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Author SHA1 Message Date
Efraim Flashner
a0400dc9a5
gnu: python-pandas: Honor #:tests? flag. 
* gnu/packages/python-science.scm (python-pandas)[arguments]: Adjust
custom 'check phase to honor the #:tests? flag.
 2021-10-25 14:01:32 +03:00
Efraim Flashner
ab961fe542
gnu: python-cython: Honor #:tests? flag. 
* gnu/packages/python-xyz.scm (python-cython)[arguments]: Adjust custom
'check phase to honor the #:tests? flag.
 2021-10-25 14:01:32 +03:00
Efraim Flashner
2de88bcd7a
gnu: python-cython: Update to 0.29.24. 
* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.24.
[arguments]: Adjust custom 'check phase to skip one test. Remove
trailing #t from phases.
 2021-10-25 14:01:32 +03:00
Guillaume Le Vaillant
988eb73d5b
gnu: gnuradio: Disable a randomly failing test. 
* gnu/packages/radio.scm (gnuradio)[arguments]: Add qa_rotator_cc to the list
  of disabled tests.
 2021-10-25 11:45:53 +02:00
Guillaume Le Vaillant
78a7c7f078
gnu: python-pyqtgraph: Disable one failing test. 
* gnu/packages/python-xyz.scm (python-pyqtgraph)[arguments]: Add test_reload
  to list of disabled tests.
 2021-10-25 11:31:56 +02:00
Guillaume Le Vaillant
f3496c2b5c
gnu: hexchat: Fix build. 
* gnu/packages/messaging.scm (hexchat)[arguments]: Use GUIX_PYTHONPATH instead
  of PYTHONPATH in 'wrap-program' phase.
 2021-10-25 11:13:04 +02:00
Ricardo Wurmus
2640da8410
gnu: java-cisd-args4j: Copy instead of unpacking input. 
* gnu/packages/java.scm (java-cisd-args4j)[arguments]: Do not unpack
build-resources input; just copy the contents.
 2021-10-24 23:26:59 +00:00
Ricardo Wurmus
41e5c12c4a
gnu: sailfish: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 21:38:25 +00:00
Ricardo Wurmus
1bf55a4850
gnu: sailfish: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in
build phases...
[inputs]: ...and in the origin snippet of "rapmap".
 2021-10-24 21:37:39 +00:00
Ricardo Wurmus
4392783232
gnu: sailfish: Do not attempt to unpack a directory. 
patch-and-repack no longer outputs a compressed archive when the input was a
directory.

* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Adjust build phase
'prepare-rapmap.
 2021-10-24 21:35:57 +00:00
Ricardo Wurmus
57c233b37b
gnu: jellyfish: Remove Ruby bindings. 
These bindings no longer build and we have no package that would need them.

