edu> ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Alex Kost <alezost@gmail.com> -;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -129,15 +129,20 @@ the traditional flat-text whatis databases.") (define-public man-pages (package (name "man-pages") - (version "3.82") + (version "4.04") (source (origin (method url-fetch) - (uri (string-append + (uri + (list + (string-append "mirror://kernel.org/linux/docs/man-pages/man-pages-" - version ".tar.xz")) + version ".tar.xz") + (string-append + "mirror://kernel.org/linux/docs/man-pages/Archive/" + "man-pages-" version ".tar.xz"))) (sha256 (base32 - "1c8q618shf469nfp55qrwjv9630fgq5abfk946xya9hw1bfp6wjl")))) + "0v8zxq4scfixy3pjpw9ankvv5v8frv62khv4xm1jpkswyq6rbqcg")))) (build-system gnu-build-system) (arguments '(#:phases (alist-delete 'configure %standard-phases) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e2d5aa1ff4..51d9cc1ce4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -463,14 +463,14 @@ script files.") (define-public gmsh (package (name "gmsh") - (version "2.8.4") + (version "2.11.0") (source (origin (method url-fetch) (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" version "-source.tgz")) (sha256 - (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr")) + (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b")) (modules '((guix build utils))) (snippet ;; Remove non-free METIS code @@ -489,7 +489,15 @@ script files.") (arguments `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" "-DENABLE_BUILD_SHARED:BOOL=ON" - "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) + "-DENABLE_BUILD_DYNAMIC:BOOL=ON") + #:phases (modify-phases %standard-phases + (replace + 'check + (lambda _ + (zero? (system* "make" "test" + ;; Disable this test. See + ;; https://geuz.org/trac/gmsh/ticket/271 + "ARGS=-E component8_in_a_box"))))))) (home-page "http://www.geuz.org/gmsh/") (synopsis "3D finite element grid generator") (description "Gmsh is a 3D finite element grid generator with a built-in diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index b8d0c9c2ac..b85ebece3c 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -195,9 +195,9 @@ the Nix package manager.") ;; ;; Note: use a short commit id; when using the long one, the limit on socket ;; file names is exceeded while running the tests. - (let ((commit "5c36edc")) + (let ((commit "f888c0b1207a92b0d7af4dcf7fb73cecd1f0b34f")) (package (inherit guix-0.9.0) - (version (string-append "0.9.0." commit)) + (version (string-append "0.9.0." (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -205,7 +205,7 @@ the Nix package manager.") (commit commit))) (sha256 (base32 - "008fv3yj1jkxxma9vp8wzmkk3m82kgchaj9y7lpcvkqzcdhz8h7p")) + "1g9yxnqg3xl3wk6ps46mbjz5gvbj9cdci7rr7in9mqcqs26llqy1")) (file-name (string-append "guix-" version "-checkout")))) (arguments (substitute-keyword-arguments (package-arguments guix-0.9.0) diff --git a/gnu/packages/patches/asymptote-gsl2.patch b/gnu/packages/patches/asymptote-gsl2.patch new file mode 100644 index 0000000000..4f73d16d7f --- /dev/null +++ b/gnu/packages/patches/asymptote-gsl2.patch @@ -0,0 +1,33 @@ +From 71ff9e769ba5d9995b367201f0d41b7a8dedab9d Mon Sep 17 00:00:00 2001 +From: John Bowman <bowman@ualberta.ca> +Date: Sat, 14 Nov 2015 01:25:56 -0700 +Subject: [PATCH] Support GSL 2.0. + +--- + gsl.cc | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/gsl.cc b/gsl.cc +index b500557..0f81dc6 100644 +--- a/gsl.cc ++++ b/gsl.cc +@@ -27,6 +27,7 @@ + #include <gsl/gsl_rng.h> + #include <gsl/gsl_randist.h> + #include <gsl/gsl_cdf.h> ++#include <gsl/gsl_version.h> + + #include "opsymbols.h" + +@@ -1088,7 +1089,11 @@ void gen_rungsl_venv(venv &ve) + addGSLDOUBLE2Func<gsl_sf_ellint_F>(SYM(F)); + addGSLDOUBLE2Func<gsl_sf_ellint_E>(SYM(E)); + addGSLDOUBLE3Func<gsl_sf_ellint_P>(SYM(P),SYM(phi),SYM(k),SYM(n)); ++#if GSL_MAJOR_VERSION >= 2 ++ addGSLDOUBLE2Func<gsl_sf_ellint_D>(SYM(D),SYM(phi),SYM(k)); ++#else + addGSLDOUBLE3Func<gsl_sf_ellint_D>(SYM(D),SYM(phi),SYM(k),SYM(n)); ++#endif + addGSLDOUBLE2Func<gsl_sf_ellint_RC>(SYM(RC),SYM(x),SYM(y)); + addGSLDOUBLE3Func<gsl_sf_ellint_RD>(SYM(RD),SYM(x),SYM(y),SYM(z)); + addGSLDOUBLE3Func<gsl_sf_ellint_RF>(SYM(RF),SYM(x),SYM(y),SYM(z)); diff --git a/gnu/packages/patches/bedtools-32bit-compilation.patch b/gnu/packages/patches/bedtools-32bit-compilation.patch deleted file mode 100644 index bc567f3f6b..0000000000 --- a/gnu/packages/patches/bedtools-32bit-compilation.patch +++ /dev/null @@ -1,171 +0,0 @@ -Fixed in upstream, see -https://github.com/arq5x/bedtools2/issues/271 - -From b47dbefcb57f8e6c4fe397f64346338620740b71 Mon Sep 17 00:00:00 2001 -From: arq5x <arq5x@virginia.edu> -Date: Wed, 15 Jul 2015 15:15:23 -0600 -Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267 - and #271? - ---- - src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------ - src/utils/general/QuickString.cpp | 27 ++++++++++++++------------- - src/utils/general/QuickString.h | 6 +++--- - 3 files changed, 29 insertions(+), 28 deletions(-) - -diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp -index 859cfdc..0fb544b 100644 ---- a/src/coverageFile/coverageFile.cpp -+++ b/src/coverageFile/coverageFile.cpp -@@ -83,11 +83,11 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) { - float depthPct = (float)basesAtDepth / (float)_totalQueryLen; - - _finalOutput = "all\t"; -- _finalOutput.append(depth); -+ _finalOutput.append(static_cast<uint32_t>(depth)); - _finalOutput.append("\t"); -- _finalOutput.append(basesAtDepth); -+ _finalOutput.append(static_cast<uint32_t>(basesAtDepth)); - _finalOutput.append("\t"); -- _finalOutput.append(_totalQueryLen); -+ _finalOutput.append(static_cast<uint32_t>(_totalQueryLen)); - _finalOutput.append("\t"); - format(depthPct); - -@@ -138,7 +138,7 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) { - - void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - { -- _finalOutput = hits.size(); -+ _finalOutput = static_cast<uint32_t>(hits.size()); - outputMgr->printRecord(hits.getKey(), _finalOutput); - } - -@@ -147,9 +147,9 @@ void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - //loop through all bases in query, printing full record and metrics for each - const Record * queryRec = hits.getKey(); - for (size_t i= 0; i < _queryLen; i++) { -- _finalOutput = i +1; -+ _finalOutput = static_cast<uint32_t>(i+1); - _finalOutput.append("\t"); -- _finalOutput.append(_depthArray[i]); -+ _finalOutput.append(static_cast<uint32_t>(_depthArray[i])); - - outputMgr->printRecord(queryRec, _finalOutput); - } -@@ -181,11 +181,11 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - size_t numBasesAtDepth = iter->second; - float coveredBases = (float)numBasesAtDepth / (float)_queryLen; - -- _finalOutput = depth; -+ _finalOutput = static_cast<uint32_t>(depth); - _finalOutput.append("\t"); -- _finalOutput.append(numBasesAtDepth); -+ _finalOutput.append(static_cast<uint32_t>(numBasesAtDepth)); - _finalOutput.append("\t"); -- _finalOutput.append(_queryLen); -+ _finalOutput.append(static_cast<uint32_t>(_queryLen)); - _finalOutput.append("\t"); - format(coveredBases); - -@@ -199,11 +199,11 @@ void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits) - size_t nonZeroBases = _queryLen - countBasesAtDepth(0); - float coveredBases = (float)nonZeroBases / (float)_queryLen; - -- _finalOutput = hits.size(); -+ _finalOutput = static_cast<uint32_t>(hits.size()); - _finalOutput.append("\t"); -- _finalOutput.append(nonZeroBases); -+ _finalOutput.append(static_cast<uint32_t>(nonZeroBases)); - _finalOutput.append("\t"); -- _finalOutput.append(_queryLen); -+ _finalOutput.append(static_cast<uint32_t>(_queryLen)); - _finalOutput.append("\t"); - format(coveredBases); - -diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp -index 0757009..a83263e 100644 ---- a/src/utils/general/QuickString.cpp -+++ b/src/utils/general/QuickString.cpp -@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (uint32_t val) { - return *this; - } - --QuickString &QuickString::operator = (size_t val) { -- clear(); -- append(val); -- return *this; --} -+// QuickString &QuickString::operator = (size_t val) { -+// clear(); -+// append(val); -+// return *this; -+// } - - QuickString &QuickString::operator = (float val) { - clear(); -@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (uint32_t num) { - return *this; - } - --QuickString &QuickString::operator += (size_t num) { -- append(num); -- return *this; --} -+// QuickString &QuickString::operator += (size_t num) { -+// append(num); -+// return *this; -+// } -+ - QuickString &QuickString::operator += (float num) { - append(num); - return *this; -@@ -273,12 +274,12 @@ void QuickString::append(int num) { - } - - void QuickString::append(uint32_t num) { -- int2str((int)num, *this, true); -+ int2str((int)num, *this, true); - } - --void QuickString::append(size_t num) { -- int2str((int)num, *this, true); --} -+// void QuickString::append(size_t num) { -+// int2str((int)num, *this, true); -+// } - - void QuickString::append(float num) { - append(ToString(num)); -diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h -index b43fdfc..6e6fa94 100644 ---- a/src/utils/general/QuickString.h -+++ b/src/utils/general/QuickString.h -@@ -38,7 +38,7 @@ class QuickString { - QuickString &operator = (char); - QuickString &operator = (int); - QuickString &operator = (uint32_t); -- QuickString &operator = (size_t); -+ //QuickString &operator = (size_t); - QuickString &operator = (float); - QuickString &operator = (double); - QuickString &operator += (const QuickString &); -@@ -47,7 +47,7 @@ class QuickString { - QuickString &operator += (char); - QuickString &operator += (int); - QuickString &operator += (uint32_t); -- QuickString &operator += (size_t); -+ //QuickString &operator += (size_t); - QuickString &operator += (float); - QuickString &operator += (double); - -@@ -74,7 +74,7 @@ class QuickString { - //for better performance. - void append(int num); - void