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2021-12-09gnu: seek: Update to 1-1.196ed4c....* gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c. [source]: Fetch from github. [build-system]: Use cmake-build-system. [arguments]: Remove all custom phases; replace 'check phase; disable tests; set configure flags. [inputs]: Add apache-thrift:include, apache-thrift:lib, and python. [native-inputs]: Remove autoconf, automake, and perl; add pkg-config. Ricardo Wurmus
2021-12-09gnu: libsvm: Install header and library....* gnu/packages/machine-learning.scm (libsvm)[arguments]: Add build phase 'build-lib; also install header file and shared library in the 'install phase. Ricardo Wurmus
2021-12-09gnu: miso: Update to 0.5.4-1.b714021....* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021. [source]: Fetch via git; simplify snippet. [inputs]: Replace samtools with samtools-1.2. [home-page]: Update to new location. Ricardo Wurmus
2021-12-09gnu: Add samtools-1.2....* gnu/packages/bioinformatics.scm (samtools-1.2): New variable. Ricardo Wurmus
2021-12-09gnu: Add htslib-for-samtools-1.2....* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable. Ricardo Wurmus
2021-12-09gnu: python2-scipy: Override native inputs....* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override; replace gfortran with gfortran-7; add gcc-7. Ricardo Wurmus
2021-12-09gnu: python2-matplotlib: Fix mpl_toolkits module....* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase 'create-init-file; restore 'sanity-check phase. Ricardo Wurmus
2021-12-09gnu: Add gfortran-7....* gnu/packages/gcc.scm (gfortran-7): New variable. Ricardo Wurmus
2021-12-08gnu: python-slepc4py: Update to 3.16.1....This is a followup 5b4d1e57b6d4931f6ee2a50abf84222fe015d045. * gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to... [propagated-inputs]: ... here. (python-slepc4py): Update to 3.16.1. Ludovic Courtès
2021-12-08gnu: python-petsc4py: Update to 3.16.1....This is a followup to 07ac13a26a0d7c8319afb42c55fc2116ec44668f. * gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1. Ludovic Courtès
2021-12-08gnu: geeqie: Fix X11 error at startup....Fixes <https://issues.guix.gnu.org/52089>. Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>. Patch provided by John Kehayias <john.kehayias@protonmail.com>. * gnu/packages/patches/geeqie-clutter.patch: New file. * gnu/packages/image-viewers.scm (geeqie)[sources]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. Ludovic Courtès
2021-12-08gnu: mumps: Allow compilation with GCC 10....Following the suggestion at <https://community.freefem.org/t/compline-on-macos-10-15-6/543>. * gnu/packages/maths.scm (mumps)[arguments]: In 'configure' phase, add '-fallow-argument-mismatch' to 'OPTF'. Ludovic Courtès
2021-12-08maint: Don't require unsupported packages such as GNOME on i686-linux....* etc/release-manifest.scm (%system-manifest): Filter out PACKAGE when it doesn't pass 'supported-package?'. Ludovic Courtès
2021-12-08services: %desktop-services: Use SDDM rather than GDM on non-x86_64....This works around the fact that Rust is currently unavailable in Guix on platforms other than x86_64-linux: https://lists.gnu.org/archive/html/guix-devel/2021-11/msg00197.html * gnu/services/desktop.scm (desktop-services-for-system): New procedure. (%desktop-services): Turn into a macro. Ludovic Courtès
2021-12-08system: Mark 'services' field as thunked....This allows us to make services dependent on (%current-system), for example. * gnu/system.scm (<operating-system>)[services]: Mark as thunked. Ludovic Courtès
2021-12-08gnu: idutils: Fix build with glibc 2.33....* gnu/packages/idutils.scm (idutils)[source]: Remove reference to 'gets' from "lib/stdio.in.h". Ludovic Courtès
2021-12-08gnu: libtorrent-rasterbar: Build with default cmake....* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Remove cmake flag. Efraim Flashner
2021-12-08gnu: tadbit: Update to 1.0.1-1.5c4c1dd....* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd. [arguments]: Remove trailing #T from build phases; pass -fcommon to test binaries; run tests conditionally. Ricardo Wurmus
2021-12-08gnu: python2-sphinx: Remove websupport test....* gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test file. Ricardo Wurmus
2021-12-08gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2....* gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to 1.1.2. [arguments]: Override; delete 'sanity-check phase. [propagated-inputs]: Override and add python2-six. (python-sphinxcontrib-websupport)[properties]: Record python2-variant. Ricardo Wurmus
2021-12-08gnu: python2-jinja2: Downgrade to 2.11.3...* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version supporting Python 2. (python-jinja2)[properties]: Record python2-variant. Ricardo Wurmus
2021-12-08gnu: python2-markupsafe: Downgrade to 1.1.1....* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1, because that's the last version to support Python 2. Ricardo Wurmus
2021-12-08gnu: ocaml-mcl: Add -fcommon to compiler flags....* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon. Ricardo Wurmus
2021-12-08gnu: paml: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS. Ricardo Wurmus
2021-12-08gnu: paml: Remove trailing #T....* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-08gnu: sambamba: Remove trailing #T....* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-08gnu: discrover: Add texlive-fonts-ec to inputs....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-fonts-ec. Ricardo Wurmus
2021-12-08gnu: discrover: Remove trailing #T....* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T from build phases. Ricardo Wurmus
2021-12-08gnu: tbsp: Update to 1.0.0-2.dc30c03....* gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03. [arguments]: Relax requirement on matplot. This may turn out to be a mistake. [inputs]: Replace python-biopython with python-biopython-1.73. Ricardo Wurmus
2021-12-08gnu: mantis: Update to 0.1-2.b6979a2....* gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2. [arguments]: Disable the use of SSE4.2 instructions. [native-inputs]: Build with GCC 7. Ricardo Wurmus
2021-12-08gnu: imp: Disable tests....* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test suite. Ricardo Wurmus
2021-12-08gnu: snap-aligner: Update to 2.0.0....* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0. Ricardo Wurmus
2021-12-08gnu: snap-aligner: Remove trailing #T....* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T from 'install phase. Ricardo Wurmus
2021-12-08gnu: snap-aligner: Run tests conditionally....* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS? option. Ricardo Wurmus
2021-12-08gnu: khmer: Cythonize source files....* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files. [arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp files from Cython sources; add 'build-extensions phase; replace 'check phase. Ricardo Wurmus
2021-12-08gnu: cwltool: Update to 3.1.20211107152837....* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837. [arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T from build phases; fix /bin/sh invocations in test files. Ricardo Wurmus
2021-12-08gnu: lollypop: Build with libsoup@2....* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to LIBSOUP-MINIMAL-2. Marius Bakke
2021-12-08gnu: rhythmbox: Adjust inputs....* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2. Marius Bakke
2021-12-08gnu: labelme: Loosen Python requirements....* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it does not require a specific version of Matplotlib. Marius Bakke
2021-12-07gnu: newick-utils: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS. Ricardo Wurmus
2021-12-07gnu: blasr: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5. Ricardo Wurmus
2021-12-07gnu: blasr: Remove trailing #T....* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase. Ricardo Wurmus
2021-12-07gnu: blasr-libcpp: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib. Ricardo Wurmus
2021-12-07gnu: htseq: Update to 0.12.3....* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3. Ricardo Wurmus
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: 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: 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
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