| Age | Commit message (Expand) | Author |
|---|
| 2018-03-17 | Merge branch 'master' into core-updates | Mark H Weaver |
| 2018-03-16 | gnu: Add pigx....* gnu/packages/bioinformatics.scm (pigx): New variable.
| Ricardo Wurmus |
| 2018-03-16 | gnu: pigx-rnaseq: Disable memory hungry test....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
| Ricardo Wurmus |
| 2018-03-16 | gnu: All snippets report errors using exceptions, else return #t....* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
| Mark H Weaver |
| 2018-03-16 | gnu: Add pigx-scrnaseq....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
| Ricardo Wurmus |
| 2018-03-16 | gnu: kentutils: Build with mariadb....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
| Ricardo Wurmus |
| 2018-03-16 | gnu: kentutils: Build with mariadb....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
| Ricardo Wurmus |
| 2018-03-15 | gnu: Add Diversitree....* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
| Leo Famulari |
| 2018-03-14 | Merge branch 'master' into core-updates | Ricardo Wurmus |
| 2018-03-11 | build-system/gnu: Add 'bootstrap' phase....This factorizes what has become a widespread idiom.
* guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable.
(bootstrap): New procedure.
(%standard-phases): Add it after 'unpack'.
* guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap.
* guix/build/asdf-build-system.scm (%standard-phases/source)
(%standard-phases): Likewise.
* guix/build/cargo-build-system.scm (%standard-phases): Likewise.
* guix/build/cmake-build-system.scm (%standard-phases): Likewise.
* guix/build/dub-build-system.scm (%standard-phases): Likewise.
* guix/build/emacs-build-system.scm (%standard-phases): Likewise.
* guix/build/font-build-system.scm (%standard-phases): Likewise.
* guix/build/go-build-system.scm (%standard-phases): Likewise.
* guix/build/haskell-build-system.scm (%standard-phases): Likewise.
* guix/build/minify-build-system.scm (%standard-phases): Likewise.
* guix/build/ocaml-build-system.scm (%standard-phases): Likewise.
* guix/build/perl-build-system.scm (%standard-phases): Likewise.
* guix/build/python-build-system.scm (%standard-phases): Likewise.
* guix/build/r-build-system.scm (%standard-phases): Likewise.
* guix/build/ruby-build-system.scm (%standard-phases): Likewise.
* guix/build/scons-build-system.scm (%standard-phases): Likewise.
* guix/build/texlive-build-system.scm (%standard-phases): Likewise.
* guix/build/waf-build-system.scm (%standard-phases): Likewise.
* gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap.
(soundtouch, cuetools, bluez-alsa): Remove 'arguments'.
(cava)[arguments]: Replace 'bootstrap.
* gnu/packages/backup.scm (rdup): Remove 'bootstrap.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Replace
'bootstrap.
* gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove
'arguments'.
* gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'.
* gnu/packages/crypto.scm (libb2): Remove #:phases.
* gnu/packages/databases.scm (guile-wiredtiger): Likewise.
* gnu/packages/debug.scm (stress-make): Remove 'bootstrap'.
* gnu/packages/documentation.scm (asciidoc): Likewise.
* gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'.
* gnu/packages/ftp.scm (weex): Remove 'arguments'.
* gnu/packages/game-development.scm (ois): Remove 'arguments'.
* gnu/packages/games.scm (pioneer): Remove 'bootstrap.
* gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap.
(arc-theme): Remove 'arguments'.
(faba-icon-theme): Remove 'bootstrap.
(arc-icon-theme): Remove 'arguments'.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/gtk.scm (guile-rsvg): Likewise.
* gnu/packages/guile.scm (mcron2): Remove 'bootstrap.
(guile-bash): Remove #:phases.
(guile-git): Remove 'bootstrap.
(guile-syntax-highlight): Remove 'arguments'.
(guile-sjson): Likewise.
* gnu/packages/java.scm (classpath-devel): Remove 'bootstrap.
* gnu/packages/kodi.scm (libdvdnav/kodi)
(libdvdread/kodi, libdvdcss/kodi): Likewise.
* gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'.
* gnu/packages/libusb.scm (hidapi): Likewise.
* gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to
'patch-stuff'; move it before 'bootstrap', without autoreconf
invocation.
(eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh'
invocation; move it before 'bootstrap.
