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Author SHA1 Message Date
Mark H Weaver c1fced68e2
gnu: libssh2: Use invoke. 
* gnu/packages/ssh.scm (libssh2)[arguments]: Use invoke in the autoreconf
phase.
 2018-03-23 04:42:44 -04:00
Mark H Weaver 4bd9f46553
gnu: libsoup: Use invoke. 
* gnu/packages/gnome.scm (libsoup)[arguments]: Use invoke in the custom
install phase.
 2018-03-23 04:42:42 -04:00
Mark H Weaver 257d8974e6
gnu: libelf: Use invoke. 
* gnu/packages/elf.scm (libelf)[arguments]: Use invoke in the configure phase.
 2018-03-23 04:42:40 -04:00
Mark H Weaver 1a3aa5bab2
gnu: libarchive: Use invoke. 
* gnu/packages/backup.scm (libarchive)[arguments]: Use invoke and remove
vestigial plumbing from the check phase.
 2018-03-23 04:42:38 -04:00
Mark H Weaver 859e8873d0
gnu: imake: Use invoke. 
* gnu/packages/xorg.scm (imake)[arguments]: Use invoke and remove vestigial
plumbing from the 'install-data' phase.
 2018-03-23 04:42:36 -04:00
Mark H Weaver 173b647fa5
gnu: perl-image-magick: Return #t from all phases. 
* gnu/packages/imagemagick.scm (perl-image-magick)[arguments]: Return #t from
the 'image-magick-flags' and 'skip-mpeg-tests' phases.
 2018-03-23 04:42:33 -04:00
Mark H Weaver a440d01ae0
gnu: imagemagick: Return #t from all phases. 
* gnu/packages/imagemagick.scm (imagemagick)[arguments]: Return #t from
the 'pre-build' and 'strip-configure-xml' phases.
 2018-03-23 04:42:31 -04:00
Mark H Weaver 8f52d8982b
gnu: ijs: Use invoke. 
* gnu/packages/ghostscript.scm (ijs)[arguments]: Use invoke in the autogen
phase.
 2018-03-23 04:42:29 -04:00
Mark H Weaver 3f27124eb3
gnu: icecat: Return #t from all phases. 
* gnu/packages/gnuzilla.scm (icecat)[arguments]: Return #t from the
'install-icons' and 'wrap-program' phases.  Use 'invoke' in the custom
configure phase.
 2018-03-23 04:42:27 -04:00
Mark H Weaver a53ced66b1
gnu: gnumach: Use invoke. 
* gnu/packages/hurd.scm (gnumach)[arguments]: Use invoke and remove vestigial
plumbing in the 'produce-image' phase.
 2018-03-23 04:42:25 -04:00
Mark H Weaver 92fcb831c0
gnu: guix: Use invoke. 
* gnu/packages/package-management.scm (guix)[arguments]: Use invoke in the
bootstrap phase.
 2018-03-23 04:42:22 -04:00
Mark H Weaver 31ca09011a
gnu: gtk+@2: Return #t from all phases. 
* gnu/packages/gtk.scm (gtk+-2)[arguments]: Return #t from
the 'disable-tests' phase.
 2018-03-23 04:42:19 -04:00
Mark H Weaver b17f723846
gnu: gnupg@1: Return #t from all phases. 
* gnu/packages/gnupg.scm (gnupg-1)[arguments]: Return #t from
the 'patch-check-sh' phase.
 2018-03-23 04:42:17 -04:00
Mark H Weaver a48d22d615
gnu: hurd-minimal: Use invoke. 
* gnu/packages/hurd.scm (hurd-minimal)[arguments]: Use invoke in the custom
build phase.
 2018-03-23 04:42:15 -04:00
Mark H Weaver fe92152133
gnu: hurd-headers: Use invoke. 
* gnu/packages/hurd.scm (hurd-headers)[arguments]: Use invoke in the custom
install phase.
