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* utils: Move base16 procedures to (guix base16).Ludovic Courtès2017-03-16
| | | | | | | | | | | | | | | * 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.
* gnu: password-store: Fix compatibility with GnuPG 2.1.19.Clément Lassieur2017-03-16
| | | | | | | | * 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>
* gnu: Add r-seurat.Raoul Jean Pierre Bonnal2017-03-16
| | | | | | * gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: sra-tools: Update to 2.8.2-1.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1. [arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
* gnu: ncbi-vdb: Install configuration files.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files".
* gnu: ncbi-vdb: Override search path for java-ngs.Ricardo Wurmus2017-03-16
| | | | | | * 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".
* gnu: ncbi-vdb: Use modify-phases syntax.Ricardo Wurmus2017-03-16
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax.
* gnu: ncbi-vdb: Update to 2.8.2.Ricardo Wurmus2017-03-16
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
* gnu: ngs-sdk: Update to 1.3.0.Ricardo Wurmus2017-03-16
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
* gnu: Add pzstd.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/compression.scm (pzstd): New variable.
* gnu: Add zstd.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/compression.scm (zstd): New variable.
* gnu: python-publicsuffix2: Update to 2.20160818.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
* gnu: awscli: Update to 1.11.63.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (awscli): Update to 1.11.63.
* gnu: python-botocore: Update to 1.5.26.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (python-botocore): Update to 1.5.26.
* gnu: python-ptyprocess: Update to 0.5.1.Tobias Geerinckx-Rice2017-03-16
| | | | * gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.
* gnu: Add prboom-plus.Kei Kebreau2017-03-15
| | | | * gnu/packages/games.scm (prboom-plus): New variable.
* gnu: Add tftp-hpa.Gábor Boskovits2017-03-15
| | | | | | * gnu/packages/networking.scm (tftp-hpa): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: guile-next: Update to 2.2.0.Andy Wingo2017-03-15
| | | | * gnu/packages/guile.scm (guile-next): Update to 2.2.0.
* gnu: profanity: Make the source URL version-agnostic.Leo Famulari2017-03-15
| | | | | * gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source URL.
* gnu: units: Update to 2.14.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/maths.scm (units): Update to 2.14.
* gnu: no-more-secrets: Update to 0.3.2.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/games.scm (no-more-secrets): Update to 0.3.2.
* gnu: mailutils: Update to 3.2.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/mail.scm (mailutils): Update to 3.2.
* gnu: Use INSTALL-FILE where appropriate.Tobias Geerinckx-Rice2017-03-15
| | | | | | | | | | | | * gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler INSTALL-FILE for COPY-FILE when invoked with redundant arguments. * gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity, edirect, fasttree, rsem, samtools-0.1): Likewise. * gnu/packages/code.scm (withershins): Likewise. * gnu/packages/conky.scm (conky): Likewise. * gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise. * gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise. * gnu/packages/engineering.scm (librecad): Likewise.
* gnu: cryptsetup: Update to 1.7.4.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4.
* gnu: man-pages: Update to 4.10.Tobias Geerinckx-Rice2017-03-15
| | | | | * gnu/packages/man.scm (man-pages): Update to 4.10. [home-page]: Use HTTPS.
* gnu: Add profanity.Mekeor Melire2017-03-15
| | | | | | * gnu/packages/messaging.scm (profanity): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: Add libstrophe.Mekeor Melire2017-03-15
| | | | | | * gnu/packages/messaging.scm (libstrophe): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: Add libmesode.Mekeor Melire2017-03-15
| | | | | | * gnu/packages/messaging.scm (libmesode): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: bitcoin-core: Update to 0.14.0.Leo Famulari2017-03-15
| | | | * gnu/packages/finance.scm (bitcoin-core): Update to 0.14.0.
* build: Prefer Guile 2.2 over 2.0.Ludovic Courtès2017-03-15
| | | | | | * configure.ac: In 'GUILE_PKG', prefer 2.2 over 2.0. Remove warning about 2.2 not being fully supported. * doc/guix.texi (Requirements): Mention Guile 2.2.x.
* tests: Expect less accurate location info in 2.2.0.Ludovic Courtès2017-03-15
| | | | * tests/guix-system.sh: Work around inaccurate location info in 2.2.0.
* store: Adjust UTF-8 test to Guile 2.2.Ludovic Courtès2017-03-15
| | | | | * tests/store.scm ("current-build-output-port, UTF-8 + garbage"): On Guile 2.2, expect REPLACEMENT CHARACTER instead of '?'.
