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2022-04-01gnu: vtk@6: Depend on Python 2.x, not 3.x....* gnu/packages/image-processing.scm (vtk-6)[native-inputs]: Replace PYTHON with PYTHON-2. Ludovic Courtès
2022-04-01gnu: libtool: Add 2.4.7....* gnu/packages/autotools.scm (libtool-2.4.7): New variable. Ludovic Courtès
2022-04-01gnu: libressl: Add 'release-monitoring-url' property....* gnu/packages/tls.scm (libressl)[properties]: New field. Ludovic Courtès
2022-04-01gnu: cl-usocket: Update to 0.8.4....* gnu/packages/lisp-xyz.scm (sbcl-usocket): Update to 0.8.4. [inputs]: Use new style. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net> jgart
2022-03-31gnu: libfido2: Fix cross-compilation....* gnu/packages/security-token.scm (libfido2)[arguments]: Set the PKG_CONFIG_EXECUTABLE variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Sébastien Lerique
2022-03-31gnu: libfido2: Use new style for inputs....* gnu/packages/security-token.scm (libfido2)[inputs]: Use new style. Sort alphabetically. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Sébastien Lerique
2022-03-31gnu: tio: Update to 1.36....* gnu/packages/terminals.scm (tio): Update to 1.36. [native-inputs]: Add pkg-config. [inputs]: Add libinih. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Raphaël Mélotte via Guix-patches
2022-03-31gnu: iverilog: Add zlib dependency for LXT dump file format support....* gnu/packages/fpga.scm (iverilog)[native-inputs]: Add zlib. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Christian Gelinek
2022-03-31gnu: gmid: Update to 1.8.3....* gnu/packages/web.scm (gmid): Update to 1.8.3. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> cage
2022-03-31gnu: plantuml: Update to 1.2022.3....* gnu/packages/uml.scm (plantuml): Update to 1.2022.3. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Collin J. Doering
2022-03-31gnu: python-velocyto: Set cache directory for Numba....* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase 'set-numba-cache-dir. Ricardo Wurmus
2022-03-31gnu: wfmash: Enable test suite....* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable tests. Add custom 'check phase based on upstream's own CI tests. [native-inputs]: Add samtools. Efraim Flashner
2022-03-31gnu: Add wfmash....* gnu/packages/bioinformatics.scm (wfmash): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: atomic-queue: Do not look for boost when cross-compiling....* gnu/packages/cpp.scm (atomic-queue)[arguments]: When cross-compiling, add a do-not-check-for-boost phase. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: atomic-queue: Run tests correctly....* gnu/packages/cpp.scm (atomic-queue)[arguments]: In the check phase, run tests instead of returning a function to run them. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: htslib: Add bzip2 and xz to inputs....htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz should be listed in inputs even though they are already present implicitly in native-inputs. Else, cross-compilation will fail. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: gsl: Force bootstrap when cross-compiling to riscv64-linux....* gnu/packages/maths.scm (gsl)[arguments]: Force an autotools bootstrap when cross-compiling to riscv64-linux. [native-inputs]: Add autoconf, automake and libtool when cross-compiling to riscv64-linux. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: python-loompy: Update to 3.0.7....* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7. [arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir; respect TESTS? argument in 'check phase. [propagated-inputs]: Add python-click, python-numba, and python-numpy-groupies. Ricardo Wurmus
2022-03-31gnu: Add python-numpy-groupies....* gnu/packages/python-science.scm (python-numpy-groupies): New variable. Ricardo Wurmus
2022-03-31gnu: Add riscv-pk....* gnu/packages/virtualization.scm (riscv-pk): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: spike: Substitute path to dtc instead of wrapping executables....* gnu/packages/virtualization.scm (spike)[arguments]: Delete the wrap-binary phase. Add a configure-dtc-path phase that substitutes the absolute path to dtc. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: python-anndata: Update to 0.8.0....* gnu/packages/python-xyz.scm (python-anndata): Update to 0.8.0. [arguments]: Remove build phase 'relax-dependency-requirements. Ricardo Wurmus
2022-03-31gnu: python-h5py: Update to 3.6.0....* gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0. [arguments]: Set HDF5_DIR variable instead of patching files. Ricardo Wurmus
