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2021-10-12Merge remote-tracking branch 'origin/master' into core-updates-frozen.Mathieu Othacehe
2021-10-12gnu: clipper: Disable non-deterministic test.Felix Gruber
This test fails/succeeds non-deterministically. * gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable non-deterministic test test_get_FDR_cutoff_mean. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-10-08gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.Lars-Dominik Braun
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
2021-10-08gnu: ngless: Fix build.Lars-Dominik Braun
Apply upstream patch to restore compatibility with current Stackage. * gnu/packages/patches/ngless-unliftio.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/bioinformatics.scm (ngless): Use it.
2021-10-08gnu: Update Haskell ecosystem.Lars-Dominik Braun
Bump packages’ versions to the lastest Stackage or Hackage release. Since packages are interdependent, do so in a single commit. 525 packages have been updated. These packages have been removed, because they fail to build, have no newer version available and no dependencies: corrode ghc-easytest ghc-edisonapi ghc-edisoncore ghc-pandoc-types ghc-regex-tdfa-text These have been removed, because they are no longer required: ghc-happy-1.19.9 ghc-prettyprinter-1.6 ghc-protolude-0.3 ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc does not use them any more. Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
2021-09-29gnu: pigx-chipseq: Update to 0.0.53.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53. [inputs]: Add r-hexbin.
2021-09-22gnu: Update some packages using old JavaScript minifier.Charles
* gnu/packages/minetest.scm (minetest-basic-trains): New variable. * gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input. * gnu/packages/ci.scm (laminar): Update uglifyjs input. * gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input. * gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-09-20gnu: Add r-presto.zimoun
* gnu/packages/bioinformatics.scm (r-presto): New variable.
2021-09-13gnu: discrover: Update package name in texlive-union.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace texlive-fonts-cm with texlive-cm.
2021-09-07Merge branch 'master' into core-updates-frozenLudovic Courtès
2021-09-06gnu: Use the non-deprecated TeX packages.Ludovic Courtès
This commit leaves 'dblatex' and 'texlive-hyperref' as users of deprecated packages, but these have many dependents. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use non-deprecated TeX Live packages. (velvet)[native-inputs]: Likewise. * gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise. (chez-web)[native-inputs]: Likewise. * gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise. * gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise. * gnu/packages/maths.scm (hypre)[native-inputs]: Likewise. * gnu/packages/music.scm (lilypond)[native-inputs]: Likewise. * gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise. * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Likewise. (python-matplotlib-documentation)[native-inputs]: Likewise. (python-ipython-documentation)[native-inputs]: Likewise. (python-nbconvert)[native-inputs]: Likewise. (python-pypandoc)[native-inputs]: Likewise. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise. * gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise. (teximpatient)[native-inputs]: Likewise. (texlive-latex-pgf)[propagated-inputs]: Likewise. (texlive-beamer)[propagated-inputs]: Likewise.
2021-09-06gnu: Add megadepth.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (megadepth): New variable.
2021-09-06gnu: Replace PYTHONPATH with GUIX_PYTHONPATH.Felix Gruber
In packages that do not use python-build-system, PYTHONPATH is generally not defined. Instead we can use GUIX_PYTHONPATH which should contain all Python dependencies. * gnu/packages/bioinformatics.scm (shorah)[arguments]: Replace PYTHONPATH with GUIX_PYTHONPATH. * gnu/packages/debug.scm (c-vise)[arguments]: Idem. * gnu/packages/gnome.scm (drawing, apostrophe, ocrfeeder)[arguments]: Idem. * gnu/packages/music.scm (a2jmidid)[arguments]: Idem. * gnu/packages/syndication.scm (gfeeds)[arguments]: Idem. * gnu/packages/xdisorg.scm (gammastep)[arguments]: Idem. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-09-01gnu: Add r-catch.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-catch): New variable.
2021-08-31gnu: Add scregseg.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scregseg): New variable.
2021-08-31gnu: python-strawc: Propagate pybind11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from here... [propagated-inputs]: ...to here.
2021-08-31gnu: python-scanpy: Propagate sinfo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move python-sinfo from here... [propagated-inputs]: ...to here.
