| Commit message (Collapse) | Author | Age |
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Gmsh bundles METIS 5 released with Apache License 2.0 since upstream commit
eaff7f6477fe876991615cfa4b5832bd5f12994b. Instead, Gmsh is linked with the
package 'metis'.
* gnu/packages/maths.scm (gmsh): Update to 4.6.0.
(propagated-inputs): Replace 'opencascade-oce' by 'opencascade-occt', add
'metis'.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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From 0d8692dfebc6ac4b515c06612ab8da4c898719eb Mon Sep 17 00:00:00 2001
From: Greg Hogan <code@greghogan.com>
Date: Tue, 29 Sep 2020 11:54:38 +0000
Subject: [PATCH] gnu: SuiteSparse: Update to 5.8.1.
* gnu/packages/maths.scm (suitesparse): Update to 5.8.1.
[arguments]: Remove unnecessary flag and use default blas and lapack.
[inputs]: Add new dependencies for SLIP_LU component.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/algebra.scm (iml)[inputs]: Correctly refer to package
inputs.
* gnu/packages/astronomy.scm (xplanet),
* gnu/packages/audio.scm (redkite, libaudec, lv2lint, lv2toweb),
* gnu/packages/bioconductor.scm (r-cummerbund),
* gnu/packages/chicken.scm (chicken),
* gnu/packages/conky.scm (conky),
* gnu/packages/cran.scm (r-latex2exp),
* gnu/packages/crates-io.scm (rust-rgb),
* gnu/packages/databases.scm (mariadb),
* gnu/packages/diffoscope.scm (reprotest),
* gnu/packages/file-systems.scm (glusterfs),
* gnu/packages/finance.scm (electron-cash),
* gnu/packages/games.scm (rinutils, ksudoku, kdiamond, kigo),
* gnu/packages/geo.scm (grass),
* gnu/packages/gnome.scm (libmediaart, gnome-contacts, geoclue),
* gnu/packages/gnucash.scm (aqbanking),
* gnu/packages/image.scm (mtpaint),
* gnu/packages/kde-internet.scm (kopete, ktorrent),
* gnu/packages/kde-utils.scm (kmousetool, kmouth, kronometer),
* gnu/packages/linphone.scm (liblinphone),
* gnu/packages/maths.scm (ppl),
* gnu/packages/mercury.scm (mercury-minimal),
* gnu/packages/music.scm (bjumblr, bschaffl, lsp-plugins,
spectacle-analyzer, helm, tap-lv2, wolf-shaper, shiru-lv2),
* gnu/packages/networking.scm (restinio),
* gnu/packages/prolog.scm (swi-prolog),
* gnu/packages/python-web.scm (gunicorn),
* gnu/packages/python-xyz.scm (python-docusign-esign),
* gnu/packages/ruby.scm (ruby-cucumber, ruby_version, ruby-addressable),
* gnu/packages/sagemath.scm (python-cypari2),
* gnu/packages/skarnet.scm (s6-linux-init),
* gnu/packages/vpn.scm (sshuttle),
* gnu/packages/web.scm (libcyaml),
* gnu/packages/xdisorg.scm (kbdd),
* gnu/packages/xorg.scm (xpra): Same.
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This reverts commit c59e9f0a03241ef3c7b8042054fd54e327f7539a because it
triggers too many rebuilds.
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* gnu/packages/maths.scm (openblas): Update to 0.3.10.
[source]: Fetch from github.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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Fixes CVE-2018-13870, CVE-2018-13869 and CVE-2018-17435.
* gnu/packages/maths.scm (hdf5-1.10): Update to 1.10.7.
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* gnu/packages/maths.scm (metamath): Update to 0.192.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/maths.scm (libflame): New variable.
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* gnu/packages/maths.scm (lrslib): Update to 7.1.
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* gnu/packages/maths.scm (octave)[source]: Remove. It had been
unnecessary since b66741edc954f0a17f1ef567e8d612cac87c7b6a.
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* gnu/packages/maths.scm (netcdf-parallel-openmpi)[arguments]: Add
'mip-setup' phase.
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* gnu/packages/maths.scm (hdf5-parallel-openmpi): Inherit from HDF5-1.10.
