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| * | gnu: python2-numpy@1.8: Provide "python2-nose".Marius Bakke2018-11-25
| | | | | | | | | | | | | | | | | | Also remove other native-inputs since they appear unnecessary. * gnu/packages/python.scm (python2-numpy-1.8)[native-inputs]: New field.
| * | gnu: diffoscope: Update to 106.Julien Lepiller2018-11-25
| | | | | | | | | | | | * gnu/packages/package-management.scm (diffoscope): Update to 106.
| * | gnu: diffoscope: Fix test failure.Julien Lepiller2018-11-25
| | | | | | | | | | | | | | | * gnu/packages/package-management.scm (diffoscope)[arguments]: Remove failing Berkeley DB test.
| * | Merge branch 'master' into core-updatesMarius Bakke2018-11-24
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| * | | gnu: python-pika: Update to 0.12.0.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-pika): Update to 0.12.0.
| * | | gnu: bless: Adjust to zlib static output.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC. [arguments]: Adjust #:make-flags accordingly.
| * | | gnu: adb: Fix FTBFS with Glibc 2.28.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/android.scm (adb)[arguments]: Add phase 'glibc-compat'.
| * | | gnu: python2-fasteners: Propagate python2-futures.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-fasteners)[properties]: New field. (python2-fasteners)[propagated-inputs]: Add PYTHON2-FUTURES.
| * | | gnu: python2-futures: Update to 3.2.0.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/python.scm (python2-futures): Update to 3.2.0.
| * | | gnu: python2-futures: Disable tests.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/python.scm (python2-futures)[arguments]: Set #:test? #f.
| * | | gnu: python-pycurl: Fix FTBFS from 7b844100464633db5455a3931858bb57c9e529e6.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | | | | | * gnu/packages/python-web.scm (python-pycurl)[arguments]: Add phase 'configure-tls-backend'.
| * | | gnu: ledger: Fix build with Boost >= 1.68.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/finance.scm (ledger)[arguments]: Add phase 'boost-compat.
| * | | gnu: mosaik: Fix FTBFS from b90289dadc8ee15848ce911a2bdcd3ae8302d58c.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
| * | | gnu: python-cheetah: Update to 3.1.0.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python2-cheetah): Rename to ... (python-cheetah): ... this. Update to 3.1.0. [arguments]: Add custom 'check' phase. [propagated-inputs]: Change PYTHON2-MARKDOWN to PYTHON-MARKDOWN. (python2-cheetah): Rewrite in terms of PACKAGE-WITH-PYTHON2.
| * | | gnu: python2-cheetah: Update home page.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-cheetah)[home-page]: Update to current.
| * | | gnu: rust: Don't depend on 'git'.Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/rust.scm (rust-1.19)[inputs]: Remove GIT. (rust-1.20)[arguments]: Disable Cargo tests that require git. (rust-1.26)[arguments]: Likewise.
| * | | gnu: mariadb: Update to 10.1.37 [security fixes].Marius Bakke2018-11-24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This release fixes CVE-2018-3282, CVE-2018-3174, CVE-2018-3143, CVE-2018-3156, and CVE-2018-3251. See <https://mariadb.com/kb/en/library/mariadb-10137-release-notes/> for details. * gnu/packages/databases.scm (mariadb): Update to 10.1.37.
| * | | Merge branch 'master' into core-updatesMarius Bakke2018-11-24
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| * | | | gnu: pt-scotch, pt-scotch32: Add Open MPI setup phase.Ludovic Courtès2018-11-23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/maths.scm (pt-scotch)[arguments]: Use 'invoke' instead of 'system*'. Add 'mpi-setup' phase. (pt-scotch32)[arguments]: Likewise.
| * | | | gnu: pigx-scrnaseq: Use latest snakemake.Ricardo Wurmus2018-11-23
| | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4 with snakemake.
| * | | | gnu: pigx-bsseq: Use latest snakemake.Ricardo Wurmus2018-11-23
| | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4 with snakemake.