* gnu/packages/bioinformatics.scm (jellyfish)[outputs]: Remove "ruby" output.
[arguments]: Remove option for building Ruby bindings.
[native-inputs]: Remove ruby.
 2021-10-24 21:34:26 +00:00
Ricardo Wurmus
da526f33f2
gnu: cutadapt: Regenerate Cython files. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
 2021-10-24 21:23:20 +00:00
Ricardo Wurmus
3eeae68af1
gnu: python-requests-unixsocket: Fix tests. 
* gnu/packages/python-web.scm (python-requests-unixsocket)[arguments]: Do not
run tests with --pep8 option; only run tests when enabled.
 2021-10-24 20:49:46 +00:00
Ricardo Wurmus
b67013c8ca
gnu: python-mpmath: Update to 1.2.1. 
* gnu/packages/python-xyz.scm (python-mpmath): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Run tests directly with pytest; set the version with setuptools.
[native-inputs]: Add python-setuptools-scm.
 2021-10-24 20:10:26 +00:00
Ricardo Wurmus
722c4685f0
gnu: java-commons-io: Replace %build-inputs with gexp. 
* gnu/packages/java.scm (java-commons-io)[arguments]: Do not use
%build-inputs; use gexp with this-package-native-inputs instead.
 2021-10-24 20:02:54 +00:00
Ricardo Wurmus
4faca03bed
gnu: python-dnaio: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
 2021-10-24 19:47:20 +00:00
Ricardo Wurmus
88919aa8a2
gnu: python-xopen: Update to 0.8.2. 
* gnu/packages/python-xyz.scm (python-xopen): Update to 0.8.2.
 2021-10-24 19:47:02 +00:00
Ricardo Wurmus
238f47c76f
gnu: macs: Fix build by setting HOME. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
 2021-10-24 19:09:35 +00:00
Ricardo Wurmus
1d01043a4f
gnu: methyldackel: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
 2021-10-24 19:01:22 +00:00
Ricardo Wurmus
2820b03509
gnu: methyldackel: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
 2021-10-24 19:00:53 +00:00
Ricardo Wurmus
cc331ad7eb
gnu: flexbar: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:50:09 +00:00
Ricardo Wurmus
084bdf9d69
gnu: flexbar: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
 2021-10-24 18:49:43 +00:00
Ricardo Wurmus
d0a1d798ee
gnu: bwa: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
 2021-10-24 18:48:53 +00:00
Ricardo Wurmus
2da99b671e
gnu: bwa: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
 2021-10-24 18:48:20 +00:00
Ricardo Wurmus
724972bcca
gnu: bowtie1: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:47:45 +00:00
Ricardo Wurmus
f336cc4fe7
gnu: bowtie: Replace invalid characters. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
 2021-10-24 18:44:57 +00:00
Ricardo Wurmus
e5a26a1f02
gnu: bowtie: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
 2021-10-24 16:59:39 +00:00
Ricardo Wurmus
2ec601580b
gnu: bowtie: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
 2021-10-24 16:58:58 +00:00
Ricardo Wurmus
7f151c9bd8
gnu: diffoscope: Update to 188. 
* gnu/packages/diffoscope.scm (diffoscope): Update to 188.
 2021-10-24 15:09:31 +00:00
Ricardo Wurmus
b142611b36
gnu: diffoscope: Disable another broken libfile test. 
* gnu/packages/diffoscope.scm (diffoscope)[arguments]: Rename build phase
'remove-berkeley-test to 'remove-broken-file-type-detection-test and delete
another test that is broken due to our `file' package.
 2021-10-24 15:09:30 +00:00
Ricardo Wurmus
1d9cf387b3
gnu: python-magic: Update to 0.4.24. 
* gnu/packages/python-xyz.scm (python-magic): Update to 0.4.24.
 2021-10-24 15:09:18 +00:00
Ricardo Wurmus
b3ac826e18
gnu: blender: Use older TBB and update header variables. 
* gnu/packages/graphics.scm (blender)[inputs]: Replace tbb with tbb-2020.
[arguments]: Don't set CPATH; set C_INCLUDE_PATH and CPLUS_INCLUDE_PATH instead.
 2021-10-24 13:28:05 +00:00
Ricardo Wurmus
78ea1ce7d5
gnu: openvdb: Use older version of TBB. 
* gnu/packages/graphics.scm (openvdb)[inputs]: Replace tbb with tbb-2020.
 2021-10-24 13:28:05 +00:00
Ricardo Wurmus
42873c2b06
gnu: tbb-for-salmon: Rename. 
* gnu/packages/tbb.scm (tbb-for-salmon): Rename this variable...
(tbb-2020): ...to this.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Rename it.
 2021-10-24 13:28:05 +00:00
Ludovic Courtès
22e753b9b1
gnu: hdf-java: Look for jars in the right place. 
* gnu/packages/maths.scm (hdf-java)[arguments]: Look for slf4j .jar
files in the right place rather than share/java.
 2021-10-23 23:19:02 +02:00
Ludovic Courtès
2dffe4767c
gnu: Use 'search-input-file' some more. 
This patch replaces occurrences of:

  (string-append (assoc-ref %build-inputs "…") "/…")

by:

  (search-input-file %build-inputs "/…")