 2018-03-23 04:42:13 -04:00
Mark H Weaver 2057ea6825
gnu: gnumach-headers: Use invoke. 
* gnu/packages/hurd.scm (gnumach-headers)[arguments]: Use invoke in the
custom install phase.
 2018-03-23 04:42:11 -04:00
Mark H Weaver ac8281214f
gnu: gmime: Return #t from all phases. 
* gnu/packages/mail.scm (gmime)[arguments]: Return #t from
the 'patch-paths-in-tests' phase.
 2018-03-23 04:42:09 -04:00
Mark H Weaver b4c4f3399c
gnu: glibc-hurd-headers: Return #t from all phases. 
* gnu/packages/base.scm (glibc/hurd-headers): Return #t from the custom
install phase.
 2018-03-23 04:42:06 -04:00
Mark H Weaver ecb67a18b0
gnu: git: Return #t from all phases. 
* gnu/packages/version-control.scm (git)[arguments]: Return #t from
the 'split' phase.  Use 'invoke' in the 'install-man-pages' phase.
 2018-03-23 04:42:04 -04:00
Mark H Weaver eb075eddfc
gnu: ghostscript: Use invoke. 
* gnu/packages/ghostscript.scm (ghostscript): Use invoke from the
custom 'build' and 'install' phases.
 2018-03-23 04:42:02 -04:00
Mark H Weaver ae7ba73124
gnu: gettext-minimal: Return #t from all phases. 
* gnu/packages/gettext.scm (gettext-minimal)[arguments]: Return #t from
the 'patch-tests' and 'link-expat' phases.
 2018-03-23 04:41:59 -04:00
Mark H Weaver e3eb53e749
gnu: geoclue: Return #t from all phases. 
* gnu/packages/gnome.scm (geoclue)[arguments]: Return #t from
the 'patch-/bin/true' phase.
 2018-03-23 04:41:57 -04:00
Mark H Weaver 0c5c788fad
gnu: gdk-pixbuf+svg: Use invoke. 
* gnu/packages/gtk.scm (gdk-pixbuf+svg): Use invoke in
the 'register-svg-loader' phase.
 2018-03-23 04:41:55 -04:00
Mark H Weaver 3e629738a3
gnu: cross-base: Use invoke in (gnu build cross-toolchain). 
* gnu/build/cross-toolchain.scm (set-cross-path/mingw, install-strip): Use
invoke.
 2018-03-23 04:41:53 -04:00
Mark H Weaver dcd5ea699f
gnu: gawk: Return #t from all phases. 
* gnu/packages/gawk.scm (gawk)[arguments]: Return #t from
the 'set-shell-file-name' phase.
 2018-03-23 04:41:51 -04:00
Mark H Weaver 21398edae2
gnu: fontconfig: Use invoke. 
* gnu/packages/fontutils.scm (fontconfig): Use invoke in the install phase.
 2018-03-23 04:41:48 -04:00
Mark H Weaver 3918ed732e
gnu: ffmpeg: Use invoke. 
* gnu/packages/video.scm (ffmpeg)[arguments]: Use invoke in the custom
configure phase.
 2018-03-23 04:41:46 -04:00
Mark H Weaver 114ef0a4c5
gnu: faad2: Use invoke. 
* gnu/packages/audio.scm (faad2)[arguments]: Use invoke in the 'bootstrap'
phase.
 2018-03-23 04:41:44 -04:00
Mark H Weaver 472415c8df
gnu: extra-cmake-modules: Return #t from all phases. 
* gnu/packages/kde-frameworks.scm (extra-cmake-modules)[arguments]: Return #t
from the 'fix-lib-path' phase.
 2018-03-23 04:41:42 -04:00
Mark H Weaver e2d90ee428
gnu: emacs: Return #t from all phases. 
* gnu/packages/emacs.scm (emacs)[arguments]: Return #t from the 'fix-/bin/pwd'
phase.
