~ruther/guix-local

8fa7de38 — Ricardo Wurmus 4 years ago 
gnu: r-flowclust: Add gsl.

* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
3e9dc275 — Mark H Weaver 4 years ago 
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.

This is a followup to commit a63231003e7bbeafb0110b077788e47e78685f20.

* gnu/packages/patches/icecat-78-makeicecat.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
c0d9ba22 — Mathieu Othacehe 4 years ago 
gnu: cuirass: Update to 1.1.0-6.df8837c.

* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
fcf7e651 — jgart 4 years ago 
gnu: python-pandocfilters: Update to 1.5.0.

* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
d49e7a59 — Mark H Weaver 4 years ago 
gnu: icecat: Fix CVE-2021-43527.

* gnu/packages/patches/icecat-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat-source): Apply it.
080a5de2 — Mark H Weaver 4 years ago 
gnu: nss: Fix CVE-2021-43527 via graft.

* gnu/packages/patches/nss-CVE-2021-43527.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/nss.scm (nss/fixed): New variable
(nss)[replacement]: New field.
345b3419 — Ricardo Wurmus 4 years ago 
gnu: openjdk16: Use MAKE-FILE-WRITABLE.

* gnu/packages/java.scm (openjdk16)[arguments]: Do not shell out to "chmod".
68e71fbb — Arne Babenhauserheide 4 years ago 
gnu: Add openjdk17.

* gnu/packages/java.scm (openjdk17): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
f697fc26 — Leo Famulari 4 years ago 
doc: Give more details about generating patches with base commit information.

* doc/contributing.texi (Submitting Patches): Talk more about '--base'.
1f5c1bc0 — Ricardo Wurmus 4 years ago 
gnu: python2-decorator: Downgrade to 4.3.0

* gnu/packages/python-xyz.scm (python2-decorator): Keep at 4.3.0.
(python-decorator)[properties]: Add python2-variant.
a2423c0c — Ricardo Wurmus 4 years ago 
gnu: ribodiff: Remove trailing #T.

* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T
from build phase.
1123d258 — Ricardo Wurmus 4 years ago 
gnu: ribodiff: Disable broken test.

* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase
'disable-plot-test.
f28f5be1 — Ricardo Wurmus 4 years ago 
gnu: python2-statsmodels: Downgrade to 0.9.0.

* gnu/packages/statistics.scm (python2-statsmodels): Downgrade to 0.9.0.
31d372cd — Ricardo Wurmus 4 years ago 
gnu: khmer: Fix build with Python 3.8.

* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
32d5fb01 — Ricardo Wurmus 4 years ago 
gnu: python-biom-format: Update to 2.1.10.

* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
fab80c36 — jgart 4 years ago 
gnu: Add trayer-srg.

* gnu/packages/wm.scm (trayer-srg): New variable.

Co-authored-by: Disseminate Dissent <disseminatedissent@protonmail.com>
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
28ad55a5 — Ricardo Wurmus 4 years ago 
gnu: pardre: Update to 2.2.5.

* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5.
[arguments]: Remove trailing #T and update comment about tests.
fc20fad6 — Ricardo Wurmus 4 years ago 
gnu: pardre: Use C++ bindings for MPI.

* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with
openmpi-c++.
2d6be35e — Ricardo Wurmus 4 years ago 
gnu: Add openmpi-c++.

* gnu/packages/mpi.scm (openmpi-c++): New variable.
df4f960c — Liliana Marie Prikler 4 years ago 
gnu: Add libconfini.

* gnu/packages/cpp.scm (libconfini): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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