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Author SHA1 Message Date
Danny Milosavljevic 91294b5361
Revert 'gnu: rust: Remove unused "ar" setting.'. 
Some versions of Rust do need it and others complain about it.
For now, revert the removal entirely.

This reverts commit ec944a1de9.
 2018-09-22 10:09:47 +02:00
Ben Woodcroft 05fb1e0017
gnu: hmmer: Update to 3.2.1. 
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2018-09-22 09:16:47 +10:00
Nicolas Goaziou 78b7b9dbe9
gnu: snap: Update to 4.2.1.4. 
* gnu/packages/education.scm (snap): Update to 4.2.1.4.
 2018-09-21 22:22:09 +02:00
Nicolas Goaziou a255142af3
gnu: emacs-org: Update to 9.1.14. 
* gnu/packages/emacs.scm (emacs-org): Update to 9.1.14.
 2018-09-21 21:55:28 +02:00
Tobias Geerinckx-Rice 1302837f6b
gnu: workrave: Update to 1.10.21. 
* gnu/packages/gnome.scm (workrave): Update to 1.10.21.
[source]: Use GIT-FILE-NAME.
 2018-09-21 20:32:27 +02:00
Tobias Geerinckx-Rice 43726c522f
gnu: emacs-password-store: Update to 1.7.3. 
* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3.
 2018-09-21 20:32:27 +02:00
Tobias Geerinckx-Rice 10fadd1e3d
gnu: filezilla: Update to 3.37.1. 
* gnu/packages/ftp.scm (filezilla): Update to 3.37.1.
 2018-09-21 19:52:27 +02:00
Tobias Geerinckx-Rice 9a32bdf8a9
gnu: wxwidgets: Update to 3.0.4. 
* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4.
 2018-09-21 19:52:26 +02:00
Tobias Geerinckx-Rice 199d72e327
gnu: python-pyparsing: Update to 2.2.1. 
* gnu/packages/python.scm (python-pyparsing): Update to 2.2.1.
[source]: Use PYPI-URI.
 2018-09-21 19:52:26 +02:00
Danny Milosavljevic ec944a1de9
gnu: rust: Remove unused "ar" setting. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "ar" setting.
 2018-09-21 17:59:09 +02:00
Ludovic Courtès 92a9f14b9d
doc: Add section about inferiors. 
* doc/guix.texi (Inferiors): New node.
(Channels): Add xref to "Inferiors".
 2018-09-21 17:04:38 +02:00
Ludovic Courtès 2dad031375
inferior: Add 'inferior-for-channels'. 
* guix/inferior.scm (%inferior-cache-directory): New variable.
(inferior-for-channels): New procedure.
 2018-09-21 17:04:38 +02:00
Ludovic Courtès c37f38bde6
channels: Add 'channel-instances->derivation'. 
* guix/channels.scm (channel-instances->derivation): New procedure.
(latest-channel-derivation): Use it.
(channel-instance-derivations): Make private.
 2018-09-21 17:04:38 +02:00
Ludovic Courtès 811b21fb15
profiles: 'packages->manifest' now accepts inferior packages. 
* guix/profiles.scm (packages->manifest)[inferiors-loaded?]: New
variable.
[inferior->entry]: New procedure.
Accept inferior packages when INFERIORS-LOADED? is true.
* tests/guix-package.sh: Add test using a manifest with an inferior.
* tests/inferior.scm ("packages->manifest"): New test.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès 2e6d64e122
inferior: Add 'inferior-package->manifest-entry'. 
* guix/inferior.scm (inferior-package->manifest-entry): New procedure.
* tests/inferior.scm (manifest-entry->list): New procedure.
("inferior-package->manifest-entry"): New test.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès eee8b303f6
inferior: Add 'inferior-package-search-paths' & co. 
* guix/inferior.scm (%inferior-package-search-paths)
(inferior-package-native-search-paths)
(inferior-package-search-paths)
(inferior-package-transitive-native-search-paths): New procedures.
* tests/inferior.scm ("inferior-package-search-paths"): New test.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès 6030396aec
inferior: Add 'inferior-package-inputs' & co. 
* guix/inferior.scm (open-inferior): Use (ice-9 match).
(inferior-package-input-field, inferior-package-inputs):
(inferior-package-native-inputs)
(inferior-package-propagated-inputs)
(inferior-package-transitive-propagated-inputs): New procedures.
* tests/inferior.scm ("inferior-package-inputs"): New test.

inputs fixlet
 2018-09-21 17:04:37 +02:00
Ludovic Courtès e1a4ffdab5
inferior: Add 'lookup-inferior-packages'. 