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* gnu/packages/maths.scm (hdf5-1.10, hdf5-parallel-openmpi): Use
'package/inherit'.
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* gnu/packages/maths.scm (hdf5): Rename to...
(hdf-1.8): ... this.
(hdf5-1.10): Adjust accordingly.
(hdf5): New variable.
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* gnu/packages/maths.scm (wxmaxima): Update to 20.06.6.
[arguments]: Add 'patch-doc-path phase.
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* gnu/packages/maths.scm (veusz): New variable.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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* gnu/packages/maths.scm (clapack): New variable.
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* gnu/packages/maths.scm (mcrl2): Update to 202006.0.
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* gnu/packages/maths.scm (sleef): New variable.
Signed-off-by: Brett Gilio <brettg@gnu.org>
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* gnu/packages/java.scm (java-junit)[arguments]: Replace install phase.
(java-hamcrest-core)[arguments]: Replace install phase.
(java-hamcrest-library)[arguments]: Replace install phase.
(java-cisd-jhdf5, java-commons-math3, java-commons-collections4)
(java-commons-io, java-commons-exec-1.1, java-commons-exec)
(java-commons-lang3, java-commons-codec, java-native-access)
(java-native-access-platform, java-hamcrest-all): Change junit and hamcrest
jar location accordingly.
(java-hamcrest-all): Use old install phase of java-hamcrest-core.
* gnu/packages/maths.scm (java-hdf): Change junit and hamcrest jar
location accordingly.
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Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix
swh) would sometimes return #f for these because the ".git" URLs are
redirects to the non-".git" URLs. Consequently, 'guix lint -c archival'
would keep saying "scheduled Software Heritage archival"; likewise, the
fallback download code would fail.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/aidc.scm,
gnu/packages/algebra.scm,
gnu/packages/android.scm,
gnu/packages/animation.scm,
gnu/packages/arcan.scm,
gnu/packages/assembly.scm,
gnu/packages/audio.scm,
gnu/packages/authentication.scm,
gnu/packages/avr.scm,
gnu/packages/axoloti.scm,
gnu/packages/backup.scm,
gnu/packages/bash.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/boost.scm,
gnu/packages/build-tools.scm,
gnu/packages/c.scm,
gnu/packages/calendar.scm,
gnu/packages/cdrom.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/chez.scm,
gnu/packages/clojure.scm,
gnu/packages/code.scm,
gnu/packages/compression.scm,
gnu/packages/compton.scm,
gnu/packages/coq.scm,
gnu/packages/cpp.scm,
gnu/packages/cran.scm,
gnu/packages/crypto.scm,
gnu/packages/curl.scm,
gnu/packages/databases.scm,
gnu/packages/datastructures.scm,
gnu/packages/debug.scm,
gnu/packages/disk.scm,
gnu/packages/distributed.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/dns.scm,
gnu/packages/docker.scm,
gnu/packages/education.scm,
gnu/packages/efi.scm,
gnu/packages/elixir.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/embedded.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/erlang.scm,
gnu/packages/fabric-management.scm,
gnu/packages/file-systems.scm,
gnu/packages/finance.scm,
gnu/packages/firmware.scm,
gnu/packages/flashing-tools.scm,
gnu/packages/fonts.scm,
gnu/packages/fontutils.scm,
gnu/packages/fpga.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/genealogy.scm,
gnu/packages/genimage.scm,
gnu/packages/geo.scm,
gnu/packages/gimp.scm,
gnu/packages/gl.scm,
gnu/packages/gnome-xyz.scm,
gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/golang.scm,
gnu/packages/gpodder.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/groff.scm,
gnu/packages/groovy.scm,
gnu/packages/gtk.scm,
gnu/packages/guile-xyz.scm,
gnu/packages/guile.scm,
gnu/packages/hardware.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-xyz.scm,
gnu/packages/hexedit.scm,
gnu/packages/i2p.scm,
gnu/packages/ibus.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/ipfs.scm,
gnu/packages/java-graphics.scm,
gnu/packages/java-maths.scm,
gnu/packages/java.scm,
gnu/packages/javascript.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/jupyter.scm,
