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* pack: Add '--format' option and Docker output support.Ludovic Courtès2017-03-16
| | | | | | | | | | | | | | | | | | | | * 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'.
* pack: Honor command-line options related to the store.Ludovic Courtès2017-03-16
| | | | | * guix/scripts/pack.scm (guix-pack): Call 'set-build-options-from-command-line'.
* memoization: Micro-optimize code produced by 'define-cache-procedure'.Ludovic Courtès2017-03-16
| | | | | | * guix/memoization.scm (%nothing): Remove. (define-cache-procedure): Make '%nothing' a local variable, with a literal list.
* services: connman: Rework service.Mathieu Othacehe2017-03-16
| | | | | | | | | | | | | | * 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>
* gexp: Add '=>' syntax to import computed modules.Ludovic Courtès2017-03-16
| | | | | | | | | | * 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'.
* 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.
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