* guix/inferior.scm (<inferior>)[packages, table]: New fields.
(open-inferior): Initialize these new fields.
(inferior-packages): Rename to...
(%inferior-packages): ... this.
(inferior-packages): New procedure; force the promise.
(%inferior-package-table, lookup-inferior-packages): New procedures.
* tests/inferior.scm ("lookup-inferior-packages")
("lookup-inferior-packages and eq?-ness"): New tests.
 2018-09-21 17:04:37 +02:00
Ludovic Courtès 9daf046c5d
inferior: Add 'inferior-package-derivation'. 
* guix/inferior.scm (read-inferior-response)
(send-inferior-request): New procedures.
(inferior-eval): Rewrite in terms of these.
(proxy, inferior-package-derivation, inferior-package->derivation)
(package-compiler): New procedures.
* tests/inferior.scm ("inferior-package-derivation"): New test.
 2018-09-21 17:04:37 +02:00
pimi 7e27393f82
gnu: Add r-pore. 
* gnu/packages/bioinformatics.scm (r-pore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-21 17:04:37 +02:00
Paul Garlick 45201bf245
gnu: hdf5-parallel-openmpi: Really enable parallel build. 
This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.

* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags.  Remove
the incompatible "--enable-cxx" flag.  Add 'mpi-setup' phase.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
 2018-09-21 17:04:37 +02:00
Paul Garlick b0d1e60fff
gnu: hdf5: Allow for absence of utility script. 
* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split'
phase to check for existence of h5fc script.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2018-09-21 17:04:37 +02:00
Danny Milosavljevic 10e066f410
gnu: rust: Remove unused "localstatedir" setting. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "localstatedir" setting.
 2018-09-21 15:21:24 +02:00
Tobias Geerinckx-Rice 118a084531
gnu: libfilezilla: Update to 0.13.2. 
* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.2.
[source]: Use HTTPS.
 2018-09-21 15:04:29 +02:00
Tobias Geerinckx-Rice 41e551b2d3
gnu: python-pyparsing: Update home page. 
* gnu/packages/python.scm (python-pyparsing)[home-page]: Update.
 2018-09-21 15:03:49 +02:00
Tobias Geerinckx-Rice eacb5dc487
gnu: emacs-mu4e-conversation: Fix typo in description. 
* gnu/packages/emacs.scm (emacs-mu4e-conversation)[description]:
Fix 'correspondant' typo.
 2018-09-21 15:03:49 +02:00
Tobias Geerinckx-Rice 93ab9a5d76
gnu: kodi: Use INVOKE. 
* gnu/packages/kodi.scm (kodi)[arguments]: Substitute INVOKE for SYSTEM*.
 2018-09-21 15:03:48 +02:00
Tobias Geerinckx-Rice 2aa137e261
gnu: crossguid: Use INVOKE. 
* gnu/packages/kodi.scm (crossguid)[arguments]: Substitute INVOKE for SYSTEM*.
 2018-09-21 15:03:48 +02:00
Mark H Weaver e67ad5532f
gnu: icecat: Update to 60.2.0-gnu1 (pre-release). 
* gnu/packages/gnuzilla.scm (icecat): Update to 60.2.0-gnu1.
[source]: Download pre-release from alpha.gnu.org.  Remove obsolete patches.
Comment out the code to delete the bundled copies of libevent, cairo,
harfbuzz, and graphite2.
[inputs]: Use the latest ffmpeg.  Comment out libevent, cairo, harfbuzz, and
graphite2.
[native-inputs]: Add rust and cargo.
[arguments]: Remove --enable-gio and --disable-gnomeui.  Add --disable-stylo.
Comment out --with-system-{libevent,harfbuzz,graphite2}, --enable-system-cairo.
Import %cargo-build-system-modules.  Add 'patch-cargo-checksums' phase.
* gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch,
gnu/packages/patches/icecat-bug-1413868-pt1.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2018-09-21 07:16:02 -04:00
Mark H Weaver c5327efb97
gnu: libvpx: Add upstream security fix. 
* gnu/packages/patches/libvpx-use-after-free-in-postproc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/video.scm (libvpx)[source]: Add patch.
 2018-09-21 07:15:59 -04:00
Tobias Geerinckx-Rice 6569549dfa
gnu: python-paramiko: Update to 2.4.2 [security fixes]. 
* gnu/packages/python-crypto.scm (python-paramiko): Update to 2.4.2.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice 101ad242be
gnu: python-paramiko: Use HTTPS home page. 