* syscalls: Adjust 'clone' to Guile 2.2.Ludovic Courtès2017-03-15
| | | | | | | | | | | | | | | | | | | Before that, something like: (call-with-container (lambda () (match (primitive-fork) …))) would hang in 'primitive-fork' as the child process (the one started in the container) would try to pthread_join the finalization thread in 'stop_finalization_thread' in libguile, not knowing that this thread is nonexistent. * guix/build/syscalls.scm (%set-automatic-finalization-enabled?!): New procedure. (without-automatic-finalization): New macro. (clone): Wrap PROC call in 'without-automatic-finalization'.
* zlib: Don't rely on EBADF being ignored by 'fport_close'.Ludovic Courtès2017-03-15
| | | | | | | | | | | | | In 2.2, 'fport_close' no longer swallows EBADF and instead raises a 'system-error' for this. This commit adjusts for 2.2. * guix/zlib.scm (close-procedure): Remove. (make-gzip-input-port): Use 'port->fdes' instead of 'fileno'. Use 'gzclose' instead of 'close-procedure'. (make-gzip-output-port): Likewise. * tests/zlib.scm ("compression/decompression pipe"): Don't check whether PARENT is closed using 'port-closed?'. Instead, use 'seek' on the underlying FD and check for EBADF.
* maint: Mention guix-patches@gnu.org in 'HACKING'.Ludovic Courtès2017-03-15
| | | | | | Fixes <http://bugs.gnu.org/25899>. * HACKING: Mention guix-patches@gnu.org.
* gnu: mariadb: Update to 10.1.22 [fixes CVE-2017-3302 and CVE-2017-3313].Marius Bakke2017-03-15
| | | | * gnu/packages/databases.scm (mariadb): Update to 10.1.22.
* gnu: python-waf: Update to 1.9.8.Efraim Flashner2017-03-15
| | | | | * gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8. [home-page]: Use https.
* gnu: direnv: Update to 2.11.3.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/shellutils.scm (direnv): Update to 2.11.3.
* gnu: conky: Update to 1.10.6.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/conky.scm (conky): Update to 1.10.6.
* gnu: obs: Update to 18.0.1.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/video.scm (obs): Update to 18.0.1.
* gnu: youtube-dl: Update to 2017.03.15.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2017.03.15.
* gnu: stress-make: Fix description.Tobias Geerinckx-Rice2017-03-15
| | | | | * gnu/packages/debug.scm (stress-make)[description]: Fix typo. Avoid ambiguous use of ‘in order’.
* gnu: znc: Update to 1.6.5.Tobias Geerinckx-Rice2017-03-15
| | | | * gnu/packages/messaging.scm (znc): Update to 1.6.5.
* gnu: grue-hunter: Correctly install documentation.Tobias Geerinckx-Rice2017-03-15
| | | | | * gnu/packages/games.scm (grue-hunter)[arguments]: Install and populate ‘/share/doc/grue-hunter’ as a directory, not a plain file.
* gnu: samtools: End installation phases with truth.Tobias Geerinckx-Rice2017-03-15
| | | | | * gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
* gnu: w3m: Update to 0.5.3+git20170102 [security fixes].Leo Famulari2017-03-14
| | | | | | | See 'NEWS' and 'ChangeLog' in the source distribution for more information about the security-related bug fixes. * gnu/packages/w3m.scm (w3m): Update to 0.5.3+git20170102.
* Revert "gnu: gitolite: Fix shebangs in hooks."Leo Famulari2017-03-14
| | | | | | | | | | This change embedded store references in the shebangs of scripts that were meant to be copied out of the store. Those scripts would break when the interpreters expected by the shebangs were garbage collected. <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25966#28> This reverts commit d0c16adb190c7244ee3ef1329cba78a015ae5d10.
* pack: Add unit test.Ludovic Courtès2017-03-14
| | | | | | | * guix/scripts/pack.scm (self-contained-tarball): Add #:tar option. [build](tar-supports-sort?): New variable. Use it. * tests/pack.scm: New file. * Makefile.am (SCM_TESTS): Add it.
* pack: Use maximum compression; use '-n' for gzip.Ludovic Courtès2017-03-14
| | | | | | | | * guix/scripts/pack.scm (<compressor>)[tar-option]: Remove. [command]: New field. (%compressors): Provide complete commands. Use '-9' or equivalent for each compressor; use '-n' for gzip. (self-contained-tarball)[build]: Adjust accordingly.
* Revert "gnu: nss: Use 'modify-phases' syntax."Marius Bakke2017-03-14
| | | | This reverts commit 87f1c7efc18f8996b0b2817a5f7b84eebe2ddf5a.
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