5ae63362ae
import cran: Distinguish Bioconductor data packages.
...
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor
data packages.
(bioconductor-data-package?): New procedure.
2017-04-05 18:38:51 +02:00
b23c1a71be
download: Update the GnuPG mirror list.
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* guix/download.scm (%mirrors) <gnupg>: Use HTTP for TU Wien mirror.
2017-04-05 07:07:35 -04:00
1c6b2d3f98
build: Export register-root procedure.
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* guix/scripts/build.scm: Export register-root procedure.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-04-05 00:53:03 +02:00
6c17422eac
utils: Fix handling of shell arguments for xz compression.
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Fixes test failures related to xz compression in tests/utils.scm.
This is a followup to commit 63102406f2
2017-04-03 23:23:39 -04:00
76c486196f
packages: Catch invalid input errors for structs.
...
Reported by Thomas Sigurdsen <thomas.sigurdsen@gmail.com>
at <https://lists.gnu.org/archive/html/help-guix/2017-04/msg00007.html >.
* guix/packages.scm (expand-input): Add 'guard' form around call to
'package-source-derivation'.
* tests/packages.scm (dummy): New test.
2017-04-04 00:10:00 +02:00
3e43166ffc
gexp: 'lower-object' raises an exception when passed an invalid object.
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* guix/gexp.scm (&gexp-error, &gexp-input-error): New error conditions.
(lower-object): Raise &gexp-input-error when 'lookup-compiler' returns #f.
* tests/gexp.scm ("lower-object & gexp-input-error?"): New test.
* guix/ui.scm (call-with-error-handling): Add case for 'gexp-input-error?'.
2017-04-04 00:10:00 +02:00
2a0d5de5a9
Merge branch 'core-updates'
2017-04-03 00:13:06 +02:00
63102406f2
guix: Compress and decompress xz archives in parallel.
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* guix/scripts/pack.scm (%compressors): Add flag '-T0' when calling "xz".
* guix/utils.scm (decompressed-port, compressed-port,
compressed-output-port): Same.
2017-04-02 14:42:20 +03:00
f264e838c0
substitute: Send ‘User-Agent’ header.
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* guix/scripts/substitute.scm (narinfo-request): Pass ‘User-Agent’ #:headers
to ‘build-request’.
2017-03-31 15:33:16 +02:00
84157bb8bf
Merge branch 'master' into core-updates
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Most conflicts are from 6fd52309b8
2017-03-30 22:59:53 +02:00
cdb3f734cf
packages: Remove "mips64el-linux" from '%hydra-supported-systems'.
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* guix/packages.scm (%hydra-supported-systems): Remove "mips64el-linux".
2017-03-29 22:50:42 +02:00
e1f02f92e9
Replace (compose not PROC) with simpler idioms.
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* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
2017-03-28 22:15:44 +02:00
1a75083b0d
import cran: Print package stream in the expected order.
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* guix/scripts/import/cran.scm (guix-import-cran): Reverse list of packages.
2017-03-28 15:54:10 +02:00
2dca8b2d51
import cran: Automatically add gfortran and zlib when needed.
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* guix/import/cran.scm (needs-fortran?, needs-zlib?): New procedures.
(description->package): Use them.
2017-03-28 15:37:47 +02:00
6dfd683dc7
download: Properly parse ftp:// URLs that lack user info.
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Fixes a regression introduced in
a4f5423415
2017-03-28 13:30:09 +02:00
bdb59b331b
derivations: Do not fetch narinfos for non-substitutable items.
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This avoids connections to substitute servers for derivations that are
not substitutable anyway, such as profiles.
Reported by Andy Wingo.
* guix/derivations.scm (substitution-oracle): Skip derivations that do
not pass 'substitutable-derivation?'.
* tests/derivations.scm ("substitution-oracle and #:substitute? #f"):
New test.
2017-03-28 10:00:05 +02:00
c17383f400
Merge branch 'master' into core-updates
2017-03-27 21:19:38 -04:00
689db38e34
ui: Support Texinfo markup in package synopses.
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* guix/ui.scm (package-field-string): New procedure.
(package-description-string): Use it.
(package-synopsis-string): New procedure.
(package->recutils): Use it.
* guix/scripts/lint.scm (check-synopsis-style)[check-texinfo-markup]:
New procedure. Use it in checks.
* tests/lint.scm: Test it.
