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* gnu: gcc@9: Fix limits.h include for cross builds.Carl Dong2019-05-06
| | | | | | | | | | | | This allows us to supply gcc-9 as an optional argument to cross-gcc, successfully constructing gcc-9-based cross-compilers. * gnu/packages/gcc.scm (gcc-9)[source](patches): Add "gcc-9-asan-fix-limits-include.patch". * gnu/packages/patches/gcc-9-asan-fix-limits-include.patch: New file. * gnu/local.mk (dist_patch_DATA): Add the patch. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: cross-base: Apply gcc 8 patch to gcc >= 8.Carl Dong2019-05-06
| | | | | | | | * gnu/packages/cross-base.scm (cross-gcc): Apply gcc 8 patch to gcc >= 8. * gnu/packages/patches/gcc-8-cross-environment-variables.patch: New file. * gnu/local.mk (dist_patch_DATA): Add the patch. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: gcc: Add 9.1.0.Carl Dong2019-05-06
| | | | | | | | | * gnu/packages/gcc.scm (gcc-9): New variable. * gnu/packages/commencement.scm (gcc-toolchain-9): New variable. * gnu/packages/patches/gcc-9-strmov-store-file-names.patch: New file. * gnu/local.mk (dist_patch_DATA): Add the patch. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: linux-libre: Update to 5.0.13.Mark H Weaver2019-05-06
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 5.0.13. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.19: Update to 4.19.40.Mark H Weaver2019-05-06
| | | | | * gnu/packages/linux.scm (%linux-libre-4.19-version): Update to 4.19.40. (%linux-libre-4.19-hash): Update hash.
* gnu: linux-libre@4.14: Update to 4.14.116.Mark H Weaver2019-05-06
| | | | | * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.116. (%linux-libre-4.14-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.173.Mark H Weaver2019-05-06
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.173.
* gnu: docker: Refer to xz by its absolute path.Maxim Cournoyer2019-05-05
| | | | | * gnu/packages/docker.scm (docker)[inputs]: Add xz. [phases]{patch-paths}: Patch the reference to xz.
* gnu: docker: Patch the reference to the docker proxy.Maxim Cournoyer2019-05-05
| | | | | | * gnu/packages/docker.scm (docker)[inputs]: Add docker-libnetwork-cmd-proxy. * gnu/packages/docker.scm (docker)[phases]{patch-paths}: Patch proxy.go to refer to the docker-proxy binary by its absolute path.
* gnu: docker: Optimize substitution macros.Maxim Cournoyer2019-05-05
| | | | | | | | | | | This change halves the time needed to patch the paths. * gnu/packages/docker.scm (docker)[phases]{patch-paths}: Allow passing multiple SOURCE-TEXT, PACKAGE and RELATIVE-PATH tuples so that the rewrite rules can be generated and processed by a single use of the SUBSTITUTE* macro. Rename SUBSTITUTE-LOOKPATH to SUBSTITUTE-LOOKPATH* and substitute-Command to SUBSTITUTE-COMMAND* to denote the change. Adapt the uses of SUBSTITUTE-LOOKPATH* and SUBSTITUTE-COMMAND*.
* gnu: docker: Make macros use a relative path as argument.Maxim Cournoyer2019-05-05
| | | | | | * gnu/packages/docker.scm (docker)[phases]: Move implementation detail inside the SUBSTITUTE-LOOKPATH and SUBSTITUTE-COMMAND macros definition, so that the relative path argument can be given as a relative path.
* gnu: docker: Harmonize LookPath regexes.Maxim Cournoyer2019-05-05
| | | | | | * gnu/packages/docker.scm (docker)[phases]: In the patch-paths phase, update the regexes used by SUBSTITUTE-LOOKPATH and SUBSTITUTE-COMMAND to match at the start of the word, like it's done later.
* gnu: docker: Cleanup extraneous comments.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/docker.scm (docker): Remove "parenthesis-balancing" comments.
* gnu: docker: Fix indentation.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/docker.scm (docker): Fix indentation using Emacs.
* gnu: Add docker-libnetwork-cmd-proxy.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/docker.scm (docker-libnetwork-cmd-proxy): New variable.
* gnu: Add docker-libnetwork.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/docker.scm (docker-libnetwork): New private variable.
* gnu: Add go-netlink.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/linux.scm (go-netlink): New variable.
* gnu: Add go-netns.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/networking.scm (go-netns): New variable.
* gnu: Add go-sctp.Maxim Cournoyer2019-05-05
| | | | * gnu/packages/networking.scm (go-sctp): New variable.
* gnu: r-chippeakanno: Update to 3.18.0.Ricardo Wurmus2019-05-06
| | | | | * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.0. [propagated-inputs]: Add r-rtracklayer.
* gnu: r-arrmnormalization: Update to 1.24.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.24.0.
* gnu: r-progeny: Update to 1.6.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-progeny): Update to 1.6.0.
* gnu: r-rbowtie2: Update to 1.6.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-rbowtie2): Update to 1.6.0.
* gnu: r-zfpkm: Update to 1.6.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.6.0.
* gnu: r-webbioc: Update to 1.56.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-webbioc): Update to 1.56.0.
* gnu: r-widgettools: Update to 1.62.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-widgettools): Update to 1.62.0.
* gnu: r-wiggleplotr: Update to 1.8.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.8.0.
* gnu: r-wrench: Update to 1.2.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-wrench): Update to 1.2.0.
* gnu: r-xcms: Update to 3.6.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-xcms): Update to 3.6.0.
* gnu: r-massspecwavelet: Update to 1.50.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.50.0.
* gnu: r-xbseq: Update to 1.16.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-xbseq): Update to 1.16.0.
* gnu: r-roar: Update to 1.20.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-roar): Update to 1.20.0.
* gnu: r-yarn: Update to 1.10.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-yarn): Update to 1.10.0.
* gnu: r-quantro: Update to 1.18.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-quantro): Update to 1.18.0.
* gnu: r-yaqcaffy: Update to 1.44.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-yaqcaffy): Update to 1.44.0.
* gnu: r-simpleaffy: Update to 2.60.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-simpleaffy): Update to 2.60.0.
* gnu: r-gcrma: Update to 2.56.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-gcrma): Update to 2.56.0.
* gnu: r-yapsa: Update to 1.10.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-yapsa): Update to 1.10.0.
* gnu: r-somaticsignatures: Update to 2.20.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.20.0.
* gnu: r-gtrellis: Update to 1.16.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.16.0.
* gnu: r-yamss: Update to 1.10.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-yamss): Update to 1.10.0.
* gnu: r-ebimage: Update to 4.26.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-ebimage): Update to 4.26.0.
* gnu: r-aucell: Update to 1.6.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-aucell): Update to 1.6.0.
* gnu: r-allelicimbalance: Update to 1.22.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.22.0.
* gnu: r-annotationtools: Update to 1.58.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.58.0.
* gnu: r-annotationfuncs: Update to 1.34.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-annotationfuncs): Update to 1.34.0.
* gnu: r-abaenrichment: Update to 1.14.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-abaenrichment): Update to 1.14.0.
* gnu: r-gofuncr: Update to 1.4.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.4.0.
* gnu: r-atacseqqc: Update to 1.8.0.Ricardo Wurmus2019-05-06
| | | | | * gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.8.0. [propagated-inputs]: Add r-edger.
* gnu: r-genomicscores: Update to 1.8.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-genomicscores): Update to 1.8.0.
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