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* 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.
* services: docker: Add new fields to support proxy.Maxim Cournoyer2019-05-05
| | | | | | | | | | The Docker proxy enables inter-container and outside-to-container loopback, and is required by the Docker registry server. * gnu/services/docker.scm (docker-configuration)[proxy, enable-proxy?]: Add fields. (docker-shepherd-service): Use them. (serialize-boolean): New function.
* 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.
* build: go-build-system: Ensure uniform unpacking directory.Maxim Cournoyer2019-05-05
| | | | | | | | | | | Depending on whether the source is a directory or an archive, we strip the source directory or preserve it, respectively. This change makes it so that whether the type of the source, it is unpacked at the expected location given by the IMPORT-PATH of the Go build system. * guix/build/go-build-system.scm: Add the (ice-9 ftw) module. (unpack): Add inner procedure to maybe strip the top level directory of an archive, document it and use it.
* build: go-build-system: Use WHEN for side-effect conditionals.Maxim Cournoyer2019-05-05
| | | | | * guix/build/go-build-system.scm (unpack): Replace single branch `if' by `when'.
* build: go-build-system: Re-ident.Maxim Cournoyer2019-05-05
| | | | * guix/build/go-build-system.scm (unpack): Fix indentation.
* 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.
* gnu: r-motifstack: Update to 1.28.0.Ricardo Wurmus2019-05-06
| | | | | * gnu/packages/bioconductor.scm (r-motifstack): Update to 1.28.0. [propagated-inputs]: Replace r-grimport with r-grimport2.
* gnu: r-motiv: Update to 1.40.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-motiv): Update to 1.40.0.
* gnu: r-rgadem: Update to 2.31.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-rgadem): Update to 2.31.0.
* gnu: r-bacon: Update to 1.12.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-bacon): Update to 1.12.0.
* gnu: r-abseqr: Update to 1.2.0.Ricardo Wurmus2019-05-06
| | | | * gnu/packages/bioconductor.scm (r-abseqr): Update to 1.2.0.
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