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12639 Commits

Author SHA1 Message Date
Ludovic Courtès af98798c7a
union: Compare inode numbers in 'file=?'. 
* guix/build/union.scm (file=?): Compare the inode of ST1 and ST2.
 2016-05-23 18:05:46 +02:00
Ludovic Courtès 86cf13033e
cve: Remove now unnecessary HTTP caching. 
* guix/cve.scm (call-with-cve-port): Use 'http-fetch' instead of
'http-fetch/cached'.
 2016-05-23 18:05:46 +02:00
Ludovic Courtès 5cdd21c7fe
cve: Keep a summarized sexp in cache instead of the full XML. 
This avoids ~20s of XML parsing when running 'guix lint -c cve'.

* guix/cve.scm (vulnerability->sexp, sexp->vulnerability)
(fetch-vulnerabilities): New procedures.
(current-vulnerabilities): Use 'fetch-vulnerabilities'.
 2016-05-23 18:05:46 +02:00
Roel Janssen f22debacb4
gnu: Add poppler-qt5. 
* gnu/packages/pdf.scm (poppler-qt5): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-05-23 14:35:23 +03:00
Ricardo Wurmus 524eee0298 gnu: Add slurm-drmaa. 
* gnu/packages/parallel.scm (slurm-drmaa): New variable.
 2016-05-23 12:55:40 +02:00
Ricardo Wurmus 0783787436 gnu: Add ParDRe. 
* gnu/packages/bioinformatics.scm (pardre): New variable.
 2016-05-23 12:55:09 +02:00
Efraim Flashner 624d4e2e6b
gnu: gnu-pw-mgr: Update to 2.0. 
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.0.
 2016-05-22 16:58:21 +03:00
Leo Famulari 13913c52d5
gnu: imagemagick: Update to 6.9.4-4. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-4.
 2016-05-22 03:51:57 -04:00
Lukas Gradl 88bb4197c4 gnu: Add python2-rope. 
* gnu/packages/python.scm (python2-rope): New variable.
 2016-05-22 14:19:52 +10:00
Kei Yamashita 3c47489766
gnu: Add gnome-calendar. 
* gnu/packages/gnome.scm (gnome-calendar): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Matthew Jordan 548994142f
gnu: Add envstore. 
* gnu/package/shellutils.scm: New file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Jan Nieuwenhuizen b9b447be64
gnu: Add sicp. 
* gnu/packages/scheme.scm (sicp): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Roel Janssen a56be436d0
gnu: Add dia. 
* gnu/packages/gnome.scm (dia): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Mathieu Lirzin 28dee3d282 build: Fix 'AM_V_at' typo. 
* Makefile.am (hydra-jobs.scm): Fix 'AM_V_at' typo.
 2016-05-21 23:09:46 +02:00
Ludovic Courtès ece6864bd0
grafts: Rename files whose name matches a graft. 
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.
 2016-05-21 01:35:14 +02:00
Ludovic Courtès cf8b312d18
grafts: Preserve empty directories when grafting. 
* guix/build/graft.scm (rewrite-directory)[rewrite-leaf]: Add case for
'directory.
Pass #:directories? #t to 'find-files'.
 2016-05-21 01:35:14 +02:00
Ludovic Courtès 30d4bc0434
substitute: Gracefully handle invalid store file names. 
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.
 2016-05-21 01:35:14 +02:00
Ludovic Courtès a773c3142d
graph: Allow store file names for 'derivation' and 'references' graphs. 
* 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.
 2016-05-21 01:35:14 +02:00
Ludovic Courtès 97507ebedc
derivations: 'derivation' sorts items in the resulting object. 
* 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.
 2016-05-21 01:35:14 +02:00
Ludovic Courtès 3cabdead6f
graph: Use absolute file name canonicalization. 
* guix/scripts/graph.scm (guix-graph): Wrap in 'with-fluids'.