gnu/packages/kodi.scm,
gnu/packages/language.scm,
gnu/packages/lego.scm,
gnu/packages/less.scm,
gnu/packages/libusb.scm,
gnu/packages/linux.scm,
gnu/packages/lirc.scm,
gnu/packages/lisp-xyz.scm,
gnu/packages/llvm.scm,
gnu/packages/logging.scm,
gnu/packages/lolcode.scm,
gnu/packages/lua.scm,
gnu/packages/lxde.scm,
gnu/packages/lxqt.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/markup.scm,
gnu/packages/maths.scm,
gnu/packages/maven.scm,
gnu/packages/mes.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/node-xyz.scm,
gnu/packages/ocaml.scm,
gnu/packages/ocr.scm,
gnu/packages/onc-rpc.scm,
gnu/packages/opencl.scm,
gnu/packages/opencog.scm,
gnu/packages/pantheon.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/perl6.scm,
gnu/packages/phabricator.scm,
gnu/packages/popt.scm,
gnu/packages/printers.scm,
gnu/packages/prolog.scm,
gnu/packages/protobuf.scm,
gnu/packages/pulseaudio.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm,
gnu/packages/qt.scm,
gnu/packages/radio.scm,
gnu/packages/rails.scm,
gnu/packages/rdf.scm,
gnu/packages/rednotebook.scm,
gnu/packages/rpc.scm,
gnu/packages/rsync.scm,
gnu/packages/ruby.scm,
gnu/packages/rust.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/security-token.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/shellutils.scm,
gnu/packages/simh.scm,
gnu/packages/sml.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/stenography.scm,
gnu/packages/sync.scm,
gnu/packages/syncthing.scm,
gnu/packages/synergy.scm,
gnu/packages/telephony.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tmux.scm,
gnu/packages/tor.scm,
gnu/packages/toys.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/vim.scm,
gnu/packages/virtualization.scm,
gnu/packages/vlang.scm,
gnu/packages/vnc.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wireservice.scm,
gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm,
tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
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* gnu/packages/maths.scm (ruby-asciimath): Update to 2.0.1.
[arguments]: Remove.
[native-inputs]: Remove bundler, add ruby-nokogiri.
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* gnu/packages/maths.scm (qalculate-gtk)[description]: Fix typo.
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* gnu/packages/maths.scm (metamath): Update to 0.183.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
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* gnu/packages/maths.scm (metamath): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
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* gnu/packages/maths.scm (maxima): Update to 5.44.0.
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* gnu/packages/maths.scm (xaos)[source]: Add file-name field.
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* gnu/packages/maths.scm (ipopt)[source]: Fix URI.
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* gnu/packages/maths.scm (ipopt)[home-page]: Use HTTPS URI.
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* gnu/packages/maths.scm (xaos): Update to 4.0.
[source]: Use git-fetch.
[native-inputs]: Add qtbase and qttools.
[arguments]: Remove #:make-flags options; replace 'configure' phase; add
'make-qt-deterministic' and 'install-data' phases.
[home-page]: Update URL.
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* gnu/packages/maths.scm (clp): Update to 1.17.6.
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* gnu/packages/maths.scm (hdf4)[arguments]: Add phase
'provide-absolute-libjpeg-reference'.
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* gnu/packages/maths.scm (nauty): Update to 2.7r1.
[arguments]: Prevent using "-march-native". Install new executable.
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* gnu/packages/maths.scm (wxmaxima): Update to 20.04.0.
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* gnu/packages/maths.scm (qhull): update to 2019.1
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/maths.scm (gsl)[arguments]: Skip the same set of tests on
powerpc as skipped on aarch64.
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* gnu/packages/maths.scm (z3): Update to 4.8.8.
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* .mailmap: change email and name for Nikita.
