| Commit message (Collapse) | Author | Age |
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* gnu/packages/gdb.scm (gdb): Update to 8.2.
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* gnu/packages/guile.scm (guile-json): Update to 1.2.0.
[license]: Change to GPL3+.
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* guix/scripts/describe.scm (display-profile-info)[number]: Use the
current generation number instead of the last generation number.
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* guix/profiles.scm (package->manifest-entry): Add #:properties and
honor it.
* guix/scripts/package.scm (package-provenance)
(package->manifest-entry*): New procedures.
(transaction-upgrade-entry, options->installable): Use
'package->manifest-entry*' instead of 'package->manifest-entry'.
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* guix/scripts/describe.scm: New file.
* Makefile.am (MODULES): Add it.
(SH_TESTS): Add tests/guix-describe.sh.
* po/guix/POTFILES.in: Add it.
* guix/scripts/pull.scm (display-profile-content): Export.
* guix/describe.scm (current-profile, current-profile-entries): Export.
* tests/guix-describe.sh: New file.
* doc/guix.texi (Features): Mention 'guix pull' and provenance tracking.
(Invoking guix pull): Link to 'guix describe'.
(Channels): Likewise.
(Invoking guix describe): New node.
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* guix/scripts/pull.scm (show-help, %options): Add '--profile'.
(build-and-install): Change 'config-dir' argument to 'profile'.
(guix-pull): Honor '--profile'.
* doc/guix.texi (Invoking guix pull): Document it.
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* gnu/packages/cran.scm (r-ggformula): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/cran.scm (r-mosaiccore): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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gnu/packages/cran.scm (r-ggstance): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/cran.scm (r-abctools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/cran.scm (r-abcrf): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/cran.scm (r-abcp2): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/emacs.scm (emacs-ess): Update to 17.11
[url]: Use github for https
[snippet]: update julia-mode substitution, only build info doc, bypass failing test
[propagated-inputs]: Add emacs-julia-mode
[description]: Mention that ESS supports Julia and JAGS (which replaces OpenBUGS)
[arguments]: Remove 'set-home' phase.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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Fixes <https://bugs.gnu.org/32652>.
* gnu/system/vm.scm (operating-system-uuid)[service-name,
file-system-digest]: New procedures.
Map these over services and file systems and hash the result.
* tests/guix-system.sh: Add test.
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* gnu/packages/dns.scm (knot): Update to 2.7.2.
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* gnu/packages/networking.scm (wireshark): Update to 2.6.3.
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* gnu/packages/curl.scm (curl)[replacement]: Update to 7.61.1.
(curl-7.61.0): Replace variable with ...
(curl-7.61.1): ... new variable.
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* gnu/packages/music.scm (libgme): Update to 0.6.2.
[native-inputs]: Add gcc-4.9.
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* doc/guix.texi (Web Services): Document 'channels' and
'package-list-expiration'.
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Previously Git pulls over HTTPS would fail with:
guix/git.scm:132:7: In procedure update-cached-checkout:
Throw to key `git-error' with args `(#<<git-error> code: -17 message: "the SSL certificate is invalid" class: 16>)'.
* gnu/services/web.scm (hpcguix-web-shepherd-service): Pass
"SSL_CERT_DIR=/etc/ssl/certs".
* doc/guix.texi (Web Services): Mention certificates.
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Reported by Paul Garlick <pgarlick@tourbillion-technology.com>.
Fixes a bug whereby "old" Guix instances (before mid-May 2018) would
fail to pull to current master.
Specifically, Paul reported being unable to upgrade from
6f84dc4314cd84550d9fc7e7afa11c495edc45a5 (a commit that predates that
addition of the 'bootstrap' phase on gnu-build-system on 'master' and
that also predates the new 'guix pull'.)
* build-aux/build-self.scm (guile-gcrypt)[arguments]: New field.
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* gnu/packages/gcc.scm (gfortran-8, gcc-objc-8, gcc-objc++-8): New
variables.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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Reported by Alex Vong <alexvong1995@gmail.com>.
* config-daemon.ac: Do not add "-L$LIBGCRYPT_LIBDIR" to LIBGCRYPT_LIBS
when "$LIBGCRYPT_LIBDIR" is empty.
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* gnu/packages/plotutils.scm (guile-present)[source](modules, snippet):
Remove.
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* gnu/packages/plotutils.scm (guile-charting)[source](modules, snippet):
Remove.
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* gnu/packages/web.scm (hpcguix-web): Update to 9ff40fc.
[arguments]: In 'wrap-program' phase, add guile-gcrypt, guile-git, and
guile-bytestructures to DEPS.
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* gnu/packages/guile.scm (guile-commonmark)[source](snippet): Change the
"modir = " and "godir = " line separately, allowing .go files to be
installed to $(libdir).
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This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2.
Sorry!
* gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages
bioconductor).
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* gnu/packages/ccache.scm (ccache): Update to 3.4.3.
[arguments]: Remove obsolete 'munge-failing-test' phase.
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* gnu/packages/fonts.scm (font-fira-code): Update to 1.205.
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* gnu/packages/mpd.scm (libmpdclient): Update to 2.15.
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Fixes <https://bugs.gnu.org/32618>.
Reported by Eric Brown <brown@fastmail.com>.
* guix/git.scm (update-cached-checkout): Remove "origin/" from default
REF. Define CANONICAL-REF and use it instead of REF.
(latest-repository-commit): Remove "origin/" from default REF.
* guix/channels.scm (%default-channels): Remove "origin/" from
'branch'.
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This fixes a regression introduced in
ca719424455465fca4b872c371daf2a46de88b33 whereby external channels would
fail to build due to the lack of (gcrypt …) modules.
* guix/channels.scm (channel-instance-derivations): Add 'guile-gcrypt'.
Pass it along CORE to 'build-channel-instance'.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
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* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
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* gnu/packages/statistics.scm (r-modelmetrics): Update to 1.2.0.
[propagated-inputs]: Add r-data-table.
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* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-2.
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* gnu/packages/statistics.scm (r-rann): Update to 2.6.
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* gnu/packages/statistics.scm (r-ggthemes): Update to 4.0.1.
[propagated-inputs]: Remove r-assertthat and r-colorspace; add r-purrr,
r-stringr, and r-tibble.
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* gnu/packages/statistics.scm (r-ztable): Update to 0.2.0.
[propagated-inputs]: Add r-flextable, r-magrittr, r-moonbook, r-officer,
r-rcolorbrewer, r-scales, and r-stringr.
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* gnu/packages/statistics.scm (r-zoo): Update to 1.8-3.
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* gnu/packages/statistics.scm (r-gtools): Update to 3.8.1.
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* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-27.
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* gnu/packages/machine-learning.scm (r-adaptivesparsity): Update to 1.6.
[propagated-inputs]: Add r-mass and r-matrix.
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* gnu/packages/cran.scm (r-codedepends): Move from here...
* gnu/packages/bioconductor.scm (r-codedepends): ...to here.
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* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
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* gnu/packages/cran.scm (r-ggpubr): Update to 0.1.8.
[propagated-inputs]: Add r-glue and r-polynom.
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