append(uint32_t num); -- void append(size_t num); -+ //void append(size_t num); - void append(float num); - void append(double num); - - diff --git a/gnu/packages/patches/boost-mips-avoid-m32.patch b/gnu/packages/patches/boost-mips-avoid-m32.patch deleted file mode 100644 index 811c9fb3aa..0000000000 --- a/gnu/packages/patches/boost-mips-avoid-m32.patch +++ /dev/null @@ -1,15 +0,0 @@ -The following patch prevents the use of the -m32 flag on mips, where it -is not understood by gcc, as well as other non-x86 architectures. - -diff -u -r boost_1_58_0.orig/tools/build/src/tools/gcc.jam boost_1_58_0/tools/build/src/tools/gcc.jam ---- boost_1_58_0.orig/tools/build/src/tools/gcc.jam 2015-04-04 19:25:07.000000000 +0200 -+++ boost_1_58_0/tools/build/src/tools/gcc.jam 2015-07-10 01:08:19.822733823 +0200 -@@ -451,7 +451,7 @@ - else - { - local arch = [ feature.get-values architecture : $(properties) ] ; -- if $(arch) != arm -+ if $(arch) = x86 - { - if $(model) = 32 - { diff --git a/gnu/packages/patches/csound-header-ordering.patch b/gnu/packages/patches/csound-header-ordering.patch new file mode 100644 index 0000000000..3640d123dd --- /dev/null +++ b/gnu/packages/patches/csound-header-ordering.patch @@ -0,0 +1,20 @@ +Prevent compilation issues with boost-1.60.0. + +Reported upstream at https://github.com/csound/csound/issues/570 + +--- Csound6.05/Opcodes/chua/ChuaOscillator.cpp 2015-04-25 14:06:22.995646234 -0500 ++++ Csound6.05/Opcodes/chua/ChuaOscillator.cpp 2015-12-21 10:31:58.182362640 -0600 +@@ -117,11 +117,12 @@ + // d = sys_variables(12); + // gnor = a*(x.^3) + b*(x.^2) + c*x + d; + +-#include <OpcodeBase.hpp> + #include <boost/numeric/ublas/vector.hpp> + using namespace boost::numeric; + #include <cmath> + ++#include <OpcodeBase.hpp> ++ + #undef CS_KSMPS + #define CS_KSMPS (opds.insdshead->ksmps) + diff --git a/gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch b/gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch new file mode 100644 index 0000000000..93a8ddc242 --- /dev/null +++ b/gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH.patch @@ -0,0 +1,46 @@ +This patch makes GTK+ look for additional modules in a list of directories +specified by the environment variable "GUIX_GTK2_PATH". This can be used +instead of "GTK_PATH" to make GTK+ find modules that are incompatible with +other major versions of GTK+. + +--- a/gtk/gtkmodules.c 2014-09-29 22:02:17.000000000 +0200 ++++ b/gtk/gtkmodules.c 2015-12-02 18:41:53.306396938 +0100 +@@ -55,6 +55,7 @@ + get_module_path (void) + { + const gchar *module_path_env; ++ const gchar *module_guix_gtk2_path_env; + const gchar *exe_prefix; + const gchar *home_dir; + gchar *home_gtk_dir = NULL; +@@ -70,6 +71,7 @@ + home_gtk_dir = g_build_filename (home_dir, ".gtk-2.0", NULL); + + module_path_env = g_getenv ("GTK_PATH"); ++ module_guix_gtk2_path_env = g_getenv ("GUIX_GTK2_PATH"); + exe_prefix = g_getenv ("GTK_EXE_PREFIX"); + + if (exe_prefix) +@@ -77,9 +79,21 @@ + else + default_dir = g_build_filename (GTK_LIBDIR, "gtk-2.0", NULL); + +- if (module_path_env && home_gtk_dir) ++ if (module_guix_gtk2_path_env && module_path_env && home_gtk_dir) ++ module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, ++ module_guix_gtk2_path_env, module_path_env, home_gtk_dir, default_dir, NULL); ++ else if (module_guix_gtk2_path_env && home_gtk_dir) ++ module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, ++ module_guix_gtk2_path_env, home_gtk_dir, default_dir, NULL); ++ else if (module_guix_gtk2_path_env && module_path_env) ++ module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, ++ module_guix_gtk2_path_env, module_path_env, default_dir, NULL); ++ else if (module_path_env && home_gtk_dir) + module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, + module_path_env, home_gtk_dir, default_dir, NULL); ++ else if (module_guix_gtk2_path_env) ++ module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, ++ module_guix_gtk2_path_env, default_dir, NULL); + else if (module_path_env) + module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, + module_path_env, default_dir, NULL); diff --git a/gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch b/gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch new file mode 100644 index 0000000000..66fd2fd1c4 --- /dev/null +++ b/gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch @@ -0,0 +1,38 @@ +This patch makes GTK+ look for additional modules in a list of directories +specified by the environment variable "GUIX_GTK3_PATH". This can be used +instead of "GTK_PATH" to make GTK+ find modules that are incompatible with +other major versions of GTK+. + +--- a/gtk/gtkmodules.c 2015-09-20 20:09:05.060590217 +0200 ++++ b/gtk/gtkmodules.c 2015-09-20 20:10:33.423124833 +0200 +@@ -52,6 +52,7 @@ + get_module_path (void) + { + const gchar *module_path_env; ++ const gchar *module_guix_gtk3_path_env; + const gchar *exe_prefix; + gchar *module_path; + gchar *default_dir; +@@ -61,6 +62,7 @@ + return result; + + module_path_env = g_getenv ("GTK_PATH"); ++ module_guix_gtk3_path_env = g_getenv ("GUIX_GTK3_PATH"); + exe_prefix = g_getenv ("GTK_EXE_PREFIX"); + + if (exe_prefix) +@@ -68,7 +70,13 @@ + else + default_dir = g_build_filename (_gtk_get_libdir (), "gtk-3.0", NULL); + +- if (module_path_env) ++ if (module_guix_gtk3_path_env && module_path_env) ++ module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, ++ module_guix_gtk3_path_env, module_path_env, default_dir, NULL); ++ else if (module_guix_gtk3_path_env) ++ module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, ++ module_guix_gtk3_path_env, default_dir, NULL); ++ else if (module_path_env) + module_path = g_build_path (G_SEARCHPATH_SEPARATOR_S, + module_path_env, default_dir, NULL); + else diff --git a/gnu/packages/patches/julia-0.3.10-fix-empty-array.patch b/gnu/packages/patches/julia-0.3.10-fix-empty-array.patch deleted file mode 100644 index b00f6549e3..0000000000 --- a/gnu/packages/patches/julia-0.3.10-fix-empty-array.patch +++ /dev/null @@ -1,13 +0,0 @@ -See https://github.com/JuliaLang/julia/issues/11817 - ---- a/src/codegen.cpp 2015-06-24 12:44:31.218674066 +0200 -+++ b/src/codegen.cpp 2015-04-23 11:19:50.000000000 +0200 -@@ -4551,7 +4551,7 @@ - #ifdef V128_BUG - "-avx", - #endif -- }; -+ ""}; - SmallVector<std::string, 4> MAttrs(mattr, mattr+sizeof(mattr)/sizeof(mattr[0])); - EngineBuilder eb = EngineBuilder(engine_module) - .setEngineKind(EngineKind::JIT) diff --git a/gnu/packages/patches/ldc-disable-tests.patch b/gnu/packages/patches/ldc-disable-tests.patch new file mode 100644 index 0000000000..3f5e6c29a1 --- /dev/null +++ b/gnu/packages/patches/ldc-disable-tests.patch @@ -0,0 +1,90 @@ +This patch fixes a failing unit test by feeding buildNormalizedPath to the +tzdata properly. Three other tests are disabled, one assumes /root and the +two others use networking. Not bad out of almost 700 tests! + +by Pjotr Prins <pjotr.guix@thebird.nl> + +diff --git a/std/datetime.d b/std/datetime.d +index 8e4ed3b..6c15bc5 100644 +--- a/std/datetime.d ++++ b/std/datetime.d +@@ -28018,6 +28018,7 @@ public: + The default directory where the TZ Database files are. It's empty + for Windows, since Windows doesn't have them. + +/ ++ + enum defaultTZDatabaseDir = "/usr/share/zoneinfo/"; + } + else version(Windows) +@@ -28069,14 +28070,13 @@ assert(tz.dstName == "PDT"); + import std.range : retro; + import std.format : format; + +- name = strip(name); +- + enforce(tzDatabaseDir.exists(), new DateTimeException(format("Directory %s does not exist.", tzDatabaseDir))); + enforce(tzDatabaseDir.isDir, new DateTimeException(format("%s is not a directory.", tzDatabaseDir))); + +- immutable file = buildNormalizedPath(tzDatabaseDir, name); ++ auto filename = "./" ~ strip(name); // make sure the prefix is not stripped ++ immutable file = buildNormalizedPath(tzDatabaseDir, filename); + +- enforce(file.exists(), new DateTimeException(format("File %s does not exist.", file))); ++ enforce(file.exists(), new DateTimeException(format("File %s does not exist in %s.", file, tzDatabaseDir))); + enforce(file.isFile, new DateTimeException(format("%s is not a file.", file))); + + auto tzFile = File(file); +diff --git a/std/path.d b/std/path.d +index 254d8f0..b0fc04d 100644 +--- a/std/path.d ++++ b/std/path.d +@@ -3080,8 +3080,11 @@ unittest + } + else + { ++ pragma(msg, "test disabled on GNU Guix"); ++/* + assert(expandTilde("~root") == "/root", expandTilde("~root")); + assert(expandTilde("~root/") == "/root/", expandTilde("~root/")); ++*/ + } + assert(expandTilde("~Idontexist/hey") == "~Idontexist/hey"); + } +diff --git a/std/socket.d b/std/socket.d +index b85d1c9..7fbf346 100644 +--- a/std/socket.d ++++ b/std/socket.d +@@ -517,6 +517,8 @@ class Protocol + + unittest + { ++ pragma(msg, "test disabled on GNU Guix"); ++/* + // getprotobyname,number are unimplemented on Android + softUnittest({ + Protocol proto = new Protocol; +@@ -530,6 +532,7 @@ unittest + assert(proto.name == "tcp"); + assert(proto.aliases.length == 1 && proto.aliases[0] == "TCP"); + }); ++*/ + } + + +@@ -859,6 +862,8 @@ class InternetHost + + unittest + { ++ pragma(msg, "test disabled on GNU Guix"); ++ /* + InternetHost ih = new InternetHost; + + ih.getHostByAddr(0x7F_00_00_01); +@@ -889,6 +894,7 @@ unittest + // writefln("aliases[%d] = %s", i, s); + // } + }); ++ */ + } + + diff --git a/gnu/packages/patches/libcmis-fix-test-onedrive.patch b/gnu/packages/patches/libcmis-fix-test-onedrive.patch new file mode 100644 index 0000000000..adf2e0b8e5 --- /dev/null +++ b/gnu/packages/patches/libcmis-fix-test-onedrive.patch @@ -0,0 +1,35 @@ +Patch from resolution of http://sourceforge.net/p/libcmis/tickets/13/ + +From 814c7845d53688b35a747cf193c2ff99e40a8652 Mon Sep 17 00:00:00 2001 +From: Jonathan Wakely <jwakely@redhat.com> +Date: Wed, 2 Sep 2015 16:35:45 +0100 +Subject: [PATCH 5/5] Remove invalid comments from test JSON file. + +--- + qa/libcmis/data/onedrive/search-result.json | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/qa/libcmis/data/onedrive/search-result.json b/qa/libcmis/data/onedrive/search-result.json +index 61d250a..2482429 100644 +--- a/qa/libcmis/data/onedrive/search-result.json ++++ b/qa/libcmis/data/onedrive/search-result.json +@@ -8,7 +8,7 @@ + }, + "name":"OneDriveFile", + "description":"", +- "parent_id":"folderA", // path: /A/Wrong File ++ "parent_id":"folderA", + "size":18047, + "upload_location":"https://apis.live.net/v5.0/wrongFileId/content/", + "comments_count":0, +@@ -32,7 +32,7 @@ + }, + "name":"OneDriveFile", + "description":"", +- "parent_id":"folderC", // path: /A/B/C/Right File ++ "parent_id":"folderC", + "size":4, + "upload_location":"https://apis.live.net/v5.0/rightFileId/content/", + "comments_count":0, +-- +2.4.3