* gnu/packages/perl.scm (perl-try-tiny)[synopsis]: Adjust for the
Texinfo markup.
2017-03-27 10:55:16 +03:00
0a5ce0d1df
profiles: Create fonts.dir/scale for all fonts directories.
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* guix/profiles.scm (fonts-dir-file): Create fonts.dir/scale files for all
fonts directories.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-03-26 12:53:52 +02:00
addce19e2d
union: Add create-all-directories? parameter to 'union-build'.
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* guix/build/union.scm (union-build): Add create-all-directories? keyword
parameter.
* tests/union.scm ("union-build #:create-all-directories? #t"): New test.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2017-03-26 12:53:48 +02:00
0371b345e8
Merge remote-tracking branch 'origin/master' into core-updates
2017-03-23 14:53:33 +02:00
4bb5e0aeb3
publish: Add '--nar-path'.
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* guix/scripts/publish.scm (show-help, %options): Add '--nar-path'.
(%default-options): Add 'nar-path'.
(guix-publish): Honor it.
2017-03-22 14:05:59 +01:00
cdd7a7d210
publish: Make the nar URL prefix a parameter.
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* guix/scripts/publish.scm (narinfo-string): Add #:nar-path and honor it.
(render-narinfo): Likewise.
(make-request-handler): Likewise.
(run-publish-server): Likewise.
* tests/publish.scm ("custom nar path"): New test.
2017-03-22 14:05:59 +01:00
46f58390cb
publish: Add '--public-key' and '--private-key'.
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* guix/scripts/publish.scm (show-help, %options): Add --public-key and
--private-key.
* doc/guix.texi (Invoking guix publish): Document it.
2017-03-22 14:05:59 +01:00
ab2a74e4db
publish: The public and private keys are now SRFI-39 parameters.
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* guix/scripts/publish.scm (%default-options): Add 'public-key-file' and
'private-key-file'.
(lazy-read-file-sexp): Remove.
(%private-key, %public-key): Turn into SRFI-39 parameters.
(signed-string, render-narinfo): Adjust accordingly.
(guix-publish): Honor 'public-key-file' and 'private-key-file' from
OPTS. Use 'parameterize'.
* guix/pk-crypto.scm (read-file-sexp): New procedure.
* tests/publish.scm: Initialize '%public-key' and '%private-key'.
2017-03-22 14:05:59 +01:00
378de69c59
Merge remote-tracking branch 'origin/master' into core-updates
2017-03-22 12:57:37 +02:00
a4f5423415
download: Handle username and password properties for FTP URIs.
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* guix/build/download.scm (ftp-fetch): Process username and password from a URI.
2017-03-21 12:15:14 +01:00
193420a803
ftp-client: Allow custom username and password for FTP servers.
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* guix/ftp-client.scm (ftp-open): Add username and password arguments.
2017-03-21 12:14:05 +01:00
d67f972bd7
download: Remove non-existent kernel mirror.
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* guix/download.scm (%mirrors) <kernel.org>: Remove www.all.kernel.org.
2017-03-19 21:18:46 -04:00
f67337e23e
Merge branch 'master' into core-updates
2017-03-19 18:52:12 -04:00
4fd06a4dd1
http-client: Avoid name clash with 'open-connection-for-uri' in 2.2.0.
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* guix/build/download.scm (open-connection-for-uri): Add note about
same-named binding in Guile 2.2.0.
* guix/http-client.scm: Use 'guix:open-connection-for-uri' for the
procedure coming from (guix build download).
* guix/scripts/lint.scm: Likewise.
* guix/scripts/substitute.scm: Likewise.
2017-03-18 00:39:50 +01:00
36626c556e
build: Require Guile >= 2.0.9.
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* configure.ac: Bump requirement to 2.0.9.
* doc/guix.texi (Requirements): Adjust accordingly.
* README (Requirements): Likewise.
* build-aux/download.scm: Remove workaround for <http://bugs.gnu.org/13095 >.
* guix/build/download.scm: Likewise.
(http-fetch)[post-2.0.7?]: Remove. Remove conditional code for not
POST-2.0.7?.
* guix/http-client.scm: Remove workaround for <http://bugs.gnu.org/13095 >.
(http-fetch)[post-2.0.7?]: Remove. Remove conditional code for not
POST-2.0.7?.
