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2017-03-16services: 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
2017-03-16gexp: 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
2017-03-16utils: 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
2017-03-16gnu: 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
2017-03-16gnu: Add r-seurat.•••* gnu/packages/bioinformatics.scm (r-seurat): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Raoul Jean Pierre Bonnal
2017-03-16gnu: 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
2017-03-16gnu: ncbi-vdb: Install configuration files.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase "install-configuration-files". Ricardo Wurmus
2017-03-16gnu: 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
2017-03-16gnu: ncbi-vdb: Use modify-phases syntax.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases syntax. Ricardo Wurmus
2017-03-16gnu: ncbi-vdb: Update to 2.8.2.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2. Ricardo Wurmus
2017-03-16gnu: ngs-sdk: Update to 1.3.0.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0. Ricardo Wurmus
2017-03-16gnu: Add pzstd.•••* gnu/packages/compression.scm (pzstd): New variable. Tobias Geerinckx-Rice
2017-03-16gnu: Add zstd.•••* gnu/packages/compression.scm (zstd): New variable. Tobias Geerinckx-Rice
2017-03-16gnu: python-publicsuffix2: Update to 2.20160818.•••* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818. Tobias Geerinckx-Rice
2017-03-16gnu: awscli: Update to 1.11.63.•••* gnu/packages/python.scm (awscli): Update to 1.11.63. Tobias Geerinckx-Rice
2017-03-16gnu: python-botocore: Update to 1.5.26.•••* gnu/packages/python.scm (python-botocore): Update to 1.5.26. Tobias Geerinckx-Rice
2017-03-16gnu: python-ptyprocess: Update to 0.5.1.•••* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1. Tobias Geerinckx-Rice
2017-03-15gnu: Add prboom-plus.•••* gnu/packages/games.scm (prboom-plus): New variable. Kei Kebreau
2017-03-15gnu: Add tftp-hpa.•••* gnu/packages/networking.scm (tftp-hpa): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Gábor Boskovits
2017-03-15gnu: guile-next: Update to 2.2.0.•••* gnu/packages/guile.scm (guile-next): Update to 2.2.0. Andy Wingo
2017-03-15gnu: profanity: Make the source URL version-agnostic.•••* gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source URL. Leo Famulari
2017-03-15gnu: units: Update to 2.14.•••* gnu/packages/maths.scm (units): Update to 2.14. Tobias Geerinckx-Rice
2017-03-15gnu: no-more-secrets: Update to 0.3.2.•••* gnu/packages/games.scm (no-more-secrets): Update to 0.3.2. Tobias Geerinckx-Rice
2017-03-15gnu: mailutils: Update to 3.2.•••* gnu/packages/mail.scm (mailutils): Update to 3.2. Tobias Geerinckx-Rice
2017-03-15gnu: Use INSTALL-FILE where appropriate.•••* 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. Tobias Geerinckx-Rice
2017-03-15gnu: cryptsetup: Update to 1.7.4.•••* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4. Tobias Geerinckx-Rice
2017-03-15gnu: man-pages: Update to 4.10.•••* gnu/packages/man.scm (man-pages): Update to 4.10. [home-page]: Use HTTPS. Tobias Geerinckx-Rice
2017-03-15gnu: Add profanity.•••* gnu/packages/messaging.scm (profanity): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Mekeor Melire
2017-03-15gnu: Add libstrophe.•••* gnu/packages/messaging.scm (libstrophe): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Mekeor Melire
2017-03-15gnu: Add libmesode.•••* gnu/packages/messaging.scm (libmesode): New variable. Signed-off-by: Leo Famulari <leo@famulari.name> Mekeor Melire
2017-03-15gnu: bitcoin-core: Update to 0.14.0.•••* gnu/packages/finance.scm (bitcoin-core): Update to 0.14.0. Leo Famulari
2017-03-15build: Prefer Guile 2.2 over 2.0.•••* 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. Ludovic Courtès
2017-03-15tests: Expect less accurate location info in 2.2.0.•••* tests/guix-system.sh: Work around inaccurate location info in 2.2.0. Ludovic Courtès
2017-03-15store: Adjust UTF-8 test to Guile 2.2.•••* tests/store.scm ("current-build-output-port, UTF-8 + garbage"): On Guile 2.2, expect REPLACEMENT CHARACTER instead of '?'. Ludovic Courtès
2017-03-15syscalls: Adjust 'clone' to Guile 2.2.•••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'. Ludovic Courtès
2017-03-15zlib: Don't rely on EBADF being ignored by 'fport_close'.•••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. Ludovic Courtès
2017-03-15maint: Mention guix-patches@gnu.org in 'HACKING'.•••Fixes <http://bugs.gnu.org/25899>. * HACKING: Mention guix-patches@gnu.org. Ludovic Courtès
2017-03-15gnu: mariadb: Update to 10.1.22 [fixes CVE-2017-3302 and CVE-2017-3313].•••* gnu/packages/databases.scm (mariadb): Update to 10.1.22. Marius Bakke
2017-03-15gnu: python-waf: Update to 1.9.8.•••* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8. [home-page]: Use https. Efraim Flashner
2017-03-15gnu: direnv: Update to 2.11.3.•••* gnu/packages/shellutils.scm (direnv): Update to 2.11.3. Tobias Geerinckx-Rice
2017-03-15gnu: conky: Update to 1.10.6.•••* gnu/packages/conky.scm (conky): Update to 1.10.6. Tobias Geerinckx-Rice
2017-03-15gnu: obs: Update to 18.0.1.•••* gnu/packages/video.scm (obs): Update to 18.0.1. Tobias Geerinckx-Rice
2017-03-15gnu: youtube-dl: Update to 2017.03.15.•••* gnu/packages/video.scm (youtube-dl): Update to 2017.03.15. Tobias Geerinckx-Rice
2017-03-15gnu: stress-make: Fix description.•••* gnu/packages/debug.scm (stress-make)[description]: Fix typo. Avoid ambiguous use of ‘in order’. Tobias Geerinckx-Rice
2017-03-15gnu: znc: Update to 1.6.5.•••* gnu/packages/messaging.scm (znc): Update to 1.6.5. Tobias Geerinckx-Rice
2017-03-15gnu: grue-hunter: Correctly install documentation.•••* gnu/packages/games.scm (grue-hunter)[arguments]: Install and populate ‘/share/doc/grue-hunter’ as a directory, not a plain file. Tobias Geerinckx-Rice
2017-03-15gnu: samtools: End installation phases with truth.•••* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE. Tobias Geerinckx-Rice
2017-03-14gnu: w3m: Update to 0.5.3+git20170102 [security fixes].•••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. Leo Famulari
2017-03-14Revert "gnu: gitolite: Fix shebangs in hooks."•••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. Leo Famulari
2017-03-14pack: Add unit test.•••* 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. Ludovic Courtès