\ No newline at end of file diff --git a/gnu/packages/patches/nss-pkgconfig.patch b/gnu/packages/patches/nss-pkgconfig.patch index 80c0c5b009..e611f69bea 100644 --- a/gnu/packages/patches/nss-pkgconfig.patch +++ b/gnu/packages/patches/nss-pkgconfig.patch @@ -7,8 +7,10 @@ Modifications: Remove optional patching in nss/Makefile. Include -L$libdir in output from "nss-config --libs". ---- nss-3.17.1/nss/config/Makefile -+++ nss-3.17.1/nss/config/Makefile +Later adapted to apply cleanly to nss-3.21. + +--- nss-3.21/nss/config/Makefile ++++ nss-3.21/nss/config/Makefile @@ -0,0 +1,40 @@ +CORE_DEPTH = .. +DEPTH = .. @@ -50,8 +52,8 @@ Modifications: + +dummy: all export libs + ---- nss-3.17.1/nss/config/nss-config.in -+++ nss-3.17.1/nss/config/nss-config.in +--- nss-3.21/nss/config/nss-config.in ++++ nss-3.21/nss/config/nss-config.in @@ -0,0 +1,145 @@ +#!/bin/sh + @@ -198,8 +200,8 @@ Modifications: + echo $libdirs +fi + ---- nss-3.17.1/nss/config/nss.pc.in -+++ nss-3.17.1/nss/config/nss.pc.in +--- nss-3.21/nss/config/nss.pc.in ++++ nss-3.21/nss/config/nss.pc.in @@ -0,0 +1,12 @@ +prefix=@prefix@ +exec_prefix=@exec_prefix@ @@ -213,14 +215,11 @@ Modifications: +Libs: -L${libdir} -lssl3 -lsmime3 -lnss3 -lnssutil3 +Cflags: -I${includedir} + ---- nss-3.17.1/nss/manifest.mn -+++ nss-3.17.1/nss/manifest.mn -@@ -10,7 +10,7 @@ +--- nss-3.21/nss/manifest.mn ++++ nss-3.21/nss/manifest.mn +@@ -10,4 +10,4 @@ RELEASE = nss --DIRS = coreconf lib cmd -+DIRS = coreconf lib cmd config - - ifdef NSS_BUILD_GTESTS - DIRS += external_tests +-DIRS = coreconf lib cmd external_tests ++DIRS = coreconf lib cmd external_tests config diff --git a/gnu/packages/patches/openimageio-boost-1.60.patch b/gnu/packages/patches/openimageio-boost-1.60.patch new file mode 100644 index 0000000000..92fc3237bb --- /dev/null +++ b/gnu/packages/patches/openimageio-boost-1.60.patch @@ -0,0 +1,47 @@ +From 875fbbd92695397bfc83d1cd5fdd4094e1d50199 Mon Sep 17 00:00:00 2001 +From: Larry Gritz <lg@larrygritz.com> +Date: Mon, 28 Dec 2015 11:46:07 -0800 +Subject: [PATCH] Python ImageCache binding fixes -- disable broken calls + +Some of these calls (thankfully undocumented and presumably unused) +are horribly broken. They compiled before, but with new Boost 1.60 +they don't even compile properly. So just comment them out on this +obsolete branch. They are fully fixed in RB-1.6 and beyond. + +--- a/src/python/py_imagecache.cpp ++++ b/src/python/py_imagecache.cpp +@@ -199,23 +199,24 @@ void declare_imagecache() + .def("destroy", &ImageCacheWrap::destroy) + .staticmethod("destroy") + .def("clear", &ImageCacheWrap::clear) +- .def("attribute", &ImageCacheWrap::attribute) ++ // .def("attribute", &ImageCacheWrap::attribute) + .def("attribute", &ImageCacheWrap::attribute_int) + .def("attribute", &ImageCacheWrap::attribute_float) +- .def("attribute", &ImageCacheWrap::attribute_double) +- .def("attribute", &ImageCacheWrap::attribute_char) ++ // .def("attribute", &ImageCacheWrap::attribute_double) ++ // .def("attribute", &ImageCacheWrap::attribute_char) + .def("attribute", &ImageCacheWrap::attribute_string) +- .def("getattribute", &ImageCacheWrap::attribute) ++ // .def("getattribute", &ImageCacheWrap::attribute) + .def("getattribute", &ImageCacheWrap::getattribute_int) + .def("getattribute", &ImageCacheWrap::getattribute_float) +- .def("getattribute", &ImageCacheWrap::getattribute_double) +- .def("getattribute", &ImageCacheWrap::getattribute_char) ++ // .def("getattribute", &ImageCacheWrap::getattribute_double) ++ // .def("getattribute", &ImageCacheWrap::getattribute_char) + .def("getattribute", &ImageCacheWrap::getattribute_string) +- .def("resolve_filename", &ImageCacheWrap::resolve_filename) +- .def("get_image_info", &ImageCacheWrap::get_image_info) +- .def("get_image_info", &ImageCacheWrap::get_image_info_old) ++ // .def("get_image_info", &ImageCacheWrap::get_image_info) ++ // .def("get_image_info", &ImageCacheWrap::get_image_info_old) + .def("get_imagespec", &ImageCacheWrap::get_imagespec) +- .def("get_pixels", &ImageCacheWrap::get_pixels) ++ // .def("get_pixels", &ImageCacheWrap::get_pixels) ++ .def("resolve_filename", &ImageCacheWrap::resolve_filename) ++ + // .def("get_tile", &ImageCacheWrap::get_tile) + // .def("release_tile", &ImageCacheWrap::release_tile) + // .def("tile_pixels", &ImageCacheWrap::tile_pixels) diff --git a/gnu/packages/patches/sudo-CVE-2015-5602.patch b/gnu/packages/patches/sudo-CVE-2015-5602.patch new file mode 100644 index 0000000000..36c90fbee7 --- /dev/null +++ b/gnu/packages/patches/sudo-CVE-2015-5602.patch @@ -0,0 +1,372 @@ +Based on the patch from https://www.sudo.ws/repos/sudo/raw-rev/c2e36a80a279 +Backported to 1.8.15 by Mark H Weaver <mhw@netris.org> + +# HG changeset patch +# User Todd C. Miller <Todd.Miller@courtesan.com> +# Date 1452475889 25200 +# Node ID c2e36a80a27927c32cba55afae78b8dc830cddc3 +# Parent 94ffd6b18431fa4b9ed0a0c3f0b7b9582a4f6bde +Rewritten sudoedit_checkdir support that checks all the dirs in the +path and refuses to follow symlinks in writable directories. +This is a better fix for CVE-2015-5602. +Adapted from a diff by Ben Hutchings. Bug #707 + +diff -r 94ffd6b18431 -r c2e36a80a279 doc/CONTRIBUTORS +--- a/doc/CONTRIBUTORS Mon Jan 04 10:47:11 2016 -0700 ++++ b/doc/CONTRIBUTORS Sun Jan 10 18:31:29 2016 -0700 +@@ -58,6 +58,7 @@ + Holloway, Nick + Hoover, Adam + Hunter, Michael T. ++ Hutchings, Ben + Irrgang, Eric + Jackson, Brian + Jackson, John R. +diff -r 94ffd6b18431 -r c2e36a80a279 doc/UPGRADE +--- a/doc/UPGRADE Mon Jan 04 10:47:11 2016 -0700 ++++ b/doc/UPGRADE Sun Jan 10 18:31:29 2016 -0700 +@@ -1,6 +1,15 @@ + Notes on upgrading from an older release + ======================================== + ++o Upgrading from a version prior to the post-1.8.15 fix for CVE-2015-5602. ++ ++ The meaning of the sudoedit_checkdir sudoers option has changed. ++ Previously, it would only check the parent directory ++ of the file to be edited. After the CVE fix, all directories ++ in the path to be edited are checked and sudoedit will refuse ++ to follow a symbolic link in a directory that is writable by ++ the invoking user. ++ + o Upgrading from a version prior to 1.8.15: + + Prior to version 1.8.15, when env_reset was enabled (the default) +diff -r 94ffd6b18431 -r c2e36a80a279 doc/sudoers.cat +--- a/doc/sudoers.cat Mon Jan 04 10:47:11 2016 -0700 ++++ b/doc/sudoers.cat Sun Jan 10 18:31:29 2016 -0700 +@@ -1275,12 +1275,15 @@ + system call. This flag is _o_f_f by default. + + sudoedit_checkdir +- If set, ssuuddooeeddiitt will refuse to edit files located in a +- directory that is writable by the invoking user unless +- it is run by root. On many systems, this option +- requires that the parent directory of the file to be +- edited be readable by the target user. This flag is +- _o_f_f by default. ++ If set, ssuuddooeeddiitt will check directories in the path to ++ be edited for writability by the invoking user. ++ Symbolic links will not be followed in writable ++ directories and ssuuddooeeddiitt will also refuse to edit a ++ file located in a writable directory. Theses ++ restrictions are not enforced when ssuuddooeeddiitt is invoked ++ as root. On many systems, this option requires that ++ all directories in the path to be edited be readable by ++ the target user. This flag is _o_f_f by default. + + sudoedit_follow By default, ssuuddooeeddiitt will not follow symbolic links + when opening files. The _s_u_d_o_e_d_i_t___f_o_l_l_o_w option can be +diff -r 94ffd6b18431 -r c2e36a80a279 doc/sudoers.man.in +--- a/doc/sudoers.man.in Mon Jan 04 10:47:11 2016 -0700 ++++ b/doc/sudoers.man.in Sun Jan 10 18:31:29 2016 -0700 +@@ -2715,10 +2715,16 @@ + .br + If set, + \fBsudoedit\fR +-will refuse to edit files located in a directory that is writable +-by the invoking user unless it is run by root. +-On many systems, this option requires that the parent directory +-of the file to be edited be readable by the target user. ++will check directories in the path to be edited for writability ++by the invoking user. ++Symbolic links will not be followed in writable directories and ++\fBsudoedit\fR ++will also refuse to edit a file located in a writable directory. ++Theses restrictions are not enforced when ++\fBsudoedit\fR ++is invoked as root. ++On many systems, this option requires that all directories ++in the path to be edited be readable by the target user. + This flag is + \fIoff\fR + by default. +diff -r 94ffd6b18431 -r c2e36a80a279 doc/sudoers.mdoc.in +--- a/doc/sudoers.mdoc.in Mon Jan 04 10:47:11 2016 -0700 ++++ b/doc/sudoers.mdoc.in Sun Jan 10 18:31:29 2016 -0700 +@@ -2549,10 +2549,16 @@ + .It sudoedit_checkdir + If set, + .Nm sudoedit +-will refuse to edit files located in a directory that is writable +-by the invoking user unless it is run by root. +-On many systems, this option requires that the parent directory +-of the file to be edited be readable by the target user. ++will check directories in the path to be edited for writability ++by the invoking user. ++Symbolic links will not be followed in writable directories and ++.Nm sudoedit ++will also refuse to edit a file located in a writable directory. ++Theses restrictions