a31a4517b6
gnu: julia-finitedifferences: Fix tests on i686-linux.
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* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
2a749f34e5
gnu: julia-benchmarktools: Fix tests on i686-linux.
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* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>:
Conditionnally disable the failing tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
7fee8a46fb
gnu: julia-datastructures: Fix tests on i686-linux.
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* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
9112bed608
gnu: libunwind-julia: Fix build on i686-linux.
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* gnu/packages/julia.scm (libunwind)[origin]<patches>: Add patch.
* gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: New file.
* gnu/local/mk (dist_patch_DATA): Register it.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:33:30 +02:00
cc491eab7e
gnu: plink-ng: Enable tests.
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* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
2021-12-04 16:00:08 +01:00
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:35:28 +01:00
88bb81b515
gnu: plink: Remove reference to %build-inputs.
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* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
2021-12-04 15:31:31 +01:00
e920101141
gnu: plink: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
2021-12-04 15:31:08 +01:00
a4e7475edc
gnu: rsem: Update to 1.3.3.
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* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
2021-12-04 15:27:39 +01:00
c45c909026
gnu: rsem: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:26:48 +01:00
5e0bcba57b
gnu: rsem: Remove references to %build-inputs.
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* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
2021-12-04 15:26:01 +01:00
23975fe27a
gnu: rsem: Remove trailing #T from snippet.
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* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
2021-12-04 15:25:26 +01:00
cfaf37d10b
gnu: prodigal: Remove reference to %outputs.
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* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:13:11 +01:00
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase.
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* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
2021-12-04 15:11:28 +01:00
e128839a94
gnu: prank: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:11:04 +01:00
114eb987cb
gnu: mash: Replace references to %build-inputs.
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* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
2021-12-04 00:32:01 +01:00
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs.
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* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
2021-12-04 00:31:20 +01:00
a6b6084649
gnu: mash: Simplify snippet.
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* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04 00:30:44 +01:00
31409a4af7
gnu: mafft: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
2021-12-04 00:22:27 +01:00
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs.
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* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
2021-12-04 00:21:27 +01:00
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04 00:19:08 +01:00
7c2ee27360
gnu: fastp: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04 00:16:10 +01:00
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
2021-12-04 00:06:43 +01:00
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
2021-12-04 00:03:54 +01:00
62e0641892
gnu: fxtract: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04 00:02:20 +01:00
4f03151ca4
gnu: delly: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-04 00:00:26 +01:00
3601fcbf65
gnu: libbigwig: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:57:24 +01:00
fd607a9efa
gnu: cd-hit: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
2021-12-03 23:56:11 +01:00
c40852a227
gnu: bowtie1: Replace reference to %outputs.
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* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-03 23:54:10 +01:00
a47a90b900
gnu: bowtie: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:52:43 +01:00
f5c38ee45f
gnu: bless: Remove reference to %build-inputs.
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* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp. Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
2021-12-03 23:51:16 +01:00
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases.
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* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
2021-12-03 23:48:46 +01:00
0e09065460
gnu: bedtools: Remove reference to %outputs.
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* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
2021-12-03 23:36:18 +01:00
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs.
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* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
2021-12-03 23:26:48 +01:00
6d4f260166
gnu: bamutils: Update to 1.0.14.
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* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
2021-12-03 13:56:02 +01:00
673cc29908
gnu: bamutils: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
361e0d9f27
gnu: bamm: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
2021-12-03 13:56:01 +01:00
4f536c4607
gnu: python2-openpyxl: Explicitly build with Python 2.
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* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value
for #:python field.
2021-12-03 13:56:01 +01:00
7fb5bfc54f
gnu: python-plastid: Update to 0.5.1.
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* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
2021-12-03 13:56:01 +01:00
e080e35dc1
gnu: glade: Remove dependency on GJS on non-x86_64.
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* gnu/packages/gnome.scm (glade3)[arguments]: Add optional
'skip-gjs-test' phase.
[native-inputs]: Provide GJS only when 'target-x86-64?'.
2021-12-02 14:59:57 +01:00
689d141cd8
gnu: Remove librsvg@2.50 from the Xfce dependency graph.
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This allows us to build Xfce on non-x86_64 platforms.
* gnu/packages/gstreamer.scm (gst-plugins-good)[inputs]: Use
'librsvg-for-system' instead of 'librsvg'.
* gnu/packages/gtk.scm (guile-rsvg)[inputs]: Likewise.
* gnu/packages/xfce.scm (xfce4-xkb-plugin)[inputs]: Likewise.
2021-12-02 14:59:57 +01:00
d371abbd0f
gnu: librsvg: Add 'librsvg-for-system' procedure.
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* gnu/packages/gnome.scm (librsvg-for-system): New procedure.
2021-12-02 14:59:56 +01:00
8477a6d743
gnu: librsvg: Reintroduce version 2.40.
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* gnu/packages/gnome.scm (librsvg-2.40): New variable.
2021-12-02 14:59:56 +01:00
37c475ebc0
gnu: prinseq: Fix use of SEARCH-INPUT-FILE.
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* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Pass missing argument
to SEARCH-INPUT-FILE.
2021-12-02 11:26:55 +01:00
f1fd313e48
gnu: gnome-shell: Do not wrap in LD_LIBRARY_PATH.
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Fixes <https://bugs.gnu.org/37123 >.
* gnu/packages/gnome.scm (gnome-shell)[arguments]: Remove LD_LIBRARY_PATH from
wrapper.
2021-12-02 10:52:45 +01:00
e1cb787870
gnu: python2-matplotlib: Disable sanity-check.
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* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Delete
'sanity-check phase.
2021-12-02 10:30:40 +01:00
a33ca53492
gnu: python2-matplotlib: Remove trailing #T.
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* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Remove
trailing #T from build phase.
2021-12-02 10:29:59 +01:00
c14ab97a03
Revert "gnu: Change source file-name suffix in rust packages."
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This reverts commit 07a80e30a1
2021-12-02 11:10:37 +02:00
e577889828
gnu: tor: Limit test suite adjustments to affected architectures.
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This is a follow-up to 68d090002a
2021-12-02 11:07:18 +02:00
24832d2ebd
gnu: python2-numpy: Delete file that depends on deleted test.
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This is a follow-up to commit ec4892c742
2021-12-02 09:45:24 +01:00
zimoun
Ricardo Wurmus
Ludovic Courtès
Efraim Flashner