 2018-03-23 04:41:39 -04:00
Mark H Weaver 3f54fd1ea5
gnu: elogind: Return #t from all phases. 
* gnu/packages/freedesktop.scm (elogin)[arguments]: Return #t from all phases.
Use invoke and remove vestigial plumbing in the 'autogen' phase.
 2018-03-23 04:41:37 -04:00
Mark H Weaver f97cb24967
gnu: dejagnu: Return #t from all phases. 
* gnu/packages/dejagnu.scm (dejagnu)[arguments]: Return #t from all phases.
Raise an exception if make check fails.
 2018-03-23 04:41:35 -04:00
Mark H Weaver fac441b365
gnu: curl: Use invoke. 
* gnu/packages/curl.scm (curl)[arguments]: Use invoke in the check phase.
 2018-03-23 04:41:33 -04:00
Mark H Weaver 95cc40a88a
gnu: autoconf@2.13: Use invoke. 
* gnu/packages/autotools.scm (autoconf-2.13)[arguments]: Use invoke in the
custom configure phase.
 2018-03-23 04:40:10 -04:00
Mark H Weaver 3d77ecfed4
gnu: apr-util: Use invoke. 
* gnu/packages/apr.scm (apr-util)[arguments]: Use invoke in the custom
configure phase.
 2018-03-23 04:40:08 -04:00
Mark H Weaver ab6e5690af
gnu: glibc/linux: Return #t from pre-configure phase. 
* gnu/packages/base.scm (glibc/linux)[arguments]: Return #t from the
pre-configure phase.
 2018-03-23 04:40:01 -04:00
Tobias Geerinckx-Rice 590594a175
gnu: openldap: Update to 2.4.46. 
* gnu/packages/openldap.scm (openldap): Update to 2.4.46.
 2018-03-23 08:28:55 +01:00
Arun Isaac 12420c800e
gnu: cmake: Re-indent. 
* gnu/packages/cmake.scm (cmake): Re-indent.
 2018-03-23 11:32:33 +05:30
Arun Isaac 89db6c6de9
gnu: cmake: Update to 3.10.2. 
* gnu/packages/cmake.scm (cmake): Update to 3.10.2.
[source]: Remove cmake-fix-tests patch.
Do not remove bundled cmlibuv.
[arguments]: Replace system* with invoke.
[inputs]: Add rhash. Sort.
[home-page]: Update URL.
* gnu/packages/patches/cmake-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Unregister it.
 2018-03-23 11:32:24 +05:30
Marius Bakke 0223db58ef
gnu: util-linux: Don't build 'nologin'. 
* gnu/packages/linux.scm (util-linux)[source](snippet): Add substitution.
 2018-03-22 18:58:06 +01:00
Marius Bakke 759ad0690b
gnu: make: End phase on #t. 
* gnu/packages/base.scm (gnu-make)[arguments]: Return #t from
'set-default-shell' phase.
 2018-03-22 18:58:06 +01:00
Marius Bakke e9b9ea1ec0
gnu: make: Fix compatibility with glibc 2.27. 
* gnu/packages/patches/make-glibc-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/base.scm (gnu-make)[source](patches): Use it.
 2018-03-22 18:58:05 +01:00
Marius Bakke 5e8cb5e698
gnu: glibc: Update to 2.27. 
* gnu/packages/base.scm (glibc/linux): Update to 2.27.
[source](patches): Add 'glibc-hidden-visibility-ldconfig.patch' and
'glibc-2.27-git-fixes.patch'.
[native-inputs]: Add BISON.
[arguments]: Remove deprecated "--enable-add-ons" from #:configure-flags.
Also remove unneeded "libc_cv_ssp=no" and "libcv_ssp_strong=no".
(glibc-2.26): New public variable.
* gnu/packages/commencement.scm (glibc-final-with-bootstrap-bash)[native-inputs]:
Add BISON-BOOT0.
* gnu/packages/patches/glibc-2.27-git-fixes.patch,
gnu/packages/patches/glibc-hidden-visibility-ldconfig.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.