are not enforced when ++.Nm sudoedit ++is invoked as root. ++On many systems, this option requires that all directories ++in the path to be edited be readable by the target user. + This flag is + .Em off + by default. +diff -r 94ffd6b18431 -r c2e36a80a279 include/sudo_compat.h +--- a/include/sudo_compat.h Mon Jan 04 10:47:11 2016 -0700 ++++ b/include/sudo_compat.h Sun Jan 10 18:31:29 2016 -0700 +@@ -182,6 +182,8 @@ + # ifndef UTIME_NOW + # define UTIME_NOW -2L + # endif ++#endif ++#if !defined(HAVE_OPENAT) || (!defined(HAVE_FUTIMENS) && !defined(HAVE_UTIMENSAT)) + # ifndef AT_FDCWD + # define AT_FDCWD -100 + # endif +diff -r 94ffd6b18431 -r c2e36a80a279 src/sudo_edit.c +--- a/src/sudo_edit.c Mon Jan 04 10:47:11 2016 -0700 ++++ b/src/sudo_edit.c Sun Jan 10 18:31:29 2016 -0700 +@@ -179,13 +179,15 @@ + } + + #ifndef HAVE_OPENAT +-/* This does not support AT_FDCWD... */ + static int + sudo_openat(int dfd, const char *path, int flags, mode_t mode) + { + int fd, odfd; + debug_decl(sudo_openat, SUDO_DEBUG_EDIT) + ++ if (dfd == AT_FDCWD) ++ debug_return_int(open(path, flags, mode)); ++ + /* Save cwd */ + if ((odfd = open(".", O_RDONLY)) == -1) + debug_return_int(-1); +@@ -207,6 +209,64 @@ + #define openat sudo_openat + #endif /* HAVE_OPENAT */ + ++#ifdef O_NOFOLLOW ++static int ++sudo_edit_openat_nofollow(int dfd, char *path, int oflags, mode_t mode) ++{ ++ debug_decl(sudo_edit_open_nofollow, SUDO_DEBUG_EDIT) ++ ++ debug_return_int(openat(dfd, path, oflags|O_NOFOLLOW, mode)); ++} ++#else ++/* ++ * Returns true if fd and path don't match or path is a symlink. ++ * Used on older systems without O_NOFOLLOW. ++ */ ++static bool ++sudo_edit_is_symlink(int fd, char *path) ++{ ++ struct stat sb1, sb2; ++ debug_decl(sudo_edit_is_symlink, SUDO_DEBUG_EDIT) ++ ++ /* ++ * Treat [fl]stat() failure like there was a symlink. ++ */ ++ if (fstat(fd, &sb1) == -1 || lstat(path, &sb2) == -1) ++ debug_return_bool(true); ++ ++ /* ++ * Make sure we did not open a link and that what we opened ++ * matches what is currently on the file system. ++ */ ++ if (S_ISLNK(sb2.st_mode) || ++ sb1.st_dev != sb2.st_dev || sb1.st_ino != sb2.st_ino) { ++ debug_return_bool(true); ++ } ++ ++ debug_return_bool(false); ++} ++ ++static int ++sudo_edit_openat_nofollow(char *path, int oflags, mode_t mode) ++{ ++ struct stat sb1, sb2; ++ int fd; ++ debug_decl(sudo_edit_openat_nofollow, SUDO_DEBUG_EDIT) ++ ++ fd = openat(dfd, path, oflags, mode); ++ if (fd == -1) ++ debug_return_int(-1); ++ ++ if (sudo_edit_is_symlink(fd, path)) { ++ close(fd); ++ fd = -1; ++ errno = ELOOP; ++ } ++ ++ debug_return_int(fd); ++} ++#endif /* O_NOFOLLOW */ ++ + /* + * Returns true if the directory described by sb is writable + * by the user. We treat directories with the sticky bit as +@@ -245,49 +305,94 @@ + debug_return_bool(false); + } + ++/* ++ * Directory open flags for use with openat(2) and fstat(2). ++ * Use O_PATH and O_DIRECTORY where possible. ++ */ ++#if defined(O_PATH) && defined(O_DIRECTORY) ++# define DIR_OPEN_FLAGS (O_PATH|O_DIRECTORY) ++#elif defined(O_PATH) && !defined(O_DIRECTORY) ++# define DIR_OPEN_FLAGS O_PATH ++#elif !defined(O_PATH) && defined(O_DIRECTORY) ++# define DIR_OPEN_FLAGS (O_RDONLY|O_DIRECTORY) ++#else ++# define DIR_OPEN_FLAGS (O_RDONLY|O_NONBLOCK) ++#endif ++ + static int + sudo_edit_open_nonwritable(char *path, int oflags, mode_t mode) + { +- char *base, *dir; ++ int dfd, fd, dflags = DIR_OPEN_FLAGS; ++#if defined(__linux__) && defined(O_PATH) ++ char *opath = path; ++#endif ++ bool is_writable; + struct stat sb; +- int dfd, fd; + debug_decl(sudo_edit_open_nonwritable, SUDO_DEBUG_EDIT) + +- base = strrchr(path, '/'); +- if (base != NULL) { +- *base++ = '\0'; +- dir = path; ++#if defined(__linux__) && defined(O_PATH) ++restart: ++#endif ++ if (path[0] == '/') { ++ dfd = open("/", dflags); ++ path++; + } else { +- base = path; +- dir = "."; ++ dfd = open(".", dflags); ++ if (path[0] == '.' && path[1] == '/') ++ path += 2; + } +-#ifdef O_PATH +- if ((dfd = open(dir, O_PATH)) != -1) { +- /* Linux kernels < 3.6 can't do fstat on O_PATH fds. */ +- if (fstat(dfd, &sb) == -1) { +- close(dfd); +- dfd = open(dir, O_RDONLY); +- if (fstat(dfd, &sb) == -1) { +- close(dfd); +- dfd = -1; +- } +- } +- } +-#else +- if ((dfd = open(dir, O_RDONLY)) != -1) { +- if (fstat(dfd, &sb) == -1) { +- close(dfd); +- dfd = -1; +- } +- } +-#endif +- if (base != path) +- base[-1] = '/'; /* restore path */ + if (dfd == -1) + debug_return_int(-1); + +- if (dir_is_writable(&sb, user_details.uid, user_details.gid, +- user_details.ngroups, user_details.groups)) { ++ for (;;) { ++ char *slash; ++ int subdfd; ++ ++ /* ++ * Look up one component at a time, avoiding symbolic links in ++ * writable directories. ++ */ ++ if (fstat(dfd, &sb) == -1) { ++ close(dfd); ++#if defined(__linux__) && defined(O_PATH) ++ /* Linux prior to 3.6 can't fstat an O_PATH fd */ ++ if (ISSET(dflags, O_PATH)) { ++ CLR(dflags, O_PATH); ++ path = opath; ++ goto restart; ++ } ++#endif ++ debug_return_int(-1); ++ } ++#ifndef O_DIRECTORY ++ if (!S_ISDIR(sb.st_mode)) { ++ close(dfd); ++ errno = ENOTDIR; ++ debug_return_int(-1); ++ } ++#endif ++ is_writable = dir_is_writable(&sb, user_details.uid, user_details.gid, ++ user_details.ngroups, user_details.groups); ++ ++ while (path[0] == '/') ++ path++; ++ slash = strchr(path, '/'); ++ if (slash == NULL) ++ break; ++ *slash = '\0'; ++ if (is_writable) ++ subdfd = sudo_edit_openat_nofollow(dfd, path, dflags, 0); ++ else ++ subdfd = openat(dfd, path, dflags, 0); ++ *slash = '/'; /* restore path */ ++ close(dfd); ++ if (subdfd == -1) ++ debug_return_int(-1); ++ path = slash + 1; ++ dfd = subdfd; ++ } ++ ++ if (is_writable) { + close(dfd); + errno = EISDIR; + debug_return_int(-1); +@@ -332,27 +437,10 @@ + if (!ISSET(oflags, O_NONBLOCK)) + (void) fcntl(fd, F_SETFL, fcntl(fd, F_GETFL, 0) & ~O_NONBLOCK); + +- /* +- * Treat [fl]stat() failure like an open() failure. +- */ +- if (fstat(fd, &sb1) == -1 || lstat(path, &sb2) == -1) { +- const int serrno = errno; ++ if (!ISSET(sflags, CD_SUDOEDIT_FOLLOW) && sudo_edit_is_symlink(fd, path)) { + close(fd); +- errno = serrno; +- debug_return_int(-1); +- } +- +- /* +- * Make sure we did not open a link and that what we opened +- * matches what is currently on the file system. +- */ +- if (!ISSET(sflags, CD_SUDOEDIT_FOLLOW)) { +- if (S_ISLNK(sb2.st_mode) || +- sb1.st_dev != sb2.st_dev || sb1.st_ino != sb2.st_ino) { +- close(fd); +- errno = ELOOP; +- debug_return_int(-1); +- } ++ fd = -1; ++ errno = ELOOP; + } + + debug_return_int(fd); + diff --git a/gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch b/gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch new file mode 100644 index 0000000000..5b78f2d909 --- /dev/null +++ b/gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch @@ -0,0 +1,24 @@ +Subject: Disable SSLv2 and SSLv3. + +The only remaining methods are TLSv1.* (the code never distinguishes +between TLSv1.0, TLSv1.1, and TLSv1.2). +--- + fm.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/fm.h b/fm.h +index 320906c..ddcd4fc 100644 +--- a/fm.h ++++ b/fm.h +@@ -1144,7 +1144,7 @@ global int ssl_path_modified init(FALSE); + #endif /* defined(USE_SSL) && + * defined(USE_SSL_VERIFY) */ + #ifdef USE_SSL +-global char *ssl_forbid_method init(NULL); ++global char *ssl_forbid_method init("2, 3"); + #endif + + global int is_redisplay init(FALSE); +-- +2.6.4 + diff --git a/gnu/packages/patches/w3m-disable-weak-ciphers.patch b/gnu/packages/patches/w3m-disable-weak-ciphers.patch new file mode 100644 index 0000000000..4780d54cb6 --- /dev/null +++ b/gnu/packages/patches/w3m-disable-weak-ciphers.patch @@ -0,0 +1,24 @@ +Subject: Disable weak ciphers + +Disable RC4, "export ciphers", and all keys < 128 bits. + +Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/w3m/+bug/1325674 +--- + url.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/url.c b/url.c +index ed6062e..e86b1f3 100644 +--- a/url.c ++++ b/url.c +@@ -326,6 +326,7 @@ openSSLHandle(int sock, char *hostname, char **p_cert) + SSL_load_error_strings(); + if (!(ssl_ctx = SSL_CTX_new(SSLv23_client_method()))) + goto eend; ++ SSL_CTX_set_cipher_list(ssl_ctx, "DEFAULT:!LOW:!RC4:!EXP"); + option = SSL_OP_ALL; + if (ssl_forbid_method) { + if (strchr(ssl_forbid_method, '2')) +-- +2.6.4 + diff --git a/gnu/packages/patches/w3m-fix-compile.patch b/gnu/packages/patches/w3m-fix-compile.patch deleted file mode 100644 index 5604052f67..0000000000 --- a/gnu/packages/patches/w3m-fix-compile.patch +++ /dev/null @@ -1,15 +0,0 @@ -https://bugs.archlinux.org/task/33397 - -diff -aur old/main.c new/main.c ---- main.c 2013-01-14 18:16:14.216210053 -0600 -+++ main.c 2013-01-14 18:17:28.816220559 -0600 -@@ -833,7 +833,8 @@ - mySignal(SIGPIPE, SigPipe); - #endif - -- orig_GC_warn_proc = GC_set_warn_proc(wrap_GC_warn_proc); -+ orig_GC_warn_proc = GC_get_warn_proc(); -+ GC_set_warn_proc(wrap_GC_warn_proc); - err_msg = Strnew(); - if (load_argc == 0) { - /* no URL specified */ diff --git a/gnu/packages/patches/w3m-force-ssl_verify_server-on.patch b/gnu/packages/patches/w3m-force-ssl_verify_server-on.patch new file mode 100644 index 0000000000..dc9f117f9d --- /dev/null +++ b/gnu/packages/patches/w3m-force-ssl_verify_server-on.patch @@ -0,0 +1,24 @@ +Subject: Force ssl_verify_server on. + +By default, SSL/TLS certificates are not verified. This enables the +verification. +--- + fm.