| Age | Commit message (Expand) | Author |
|---|
| 2017-03-17 | gnu: snakemake: Update to 3.11.2....* gnu/packages/python.scm (snakemake): Update to 3.11.2.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-minimal: Fix remaining reproducibility problems....Fixes <https://bugs.gnu.org/25598>.
* gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining
reproducibility fixes to "build-reproducibly" phase.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r: Rename to r-minimal....* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-with-recommended-packages....* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r: Do not build recommended packages....* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-survival: Move to set of recommended R packages....* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
packages.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-spatial....* gnu/packages/statistics.scm (r-spatial): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-rpart: Move to the set of recommended packages....* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
packages.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-nnet: Move to set of recommended R packages....* gnu/packages/machine-learning.scm (r-nnet): Move from here...
* gnu/packages/statistics.scm (r-nnet): ...to here because the other
recommended R packages are here.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-mgcv: Move to set of recommended R packages....* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
packages.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-nlme....* gnu/packages/statistics.scm (r-nlme): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-matrix: Move to set of recommended R packages....* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
packages.
| Ricardo Wurmus |
| 2017-03-17 | gnu: r-lattice: Move to other recommended R packages....* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-kernsmooth....* gnu/packages/statistics.scm (r-kernsmooth): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-foreign....* gnu/packages/statistics.scm (r-foreign): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-codetools....* gnu/packages/statistics.scm (r-codetools): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-cluster....* gnu/packages/statistics.scm (r-cluster): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-class....* gnu/packages/statistics.scm (r-class): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-mass....* gnu/packages/statistics.scm (r-mass): New variable.
| Ricardo Wurmus |
| 2017-03-17 | gnu: Add r-boot....* gnu/packages/statistics.scm (r-boot): New variable.
| Ricardo Wurmus |
| 2017-03-17 | doc: Really document 'guix pack --format'....* doc/guix.texi (Invoking guix pack): Properly document --format.
| Ludovic Courtès |
| 2017-03-17 | gnu: youtube-dl: Update to 2017.03.16....* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
| Tobias Geerinckx-Rice |
| 2017-03-16 | gnu: asciidoc: Use local docbook-xml package....* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml.
[arguments]: Add 'make-local-docbook-xml' phase.
| Kei Kebreau |
| 2017-03-17 | gnu: Add knot....* gnu/packages/dns.scm (knot): New variable.
| Tobias Geerinckx-Rice |
| 2017-03-17 | gnu: Add liburcu....* gnu/packages/datastructures.scm (liburcu): New variable.
| Tobias Geerinckx-Rice |
| 2017-03-17 | gnu: dns: Fix typo and use @dfn in descriptions....* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms.
(yadifa)[description]: Likewise, and fix a typo.
| Tobias Geerinckx-Rice |
| 2017-03-16 | gnu: linux-libre: Update to 4.10.3....* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3.
(%linux-libre-hash): Update hash.
| Leo Famulari |
| 2017-03-16 | gnu: linux-libre@4.4: Update to 4.4.54....* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
| Leo Famulari |
| 2017-03-16 | gnu: linux-libre@4.9: Update to 4.9.15....* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
| Leo Famulari |
| 2017-03-16 | gnu: qemu: Fix CVE-2017-{2620,2630}....* gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/qemu.scm (qemu)[source]: Use them.
| Leo Famulari |
| 2017-03-16 | gnu: virglrenderer: Fix CVE-2017-6386....* gnu/packages/patches/virglrenderer-CVE-2017-6386.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/spice.scm (virglrenderer)[source]: Use it.
| Leo Famulari |
| 2017-03-16 | doc: Reorganize categories....* doc/guix.texi: Move "guix build" to the "Software Development"
category; add "guix pack".
| Ludovic Courtès |
| 2017-03-16 | doc: Mention 'guix pack' reproducibility....* doc/guix.texi (Invoking guix pack): Mention reproducibility.
| Ludovic Courtès |
| 2017-03-16 | pack: Allow for "-S /opt/foo="....Reported by Andy Wingo.
* guix/scripts/pack.scm (%options): Use 'string-split' instead of
'string-tokenize'.
| Ludovic Courtès |
| 2017-03-16 | pack: Honor symlinks in the Docker back-end....* guix/docker.scm (symlink-source, topmost-component): New procedures.
(build-docker-image): Add #:symlinks parameter and honor it. Remove
hard-coded /bin symlink.
* guix/scripts/pack.scm (docker-image): Pass #:symlinks to
'build-docker-image'.
| Ludovic Courtès |
| 2017-03-16 | docker: Build images in a reproducible fashion....* guix/docker.scm (%tar-determinism-options): New variable.