| * | | | gnu: pigx-chipseq: Use latest snakemake.Ricardo Wurmus2018-11-23
| | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4 with snakemake.
| * | | | gnu: python-gevent: Update to 1.3.7.Ricardo Wurmus2018-11-23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-gevent): Update to 1.3.7. [arguments]: Find headers for greenlet in phase "do-not-use-bundled-sources". [propagated-inputs]: Add python-objgraph.
| * | | | gnu: Add python-objgraph.Ricardo Wurmus2018-11-23
| | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-objgraph): New variable.
| * | | | gnu: python-loompy: Remove python-typing.Ricardo Wurmus2018-11-23
| | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove python-typing.
| * | | | gnu: podofo: Add patch to fix build.Ricardo Wurmus2018-11-22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/podofo-cmake-3.12.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (podofo)[source]: Add patch.
| * | | | gnu: jalv: Build with python-2.Efraim Flashner2018-11-22
| | | | | | | | | | | | | | | | | | | | * gnu/packages/audio.scm (jalv)[arguments]: Build with python-2.
| * | | | gnu: python-scikit-learn: Update to 0.20.1.Marius Bakke2018-11-22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.20.1. [source](patches): Remove. [arguments]: Skip network tests with pytest instead of deleting files. Make sure $HOME is writable. (python2-scikit-learn): Rewrite in terms of PACKAGE-WITH-PYTHON2.
| * | | | Merge branch 'master' into core-updatesMarius Bakke2018-11-22
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| * | | | | gnu: python-tblib: Fix test failure with Python 3.7.Marius Bakke2018-11-22
| | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-tblib)[arguments]: Add 'adjust-tests' phase.
| * | | | | gnu: python-numpy: Update to 1.15.4.Marius Bakke2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-numpy): Update to 1.15.4.
| * | | | | Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner2018-11-21
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| * | | | | | gnu: libbytesize: Make .mo file builds reproducible.Ludovic Courtès2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/c.scm (libbytesize)[sources](modules, snippet): New fields. [arguments]: Add #:configure-flags and #:phases.
| * | | | | | gnu: emacs-pdf-tools: Fix build with recent Poppler.Ludovic Courtès2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/emacs-pdf-tools-poppler.patch: New file. * gnu/packages/emacs.scm (emacs-pdf-tools)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
| * | | | | | gnu: emacs-pdf-tools: Use 'git-fetch'.Ludovic Courtès2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/emacs.scm (emacs-pdf-tools)[source]: Switch to GIT-FETCH. [arguments]: In 'emacs-patch-variables' phase, make files writable.
| * | | | | | gnu: casync: Fix build with glibc 2.28.Ludovic Courtès2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/casync-renameat2-declaration.patch: New file. * gnu/packages/sync.scm (casync)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
| * | | | | | gnu: ntk: Don't use bundled waf.Efraim Flashner2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/fltk.scm (ntk)[inputs]: Add python-waf. [arguments]: Add custom phase to replace vendored waf.
| * | | | | | gnu: python-waf: Use a proper directory structure.Efraim Flashner2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fixes <https://bugs.gnu.org/25634>. * gnu/packages/python.scm (python-waf): Replace custom 'install phase to install "waf" binary into the bin directory. Remove the 'wrap phase. * gnu/packages/video.scm (mpv)[arguments]: Adjust the 'setup-waf phase accordingly.
| * | | | | | gnu: python-astroid: Update to 2.0.4.Efraim Flashner2018-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm (python-astroid): Update to 2.0.4. [source]: Switch to pypi source. [native-inputs]: Add python-dateutil, python-nose, python-pytest, python-pytest-runner. [arguments]: Add phase to remove spurious test failure. Update custom 'check phase. (python2-astroid): Update to 1.6.5. [source]: Use pypi source. [arguments]: Add phase to remove spurious test failure.
