Commit 87961fc965 inadvertently modified the
patch set for glibc-2.31. This change restores the original patch set.
Fixes: <https://bugs.gnu.org/49516>.
* gnu/packages/base.scm (glibc-2.31) [source]: Use the same patches as glibc,
but replace glibc-hurd-clock_gettime_monotonic.patch with
glibc-2.31-hurd-clock_gettime_monotonic.patch, and add
glibc-hurd-signal-sa-siginfo.patch.
* gnu/packages/patches/glibc-2.31-hurd-clock_gettime_monotonic.patch: Add it.
* gnu/packages/patches/glibc-hurd-signal-sa-siginfo.patch: Add it.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
Re-testing 'guix package -A' using the default line buffering set in (guix
ui), there doesn't seem to be a performance gain to use block buffering, so
remove this extraneous side effect.
* guix/utils.scm (pretty-print-table): Do not set buffering mode to block.
Reported-by: Ludovic Courtès <ludo@gnu.org>
* gnu/packages/tex.scm (biber): Update to 2.16.
[source]: Remove 'patches'.
[inputs]: Add 'perl-io-string', 'perl-parse-recdescent', and
'perl-unicode-collate' (upstream appears to have fixed the issue
initially mentioned as a comment: recent issue was closed after
telling user to use perl-unicode-collate 1.29, which is the one
available; see <https://github.com/plk/biber/issues/378>.)
* gnu/packages/patches/biber-fix-encoding-write.patch,
gnu/packages/patches/biber-sortinithash.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
texlive-latex-pdftexcmds moved to a different directory in TeX Live 2021.
* gnu/packages/tex.scm (texlive-latex-pdftexcmds): Update hash and paths.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Use version 20210325 for the tarballs, which is the latest one available on
the historical releases repository. And use subversion tag 2021.3 which is
the latest one available as well.
TeX Live dropped support for using the system’s poppler library after the
2020 version. Quoting from `m4/kpse-xpdf-flags.m4`:
# Support for our semi-homegrown libs/xpdf library. This is derived
# from xpdf source code, but xpdf does not distribute it as a library.
# It is used by pdftex (and nothing else) to read PDF images.
# Other engines use the semi-homegrown pplib library (q.v.) for that.
# The well-known poppler library is also originally derived from xpdf
# source code, but has been greatly revised and extended. TL used to
# (sort of) support poppler as the system xpdf, but after the TL 2020
# release we dropped this, because we switched XeTeX to use pplib, and
# nothing else used poppler. (No engines ever used poppler to generate
# their PDF output).
#
# poppler is aggressively developed, with requirements for new compilers
# and language versions. That's fine for them, but since we don't need
# anything new, it has become too time-consuming and problematic to
# continue to support it in the TL sources, when we don't have any
# requirement for it.
Therefore the main change in this commit is making the texlive-bin package
use the embedded pplib and xpdf libraries.
Another noteworthy change is to texlive-latex-l3packages, which now needs
to ship a few pre-generated files that cannot be reproduced during the
build process (the comments in the package definition have more details).
* guix/build-system/texlive.scm (%texlive-tag): Set to “texlive-2021.3”.
(%texlive-revision): Set to 59745.
* gnu/packages/tex.scm (hyph-utf8-scripts, texlive-docstrip,
texlive-unicode-data texlive-hyphen-base, texlive-metafont, texlive-cm,
texlive-courier, texlive-lm, texlive-knuth-lib, texlive-tex-plain,
texlive-hyphen-finnish, texlive-hyphen-german, texlive-hyph-utf8,
texlive-dehyph-exptl, texlive-kpathsea, texlive-latex-fancyvrb,
texlive-graphics-def, texlive-latex-graphics, texlive-hyperref,
texlive-oberdiek, texlive-latex-tools, texlive-latex-l3kernel,
texlive-l3build, texlive-luaotfload, texlive-latex-amsmath, texlive-amscls,
texlive-babel, texlive-generic-babel-german, texlive-babel-swedish,
texlive-psnfss, texlive-latex-draftwatermark, texlive-latex-etoc,
texlive-etoolbox, texlive-latex-polyglossia, texlive-tex-texinfo,
texlive-latex-bookmark, texlive-latex-cmap, texlive-latex-fancyhdr,
texlive-latex-kvoptions, texlive-latex-eso-pic, texlive-latex-multirow,
texlive-latex-parskip, texlive-latex-pdfpages, texlive-metapost,
texlive-latex-acmart, texlive-latex-preview, texlive-latex-acronym,
texlive-pdftex, texlive-latex-media9, texlive-latex-ocgx2,
texlive-latex-ms, texlive-latex-pgf, texlive-latex-pgf-generic,
texlive-latex-koma-script, texlive-generic-ltxcmds, texlive-bibtex,
texlive-context-base, texlive-context, texlive-beamer, texlive-pstricks,
texlive-tools, texlive-latex-xkeyval, texlive-csquotes, texlive-biblatex,
texlive-todonotes, texlive-microtype, texlive-caption, texlive-fontaxes,
texlive-cabin, texlive-newtx, texlive-xcharter, texlive-adjustbox,
texlive-tcolorbox): Update hash.
(texlive-extra-src, texlive-texmf-src): Update version to
“20210325”. Update hash.
(texlive-bin)[source]: Update version to “20210325”. Update hash. Preserve
‘libs/pplib’ and ‘libs/xpdf’.
[inputs]: Update hash for ‘texlive-scripts’. Remove ‘poppler’.
[arguments]: Remove “--with-system-poppler” and “--with-system-xpdf” from
‘#:configure-flags’. Remove build phase ‘use-code-for-new-poppler’.