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/fm.h b/fm.h +index 8378939..320906c 100644 +--- a/fm.h ++++ b/fm.h +@@ -1135,7 +1135,7 @@ global int view_unseenobject init(TRUE); + #endif + + #if defined(USE_SSL) && defined(USE_SSL_VERIFY) +-global int ssl_verify_server init(FALSE); ++global int ssl_verify_server init(TRUE); + global char *ssl_cert_file init(NULL); + global char *ssl_key_file init(NULL); + global char *ssl_ca_path init(NULL); +-- +2.6.4 + diff --git a/gnu/packages/patches/w3m-libgc.patch b/gnu/packages/patches/w3m-libgc.patch new file mode 100644 index 0000000000..0dc6a4027c --- /dev/null +++ b/gnu/packages/patches/w3m-libgc.patch @@ -0,0 +1,28 @@ +This patch fixes w3m compilation with libgc > 7.2. + +Reported: +https://bugs.archlinux.org/task/33397 + +Patch with explanation: +http://anonscm.debian.org/cgit/collab-maint/w3m.git/commit/?id=770eec8304bdbe458 +--- + main.c | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/main.c b/main.c +index b421943..249eb1a 100644 +--- a/main.c ++++ b/main.c +@@ -833,7 +833,8 @@ main(int argc, char **argv, char **envp) + mySignal(SIGPIPE, SigPipe); + #endif + +- orig_GC_warn_proc = GC_set_warn_proc(wrap_GC_warn_proc); ++ orig_GC_warn_proc = GC_get_warn_proc(); ++ GC_set_warn_proc(wrap_GC_warn_proc); + err_msg = Strnew(); + if (load_argc == 0) { + /* no URL specified */ +-- +2.6.4 + diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm index 6166226dce..e9a247142d 100644 --- a/gnu/packages/plotutils.scm +++ b/gnu/packages/plotutils.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -21,11 +22,21 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) + #:use-module (gnu packages algebra) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages xorg) #:use-module (gnu packages image) + #:use-module (gnu packages ghostscript) #:use-module (gnu packages guile) + #:use-module (gnu packages gl) #:use-module (gnu packages gtk) + #:use-module (gnu packages maths) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages readline) + #:use-module (gnu packages texinfo) + #:use-module (gnu packages texlive) #:use-module (gnu packages compression) #:use-module (gnu packages)) @@ -156,3 +167,61 @@ just-in-time graph generation, handles date and time data nicely, and has basic statistical capabilities. It allows significant user control over colors, styles, options and details.") (license license:gpl2+))) + +(define-public asymptote + (package + (name "asymptote") + (version "2.35") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/asymptote/" + version "/asymptote-" version ".src.tgz")) + (sha256 + (base32 + "11f28vxw0ybhvl7vxmqcdwvw7y6gz55ykw9ybgzb2px6lsvgag7z")) + (patches (list (search-patch "asymptote-gsl2.patch"))))) + (build-system gnu-build-system) + ;; Note: The 'asy' binary retains a reference to docdir for use with its + ;; "help" command in interactive mode, so adding a "doc" output is not + ;; currently useful. + (native-inputs + `(("gs" ,ghostscript) ;For tests + ("texinfo" ,texinfo) ;For generating documentation + ("texlive" ,texlive) ;For tests and documentation + ("perl" ,perl))) + (inputs + `(("fftw" ,fftw) + ("freeglut" ,freeglut) + ("gsl" ,gsl) + ("libgc" ,libgc) + ("python" ,python-2) + ("readline" ,readline) + ("zlib" ,zlib))) + (arguments + `(#:configure-flags + (list (string-append "--enable-gc=" (assoc-ref %build-inputs "libgc")) + (string-append "--with-latex=" + (assoc-ref %outputs "out") + "/share/texmf/tex/latex") + (string-append "--with-context=" + (assoc-ref %outputs "out") + "/share/texmf/tex/context/third")) + #:phases (modify-phases %standard-phases + (add-before 'build 'patch-pdf-viewer + (lambda _ + ;; Default to a free pdf viewer + (substitute* "settings.cc" + (("defaultPDFViewer=\"acroread\"") + "defaultPDFViewer=\"gv\""))))))) + (home-page "http://asymptote.sourceforge.net") + (synopsis "Script-based vector graphics language") + (description + "Asymptote is a powerful descriptive vector graphics language for +technical drawing, inspired by MetaPost but with an improved C++-like syntax. +Asymptote provides for figures the same high-quality level of typesetting that +LaTeX does for scientific text.") + ;; Most source files do not contain license statements, but the README + ;; contains: "All source files in the Asymptote project, unless explicitly + ;; noted otherwise, are released under version 3 (or later) of the GNU + ;; Lesser General Public License" + (license license:lgpl3+))) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 2977f94660..fd36f8d694 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -121,7 +121,7 @@ a focus on simplicity and productivity.") (define-public ruby-2.1 (package (inherit ruby) - (version "2.1.6") + (version "2.1.8") (source (origin (method url-fetch) @@ -130,7 +130,7 @@ a focus on simplicity and productivity.") "/ruby-" version ".tar.bz2")) (sha256 (base32 - "1sbcmbhadcxk0509svwxbm2vvgmpf3xjxr1397bgp9x46nz36lkv")))) + "11rkbfc90cg9p9mzg32475alf3ddcn9q8a3ar3fwm5xskic0n395")))) (arguments `(#:test-target "test" #:parallel-tests? #f @@ -490,7 +490,7 @@ supported: XML Markup and XML Events.") (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) #t))))) (native-inputs - `(("jdk" ,icedtea7 "jdk"))) + `(("jdk" ,icedtea "jdk"))) (synopsis "Ruby-to-Java bridge using the Java Native Interface") (description "RJB is a bridge program that connects Ruby and Java via the Java Native Interface.") @@ -2942,3 +2942,39 @@ programs to concentrate on the implementation of network protocols. It can be used to create both network servers and clients.") (home-page "http://rubyeventmachine.com") (license (list license:ruby license:gpl3)))) ; GPLv3 only AFAICT + +(define-public ruby-ansi + (package + (name "ruby-ansi") + (version "1.5.0") + (source + (origin + (method url-fetch) + ;; Fetch from GitHub as the gem does not contain testing code. + (uri (string-append "https://github.com/rubyworks/ansi/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1zdip30hivyipi8hndhb457bhiz033awd00bgrsk5axjrwp6zhly")))) + (build-system ruby-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Disable testing to break the cycle ansi, ae, ansi, as well as the + ;; cycle ansi, qed, ansi. Instead simply test that the library can + ;; be require'd. + (replace 'check + (lambda _ + (zero? (system* "ruby" "-Ilib" "-r" "ansi"))))))) + (synopsis "ANSI escape code related libraries") + (description + "This package is a collection of ANSI escape code related libraries +enabling ANSI colorization and stylization of console output. Included in the +library are the @code{Code} module, which defines ANSI codes as constants and +methods, a @code{Mixin} module for including color methods, a @code{Logger}, a +@code{ProgressBar}, and a @code{String} subclass. The library also includes a +@code{Terminal} module which provides information about the current output +device.") + (home-page "http://rubyworks.github.io/ansi") + (license license:bsd-2))) diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index ac3a17d512..1adc8aa218 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -98,14 +98,14 @@ anywhere.") (define-public samba (package (name "samba") - (version "4.3.2") + (version "4.3.3") (source (origin (method url-fetch) (uri (string-append "https://www.samba.org/samba/ftp/stable/samba-" version ".tar.gz")) (sha256 (base32 - "0xcs2bcim421mlk6l9rcrkx4cq9y41gfssyfa7xzdw5draar3631")))) + "1pvh78d5magc7lriyx7v9k7crlgxccmsy2mqn0j9xcnb78qj2bg6")))) (build-system gnu-build-system) (arguments '(#:phases @@ -236,14 +236,14 @@ many event types, including timers, signals, and the classic file descriptor eve (define-public ldb (package (name "ldb") - (version "1.1.23") + (version "1.1.24") (source (origin (method url-fetch) (uri (string-append "https://www.samba.org/ftp/ldb/ldb-" version ".tar.gz")) (sha256 (base32 - "0ncmwgga6q9v7maiywgw21w6rb3149m1w2ca11yq8k5j0izjz2wg")))) + "08ab66qzigfsfxqdvp6lx1knwsl3sqsww309xbq17l7hfcjgbsa5")))) (build-system gnu-build-system) (arguments '(#:phases diff --git a/gnu/packages/skribilo.scm b/gnu/packages/skribilo.scm index a1b3fe7c53..52ed1c34e3 100644 --- a/gnu/packages/skribilo.scm +++ b/gnu/packages/skribilo.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +23,7 @@ #:use-module (guix build-system gnu) #:use-module (gnu packages guile) #:use-module (gnu packages lout) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages plotutils) #:use-module (gnu packages imagemagick) #:use-module (gnu packages ghostscript)) @@ -30,14 +31,14 @@ (define-public skribilo (package (name "skribilo") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/skribilo/skribilo-" version ".tar.gz")) (sha256 (base32 - "0wwi996403wzcp8s8iyc2p6w7f9v39lwmy35ysdd3wc31i5dy19q")))) + "04d8xa76jvlz25jnc6p1gzsplwcwcqrmi3f7ixdhddhl1chyz66y")))) (build-system gnu-build-system) (arguments ;; Make the modules available under the usual location. @@ -62,6 +63,8 @@ #:parallel-build? #f)) + (native-inputs `(("pkg-config" ,pkg-config))) + (inputs `(("guile" ,guile-2.0) ("imagemagick" ,imagemagick) ("ghostscript" ,ghostscript) ; for 'convert' diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 81258d38f5..8bd87582ef 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -27,6 +27,7 @@ #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) @@ -53,7 +54,7 @@ (define-public r (package (name "r") - (version "3.2.2") + (version "3.2.3") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -61,7 +62,7 @@ version ".tar.gz")) (sha256 (base32 - "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw")))) + "1hdnv77ralzcx5k5b88jq1r8l6zqnywpq00g2qs949rqh63psfxr")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -1497,3 +1498,448 @@ grobs.") and draw tables.") (license license:gpl2+))) +(define-public r-rsqlite + (package + (name "r-rsqlite") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "RSQLite" version)) + (sha256 + (base32 + "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f")))) + (properties `((upstream-name . "RSQLite"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/rstats-db/RSQLite") + (synopsis "SQLite interface for R") + (description + "This package embeds the SQLite database engine in R and provides an +interface compliant with the DBI package. The source for the SQLite +engine (version 3.8.6) is included.") + (license license:lgpl2.0+))) + +(define-public r-rcurl + (package + (name "r-rcurl") + (version "1.95-0.1.2") + (source (origin + (method url-fetch) + (uri (string-append "http://www.bioconductor.org/packages/" + "release/extra/src/" + "contrib/RCurl_" version ".tar.gz")) + (sha256 + (base32 + "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc")))) + (properties `((upstream-name . "RCurl"))) + (build-system r-build-system) + (inputs + `(("libcurl" ,curl))) + (propagated-inputs + `(("r-bitops" ,r-bitops))) + (home-page "http://www.omegahat.org/RCurl") + (synopsis "General network client interface for R") + (description + "The package allows one to compose general HTTP requests and provides +convenient functions to fetch URIs, GET and POST forms, etc. and process the +results returned by the Web server. This provides a great deal of control +over the HTTP/FTP/... connection and the form of the request while providing a +higher-level interface than is available just using R socket connections. +Additionally, the underlying implementation is robust and extensive, +supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, +ldap, and also supports cookies, redirects, authentication, etc.") + (license license:bsd-3))) + +(define-public r-xml + (package + (name "r-xml") + (version "3.98-1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "XML" version)) + (sha256 + (base32 + "0j9ayp8a35g0227a4zd8nbmvnbfnj5w687jal6qvj4lbhi3va7sy")))) + (properties + `((upstream-name . "XML"))) + (build-system r-build-system) + (inputs + `(("libxml2" ,libxml2))) + (propagated-inputs + `(("r-rcurl" ,r-rcurl))) + (home-page "http://www.omegahat.org/RSXML") + (synopsis "Tools for parsing and generating XML within R") + (description + "Many approaches for both reading and creating XML (and HTML) +documents (including DTDs), both local and accessible via HTTP or FTP. Also +offers access to an XPath \"interpreter\".") + (license license:bsd-2))) + +(define-public r-lambda-r + (package + (name "r-lambda-r") + (version "1.1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "lambda.r" version)) + (sha256 + (base32 + "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa")))) + (properties `((upstream-name . "lambda.r"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/lambda.r") + (synopsis "Functional programming extension for R") + (description + "This package provides a language extension to efficiently write +functional programs in R. Syntax extensions include multi-part function +definitions, pattern matching, guard statements, built-in (optional) type +safety.") + (license license:lgpl3+))) + +(define-public r-futile-options + (package + (name "r-futile-options") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "futile.options" version)) + (sha256 + (base32 + "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f")))) + (properties + `((upstream-name . "futile.options"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/futile.options") + (synopsis "Options management framework") + (description + "The futile.options subsystem provides an easy user-defined options +management system that is properly scoped. This means that options created +via @code{futile.options} are fully self-contained and will not collide with +options defined in other packages.") + (license license:lgpl3+))) + +(define-public r-futile-logger + (package + (name "r-futile-logger") + (version "1.4.1") + (source (origin + (method url-fetch) + (uri (cran-uri "futile.logger" version)) + (sha256 + (base32 + "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51")))) + (properties `((upstream-name . "futile.logger"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-options" ,r-futile-options) + ("r-lambda-r" ,r-lambda-r))) + (home-page "http://cran.r-project.org/web/packages/futile.logger") + (synopsis "Logging utility for R") + (description + "This package provides a simple yet powerful logging utility. Based +loosely on log4j, futile.logger takes advantage of R idioms to make logging a +convenient and easy to use replacement for @code{cat} and @code{print} +statements.") + (license license:lgpl3+))) + +(define-public r-snow + (package + (name "r-snow") + (version "0.4-1") + (source (origin + (method url-fetch) + (uri (cran-uri "snow" version)) + (sha256 + (base32 + "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/snow") + (synopsis "Support for simple parallel computing in R") + (description + "The snow package provides support for simple parallel computing on a +network of workstations using R. A master R process calls @code{makeCluster} +to start a cluster of worker processes; the master process then uses functions +such as @code{clusterCall} and @code{clusterApply} to execute R code on the +worker processes and collect and return the results on the master.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-sparsem + (package + (name "r-sparsem") + (version "1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "SparseM" version)) + (sha256 + (base32 + "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz")))) + (properties + `((upstream-name . "SparseM"))) + (build-system r-build-system) + (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") + (synopsis "Sparse linear algebra") + (description + "This package provides some basic linear algebra functionality for sparse +matrices. It includes Cholesky decomposition and backsolving as well as +standard R subsetting and Kronecker products.") + (license license:gpl2+))) + +(define-public r-dt + (package + (name "r-dt") + (version "0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "DT" version)) + (sha256 + (base32 + "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj")))) + (properties + `((upstream-name . "DT"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-magrittr" ,r-magrittr))) + (home-page "http://rstudio.github.io/DT") + (synopsis "R wrapper of the DataTables JavaScript library") + (description + "This package allows for data objects in R to be rendered as HTML tables +using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). +The 'DataTables' library has been included in this R package.") + ;; The DT package as a whole is distributed under GPLv3. The DT package + ;; inludes other software components under different licenses: + ;; + ;; * Expat: jQuery, jquery.highlight.js, DataTables + ;; * ASL2.0: selectize.js + ;; * WTFPL: noUiSlider + (license (list license:gpl3 + license:expat + license:asl2.0 + (license:non-copyleft "http://www.wtfpl.net/txt/copying/"))))) + +(define-public r-base64enc + (package + (name "r-base64enc") + (version "0.1-3") + (source (origin + (method url-fetch) + (uri (cran-uri "base64enc" version)) + (sha256 + (base32 + "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd")))) + (build-system r-build-system) + (home-page "http://www.rforge.net/base64enc") + (synopsis "Tools for Base64 encoding") + (description + "This package provides tools for handling Base64 encoding. It is more +flexible than the orphaned \"base64\" package.") + (license license:gpl2+))) + +(define-public r-r-methodss3 + (package + (name "r-r-methodss3") + (version "1.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.methodsS3" version)) + (sha256 + (base32 + "1dg4bbrwr8jcsqisjrrwxs942mrjq72zw8yvl2br4djdm0md8zz5")))) + (properties `((upstream-name . "R.methodsS3"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/R.methodsS3") + (synopsis "S3 methods simplified") + (description + "This package provides methods that simplify the setup of S3 generic +functions and S3 methods. Major effort has been made in making definition of +methods as simple as possible with a minimum of maintenance for package +developers. For example, generic functions are created automatically, if +missing, and naming conflict are automatically solved, if possible. The +method @code{setMethodS3()} is a good start for those who in the future may +want to migrate to S4.") + (license license:lgpl2.1+))) + +(define-public r-r-oo + (package + (name "r-r-oo") + (version "1.19.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.oo" version)) + (sha256 + (base32 + "15rm1qb9a212bqazhcpk7m48hcp7jq8rh4yhd9c6zfyvdqszfmsb")))) + (properties `((upstream-name . "R.oo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3))) + (home-page "https://github.com/HenrikBengtsson/R.oo") + (synopsis "R object-oriented programming with or without references") + (description + "This package provides methods and classes for object-oriented +programming in R with or without references. Large effort has been made on +making definition of methods as simple as possible with a minimum of +maintenance for package developers.") + (license license:lgpl2.1+))) + +(define-public r-r-utils + (package + (name "r-r-utils") + (version "2.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.utils" version)) + (sha256 + (base32 + "03pi6pkcsq65fv7cn4x74cj050dc8x5d4xyg930p6f7flk788xaz")))) + (properties `((upstream-name . "R.utils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo))) + (home-page "https://github.com/HenrikBengtsson/R.utils") + (synopsis "Various programming utilities") + (description + "This package provides utility functions useful when programming and +developing R packages.") + (license license:lgpl2.1+))) + +(define-public r-r-cache + (package + (name "r-r-cache") + (version "0.12.