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2018-11-18gnu: hurd: Build against glibc 2.28....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. Ludovic Courtès
2018-11-18gnu: spice: Run tests sequentially....* gnu/packages/spice.scm (spice)[arguments]: Add #:parallel-tests?. Ludovic Courtès
2018-11-18gnu: qt@5: Fix build failure on glibc 2.28....* 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. Ludovic Courtès
2018-11-18gnu: linkchecker: Use 'git-file-name' for the source....* gnu/packages/web.scm (linkchecker)[source]: Add missing 'file-name' field. Efraim Flashner
2018-11-18gnu: python-pytest-localserver: Update to 0.5.0....* gnu/packages/check.scm (python-pytest-localserver): Update to 0.5.0. Efraim Flashner
2018-11-18gnu: python-pytest-localserver: Fix test suite....* gnu/packages/check.scm (python-pytest-localserver): Replace custom 'check phase. Efraim Flashner
2018-11-18gnu: libgtextutils: Re-instate custom bootstrap phase....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. Efraim Flashner
2018-11-17gnu: nss: Make tests deterministic....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. Ludovic Courtès
2018-11-17gnu: Add libfaketime....* gnu/packages/check.scm (libfaketime): New variable. Ludovic Courtès
2018-11-14gnu: bioinformatics: Return #t from all phases and snippets....* 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. Mark H Weaver
2018-11-14gnu: databases: Return #t from all phases....* gnu/packages/databases.scm (4store, go-gopkg.in-mgo.v2, mongodb) (sparql-query, tdb, sqlcipher, python-sqlparse, mongo-tools): Return #t from all phases, use invoke where appropriate, and remove vestigial plumbing. Mark H Weaver
2018-11-14gnu: compression: Return #t from all phases....* gnu/packages/compression.scm (perl-compress-raw-zlib, java-snappy) (java-iq80-snappy, pzstd, java-tukaani-xz): Return #t from all phases. Mark H Weaver
2018-11-14gnu: check: Return #t from all phases....* gnu/packages/check.scm (cmdtest, python-pytest-cov, python-fixtures) (python-pytest-localserver, python-pytest-flakes) (python2-coverage-test-runner, python-pylint, python-behave-web-api): Return #t from all phases, and use invoke where appropriate. Mark H Weaver
2018-11-14gnu: audio: Return #t from all phases....* gnu/packages/audio.scm (clalsadrv, jack-2, libsbsms, zita-convolver) (zita-resampler, zita-alsa-pcmi, gsm, cava): Return #t from all phases. (ladspa): Use 'modify-phases'. Return #t from all phases. Mark H Weaver
2018-11-14gnu: xorg: Return #t from all phases....* gnu/packages/xorg.scm (xcompmgr) * gnu/packages/xdisorg.scm (xdotool, scrot, unclutter, xscreensaver) (tint2, nxbelld, xautolock): Return #t from all phases. Mark H Weaver
2018-11-14gnu: xml: Return #t from all phases....* gnu/packages/xml.scm (python-libxml2, perl-xml-sax, xlsx2csv, libxls) (java-kxml2): Return #t from all phases. Mark H Weaver
2018-11-14gnu: video: Return #t from all phases....* gnu/packages/video.scm (youtube-dl-gui, avidemux, xvid, twitchy, aegisub): Return #t from all phases, use invoke where appropriate, and remove vestigial plumbing. Mark H Weaver
2018-11-14gnu: perl: Return #t from all phases....* gnu/packages/gd.scm (perl-gd-securityimage) * gnu/packages/libevent.scm (perl-ev) * gnu/packages/markup.scm (perl-text-markdown-discount) * gnu/packages/perl-check.scm (perl-test2-bundle-extended) * gnu/packages/perl.scm (perl-digest-md5, perl-encode-hanextra) (perl-ipc-run, perl-pathtools) * gnu/packages/photo.scm (perl-image-exiftool): Return #t from all phases. Mark H Weaver
2018-11-14gnu: networking: Return #t from all phases....* gnu/packages/networking.scm (miredo, tcp-wrappers, librdkafka, ifstatus) (iodine, httpstat, perl-socket6, perl-netaddr-ip, libproxy, openvswitch) (libnet, asio): Return #t from all phases. Mark H Weaver
2018-11-14gnu: linux: Return #t from all phases....* gnu/packages/linux.scm (iproute, ntfs-3g, cpupower, radeontop, tlp): Return #t from all phases. Mark H Weaver
2018-11-14gnu: image: Return #t from all phases....* gnu/packages/image.scm (libpng-apng, pngcrush, leptonica, zimg) (perceptualdiff): Return #t from all phases. Mark H Weaver
2018-11-14gnu: admin: Return #t from all phases....* gnu/packages/admin.scm (daemon-tools, rottlog, wpa-supplicant-minimal) (wakelan, cpulimit, nmap, sunxi-tools): Return #t from all phases. Mark H Weaver
2018-11-14gnu: texlive-bin: Fix substitution regexp....This is a followup to commit be200ef316478585059041a33d8f4287017dea5a. * gnu/packages/tex.scm (texlive-bin)[arguments]: In 'disable-failing-test' phase, escape "|" characters. Ludovic Courtès
2018-11-14Merge branch 'master' into core-updatesMarius Bakke
2018-11-14gnu: aide: Provide libpcre.a and libz.a....* gnu/packages/admin.scm (aide)[inputs]: Add PCRE:STATIC and ZLIB:STATIC. Marius Bakke
2018-11-14gnu: xf86-video-r128: Update to 6.12.0....* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0. Marius Bakke
2018-11-14gnu: mtools: Update to 4.0.20....* gnu/packages/mtools.scm (mtools): Update to 4.0.20. [source](uri): Change to 'bz2' compressed tarball. Marius Bakke
2018-11-14gnu: nano: Update to 3.2....* gnu/packages/nano.scm (nano): Update to 3.2. Marius Bakke
2018-11-14gnu: sudo: Update to 1.8.26....* gnu/packages/admin.scm (sudo): Update to 1.8.26. Marius Bakke
2018-11-14gnu: feh: Update to 3.0....* gnu/packages/image-viewers.scm (feh): Update to 3.0. Marius Bakke
2018-11-14gnu: Add jamm....* gnu/packages/bioinformatics.scm (jamm): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-ouch....* gnu/packages/cran.scm (r-ouch): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-activity....* gnu/packages/cran.scm (r-activity): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-circular....* gnu/packages/cran.scm (r-circular): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-overlap....* gnu/packages/cran.scm (r-overlap): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-acdm....* gnu/packages/cran.scm (r-acdm): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-acd....* gnu/packages/cran.scm (r-acd): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-abn....* gnu/packages/cran.scm (r-abn): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-rjags....* gnu/packages/cran.scm (r-rjags): New variable. Ricardo Wurmus
2018-11-14gnu: Add jags....* gnu/packages/statistics.scm (jags): New variable. Ricardo Wurmus
2018-11-13gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4....* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4. Ricardo Wurmus
2018-11-13gnu: r-org-mm-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-dm-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-ce-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-hs-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-genomationdata: Update to 1.14.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0. Ricardo Wurmus
2018-11-13gnu: r-go-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-genomeinfodbdata: Update to 1.2.0....* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0. Ricardo Wurmus
2018-11-13gnu: spice-vdagent: Fix typo in desktop file....Fixes <https://bugs.gnu.org/33346>. * gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in 'patch-spice-vdagent.desktop' phase. Taegil Bae
2018-11-14gnu: ImageMagick: Update to 6.9.10-14....* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14. Alex Vong
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