* gnu/packages/python-crypto.scm (python-paramiko)[home-page]: Use HTTPS.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice a1d6610e84
gnu: python-rencode: Update to 1.0.5. 
* gnu/packages/python.scm (python-rencode): Update to 1.0.5.
[arguments]: Add a 'delete-bogus-test' phase.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice e36058634d
gnu: python-hdf4: Use INVOKE. 
* gnu/packages/python.scm (python-hdf4)[arguments]: Substitute INVOKE
for SYSTEM*.
 2018-09-21 13:18:42 +02:00
Tobias Geerinckx-Rice 6f05556ba7
gnu: s6: Update to 2.7.2.1. 
* gnu/packages/skarnet.scm (s6): Update to 2.7.2.1.
 2018-09-21 13:18:41 +02:00
Tobias Geerinckx-Rice 174988fa05
gnu: perl-xml-compile: Update to 1.60. 
* gnu/packages/xml.scm (perl-xml-compile): Update to 1.60.
[propagated-inputs]: Add perl-carp, perl-scalar-list-utils, and
perl-types-serialiser.
 2018-09-21 13:18:41 +02:00
Nicolas Goaziou 1df40d3dbf
gnu: emacs-orgalist: Update to 1.9. 
* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.9.
 2018-09-21 11:52:12 +02:00
Tobias Geerinckx-Rice 3752b683dc
gnu: openscenegraph: Update to 3.6.3. 
* gnu/packages/graphics.scm (openscenegraph): Update to 3.6.3.
[source]: Use GIT-FILE-NAME.
[inputs]: Remove unused pth and qtbase.
 2018-09-21 10:25:33 +02:00
Tobias Geerinckx-Rice 29ddbc5607
gnu: python-pydot: Update to 1.2.4. 
* gnu/packages/graphviz.scm (python-pydot): Update to 1.2.4.
[arguments]: Run the test suite.
[native-inputs]: Add python-chardet.
 2018-09-21 10:25:32 +02:00
Tobias Geerinckx-Rice 1779aaa09a
Add 'GNU Guix' comment to all (gnu packages) headers. 
* gnu/packages/debian.scm, gnu/packages/syndication.scm: Add comments.
 2018-09-21 10:25:32 +02:00
Tobias Geerinckx-Rice 4aa64e3a81
gnu: ubuntu-keyring: Update to 2018.09.18.1. 
* gnu/packages/debian.scm (ubuntu-keyring): Update to 2018.09.18.1.
 2018-09-21 10:25:32 +02:00
Tobias Geerinckx-Rice eeecbe09cc
gnu: perl-dbd-mysql: Update to 4.048. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.048.
 2018-09-21 10:25:31 +02:00
Danny Milosavljevic e0b07ccc1a
gnu: rust: Work around mtime bug in rust build helpers. 
* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[fix-mtime-bug]:
Delete.
[reset-timestamps-after-changes]: Modify.
(rust-1.24): Don't delete "fix-mtime-bug" since now it doesn't ever
get created.
 2018-09-21 01:35:00 +02:00
Danny Milosavljevic 1bfaae25fa
gnu: rust@1.20.0: Fix tests. 
* gnu/packages/rust.scm (rust-1.23)[arguments]<#:phases>
[patch-cargo-tests, ignore-glibc-2.27-incompatible-test,fix-mtime-bug]: Move
to...
(rust-1.20): ... here.
 2018-09-21 01:31:10 +02:00
Mark H Weaver 83e8b1d794
gnu: linux-libre: Update to 4.18.9. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.9.
(%linux-libre-hash): Update hash.
 2018-09-20 18:04:56 -04:00
Mark H Weaver c57a2a12b1
gnu: linux-libre@4.14: Update to 4.14.71. 
* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.71.
(%linux-libre-4.14-hash): Update hash.
 2018-09-20 18:04:48 -04:00
Mark H Weaver 41d6afb266
gnu: linux-libre@4.9: Update to 4.9.128. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.128.
 2018-09-20 18:04:42 -04:00
Mark H Weaver c6ede267e6
gnu: linux-libre@4.4: Update to 4.4.157. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.157.
 2018-09-20 18:04:35 -04:00
fis trivial ea2364621a
gnu: qbittorrent: Update to 4.1.3. 
* gnu/packages/bittorrent.scm (qbittorrent): Update to 4.1.3.
[inputs]: Use python-wrapper instead of python.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-20 15:31:17 -04:00
fis trivial f5c10a94ef
gnu: gprolog: Update to 1.4.5. 
* gnu/packages/gprolog.scm (gprolog): Update to 1.4.5.
[source]: Add an alternate source URL.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2018-09-20 15:27:43 -04:00