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2021-12-07gnu: clipper: Update to 2.0.1.•••* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1. [source]: Add snippet to remove pre-compiled files. [arguments]: Disable tests, delete 'sanity-check phase, and add 'use-python3-for-cython phase. Ricardo Wurmus
2021-12-07gnu: pbbam: Update to 1.7.0.•••* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper. Ricardo Wurmus
2021-12-07gnu: dovecot-pigeonhole: Update to 0.5.17.1.•••* gnu/packages/mail.scm (dovecot-pigeonhole): Update to 0.5.17.1. Tobias Geerinckx-Rice
2021-12-07gnu: dovecot: Update to 2.3.17.1.•••* gnu/packages/mail.scm (dovecot): Update to 2.3.17.1. Tobias Geerinckx-Rice
2021-12-07gnu: bwa-pssm: Fix build.•••* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error. Ricardo Wurmus
2021-12-07gnu: Add pbcopper.•••* gnu/packages/bioinformatics.scm (pbcopper): New variable. Ricardo Wurmus
2021-12-07gnu: giac: Update to 1.7.0-43.•••* gnu/packages/algebra.scm (giac): Update to 1.7.0-43. Nicolas Goaziou
2021-12-07gnu: python-ndg-httpsclient: Add missing input.•••* gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add python-pyasn1. Ricardo Wurmus
2021-12-07gnu: fsom: Build with GCC 6.•••* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T. Ricardo Wurmus
2021-12-07gnu: python-velocyto: Remove generated C files.•••* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files. Ricardo Wurmus
2021-12-07gnu: python-schema-salad: Update to 8.2.20211116214159.•••* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.2.20211116214159. [arguments]: Remove trailing #T. [propagated-inputs]: Replace python-cachecontrol-0.11 with python-cachecontrol. [native-inputs]: Add python-black. Ricardo Wurmus
2021-12-07gnu: taxtastic: Update to 0.9.2.•••* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase. Ricardo Wurmus
2021-12-07gnu: taxtastic: Run tests conditionally.•••* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option. Ricardo Wurmus
2021-12-07gnu: python-dendropy: Update to 4.5.1.•••* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests. Ricardo Wurmus
2021-12-07gnu: make-gccgo: Override empty GOROOT/GCCGOTOOLDIR•••gnu/packages/gcc.scm (make-gccgo)[arguments]: Set tool paths (GOROOT and GCCGOTOOLDIR) even if they are already set to "". Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Sarah Morgensen
2021-12-07gnu: python-cooler: Use python-cytoolz-for-cooler.•••* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler. Ricardo Wurmus
2021-12-07gnu: Add python-cytoolz-for-cooler.•••* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable. Ricardo Wurmus
2021-12-07gnu: python-sparse: Update to 0.13.0.•••* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0. Ricardo Wurmus
2021-12-07gnu: Add diffr.•••* gnu/packages/rust-apps.scm (diffr): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> jgart
2021-12-07gnu: python-dask: Update to 2021.11.2.•••* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2. [source]: Fetch from github. [arguments]: Remove phase 'disable-broken-tests. Ricardo Wurmus
2021-12-07gnu: python-dask: Run tests conditionally.•••* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option. Ricardo Wurmus
2021-12-07gnu: python-dask: Add missing input for tests.•••* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add python-pytest-rerunfailures. Ricardo Wurmus
2021-12-07gnu: Add rust-diffr-lib-0.1.•••* gnu/packages/crates-io.scm (rust-diffr-lib-0.1): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> jgart
2021-12-07gnu: phylip: Update to 3.697.•••* gnu/packages/bioinformatics.scm (phylip): Update to 3.697. Ricardo Wurmus
2021-12-07gnu: phylip: Pass -fcommon to compiler.•••* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS. Ricardo Wurmus
2021-12-07gnu: phylip: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-07gnu: Add dutree.•••* gnu/packages/rust-apps.scm (dutree): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> jgart
2021-12-07gnu: subread: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-07gnu: subread: Update to 2.0.3.•••* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3. Ricardo Wurmus
2021-12-07gnu: subread: Update home page..•••* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page. Ricardo Wurmus
2021-12-07gnu: subread: Pass -fcommon to compiler.•••* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags. Ricardo Wurmus
2021-12-07gnu: python-pytest-console-scripts: Update to 1.2.1.•••* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to 1.2.1. Ricardo Wurmus
2021-12-07gnu: Add python-pytest-rerunfailures.•••* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable. Ricardo Wurmus
2021-12-07gnu: mcl: Add -fcommon to compiler flags.•••* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS. Ricardo Wurmus
2021-12-07gnu: python-cytoolz: Update to 0.11.2.•••* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2. [source]: Add snippet. Ricardo Wurmus
2021-12-07gnu: hisat: Update to 0.1.6.•••* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6. Ricardo Wurmus
2021-12-07gnu: hisat: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from build phase. Ricardo Wurmus
2021-12-07gnu: hisat: Remove invalid characters.•••* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes. Ricardo Wurmus
2021-12-07gnu: crossmap: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1. [source]: Add snippet to remove generated files. Ricardo Wurmus
2021-12-07gnu: Remove python2-bx-python.•••* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable. Ricardo Wurmus
2021-12-07gnu: python-bx-python: Update to 0.8.12.•••* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12. [propagated-inputs]: Remove python-six. [arguments]: Remove. Tests are still not run, though. Ricardo Wurmus
2021-12-07gnu: Remove pbtranscript-tofu.•••Upstream has disappeared and it depends on Python 2, which is no longer supported. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable. Ricardo Wurmus
2021-12-07gnu: python-pyfit-sne: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1. [arguments]: Disable tests explicitly. Ricardo Wurmus
2021-12-07gnu: guile-netlink: Update to 1.1.1.•••* gnu/packages/guile.scm (guile-netlink): Update to 1.1.1. Julien Lepiller
2021-12-06gnu: emacs-csv-mode: Update to 1.17.•••* gnu/packages/emacs-xyz.scm (emacs-csv-mode): Update to 1.17. Nicolas Goaziou
2021-12-06gnu: helm: Fix build with GCC 9 and later.•••* gnu/packages/music.scm (helm)[origin]: Add patch. * gnu/packages/patches/helm-fix-gcc-9-build.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Pierre Langlois
2021-12-06tests: patchwork: Use the default PostgreSQL.•••* gnu/tests/web.scm (patchwork-os)[services]: Change from POSTGRESQL-10 to POSTGRESQL. Marius Bakke
2021-12-06gnu: patchwork: Adjust for python-build-system change.•••This is a follow-up to commit db5646d957895944007c1bb44fcd998ea392f168, et.al. * gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more site-packages call. Marius Bakke
2021-12-06gnu: f-seq: Update name of commons-cli JAR.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of commons-cli JAR. Ricardo Wurmus
2021-12-06gnu: f-seq: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from build phase. Ricardo Wurmus
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