 2018-03-22 18:58:05 +01:00
Mark H Weaver e0f9f85f8d
gnu: tzdata-for-tests: Update to 2018c. 
* gnu/packages/base.scm (tzdata-for-tests): Replace with a simple hidden copy
of 'tzdata'.
 2018-03-21 20:43:21 -04:00
Ludovic Courtès e288572710
gnu: gcc: Adjust 'strmov' patch for string constants in variables. 
Fixes <https://bugs.gnu.org/30395>.

* gnu/packages/patches/gcc-strmov-store-file-names.patch: Update patch
to deal with string constants stored in 'static' variables.
 2018-03-20 23:39:51 +01:00
Mark H Weaver ac21be848a
Merge branch 'master' into core-updates 2018-03-20 14:22:06 -04:00
Mark H Weaver d3da21d222
gnu: aspell: Return #t from all phases. 
* gnu/packages/aspell.scm (aspell)[arguments]: Return #t from
the 'wrap-aspell' phase.
 2018-03-20 14:18:12 -04:00
Mark H Weaver bca2413141
gnu: itstool: Return #t from all phases. 
* gnu/packages/glib.scm (itstool)[arguments]: Return #t from
the 'wrap-program' phase.
 2018-03-20 14:18:11 -04:00
Mark H Weaver 2e7c3e065b
gnu: webkitgtk: Return #t from all phases. 
* gnu/packages/webkit.scm (webkitgtk)[arguments]: Return #t from
the 'add-gst-plugins-base-include-path' phase.
 2018-03-20 14:18:09 -04:00
Mark H Weaver 0392030d6a
gnu: orc: Return #t from all phases. 
* gnu/packages/gstreamer.scm (orc)[arguments]: Return #t from
the 'disable-faulty-test' phase.
 2018-03-20 14:18:07 -04:00
ng0 4a78fd4617
Correct name and Email for ng0. 
* .mailmap: Correct name and Email for ng0.
* Makefile.am, doc/guix.texi, etc/completion/fish/guix.fish
gnu/packages/accessibility.scm, gnu/packages/admin.scm,
gnu/packages/audio.scm, gnu/packages/autotools.scm,
gnu/packages/cdrom.scm, gnu/packages/check.scm,
gnu/packages/cinnamon.scm, gnu/packages/compression.scm,
gnu/packages/crypto.scm, gnu/packages/databases.scm,
gnu/packages/django.scm, gnu/packages/dns.scm,
gnu/packages/emacs.scm, gnu/packages/enlightenment.scm,
gnu/packages/fonts.scm, gnu/packages/fontutils.scm,
gnu/packages/forth.scm, gnu/packages/fvwm.scm,
gnu/packages/games.scm, gnu/packages/gl.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm,
gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm,
gnu/packages/guile.scm, gnu/packages/haskell-check.scm,
gnu/packages/haskell-crypto.scm, gnu/packages/haskell.scm,
gnu/packages/image-viewers.scm, gnu/packages/image.scm,
gnu/packages/irc.scm, gnu/packages/language.scm,
gnu/packages/libcanberra.scm, gnu/packages/linux.scm,
gnu/packages/lisp.scm, gnu/packages/lolcode.scm,
gnu/packages/lxde.scm, gnu/packages/lxqt.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm,
gnu/packages/mate.scm, gnu/packages/maths.scm,
gnu/packages/mc.scm, gnu/packages/messaging.scm,
gnu/packages/music.scm, gnu/packages/ncurses.scm,
gnu/packages/networking.scm, gnu/packages/nickle.scm,
gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/python-crypto.scm, gnu/packages/python-web.scm,
gnu/packages/python.scm, gnu/packages/qt.scm,
gnu/packages/ruby.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/serialization.scm,
gnu/packages/shells.scm, gnu/packages/ssh.scm,
gnu/packages/suckless.scm, gnu/packages/tbb.scm,
gnu/packages/telephony.scm, gnu/packages/text-editors.scm,
gnu/packages/textutils.scm, gnu/packages/time.scm,
gnu/packages/tls.scm, gnu/packages/tor.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vim.scm, gnu/packages/web.scm,
gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xfce.scm, gnu/packages/xml.scm,
gnu/packages/xorg.scm, gnu/services/certbot.scm,
gnu/services/desktop.scm, gnu/services/version-control.scm,
gnu/services/web.scm, guix/import/hackage.scm,
guix/licenses.scm: Likewise.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2018-03-20 17:17:58 +01:00
Kei Kebreau f812145e3e
gnu: ruby-sanitize: Update to 4.6.3. 