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.cache" version)) + (sha256 + (base32 + "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx")))) + (properties `((upstream-name . "R.cache"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.cache") + (synopsis "Light-weight caching of objects and results") + (description + "This package provides methods for caching or memoization of objects and +results. With this package, any R object can be cached in a key-value storage +where the key can be an arbitrary set of R objects. The cache memory is +persistent (on the file system).") + (license license:lgpl2.1+))) + +(define-public r-r-rsp + (package + (name "r-r-rsp") + (version "0.20.0") + (source (origin + (method url-fetch) + (uri (cran-uri "R.rsp" version)) + (sha256 + (base32 + "06vq9qq5hdz3hqc99q82622mab6ix7jwap20h4za6ap6gnwqs0fv")))) + (properties `((upstream-name . "R.rsp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-cache" ,r-r-cache) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.rsp") + (synopsis "Dynamic generation of scientific reports") + (description + "The RSP markup language provides a powerful markup for controlling the +content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr +documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary +to many other literate programming languages, with RSP it is straightforward +to loop over mixtures of code and text sections, e.g. in month-by-month +summaries. RSP has also several preprocessing directives for incorporating +static and dynamic contents of external files (local or online) among other +things. RSP is ideal for self-contained scientific reports and R package +vignettes.") + (license license:lgpl2.1+))) + +(define-public r-matrixstats + (package + (name "r-matrixstats") + (version "0.15.0") + (source (origin + (method url-fetch) + (uri (cran-uri "matrixStats" version)) + (sha256 + (base32 + "1068k85s6rlwfzlszw790c2rndydvrsw7rpck6k6z17896m8drfa")))) + (properties `((upstream-name . "matrixStats"))) + (build-system r-build-system) + (native-inputs + `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes + (home-page "https://github.com/HenrikBengtsson/matrixStats") + (synopsis "Methods applying to vectors and matrix rows and columns") + (description + "This package provides methods operating on rows and columns of matrices, +e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are +also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and +@code{weightedMedians()}. All methods have been optimized for speed and +memory usage.") + (license license:artistic2.0))) + +(define-public r-viridis + (package + (name "r-viridis") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "viridis" version)) + (sha256 + (base32 + "0zz9i874s1fwhl9bcbiprlzaz7zsy1rj6c729zn3k525d63qbnj7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra))) + (home-page "https://github.com/sjmgarnier/viridis") + (synopsis "Matplotlib default color map") + (description + "This package is a port of the new @url{matplotlib, +http://matplotlib.org/} color maps (@code{viridis}--the default--, +@code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are +designed in such a way that they will analytically be perfectly +perceptually-uniform, both in regular form and also when converted to +black-and-white. They are also designed to be perceived by readers with the +most common form of color blindness.") + (license license:x11))) + +(define-public r-plotly + (package + (name "r-plotly") + (version "2.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "plotly" version)) + (sha256 + (base32 + "16pqycns8qf0y1j21n009qf242lv0izwyidlx40zv88izxhg1vs0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest) + ("r-ggplot2" ,r-ggplot2) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-viridis" ,r-viridis))) + (home-page "https://plot.ly/r") + (synopsis "Create interactive web graphics") + (description + "This package enables the translation of ggplot2 graphs to an interactive +web-based version and/or the creation of custom web-based visualizations +directly from R. Once uploaded to a plotly account, plotly graphs (and the +data behind them) can be viewed and modified in a web browser.") + (license license:x11))) + diff --git a/gnu/packages/texlive.scm b/gnu/packages/texlive.scm index b6c996edfa..0b2dec41f6 100644 --- a/gnu/packages/texlive.scm +++ b/gnu/packages/texlive.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> ;;; @@ -129,30 +129,29 @@ #:tests? ,(not (string-prefix? "mips64" (or (%current-target-system) (%current-system)))) #:phases - (alist-cons-after - 'install 'postinst - (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share")) - (texlive-extra (assoc-ref inputs "texlive-extra-src")) - (unpack (assoc-ref %standard-phases 'unpack)) - (patch-source-shebangs - (assoc-ref %standard-phases 'patch-source-shebangs))) - ;; Create symbolic links for the latex variants and their - ;; man pages. - (with-directory-excursion (string-append out "/bin/") - (for-each symlink - '("pdftex" "pdftex" "xetex" "luatex") - '("latex" "pdflatex" "xelatex" "lualatex"))) - (with-directory-excursion (string-append share "/man/man1/") - (symlink "luatex.1" "lualatex.1")) - ;; Unpack texlive-extra and install tlpkg. - (mkdir "texlive-extra") - (with-directory-excursion "texlive-extra" - (apply unpack (list #:source texlive-extra)) - (apply patch-source-shebangs (list #:source texlive-extra)) - (system* "mv" "tlpkg" share)))) - %standard-phases))) + (modify-phases %standard-phases + (add-after 'install 'postint + (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share")) + (texlive-extra (assoc-ref inputs "texlive-extra-src")) + (unpack (assoc-ref %standard-phases 'unpack)) + (patch-source-shebangs + (assoc-ref %standard-phases 'patch-source-shebangs))) + ;; Create symbolic links for the latex variants and their + ;; man pages. + (with-directory-excursion (string-append out "/bin/") + (for-each symlink + '("pdftex" "pdftex" "xetex" "luatex") + '("latex" "pdflatex" "xelatex" "lualatex"))) + (with-directory-excursion (string-append share "/man/man1/") + (symlink "luatex.1" "lualatex.1")) + ;; Unpack texlive-extra and install tlpkg. + (mkdir "texlive-extra") + (with-directory-excursion "texlive-extra" + (apply unpack (list #:source texlive-extra)) + (apply patch-source-shebangs (list #:source texlive-extra)) + (system* "mv" "tlpkg" share)))))))) (synopsis "TeX Live, a package of the TeX typesetting system") (description "TeX Live provides a comprehensive TeX document production system. @@ -182,42 +181,40 @@ This package contains the binaries.") (guix build utils) (srfi srfi-26)) #:phases - (alist-cons-before - 'texmf-config 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((share (string-append (assoc-ref outputs "out") "/share"))) - (mkdir-p share) - (system* "mv" "texmf-dist" share))) - (alist-cons-after - 'patch-source-shebangs 'texmf-config - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share")) - (texmfroot (string-append share "/texmf-dist/web2c")) - (texmfcnf (string-append texmfroot "/texmf.cnf")) - (texlive-bin (assoc-ref inputs "texlive-bin")) - (texbin (string-append texlive-bin "/bin")) - (tlpkg (string-append texlive-bin "/share/tlpkg"))) - ;; Register SHARE as TEXMFROOT in texmf.cnf. - (substitute* texmfcnf - (("TEXMFROOT = \\$SELFAUTOPARENT") - (string-append "TEXMFROOT = " share))) - ;; Register paths in texmfcnf.lua, needed for context. - (substitute* (string-append texmfroot "/texmfcnf.lua") - (("selfautodir:") out) - (("selfautoparent:") (string-append share "/"))) - ;; Set path to TeXLive Perl modules - (setenv "PERL5LIB" - (string-append (getenv "PERL5LIB") ":" tlpkg)) - ;; Configure the texmf-dist tree; inspired from - ;; http://slackbuilds.org/repository/13.37/office/texlive/ - (setenv "PATH" (string-append (getenv "PATH") ":" texbin)) - (setenv "TEXMFCNF" texmfroot) - (system* "updmap-sys" "--nohash" "--syncwithtrees") - (system* "mktexlsr") - (system* "fmtutil-sys" "--all"))) - (map (cut assq <> %standard-phases) - '(set-paths unpack patch-source-shebangs)))))) + (modify-phases (map (cut assq <> %standard-phases) + '(set-paths unpack patch-source-shebangs)) + (add-after 'patch-source-shebangs 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((share (string-append (assoc-ref outputs "out") "/share"))) + (mkdir-p share) + (system* "mv" "texmf-dist" share)))) + (add-after 'install 'texmf-config + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share")) + (texmfroot (string-append share "/texmf-dist/web2c")) + (texmfcnf (string-append texmfroot "/texmf.cnf")) + (texlive-bin (assoc-ref inputs "texlive-bin")) + (texbin (string-append texlive-bin "/bin")) + (tlpkg (string-append texlive-bin "/share/tlpkg"))) + ;; Register SHARE as TEXMFROOT in texmf.cnf. + (substitute* texmfcnf + (("TEXMFROOT = \\$SELFAUTOPARENT") + (string-append "TEXMFROOT = " share))) + ;; Register paths in texmfcnf.lua, needed for context. + (substitute* (string-append texmfroot "/texmfcnf.lua") + (("selfautodir:") out) + (("selfautoparent:") (string-append share "/"))) + ;; Set path to TeXLive Perl modules + (setenv "PERL5LIB" + (string-append (getenv "PERL5LIB") ":" tlpkg)) + ;; Configure the texmf-dist tree; inspired from + ;; http://slackbuilds.org/repository/13.37/office/texlive/ + (setenv "PATH" (string-append (getenv "PATH") ":" texbin)) + (setenv "TEXMFCNF" texmfroot) + (system* "updmap-sys" "--nohash" "--syncwithtrees") + (system* "mktexlsr") + (system* "fmtutil-sys" "--all"))))))) (synopsis "TeX Live, a package of the TeX typesetting system") (description "TeX Live provides a comprehensive TeX document production system. diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 537a840247..f2c60ddadf 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> -;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015 Roel Janssen <roel@gnu.org> ;;; @@ -25,6 +25,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) + #:use-module (guix build-system cmake) #:use-module (gnu packages autotools) #:use-module (gnu packages python)) @@ -95,7 +96,7 @@ libenca and several charset conversion libraries and tools.") (define-public utf8proc (package (name "utf8proc") - (version "1.1.6") + (version "1.3.1") (source (origin (method url-fetch) @@ -104,23 +105,15 @@ libenca and several charset conversion libraries and tools.") version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0wmsi672knii0q70wh6a3ll0gv7qk33c50zbpzasrs3b16bqy659")))) + (base32 "1k48as5kjkar4yj3dwxyll8ykj4k723ib5a6mnw1g86q3zi0zdl3")))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no "check" target - #:make-flags '("CC=gcc") + #:make-flags (list "CC=gcc" + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases - (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((lib (string-append (assoc-ref outputs "out") "/lib/")) - (include (string-append (assoc-ref outputs "out") "/include/"))) - (install-file "utf8proc.h" include) - (for-each (lambda (file) - (install-file file lib)) - '("libutf8proc.a" "libutf8proc.so")))) - ;; no configure script - (alist-delete 'configure %standard-phases)))) + (modify-phases %standard-phases + (delete 'configure)))) (home-page "http://julialang.org/utf8proc/") (synopsis "C library for processing UTF-8 Unicode data") (description "utf8proc is a small C library that provides Unicode @@ -201,3 +194,26 @@ files. This file format is more compact and more readable than XML. And unlike XML, it is type-aware, so it is not necessary to do string parsing in application code.") (license license:lgpl2.1+))) + +(define-public pfff + (package + (name "pfff") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pfff/pfff/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "00m553aa277iarxj6dalmklyb64r7ias49bfwzbacsfg8h3kar8m")))) + (build-system cmake-build-system) + (home-page "http://biit.cs.ut.ee/pfff/") + (synopsis "Probabilistic fast file fingerprinting tool") + (description + "pfff is a tool for calculating a compact digital fingerprint of a file +by sampling randomly from the file instead of reading it in full. +Consequently, the computation has a flat performance characteristic, +correlated with data variation rather than file size. pfff can be as reliable +as existing hashing techniques, with provably negligible risk of collisions.") + (license license:bsd-3))) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 63a623d05e..340027e849 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -66,7 +66,6 @@ #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages qt) - #:use-module (gnu packages samba) #:use-module (gnu packages sdl) #:use-module (gnu packages ssh) #:use-module (gnu packages texinfo) @@ -736,7 +735,6 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") ("mpg123" ,mpg123) ("pulseaudio" ,pulseaudio) ("rsound" ,rsound) - ("samba" ,samba) ("vapoursynth" ,vapoursynth) ("waf" ,(origin (method url-fetch) @@ -805,7 +803,7 @@ projects while introducing many more.") (define-public youtube-dl (package (name "youtube-dl") - (version "2015.12.29") + (version "2016.01.09") (source (origin (method url-fetch) (uri (string-append "http://youtube-dl.org/downloads/" @@ -813,7 +811,7 @@ projects while introducing many more.") version ".tar.gz")) (sha256 (base32 - "0232wiq8mjs5ngmlcvf0292icrhvzr9mkwy2km0g0djznsf7rxjg")))) + "0kchbjn52smhhjcrgqcz4hdkz0wl0i73blz3m04ncb0ykbazwg26")))) (build-system python-build-system) (native-inputs `(("python-setuptools" ,python-setuptools))) (home-page "http://youtube-dl.org") diff --git a/gnu/packages/w3m.scm b/gnu/packages/w3m.scm index d114d0a69e..45c9375def 100644 --- a/gnu/packages/w3m.scm +++ b/gnu/packages/w3m.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> +;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; ;;; This file is part of GNU Guix. ;;; @@ -43,8 +44,10 @@ "1qx9f0kprf92r1wxl3sacykla0g04qsi0idypzz24b7xy9ix5579")) ;; cf. https://bugs.archlinux.org/task/33397 - (patches (list (search-patch "w3m-fix-compile.patch"))) - (patch-flags '("-p0")))) + (patches (list (search-patch "w3m-libgc.patch") + (search-patch "w3m-force-ssl_verify_server-on.patch") + (search-patch "w3m-disable-sslv2-and-sslv3.patch") + (search-patch "w3m-disable-weak-ciphers.patch"))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target #:phases (alist-cons-before diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index d22aacd12f..dd05446603 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) + #:use-module (gnu packages libreoffice) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -52,14 +53,14 @@ (define-public webkitgtk (package (name "webkitgtk") - (version "2.8.5") + (version "2.10.4") (source (origin (method url-fetch) (uri (string-append "http://www.webkitgtk.org/releases/" name "-" version ".tar.xz")) (sha256 (base32 - "082dw0d8jxvsapx30ypmy5h2srzfzi42c3zr9pbkzx1m959hq7rx")))) + "0mghsbfnmmf6nsf7cb3ah76s77aigkzf3k6kw96wgh6all6jdy6v")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no tests @@ -105,6 +106,7 @@ ("gst-plugins-base" ,gst-plugins-base) ("gtk+-2" ,gtk+-2) ("harfbuzz" ,harfbuzz) + ("hyphen" ,hyphen) ("icu4c" ,icu4c) ("libjpeg" ,libjpeg) ("libnotify" ,libnotify) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 8288869a9f..7419c61d3a 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2015 Raimon Grau <raimonster@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -707,3 +708,27 @@ Cflags: -I${includedir} C++ programming langauge.") (home-page "http://www.grinninglizard.com/tinyxml/index.html") (license license:zlib))) + +(define-public xmlstarlet + (package + (name "xmlstarlet") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/xmlstar/xmlstarlet/" + version "/xmlstarlet-" version ".tar.gz")) + (sha256 + (base32 + "1jp737nvfcf6wyb54fla868yrr39kcbijijmjpyk4lrpyg23in0m")))) + (build-system gnu-build-system) + (inputs + `(("libxslt" ,libxslt) + ("libxml2" ,libxml2))) + (home-page "http://xmlstar.sourceforge.net/") + (synopsis "Command line XML toolkit") + (description "XMLStarlet is a set of command line utilities which can be +used to transform, query, validate, and edit XML documents. XPath is used to +match and extract data, and elements can be added, deleted or modified using +XSLT and EXSLT.") + (license license:x11))) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 42422a3c56..82a5d994d2 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr> +;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org> ;;; Copyright © 2015 Cyrill Schenkel <cyrill.schenkel@gmail.com> ;;; ;;; This file is part of GNU Guix. @@ -5375,14 +5376,14 @@ Intrinsics (Xt) Library.") (define-public xterm (package (name "xterm") - (version "320") + (version "322") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.invisible-island.net/xterm/" "xterm-" version ".tgz")) (sha256 (base32 - "19r4rs5pjq944m7aiqligazf6wgmv4f023x3bx183h1l8dbvn3d6")))) + "1mh9s5g3fs64iimnl7axk0isb5306dyshisxlv5gr8vn7ysl3nws")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-wide-chars" "--enable-256-color" diff --git a/gnu/services.scm b/gnu/services.scm index 0e1c74bda8..f302816e9e 100644 --- a/gnu/services.scm +++ b/gnu/services.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2015, 2016 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -63,6 +63,7 @@ system-service-type boot-service-type + cleanup-service-type activation-service-type activation-service->script %linux-bare-metal-service @@ -208,23 +209,8 @@ containing the given entries." (define (compute-boot-script _ mexps) (mlet %store-monad ((gexps (sequence %store-monad mexps))) (gexp->file "boot" - #~(begin - (use-modules (guix build utils)) - - ;; Clean out /tmp and /var/run. - ;; - ;; XXX This needs to happen before service activations, so - ;; it has to be here, but this also implicitly assumes - ;; that /tmp and /var/run are on the root partition. - (false-if-exception (delete-file-recursively "/tmp")) - (false-if-exception (delete-file-recursively "/var/run")) - (false-if-exception (mkdir "/tmp")) - (false-if-exception (chmod "/tmp" #o1777)) - (false-if-exception (mkdir "/var/run")) - (false-if-exception (chmod "/var/run" #o755)) - - ;; Activate the system and spawn dmd. - #$@gexps)))) + ;; Clean up and activate the system, then spawn dmd. + #~(begin #$@gexps)))) (define (boot-script-entry mboot) "Return, as a monadic value, an entry for the boot script in the system @@ -247,6 +233,53 @@ directory." ;; The service that produces the boot script. (service boot-service-type #t)) +(define (cleanup-gexp _) + "Return as a monadic value a gexp to clean up /tmp and similar places upon +boot." + (define %modules + '((guix build utils))) + + (mlet %store-monad ((modules (imported-modules %modules)) + (compiled (compiled-modules %modules))) + (return #~(begin + (eval-when (expand load eval) + ;; Make sure 'use-modules' below succeeds. + (set! %load-path (cons #$modules %load-path)) + (set! %load-compiled-path + (cons #$compiled %load-compiled-path))) + + (use-modules (guix build utils)) + + ;; Clean out /tmp and /var/run. + ;; + ;; XXX This needs to happen before service activations, so it + ;; has to be here, but this also implicitly assumes that /tmp + ;; and /var/run are on the root partition. + (letrec-syntax ((fail-safe (syntax-rules () + ((_ exp rest ...) + (begin + (catch 'system-error + (lambda () exp) + (const #f)) + (fail-safe rest ...))) + ((_) + #t)))) + ;; Ignore I/O errors so the system can boot. + (fail-safe + (delete-file-recursively "/tmp") + (delete-file-recursively "/var/run") + (mkdir "/tmp") + (chmod "/tmp" #o1777) + (mkdir "/var/run") + (chmod "/var/run" #o755))))))) + +(define cleanup-service-type + ;; Service that cleans things up in /tmp and similar. + (service-type (name 'cleanup) + (extensions + (list (service-extension boot-service-type + cleanup-gexp))))) + (define* (file-union name files) ;FIXME: Factorize. "Return a <computed-file> that builds a directory containing all of FILES. Each item in FILES must be a list where the first element is the file name to diff --git a/gnu/system.scm b/gnu/system.scm index 6dfcc0fe3a..4aedb7ee36 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -295,8 +295,12 @@ a container or that of a \"bare metal\" system." %boot-service ;; %DMD-ROOT-SERVICE must come first so that the gexp that execs - ;; dmd comes last in the boot script (XXX). - %dmd-root-service %activation-service + ;; dmd comes last in the boot script (XXX). Likewise, the cleanup + ;; service must come last so that its gexp runs before activation + ;; code. + %dmd-root-service + %activation-service + (service cleanup-service-type #f) (pam-root-service (operating-system-pam-services os)) (account-service (append (operating-system-accounts os) |