(gpm): Replace 'bootstrap'.
(f2fs-tools): Remove 'arguments'.
(rng-tools): Remove #:phases.
* gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to
'copy-intltool-makefile'; remove "autoreconf" invocation and move before
'bootstrap'.
(libmesode): Remove 'arguments'.
(libstrophe): Likewise.
* gnu/packages/microcom.scm (microcom): Likewise.
* gnu/packages/networking.scm (libnet): Remove 'bootstrap.
* gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'.
* gnu/packages/package-management.scm (guix): Replace 'bootstrap.
* gnu/packages/sawfish.scm (librep): Remove 'arguments'.
* gnu/packages/version-control.scm (findnewest): Likewise.
* gnu/packages/video.scm (liba52, handbrake, motion): Replace
'bootstrap.
* gnu/packages/web.scm (fcgiwrap): Remove #:phases.
(tidy): Replace 'bootstrap.
(gumbo-parser): Remove #:phases.
* gnu/packages/wget.scm (wget2): Replace 'bootstrap.
* gnu/packages/wm.scm (i3lock-color): Remove #:phases.
* gnu/packages/xdisorg.scm (xclip): Likewise.
* gnu/packages/xml.scm (libxls): Replace 'bootstrap'.
* gnu/packages/xorg.scm (xf86-video-freedreno)
(xf86-video-intel): Remove #:phases.
* gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
| Ludovic Courtès |
| 2018-03-11 | gnu: Add pigx-bsseq....* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
| Ricardo Wurmus |
| 2018-03-11 | gnu: Add pigx-chipseq....* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
| Ricardo Wurmus |
| 2018-03-09 | gnu: r-rhdf5lib: Make build reproducible....* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
| Ricardo Wurmus |
| 2018-03-08 | gnu: Add r-phangorn....* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
| Ricardo Wurmus |
| 2018-03-08 | gnu: r-ape: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
| Ricardo Wurmus |
| 2018-03-08 | gnu: r-dropbead: Update to 0-2.d746c6f....* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
| Ricardo Wurmus |
| 2018-03-07 | gnu: Add pigx-rnaseq....* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
| Ricardo Wurmus |
| 2018-03-06 | gnu: samtools: Update to 1.7....* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
| Ricardo Wurmus |
| 2018-03-06 | gnu: htslib: Update to 1.7....* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
| Ricardo Wurmus |
| 2018-03-06 | gnu: r-rhdf5: Make build reproducible....* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
| Ricardo Wurmus |
| 2018-03-04 | gnu: piranha: Declare a source file-name....* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
| Efraim Flashner |
| 2018-03-04 | gnu: libdivsufsort: Declare a source file-name....* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
| Efraim Flashner |
| 2018-03-04 | gnu: seek: Declare a source file-name....* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
| Efraim Flashner |
| 2018-03-04 | gnu: r-dropbead: Declare a source file-name....* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
| Efraim Flashner |
| 2018-03-03 | gnu: Add dropseq-tools....* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-picard-2.10.3....* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-htsjdk-2.10.1....* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-htsjdk-latest....* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-alignment-4.0....* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-phylo-4.0....* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-core-4.0....* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-alignment....* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-phylo....* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-forester-1.005....* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-forester....* gnu/packages/bioinformatics.scm (java-forester): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-core....* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add fastqc....* gnu/packages/bioinformatics.scm (fastqc): New variable.
| Ricardo Wurmus |
| 2018-03-02 | gnu: cutadapt: Update to 1.16....* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-scran: Update to 1.6.8....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-wgcna: Update to 1.63....* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-topgo: Update to 2.30.1....* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-genomicranges: Update to 1.30.3....* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-limma: Update to 3.34.9....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-edger: Update to 3.20.9....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-shortread: Update to 1.36.1....* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
| Ricardo Wurmus |
| 2018-03-01 | gnu: r-dexseq: Update to 1.24.3....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
| Ricardo Wurmus |
| 2018-02-22 | gnu: r-qtl: Update to 1.42-8....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
| Ricardo Wurmus |
| 2018-02-19 | gnu: r-delayedmatrixstats: Update to 1.0.3....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
| Ricardo Wurmus |
| 2018-02-19 | gnu: r-scater: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
| Ricardo Wurmus |
| 2018-02-19 | gnu: r-gviz: Update to 1.22.3....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
| Ricardo Wurmus |