2022-03-31gnu: python2-h5py: Detach version and source from python-h5py....* gnu/packages/python-xyz.scm (python2-h5py): Override source and version field. (python-h5py)[properties]: Record python2-variant. Ricardo Wurmus
2022-03-30gnu: weechat: Update to 3.5....* gnu/packages/irc.scm (weechat): Update to 3.5. [inputs]: Add zstd:lib. Efraim Flashner
2022-03-30gnu: msmtp: Update to 1.8.20....* gnu/packages/mail.scm (msmtp): Update to 1.8.20. Efraim Flashner
2022-03-30gnu: ncdu-2: Update to 2.1.1....* gnu/packages/ncdu.scm (ncdu-2): Update to 2.1.1. Efraim Flashner
2022-03-30gnu: ncdu2: Set upstream name....* gnu/packages/ncdu.scm (ncdu-2)[properties]: New field. Efraim Flashner
2022-03-30gnu: anonip: Update to 1.1.0....* gnu/packages/web.scm (anonip): Update to 1.1.0. [source]: Fetch from git. [arguments]: Run tests with pytest. [native-inputs]: Add python-pytest and python-pytest-cov. Ricardo Wurmus
2022-03-30lsof: Prevent mass-rebuild....* gnu/packages/lsof.scm (lsof): Set LINUX_CONF_CC variable only when cross-compiling. Mathieu Othacehe
2022-03-30gnu: lbzip2: Fix cross-compilation....* gnu/packages/compression.scm (lbzip2)[arguments]: Search (or native-inputs inputs) for gnulib-tool.py. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Brian Kubisiak
2022-03-30gnu: lsof: Fix cross-compilation....* gnu/packages/lsof (lsof)[arguments]: Add LINUX_CONF_CC environment variable. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Brian Kubisiak
2022-03-29gnu: Mutt: Update to 2.2.2....* gnu/packages/mail.scm (mutt): Update to 2.2.2. Leo Famulari
2022-03-29gnu: linux-libre 4.9: Update to 4.9.309....* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.309. (linux-libre-4.9-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 4.14: Update to 4.14.274....* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.274. (linux-libre-4.14-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 4.19: Update to 4.19.237....* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.237. (linux-libre-4.19-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 5.4: Update to 5.4.188....* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.188. (linux-libre-5.4-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 5.10: Update to 5.10.109....* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.109. (linux-libre-5.10-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 5.15: Update to 5.15.32....* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.32. (linux-libre-5.15-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 5.16: Update to 5.16.18....* gnu/packages/linux.scm (linux-libre-5.16-version): Update to 5.16.18. (linux-libre-5.16-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: linux-libre 5.17: Update to 5.17.1....* gnu/packages/linux.scm (linux-libre-5.17-version): Update to 5.17.1. (linux-libre-5.17-pristine-source): Update hash. Leo Famulari
2022-03-29gnu: gmid: Update to 1.8.2....* gnu/packages/web.scm (gmid): Update to 1.8.2. [native-inputs]: Remove which. Signed-off-by: Leo Famulari <leo@famulari.name> cage
2022-03-29gnu: git-annex: Update to 10.20220322....* gnu/packages/haskell-apps.scm (git-annex): Update to 10.20220322. [inputs]: Add ghc-http-client-restricted. Signed-off-by: Leo Famulari <leo@famulari.name> Kyle Meyer
2022-03-29gnu: Add ghc-http-client-restricted....* gnu/packages/haskell-web.scm (ghc-http-client-restricted): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Kyle Meyer
2022-03-29gnu: ghc-http-client-tls: Update to 0.3.6.1....* gnu/packages/haskell-web.scm (ghc-http-client-tls): Update to 0.3.6.1. Signed-off-by: Leo Famulari <leo@famulari.name> Kyle Meyer
2022-03-29gnu: ghc-http-client: Update to 0.7.11....* gnu/packages/haskell-web.scm (ghc-http-client): Update to 0.7.11. [inputs]: Add ghc-iproute. Signed-off-by: Leo Famulari <leo@famulari.name> Kyle Meyer
2022-03-29gnu: r-signac: Update to 1.6.0-2.458e647....* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647. [propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings, r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-03-29gnu: plink-ng: Update to 2.00a3-20220315....* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315. Ricardo Wurmus
2022-03-29gnu: Add r-cytobackbone....* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-03-29gnu: pigx-sars-cov2-ww: Update to 0.0.5....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5. [source]: Remove patch. [arguments]: Disable tests. * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
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