* guix/serialization.scm (read-latin1-string): Remove mention of 2.0.9.
* tests/nar.scm: Use (ice-9 control).
(let/ec): Remove.
2017-03-18 00:39:49 +01:00
5461115e8f
pack: Add '--target'.
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* guix/scripts/pack.scm (self-contained-tarball): Add #:target.
(docker-image): Add #:target.
[build]: Pass it to 'build-docker-image'.
(%options, show-help): Add '--target'.
(guix-pack): Pass TARGET to 'profile-derivation' and to 'build-image'.
* guix/docker.scm (build-docker-image): Add #:system parameter and honor it.
* doc/guix.texi (Invoking guix pack): Document '--target'.
(Additional Build Options): Refer to the Autoconf manual instead of the
obsolete 'configure.info' for cross-compilation.
2017-03-18 00:38:41 +01:00
176febe377
profiles: Packages in a profile can be cross-compiled.
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* guix/profiles.scm (profile-derivation): Add #:target parameter; pass
it to 'gexp->derivation'.
* tests/profiles.scm ("profile-derivation, cross-compilation"): New test.
2017-03-17 23:25:53 +01:00
48b444304e
pack: Move absolute file name to <compressor>.
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* guix/scripts/pack.scm (<compressor>)[package]: Remove.
[command]: Document as being a gexp with an absolute file name.
(%compressors): Adjust accordingly.
(self-contained-tarball): Simplify PATH expression. Move 'string-join'
for the compressor command on the build side.
(docker-image): Simplify PATH expression.
* tests/pack.scm (%gzip-compressor): Adjust accordingly.
2017-03-17 23:25:53 +01:00
4ed64c534a
build/cargo-build-system: Make cargo-build-system install working packages.
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* guix/build/cargo-build-system.scm (configure): Remove proprietary
dependencies. Add rust dependencies and configure Cargo to find them.
(build): Also build libraries, not just applications.
(file-sha256): New variable.
(generate-checksums): New variable. Export it.
(touch): New variable.
(install): Generate checksums so Cargo accepts the package.
2017-03-17 16:48:09 +01:00
25fb58a3be
build-system/cargo (cargo-build): Add cargo-build-flags, remove configure-flags.
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* guix/build-system/cargo.scm (cargo-build): Add cargo-build-flags,
remove configure-flags.
2017-03-17 16:48:08 +01:00
2d7c4ae3ee
gnu: r: Rename to r-minimal.
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* 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".
2017-03-17 10:14:02 +01:00
aeb64f3cb2
gnu: r: Do not build recommended packages.
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* 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.
2017-03-17 10:14:02 +01:00
db3f2b61ad
pack: Allow for "-S /opt/foo=".
...
Reported by Andy Wingo.
* guix/scripts/pack.scm (%options): Use 'string-split' instead of
'string-tokenize'.
2017-03-16 22:50:15 +01:00
9e84ea3673
pack: Honor symlinks in the Docker back-end.
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* 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'.
2017-03-16 22:50:15 +01:00
54241dc8e6
docker: Build images in a reproducible fashion.
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* guix/docker.scm (%tar-determinism-options): New variable.
(build-docker-image): Use it on the two 'tar' invocations.
2017-03-16 22:50:15 +01:00
84dda5a9c0
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'.
2017-03-16 22:50:15 +01:00
b1edfbc37f
pack: Add '--format' option and Docker output support.
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* 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 1545a012cb01445711db03476a23ff
2017-03-16 22:50:15 +01:00
2971f39c33
pack: Honor command-line options related to the store.
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* guix/scripts/pack.scm (guix-pack): Call
'set-build-options-from-command-line'.
2017-03-16 22:50:15 +01:00
146db52a18
memoization: Micro-optimize code produced by 'define-cache-procedure'.
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* guix/memoization.scm (%nothing): Remove.
(define-cache-procedure): Make '%nothing' a local variable, with a
literal list.
2017-03-16 22:50:15 +01:00
d938a58bee
gexp: Add '=>' syntax to import computed modules.
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* 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'.
2017-03-16 22:50:14 +01:00
4c0c4db070
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.
2017-03-16 22:50:14 +01:00
4b7e5c1131
Merge branch 'master' into core-updates
2017-03-15 17:52:26 +01:00
70dfdd501a
syscalls: 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'.
2017-03-15 15:19:53 +01:00
Ricardo Wurmus