* doc/guix.texi (Miscellaneous Services): Use 'search-input-file' in R
Shiny example.
* gnu/packages/admin.scm (screenfetch): Use 'search-input-file'.
(ufetch): Likewise.
(hosts): Likewise.
* gnu/packages/backup.scm (dirvish): Likewise.
* gnu/packages/code.scm (colormake): Likewise.
* gnu/packages/compression.scm (makeself-safeextract): Likewise.
* gnu/packages/debug.scm (scanmem): Likewise.
* gnu/packages/education.scm (snap): Likewise.
(omnitux): Likewise.
* gnu/packages/emacs-xyz.scm (epipe): Likewise.
* gnu/packages/games.scm (openttd-opensfx): Likewise.
(openttd-openmsx): Likewise.
(openrct2-title-sequences):  Likewise.
(openrct2-objects):  Likewise.
(mrrescue):  Likewise.
(0ad-data):  Likewise.
(xonotic-data):  Likewise.
(drascula):  Likewise.
(make-lure-package):  Likewise.
(make-queen-package):  Likewise.
(sky):  Likewise.
* gnu/packages/gnome.scm (network-manager): Likewise.
* gnu/packages/gnuzilla.scm (icedove): Likewise.
* gnu/packages/guile-xyz.scm (guile-shapefile): Likewise.
* gnu/packages/hurd.scm (netdde): Likewise.
* gnu/packages/javascript.scm (js-context-menu): Likewise.
(js-commander): Likewise.
(js-xmldom-sre): Likewise.
* gnu/packages/kde-frameworks.scm (krunner): Likewise.
* gnu/packages/kodi.scm (kodi-cli): Likewise.
* gnu/packages/libreoffice.scm (hunspell-dict-pl): Likewise.
* gnu/packages/linux.scm (e2fsck/static): Likewise.
* gnu/packages/markup.scm (markdown): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
* gnu/packages/multiprecision.scm (libtomcrypt): Likewise.
* gnu/packages/networking.scm (batctl): Likewise.
* gnu/packages/python-xyz.scm (python-pymediainfo): Likewise.
* gnu/packages/shells.scm (fish-foreign-env): Likewise.
* gnu/packages/tex.scm (texlive-fonts-iwona): Likewise.
* gnu/packages/upnp.scm (miniupnpc): Likewise.
* gnu/packages/version-control.scm (git-annex-remote-rclone): Likewise.
* gnu/packages/virtualization.scm (qemu): Likewise.
* gnu/packages/web.scm (icedtea-web): Likewise.
* gnu/packages/wm.scm (stumpish): Likewise.
 2021-10-23 23:05:21 +02:00
Josselin Poiret
e5f21c7e38
gnu: qpdfview: Fix build. 
* gnu/packages/pdf.scm (qpdfview)[arguments]: Fix 'configure' phase.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2021-10-22 11:12:18 +02:00
Ricardo Wurmus
bcad95d054
gnu: lilypond: Remove trailing #t from build phases. 
* gnu/packages/music.scm (lilypond)[arguments]: Remove trailing #t from build
phases.
 2021-10-21 21:55:07 +00:00
Ricardo Wurmus
751b68981c
gnu: lilypond: Fix build with Ghostscript 9.54. 
* gnu/packages/music.scm (lilypond)[arguments]: Add build phase
'adjust-to-API-change.
 2021-10-21 21:53:46 +00:00
Ricardo Wurmus
000b34085b
gnu: pdfpc: Update to 4.5.0. 
* gnu/packages/pdf.scm (pdfpc): Update to 4.5.0.
[inputs]: Add discount, json-glib, and webkitgtk.
[license]: Update license from GPLv2+ to GPLv3+.
[arguments]: Work around a bug in Vala in new build phase
'fix-vala-API-conflict.
 2021-10-21 21:29:54 +00:00
Ricardo Wurmus
3d03f4c4ca
gnu: texlive-lh: Install more files. 
* gnu/packages/tex.scm (texlive-lh)[outputs]: Add a "doc" output.
[arguments]: Override the 'copy-files phase to install many more files in the
correct locations.
 2021-10-21 18:02:04 +00:00
Ricardo Wurmus
7fdd112815
gnu: lepton-eda: Pass -fcommon. 
* gnu/packages/engineering.scm (lepton-eda)[arguments]: Add -fcommon to
CFLAGS.
 2021-10-21 17:54:55 +00:00
Ricardo Wurmus
9380f4e43d
gnu: geda-gaf: Update to 1.10.2. 
* gnu/packages/engineering.scm (geda-gaf): Update to 1.10.2.
[native-inputs]: Add groff.
 2021-10-21 17:36:33 +00:00
Ricardo Wurmus
fc15512be4
gnu: gtksheet: Fix build. 
* gnu/packages/gtk.scm (gtksheet)[arguments]: Pass -fcommon option to GCC;
rename phase 'rename-type to 'patch-for-compatibility and update a reference
to a renamed macro.
 2021-10-21 15:58:06 +00:00
Ricardo Wurmus
dd49a72af7
gnu: gxtuner: Add phase to target specific glib API version. 
* gnu/packages/music.scm (gxtuner)[arguments]: Fix build by adding build phase
'target-specific-glib-API-version.
 2021-10-21 15:49:12 +00:00
Ricardo Wurmus
777dfcd9e0
gnu: gerbv: Fix linker error by adding -fcommon to CFLAGS. 
* gnu/packages/engineering.scm (gerbv)[arguments]: Set -fcommon option.
 2021-10-21 15:25:51 +00:00
Ricardo Wurmus
0ab197f31f
gnu: peek: Add missing input. 
* gnu/packages/video.scm (peek)[inputs]: Add python-wrapper.
 2021-10-21 15:09:29 +00:00
Ricardo Wurmus
727f05e1e2
gnu: awscli: Update to 1.20.64. 
* gnu/packages/python-web.scm (awscli): Update to 1.20.64.
[arguments]: Remove trailing #t.
[propagated-inputs]: Replace python-colorama with python-colorama-for-awscli;
replace python-docutils with python-docutils-0.15.
 2021-10-19 13:23:27 +00:00
Ricardo Wurmus
d5f89c0b93
gnu: python-boto3: Update to 1.18.64. 
* gnu/packages/python-xyz.scm (python-boto3): Update to 1.18.64.
[arguments]: Remove trailing #t.
[native-inputs]: Add python-pytest.
 2021-10-19 13:22:52 +00:00
Ricardo Wurmus
fcd17fdeac
gnu: python-botocore: Update to 1.21.64. 
* gnu/packages/python-xyz.scm (python-botocore): Update to 1.21.64.
 2021-10-19 13:22:33 +00:00