This fixes CVE-2018-3740.

* gnu/packages/ruby.scm (ruby-sanitize): Update to 4.6.3.
 2018-03-20 11:20:33 -04:00
宋文武 32745b71e1
gnu: cdogs-sdl: Update to commit bab20313. 
Fixes <https://bugs.gnu.org/30623>.

* gnu/packages/games.scm (cdogs-sdl): Update to commit
bab2031369b9ea2dbeb7eedbde10a43dd8ca83db.
[source]: Use git-fetch.
 2018-03-20 22:33:18 +08:00
Sahithi Yarlagadda c56739df6b
gnu: Add r-dyn. 
* gnu/packages/cran.scm (r-dyn): New variable.
 2018-03-20 15:00:52 +01:00
Ricardo Wurmus 4f1e4f33a0
gnu: pigx-bsseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
 2018-03-20 14:56:44 +01:00
Marius Bakke dc7e07c9b9
Merge branch 'staging' 2018-03-20 14:13:05 +01:00
Ricardo Wurmus 616446ffbf
gnu: pigx-rnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
 2018-03-20 12:20:51 +01:00
Marius Bakke 4735610ee3
gnu: poppler: Update to 0.63.0. 
* gnu/packages/pdf.scm (poppler): Update to 0.63.0.
 2018-03-20 11:57:26 +01:00
Marius Bakke 019c0eda94
gnu: fontconfig: Update to 2.13.0. 
* gnu/packages/patches/fontconfig-remove-debug-printf.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/fontutils.scm (fontconfig): Update to 2.13.0.
[source](patches): Remove.
[propagated-inputs]: Add UTIL-LINUX.
 2018-03-20 11:57:25 +01:00
Marius Bakke 7428581f8d
gnu: freetype: Update to 2.9. 
* gnu/packages/fontutils.scm (freetype): Update to 2.9.
 2018-03-20 11:57:25 +01:00
Ricardo Wurmus e35924865e
Revert "gnu: wayland: Disable failing tests." 
This reverts commit e923cee1b9.
 2018-03-20 11:47:00 +01:00
Mark H Weaver 647888845c
Merge branch 'master' into core-updates 2018-03-20 00:49:05 -04:00
Tobias Geerinckx-Rice c657716ede
gnu: dnsmasq: Fix description typos. 
* gnu/packages/dns.scm (dnsmasq)[description]: Fix some typos.
 2018-03-20 02:03:52 +01:00
Tobias Geerinckx-Rice 4e6c51d4eb
gnu: dnsmasq: Update to 2.79. 
* gnu/packages/dns.scm (dnsmasq): Update to 2.79.
 2018-03-20 02:03:52 +01:00
Marius Bakke a3e2b72ca9
gnu: certbot: Update to 0.22.1. 
* gnu/packages/tls.scm (python-acme, certbot): Update to 0.22.1.
 2018-03-20 01:40:07 +01:00
Marius Bakke 818e6d9704
gnu: python-cryptography: Update to 2.2. 
* gnu/packages/python-crypto.scm (python-cryptography-vectors,
python-cryptography): Update to 2.2.
 2018-03-20 01:25:10 +01:00
Marius Bakke c9838530d3
gnu: imlib2: Update to 1.5.1. 