(build-docker-image): Use it on the two 'tar' invocations.
| Ludovic Courtès |
| 2017-03-16 | pack: Use a fixed timestamp in Docker images....* guix/docker.scm (build-docker-image): Add #:creation-time parameter.
Use SRFI-19 'date->string' instead of 'strftime' et al.
* guix/scripts/pack.scm (docker-image)[build]: Pass #:creation-time to
'build-docker-image'.
| Ludovic Courtès |
| 2017-03-16 | pack: Add '--format' option and Docker output support....* guix/docker.scm: Remove dependency on (guix store) and (guix utils).
Use (guix build store-copy). Load (json) lazily.
(build-docker-image): Remove #:system. Add #:closure, #:compressor, and
'image' parameters. Use 'uname' to determine the architecture. Remove
use of 'call-with-temporary-directory'. Use 'read-reference-graph' to
compute ITEMS. Honor #:compressor.
* guix/scripts/pack.scm (docker-image): New procedure.
(%default-options): Add 'format'.
(%formats): New variable.
(%options, show-help): Add '--format'.
(guix-pack): Honor '--format'.
* guix/scripts/archive.scm: Remove '--format' option. This reverts
commits 1545a012cb7cd78e25ed99ecee26df457be590e9,
01445711db6771cea6122859c3f717f130359f55, and
03476a23ff2d4175b7d3c808726178f764359bec.
* doc/guix.texi (Invoking guix pack): Document '--format'.
(Invoking guix archive): Remove documentation of '--format'.
| Ludovic Courtès |
| 2017-03-16 | pack: Honor command-line options related to the store....* guix/scripts/pack.scm (guix-pack): Call
'set-build-options-from-command-line'.
| Ludovic Courtès |
| 2017-03-16 | memoization: Micro-optimize code produced by 'define-cache-procedure'....* guix/memoization.scm (%nothing): Remove.
(define-cache-procedure): Make '%nothing' a local variable, with a
literal list.
| Ludovic Courtès |
| 2017-03-16 | services: connman: Rework service....* gnu/services/networking.scm (connman-service): Remove.
(<connman-configuration>): New record specifying the package
to be used (connman) and whether vpn plugin shall be
disabled (disable-vpn?).
(connman-configuration): New exported variable.
(connman-configuration?): New exported variable.
(connman-service-type): Export it.
* doc/guix.texi (Networking Services): Adjust accordingly.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Mathieu Othacehe |
| 2017-03-16 | gexp: Add '=>' syntax to import computed modules....* guix/gexp.scm (imported-files)[file-pair]: Add case for pairs where
the cdr is not a string.
(imported-modules): Support '=>' syntax in MODULES.
* tests/gexp.scm ("imported-files with file-like objects")
("gexp->derivation & with-imported-module & computed module"): New tests.
* doc/guix.texi (G-Expressions): Document '=>' syntax for
'with-imported-modules'.
| Ludovic Courtès |
| 2017-03-16 | utils: Move base16 procedures to (guix base16)....* guix/utils.scm (bytevector->base16-string, base16-string->bytevector):
Move to...
* guix/base16.scm: ... here. New file.
* tests/utils.scm ("bytevector->base16-string->bytevector"): Move to...
* tests/base16.scm: ... here. New file.
* Makefile.am (MODULES): Add guix/base16.scm.
(SCM_TESTS): Add tests/base16.scm.
* build-aux/download.scm, guix/derivations.scm,
guix/docker.scm, guix/import/snix.scm, guix/pk-crypto.scm,
guix/scripts/authenticate.scm, guix/scripts/download.scm,
guix/scripts/hash.scm, guix/store.scm, tests/hash.scm,
tests/pk-crypto.scm: Adjust imports accordingly.
| Ludovic Courtès |
| 2017-03-16 | gnu: password-store: Fix compatibility with GnuPG 2.1.19....* gnu/packages/patches/password-store-gnupg-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/password-utils.scm (password-store)[source]: Use it.
Signed-off-by: Clément Lassieur <clement@lassieur.org>
| Clément Lassieur |
| 2017-03-16 | gnu: Add r-seurat....* gnu/packages/bioinformatics.scm (r-seurat): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Raoul Jean Pierre Bonnal |
| 2017-03-16 | gnu: sra-tools: Update to 2.8.2-1....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
| Ricardo Wurmus |
| 2017-03-16 | gnu: ncbi-vdb: Install configuration files....* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
| Ricardo Wurmus |
| 2017-03-16 | gnu: ncbi-vdb: Override search path for java-ngs....* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
| Ricardo Wurmus |
| 2017-03-16 | gnu: ncbi-vdb: Use modify-phases syntax....* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
| Ricardo Wurmus |
| 2017-03-16 | gnu: ncbi-vdb: Update to 2.8.2....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
| Ricardo Wurmus |
