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* gnu: Add envstore.Matthew Jordan2016-05-21
| | | | | | * gnu/package/shellutils.scm: New file. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add sicp.Jan Nieuwenhuizen2016-05-21
| | | | | | * gnu/packages/scheme.scm (sicp): New variable. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add dia.Roel Janssen2016-05-21
| | | | | | * gnu/packages/gnome.scm (dia): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* build: Fix 'AM_V_at' typo.Mathieu Lirzin2016-05-21
| | | | * Makefile.am (hydra-jobs.scm): Fix 'AM_V_at' typo.
* grafts: Rename files whose name matches a graft.Ludovic Courtès2016-05-21
| | | | | | | | | Fixes <http://bugs.gnu.org/23132>. Reported by Mark H Weaver <mhw@netris.org>. * guix/build/graft.scm (rename-matching-files): New procedure. (rewrite-directory): Use it. * tests/grafts.scm ("graft-derivation, renaming"): New test.
* grafts: Preserve empty directories when grafting.Ludovic Courtès2016-05-21
| | | | | | * guix/build/graft.scm (rewrite-directory)[rewrite-leaf]: Add case for 'directory. Pass #:directories? #t to 'find-files'.
* substitute: Gracefully handle invalid store file names.Ludovic Courtès2016-05-21
| | | | | | | | | | | Before, something like: echo have /gnu/foo | ./test-env guix substitute --query would lead to an ugly backtrace. * guix/scripts/substitute.scm (narinfo-cache-file): Call 'leave' when 'store-hash-part' returns #f.
* graph: Allow store file names for 'derivation' and 'references' graphs.Ludovic Courtès2016-05-21
| | | | | | | | | | | | | | * guix/scripts/graph.scm (%derivation-node-type)[convert]: Add 'derivation-path?' and catch-all clauses. (%reference-node-type)[convert]: Add 'store-path?' and catch-all clauses. (assert-package, nodes-from-package): New procedures. (%package-node-type, %bag-node-type,%bag-with-origins-node-type) (%bag-emerged-node-type): Add 'convert' field (guix-graph): Rename 'packages' to 'items' and allow 'store-path?' arguments. * guix/graph.scm (<node-type>)[convert]: Adjust comment. * doc/guix.texi (Invoking guix graph): Document it.
* derivations: 'derivation' sorts items in the resulting object.Ludovic Courtès2016-05-21
| | | | | | | | | | | | * guix/derivations.scm (derivation-input<?): New procedure. (write-derivation)[coalesce-duplicate-inputs]: Remove. Remove calls to 'sort'. (coalesce-duplicate-inputs): New procedure. (derivation-hash): Sort INPUTS and use 'coalesce-duplicate-inputs'. (derivation)[input->derivation-input] [coalesce-duplicate-inputs]: New procedures. Sort OUTPUTS, INPUTS, and ENV-VARS. * tests/derivations.scm ("read-derivation vs. derivation"): New test.
* graph: Use absolute file name canonicalization.Ludovic Courtès2016-05-21
| | | | * guix/scripts/graph.scm (guix-graph): Wrap in 'with-fluids'.
* gnu: linux-libre: Update to 4.5.5.Mark H Weaver2016-05-20
| | | | * gnu/packages/linux.scm (linux-libre): Update to 4.5.5.
* gnu: linux-libre-4.4: Update to 4.4.11.Mark H Weaver2016-05-20
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.11.
* ant-build-system: Add unpack phase.Ricardo Wurmus2016-05-20
| | | | | * guix/build/ant-build-system.scm (unpack): New procedure. (%standard-phases): Use it.
* gnu: Add default gcc-objc++.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/gcc.scm (gcc-objc++): New variable.
* gnu: Add gcc-objc++-4.9.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/gcc.scm (gcc-objc++-4.9): New variable.
* gnu: Add default gcc-objc.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/gcc.scm (gcc-objc): New variable.
* gnu: Add gcc-objc-4.9.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/gcc.scm (gcc-objc-4.9): New variable.
* gnu: r-rcpparmadillo: Update to 0.6.700.6.0.Ricardo Wurmus2016-05-20
| | | | | | * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.6.700.6.0. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 6.700.6.
* gnu: armadillo: Update to 6.700.7.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/maths.scm (armadillo): Update to 6.700.7.
* gnu: r-genomation: Update to 1.4.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
* gnu: r-jsonlite: Update to 0.9.20.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/web.scm (r-jsonlite): Update to 0.9.20.
* gnu: r-plotly: Update to 3.6.0.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-plotly): Update to 3.6.0.
* gnu: r-matrixstats: Update to 0.50.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-matrixstats): Update to 0.50.2.
* gnu: r-r-rsp: Update to 0.30.0.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-r-rsp): Update to 0.30.0.
* gnu: r-rmarkdown: Update to 0.9.6.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 0.9.6.
* gnu: r-plotrix: Update to 3.6-2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-plotrix): Update to 3.6-2.
* gnu: r-devtools: Update to 1.11.1.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-devtools): Update to 1.11.1.
* gnu: r-git2r: Update to 0.15.0.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-git2r): Update to 0.15.0.
* gnu: r-openssl: Update to 0.9.3.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-openssl): Update to 0.9.3.
* gnu: r-testthat: Update to 1.0.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-testthat): Update to 1.0.2.
* gnu: r-knitr: Update to 1.13.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-knitr): Update to 1.13.
* gnu: r-highr: Update to 0.6.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-highr): Update to 0.6.
* gnu: r-formatr: Update to 1.4.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-formatr): Update to 1.4.
* gnu: r-evaluate: Update to 0.9.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-evaluate): Update to 0.9.
* gnu: r-bh: Update to 1.60.0-2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-bh): Update to 1.60.0-2.
* gnu: r-dbi: Update to 0.4-1.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-dbi): Update to 0.4-1.
* gnu: r-rcpp: Update to 0.12.5.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5.
* gnu: r-genomicfeatures: Update to 1.24.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
* gnu: r-summarizedexperiment: Update to 1.2.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
* gnu: r-biocparallel: Update to 1.6.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
* gnu: r-annotationdbi: Update to 1.34.2.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
* gnu: r-variantannotation: Update to 1.18.1.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
* gnu: r-genomeinfodb: Update to 1.8.1.Ricardo Wurmus2016-05-20
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
* gnu: btrfs-progs: Update to 4.5.3.Leo Famulari2016-05-19
| | | | * gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3.
* gnu: jemalloc: Update to 4.2.0.Jelle Licht2016-05-19
| | | | | | * gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283.Leo Famulari2016-05-19
| | | | | | | | | * gnu/packages/patches/expat-CVE-2015-1283-refix.patch, gnu/packages/patches/expat-CVE-2016-0718.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/xml.scm (expat)[replacement]: New field. (expat/fixed): New variable. [source]: Use new patches.
* gnu: flann: Do not install .a files.Ludovic Courtès2016-05-19
| | | | * gnu/packages/maths.scm (flann)[arguments]: Add #:phases.
* gnu: python: Add 'python' variables for different major/minor versions.Hartmut Goebel2016-05-19
| | | | | | | | | | | | * gnu/packages/python.scm (python-2): Rename variable to... (python-2.7): ...this. (python-2): Refer to "python-2.7". (python): Rename variable to... (python-3.4): ...this. (python-3): Refer to "python-3.4". (python): Refer to "python-3". Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: flann: Strip .mex file.Ludovic Courtès2016-05-19
| | | | * gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories.
* gnu: Add r-biased-urn.Ben Woodcroft2016-05-19
| | | | * gnu/packages/statistics.scm (r-biased-urn): New variable.
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