(texlive-hyphen-schoolfinnish): Add public variable.
(texlive-hyphen-macedonian): Add 8bit patterns. Update hash.
(texlive-latex-base)[template]: Update hash.
[arguments]: Set ‘LUAINPUTS’ environment variable in build phase.
[native-inputs]: Update hash for ‘texlive-luatexconfig’.
[propagated-inputs]: Add ‘texlive-hyphen-schoolfinnish’,
‘texlive-latex-l3kernel’ and ‘texlive-latex-l3packages’.
(texlive-latex-l3packages)[source]: Use ‘texlive-origin’. Update hash. Add
generated files.
[arguments]: Adjust paths for ‘TEXINPUTS’ environment variable. Add build
phase ‘copy-generated-files’.
(texlive-texmf, texlive): Update version to “20210325”.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
The package texlive-latex-base in TeX Live 2021 will depend on
texlive-latex-l3kernel and texlive-latex-l3packages. Therefore we need to
remove their build dependency on texlive-latex-base to avoid a circular
dependency.
l3kernel and l3packages don’t need LaTeX during build, just IniTeX.
So to make them use it, modify texlive-build-system to allow disabling
the #:texlive-latex-base and #:tex-format parameters, and also add
a #:tex-engine parameter.
We also need to add texlive-docstrip as a native input, which was
previously provided by texlive-latex-base.
* gnu/packages/tex.scm (texlive-latex-l3kernel,
texlive-latex-l3packages)[arguments]: Add ‘#:tex-engine’, ‘#:tex-format’
and ‘#:texlive-latex-base’ parameters.
[native-inputs]: Add ‘texlive-docstrip’.
* guix/build-system/texlive.scm (lower)[build-inputs]: Don’t add
‘texlive-latex-base’ if its keyword parameter is false.
(texlive-build): Add ‘tex-engine’ keyword parameter.
[builder]: If a ‘tex-engine’ parameter was passed, use it. Otherwise, use
‘tex-format’ as the engine.
* guix/build/texlive-build-system.scm (compile-with-latex): Add ‘engine’
parameter. If the ‘format’ parameter is false, add “-ini” option to the
command line.
(build): Add ‘tex-engine’ parameter. Pass it down to ‘compile-with-latex’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
Fixes <https://issues.guix.gnu.org/48552>.
* gnu/packages/build-tools.scm (meson): Update to 0.59.0, which includes a
reproduceability fix for builds that link against multiple LLVM libraries.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* guix/import/hackage.scm (hackage-module->sexp)[dependencies]
[native-dependencies]: Make into a list of symbols.
[maybe-inputs]: Wrap INPUTS in 'list' instead of 'quasiquote'.
* tests/hackage.scm (match-ghc-foo)
(match-ghc-foo-6)
(match-ghc-foo-revision)
(match-ghc-foo-import): Adjust accordingly.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* guix/import/opam.scm (opam->guix-package): Wrap INPUTS and
NATIVE-INPUTS in 'list' instead of 'quasiquote'.
(dependency-list->inputs): Return a list of symbols.
* tests/opam.scm ("opam->guix-package"): Adjust accordingly.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* guix/import/egg.scm (egg->guix-package): Generate dependency list from
a list of symbols.
[egg-parse-dependency]: Return a list of symbols.
[maybe-inputs]: Wrap INPUTS in 'list' instead of 'quasiquote'.
* tests/egg.scm (match-chicken-foo): Adjust accordingly.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
The cleanup notably:
* Builds and installs the documentation into a separate doc output (in
the process moving around some files erroneously installed into the root
directory); and
* Removes unnecessary inputs and moves some inputs into
propagated-inputs (the candidates of which were determined with a search
for "include.*LIBNAME" in include/deal.II).
* gnu/packages/maths.scm (dealii): Reword comments.
[version]: Update to 9.3.1.
[outputs]: New field including doc output.
[native-inputs]: New field.
[inputs]: Sort them. Remove p4est (deal.II interfaces with it only when
MPI is enabled). Move boost, suitesparse and tbb to...
[propagated-inputs]: ...here. New field including hdf5, which is
actually supported in deal.II without MPI.
[arguments]<#:tests?>: New argument. The tests were not being run before
anyway.
<#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag.
[-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md,
README.md, detailed.log and summary.log files from being installed in
the root directory (though note that the logs are removed in the new
remove-build-logs phase).
[-DDEAL_II_DOCHTML_RELDIR]: New flag.
[-DDEAL_II_COMPILE_EXAMPLES]: New flag.
[-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory
from being installed in the root directory.
[-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been
resolved.
<#:phases>{remove-build-logs}: New phase.
[home-page]: Add trailing slash.
(dealii-openmpi): Use package/inherit.
[inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer
interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi,
p4est-openmpi, petsc-openmpi and slepc-openmpi to...
[propagated-inputs]: ...here. New field.
[arguments]<#:configure-flags>: Rename cf variable to flags.
<#:phases>{mpi-setup}: Remove phase which is unused because the tests
are disabled.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Eric Bavier
Chris Marusich
Joseph LaFreniere
Ludovic Courtès
Maxim Cournoyer
Giacomo Leidi
Nathan Benedetto Proença
Thiago Jung Bauermann
Maxime Devos
Lars-Dominik Braun
Guillaume Le Vaillant
Michael Rohleder
Kaelyn Takata
Sarah Morgensen
Ivan Gankevich
Paul A. Patience
Efraim Flashner
Tanguy Le Carrour
raingloom
Matthew James Kraai
Raghav Gururajan