* gnu/packages/image.scm (imlib2): Update to 1.5.1.
 2018-03-20 01:24:48 +01:00
Marius Bakke 264cb77646
gnu: imagemagick: Update to 6.9.9-39. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-39.
 2018-03-20 01:09:16 +01:00
Marius Bakke 0d729c5b14
gnu: zziplib: Correct license. 
* gnu/packages/compression.scm (zziplib)[license]: Add MPL1.1.
 2018-03-20 01:06:43 +01:00
Marius Bakke 3f986ff657
gnu: zziplib: Update to 0.13.69. 
* gnu/packages/compression.scm (zziplib): Update to 0.13.69.
[home-page]: Use new GitHub home.
[source](uri): Adjust accordingly.
[arguments]: Remove.
 2018-03-20 00:56:04 +01:00
Marius Bakke 712be306a8
gnu: rofi: Update to 1.5.1. 
* gnu/packages/xdisorg.scm (rofi): Update to 1.5.1.
 2018-03-20 00:34:00 +01:00
Marius Bakke dbc75dadb5
Revert "Revert "gnu: patchelf: Update argument phase."" 
This change only affects armhf, which doesn't use PatchELF.  My bad!

This reverts commit b1d096f869.
 2018-03-20 00:20:59 +01:00
Marius Bakke b1d096f869
Revert "gnu: patchelf: Update argument phase." 
It causes too many rebuilds this late in the 'staging' cycle.

This reverts commit c1d1cd817c.
 2018-03-20 00:06:34 +01:00
Leo Famulari d41ad1d553
gnu: uwsgi: Update to 2.0.17 [fixes CVE-2018-7490]. 
* gnu/packages/web.scm (uwsgi): Update to 2.0.17.
[source]: Use HTTPS URL.
 2018-03-19 18:56:26 -04:00
Ludovic Courtès cfbf6de18c
gnu: mcron: Update to 1.1 and deprecate "mcron2". 
* gnu/packages/guile.scm (mcron): Update to 1.1.
[native-inputs]: Add TZDATA-FOR-TESTS.
[arguments]: New field.
(mcron2): Define using 'deprecated-package'.
* gnu/services/mcron.scm: Replace 'mcron2' with 'mcron'.
* doc/guix.texi (Scheduled Job Execution): Likewise.
* gnu/tests/base.scm (%mcron-os): Remove comment about mcron2.
 2018-03-19 23:19:49 +01:00
Mark H Weaver f88028c432
gnu: linux-libre: Update to 4.15.11. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.11.
(%linux-libre-hash): Update hash.
 2018-03-19 18:02:29 -04:00
Mark H Weaver dd07a549d0
gnu: linux-libre@4.14: Update to 4.14.28. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.28.
(%linux-libre-4.14-hash): Update hash.
 2018-03-19 18:01:49 -04:00
Mark H Weaver cc367c7c7a
gnu: linux-libre@4.9: Update to 4.9.88. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.88.
 2018-03-19 18:01:12 -04:00
Mark H Weaver 75abeb73e3
gnu: linux-libre@4.4: Update to 4.4.122. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.122.
 2018-03-19 18:00:37 -04:00
Tobias Geerinckx-Rice 9010123565
gnu: weechat: Update to 2.1. 
* gnu/packages/irc.scm (weechat): Update to 2.1.
 2018-03-19 22:26:41 +01:00
Tobias Geerinckx-Rice 1d9b041c2e
gnu: perl-xml-compile-soap: Update to 3.24. 
* gnu/packages/xml.scm (perl-xml-compile-soap): Update to 3.24.
 2018-03-19 22:26:41 +01:00
Tobias Geerinckx-Rice fa3fff430b
gnu: perl-xml-simple: Update to 2.25. 
* gnu/packages/xml.scm (perl-xml-simple): Update to 2.25.
 2018-03-19 22:26:40 +01:00
Tobias Geerinckx-Rice 8d0d14479d
gnu: perl-math-random-secure: Fix typo. 