| * | | | | | Merge branch 'master' into core-updatesMarius Bakke2018-11-20
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| * | | | | | | gnu: hurd: Build against glibc 2.28.Ludovic Courtès2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Version 2.28 of glibc is the first in a long time that fully supports GNU/Hurd. This change updates the Hurd and Mach to provide the features glibc 2.28 expects and adjusts the cross-compilation tool chain for "i586-pc-gnu". * gnu/packages/base.scm (glibc/linux): Rename to... (glibc): ... this. [propagated-inputs]: Add 'hurd-target?' case. [arguments]: Use '--disable-werror' when 'hurd-target?'. Add 'augment-libc.so' phase when 'hurd-target?'. [native-inputs]: Add MIG and PERL when 'hurd-target?'. (glibc/hurd, glibc-for-target): Remove (glibc/hurd-headers): Inherit from GLIBC, not GLIBC/HURD. [arguments]: Remove "--enable-obsolete-rpc" configure flag and 'patch-configure-script' phase. * gnu/packages/cross-base.scm (cross-kernel-headers)[xglibc/hurd-headers]: Move 'set-cross-headers-path' after 'unpack'. * gnu/packages/cross-base.scm (cross-libc)[cross-libc-for-target]: Remove. Pass "--disable-werror" when TARGET matches 'hurd-triplet?'. * gnu/packages/hurd.scm (hurd-target?, patch-url): New procedures. (gnumach-headers)[source](patches, modules, snippet): New fields. (hurd-headers): Use Git commit 98b3390. [native-inputs]: Add AUTOCONF and AUTOMAKE. [arguments]: Add "ac_cv_func_*" configure flags. (hurd-minimal)[native-inputs]: Remove. [arguments]: In 'build' phase, build "include/assert-backtrace.h" first.
| * | | | | | | gnu: spice: Run tests sequentially.Ludovic Courtès2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/spice.scm (spice)[arguments]: Add #:parallel-tests?.
| * | | | | | | gnu: qt@5: Fix build failure on glibc 2.28.Ludovic Courtès2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/qt-5-renameat2.patch: New file. * gnu/packages/qt.scm (qt)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
| * | | | | | | gnu: linkchecker: Use 'git-file-name' for the source.Efraim Flashner2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/web.scm (linkchecker)[source]: Add missing 'file-name' field.
| * | | | | | | gnu: python-pytest-localserver: Update to 0.5.0.Efraim Flashner2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/check.scm (python-pytest-localserver): Update to 0.5.0.
| * | | | | | | gnu: python-pytest-localserver: Fix test suite.Efraim Flashner2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/check.scm (python-pytest-localserver): Replace custom 'check phase.
| * | | | | | | gnu: libgtextutils: Re-instate custom bootstrap phase.Efraim Flashner2018-11-18
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The source lacks a standard bootstrap script so the bootstrap phase is skipped otherwise. * gnu/packages/textutils.smc (libgtextutils)[arguments]: Replace 'bootstrap phase with upstream's bootstrap phase.
| * | | | | | | gnu: nss: Make tests deterministic.Ludovic Courtès2018-11-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Tests would fail once certificates had expired, along these lines: chains.sh: Verifying certificate(s) PayPalEE.cert with flags -d AllDB -pp -o OID.2.16.840.1.114412.1.1 vfychain -d AllDB -pp -vv -o OID.2.16.840.1.114412.1.1 /tmp/guix-build-nss-3.39.drv-0/nss-3.39/nss/tests/libpkix/certs/PayPalEE.cert Chain is bad! PROBLEM WITH THE CERT CHAIN: CERT 0. PayPalEE : ERROR -8181: Peer's Certificate has expired. Returned value is 1, expected result is pass Using 'faketime' allows us to get deterministic results. * gnu/packages/gnuzilla.scm (nss)[arguments]: In 'check' phase, run 'all.sh' under 'faketime'. [native-inputs]: Add LIBFAKETIME.
| * | | | | | | gnu: Add libfaketime.Ludovic Courtès2018-11-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/check.scm (libfaketime): New variable.
| * | | | | | | gnu: bioinformatics: Return #t from all phases and snippets.Mark H Weaver2018-11-14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk) (codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish) (salmon): Return #t from all phases and snippets, use 'invoke' where appropriate, and remove vestigal plumbing.
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