* Makefile.am, doc/guix.texi, etc/completion/fish/guix.fish,
gnu/packages/accessibility.scm, gnu/packages/admin.scm,
gnu/packages/audio.scm, gnu/packages/autotools.scm, gnu/packages/cdrom.scm,
gnu/packages/check.scm, gnu/packages/cinnamon.scm,
gnu/packages/compression.scm, gnu/packages/crypto.scm,
gnu/packages/databases.scm, gnu/packages/django.scm, gnu/packages/dns.scm,
gnu/packages/elixir.scm, gnu/packages/emacs-xyz.scm, gnu/packages/emacs.scm,
gnu/packages/enlightenment.scm, gnu/packages/erlang.scm,
gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/forth.scm,
gnu/packages/fvwm.scm, gnu/packages/games.scm, gnu/packages/gl.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm, gnu/packages/gnupg.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm, gnu/packages/guile-xyz.scm,
gnu/packages/haskell-apps.scm, gnu/packages/haskell-check.scm,
gnu/packages/haskell-crypto.scm, gnu/packages/haskell-xyz.scm,
gnu/packages/haskell.scm, gnu/packages/image-viewers.scm,
gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/language.scm,
gnu/packages/libcanberra.scm, gnu/packages/linux.scm,
gnu/packages/lisp-xyz.scm, gnu/packages/lisp.scm, gnu/packages/lolcode.scm,
gnu/packages/lxde.scm, gnu/packages/lxqt.scm, gnu/packages/mail.scm,
gnu/packages/markup.scm, gnu/packages/mate.scm, gnu/packages/maths.scm,
gnu/packages/mc.scm, gnu/packages/messaging.scm, gnu/packages/music.scm,
gnu/packages/ncurses.scm, gnu/packages/networking.scm,
gnu/packages/nickle.scm, gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/python-compression.scm, gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm, gnu/packages/python-xyz.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/ruby.scm,
gnu/packages/rust.scm, gnu/packages/scheme.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/ssh.scm, gnu/packages/suckless.scm, gnu/packages/tbb.scm,
gnu/packages/telephony.scm, gnu/packages/text-editors.scm,
gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm,
gnu/packages/tor.scm, gnu/packages/version-control.scm,
gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/web.scm,
gnu/packages/wm.scm, gnu/packages/xdisorg.scm, gnu/packages/xfce.scm,
gnu/packages/xml.scm, gnu/packages/xorg.scm, gnu/services/certbot.scm,
gnu/services/desktop.scm, gnu/services/version-control.scm,
gnu/services/web.scm, guix/import/hackage.scm, guix/licenses.scm: Likewise.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/patches/glm-restore-install-target.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/maths.scm (glm): Update to 0.9.9.8.
[arguments]: New field.
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* gnu/packages/maths.scm (flann): Update to 1.9.1.
[source]: Use 'git-fetch'.
[home-page]: Change to github.com.
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Octave support currently fails to build and is not used by any other
package in Guix.
* gnu/packages/maths.scm (flann)[outputs]: Remove "octave" output.
[inputs]: Remove OCTAVE-CLI.
[arguments]: Remove 'set-octave-directory' phase.
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Conflicts:
gnu/local.mk
gnu/packages/backup.scm
gnu/packages/emacs-xyz.scm
gnu/packages/guile.scm
gnu/packages/lisp.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/web.scm
gnu/packages/xorg.scm
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* gnu/packages/maths.scm (hdf5-blosc): New variable.
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Conflicts:
etc/news.scm
gnu/local.mk
gnu/packages/bootloaders.scm
gnu/packages/linphone.scm
gnu/packages/linux.scm
gnu/packages/tls.scm
gnu/system.scm
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* gnu/packages/maths.scm (dune-*): Update to version 2.7.
(dune-uggrid)[source] Download from Git, as no release tarball for
version 2.7 exists.
(dune-alugrid,dune-subgrid,dune-pdelab)[source] Use commit hashes as no
tags for version 2.7 exist (yet?).
(dune-istl)[source](patches) Add patch required to build version 2.7
without openmpi.
* gnu/packages/patches/dune-istl-2.7-fix-non-mpi-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/patches/libqalculate-3.8.0-libcurl-ssl-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/maths.scm (libqalculate)[source]: Use it.
Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
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* gnu/packages/maths.scm (dune-localfunctions)[arguments]: Add phase
'hide-gfortran'.
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* gnu/packages/maths.scm (dune-istl)[arguments]: Add phase 'hide-gfortran'.
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* gnu/packages/maths (dune-subgrid): Fix grammar.
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