* gnu/packages/crypto.scm (perl-math-random-secure)[description]: Fix
the spelling of ‘millennia’.
 2018-03-19 22:26:30 +01:00
Ricardo Wurmus 9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
 2018-03-19 21:06:51 +01:00
Ricardo Wurmus 096589035e
gnu: bismark: Fix references to gunzip. 
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
 2018-03-19 21:06:51 +01:00
Ricardo Wurmus 51237011bf
gnu: pigx-scrnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
 2018-03-19 21:06:50 +01:00
Efraim Flashner 203631d9ad
patchelf: Use 'https' for source uri. 
* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
 2018-03-19 21:48:43 +02:00
Efraim Flashner 05666fb8db
patchelf: Use 'https' for source uri. 
* gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri.
 2018-03-19 21:48:06 +02:00
Efraim Flashner c1d1cd817c
gnu: patchelf: Update argument phase. 
* gnu/packages/elf.scm (patchelf)[arguments]: Use 'modify-phases'
syntax.  Replace 'system*' with 'invoke'.
 2018-03-19 21:48:06 +02:00
Efraim Flashner c24f1f1614
gnu: patchelf: Use 'target-arm32?' for armhf-linux case. 
* gnu/packages/elf.scm (patchelf)[inputs]: Replace armhf-linux detection
logic with 'target-arm32?' macro.
[arguments]: Same.
 2018-03-19 21:48:03 +02:00
Leo Famulari 9687d4042a
gnu: python-paramiko: Update to 2.1.5. 
* gnu/packages/python-crypto.scm (python-paramiko, python2-paramiko):
Update to 2.1.5.
 2018-03-19 14:34:55 -04:00
Tobias Geerinckx-Rice fe15613cdf
gnu: perl-net-ssleay: Update to 1.85. 
* gnu/packages/tls.scm (perl-net-ssleay): Update to 1.85.
 2018-03-19 19:27:41 +01:00
Tobias Geerinckx-Rice b824534bb8
gnu: perl-http-message: Update to 6.15. 
* gnu/packages/web.scm (perl-http-message): Update to 6.15.
[source]: Update URI.
[native-inputs]: Add perl-try-tiny.
 2018-03-19 19:27:40 +01:00
Tobias Geerinckx-Rice a768e41523
gnu: r-minimal, r: Update to 3.4.4. 
There seem to be no dependency updates as far as I could find.

* gnu/packages/statistics.scm (r-minimal): Update to 3.4.4.
 2018-03-19 19:22:32 +01:00
Leo Famulari 6969ad0edd
gnu: python-pynacl: Update to 1.2.0. 
* gnu/packages/python-crypto.scm (python-pynacl): Update to 1.2.0.
[native-inputs]: Add python-hypothesis.
 2018-03-19 12:37:51 -04:00
Ricardo Wurmus d8f08c85ad
gnu: pigx: Update to 0.0.2. 
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
 2018-03-19 16:55:43 +01:00
Ricardo Wurmus d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1. 
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 16:55:43 +01:00
Tobias Geerinckx-Rice 504be7db58
gnu: bash-completion: Update to 2.8. 
* gnu/packages/bash.scm (bash-completion): Update to 2.8.
* gnu/packages/patches/bash-completion-directories.patch: Update context.
 2018-03-19 14:44:13 +01:00
Tobias Geerinckx-Rice 39c6af4774
gnu: hdparm: Update to 9.55. 
* gnu/packages/linux.scm (hdparm): Update to 9.55.
 2018-03-19 14:41:47 +01:00
Tobias Geerinckx-Rice eaa69a7996
gnu: libtirpc: Update to 1.0.3. 
* gnu/packages/onc-rpc.scm (libtirpc): Update to 1.0.3.
[source]: Remove patch.
* gnu/packages/patches/libtirpc-missing-headers.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-03-19 13:25:27 +01:00