 2016-05-21 01:35:14 +02:00
Mark H Weaver 3c9a7185e4
gnu: linux-libre: Update to 4.5.5. 
* gnu/packages/linux.scm (linux-libre): Update to 4.5.5.
 2016-05-20 18:58:15 -04:00
Mark H Weaver 4483a1185d
gnu: linux-libre-4.4: Update to 4.4.11. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.11.
 2016-05-20 18:58:06 -04:00
Ricardo Wurmus 932f2b70a6
ant-build-system: Add unpack phase. 
* guix/build/ant-build-system.scm (unpack): New procedure.
(%standard-phases): Use it.
 2016-05-20 15:24:32 +02:00
Ricardo Wurmus 987a118334
gnu: Add default gcc-objc++. 
* gnu/packages/gcc.scm (gcc-objc++): New variable.
 2016-05-20 15:19:48 +02:00
Ricardo Wurmus a5948c0d41
gnu: Add gcc-objc++-4.9. 
* gnu/packages/gcc.scm (gcc-objc++-4.9): New variable.
 2016-05-20 15:19:48 +02:00
Ricardo Wurmus 8b196ad208
gnu: Add default gcc-objc. 
* gnu/packages/gcc.scm (gcc-objc): New variable.
 2016-05-20 15:19:48 +02:00
Ricardo Wurmus 2d69c1616d
gnu: Add gcc-objc-4.9. 
* gnu/packages/gcc.scm (gcc-objc-4.9): New variable.
 2016-05-20 15:19:33 +02:00
Ricardo Wurmus 813efdded1
gnu: r-rcpparmadillo: Update to 0.6.700.6.0. 
* 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.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 945eef85c5
gnu: armadillo: Update to 6.700.7. 
* gnu/packages/maths.scm (armadillo): Update to 6.700.7.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 7740f58128
gnu: r-genomation: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus f6225d135c
gnu: r-jsonlite: Update to 0.9.20. 
* gnu/packages/web.scm (r-jsonlite): Update to 0.9.20.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus c969453e1c
gnu: r-plotly: Update to 3.6.0. 
* gnu/packages/statistics.scm (r-plotly): Update to 3.6.0.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 95513f284f
gnu: r-matrixstats: Update to 0.50.2. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.50.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus b8f6a97ebd
gnu: r-r-rsp: Update to 0.30.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.30.0.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus f0c56a2411
gnu: r-rmarkdown: Update to 0.9.6. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 0.9.6.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 2f7ac060ff
gnu: r-plotrix: Update to 3.6-2. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 133f27b06a
gnu: r-devtools: Update to 1.11.1. 
* gnu/packages/statistics.scm (r-devtools): Update to 1.11.1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 3624ad7150
gnu: r-git2r: Update to 0.15.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.15.0.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus c1e2c9d41a
gnu: r-openssl: Update to 0.9.3. 
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.3.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 383f6337a0
gnu: r-testthat: Update to 1.0.2. 
* gnu/packages/statistics.scm (r-testthat): Update to 1.0.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 1b206aeb00
gnu: r-knitr: Update to 1.13. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.13.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d5130e6345
gnu: r-highr: Update to 0.6. 
* gnu/packages/statistics.scm (r-highr): Update to 0.6.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus df25b0048a
gnu: r-formatr: Update to 1.4. 
* gnu/packages/statistics.scm (r-formatr): Update to 1.4.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 84e5368719
gnu: r-evaluate: Update to 0.9. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.9.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 9a0ccf43cc
gnu: r-bh: Update to 1.60.0-2. 
* gnu/packages/statistics.scm (r-bh): Update to 1.60.0-2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus a76b3f6914
gnu: r-dbi: Update to 0.4-1. 
* gnu/packages/statistics.scm (r-dbi): Update to 0.4-1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus eb1a5b65c0
gnu: r-rcpp: Update to 0.12.5. 
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d7420566a9
gnu: r-biocparallel: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
 2016-05-20 15:18:23 +02:00