2021-08-12Merge branch 'master' into core-updates-frozenMarius Bakke
Conflicts: gnu/packages/algebra.scm gnu/packages/games.scm gnu/packages/golang.scm gnu/packages/kerberos.scm gnu/packages/mail.scm gnu/packages/python.scm gnu/packages/ruby.scm gnu/packages/scheme.scm gnu/packages/tex.scm gnu/packages/tls.scm gnu/packages/version-control.scm
2021-07-29Merge branch 'master' into core-updates-frozenMarius Bakke
Conflicts: gnu/packages/bioinformatics.scm gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/emacs-xyz.scm gnu/packages/gpodder.scm gnu/packages/music.scm gnu/packages/patches/glibc-bootstrap-system.patch gnu/packages/python-xyz.scm gnu/packages/shells.scm gnu/packages/statistics.scm
2021-08-30gnu: Add python-coolbox.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
2021-08-30gnu: python-scanpy: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1. [arguments]: Bulid with flit; update list of broken tests. [native-inputs]: Add python-flit and python-anndata:source.
2021-08-30gnu: Add python-dna-features-viewer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
2021-08-30gnu: Add python-pybbi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
2021-08-27gnu: Add python-strawc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
2021-08-27gnu: Add r-cytonorm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
2021-08-25gnu: Add ivar.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ivar): New variable.
2021-08-20gnu: fastp: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1. [arguments]: Set PREFIX instead of BINDIR.
2021-08-11gnu: pigx-rnaseq: Update to 0.0.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
2021-08-13gnu: pigx-rnaseq: Update to 0.0.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
2021-08-05gnu: pigx-sars-cov2-ww: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
2021-08-03gnu: Add r-spectre.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
2021-07-26gnu: Add seqan 3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqan): Rename this variable... (seqan-2): ...to this. (seqan): New variable for seqan3. (flexbar)[native-inputs]: Update name for seqan 2.
2021-07-26gnu: Add segemehl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (segemehl): New variable.
2021-07-24gnu: Use 'search-input-directory' and 'search-input-file' where appropriate.Ludovic Courtès
This changes some of the remaining uses of this idiom: (string-append (assoc-ref inputs "LABEL") "FILE") to one of: (search-input-file inputs "FILE") (search-input-directory inputs "FILE") * gnu/packages/axoloti.scm (axoloti-patcher): Use 'search-input-directory'. (axoloti-patcher-next): Likewise. * gnu/packages/bioinformatics.scm (java-picard): Likewise. * gnu/packages/bootloaders.scm (grub-hybrid): Likewise. (u-boot-puma-rk3399): Likewise. (u-boot-rock64-rk3328): Likewise. (u-boot-firefly-rk3399): Likewise. (u-boot-rockpro64-rk3399): Likewise. (u-boot-pinebook-pro-rk3399): Likewise. * gnu/packages/cran.scm (r-shiny): Likewise. (r-shinytree): Likewise. * gnu/packages/education.scm (anki): Likewise. * gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Likewise. (emacs-rime): Likewise. * gnu/packages/emulators.scm (dolphin-emu): Likewise. * gnu/packages/games.scm (bsd-games): Likewise. (seahorse-adventures): Likewise. (einstein): Likewise. * gnu/packages/gimp.scm (gimp-fourier): Likewise. * gnu/packages/gnome.scm (gspell): Likewise. * gnu/packages/guile-xyz.scm (guile-libyaml): Likewise. * gnu/packages/java.scm (icedtea-7): Likewise. * gnu/packages/language.scm (nimf): Likewise. * gnu/packages/lxde.scm (spacefm): Likewise. * gnu/packages/mail.scm (claws-mail): Likewise. * gnu/packages/netpbm.scm (netpbm): Likewise. * gnu/packages/networking.scm (blueman): Likewise. * gnu/packages/scheme.scm (scm): Likewise. * gnu/packages/security-token.scm (python-fido2): Likewise. * gnu/packages/syndication.scm (rtv): Likewise. * gnu/packages/tls.scm (acme-client): Likewise. * gnu/packages/web.scm (netsurf): Likewise. * gnu/packages/wine.scm (wine-staging): Likewise. * gnu/packages/wxwidgets.scm (wxwidgets): Likewise.
2021-07-24gnu: Use 'search-input-file' when looking for .jar files.Ludovic Courtès
* gnu/packages/bioinformatics.scm (java-picard-1.113): Use 'search-input-file' when looking for *.jar. (fastqc): Likewise. * gnu/packages/groovy.scm (groovy): Likewise. * gnu/packages/java.scm (ant-bootstrap): Likewise. (ecj-bootstrap): Likewise. (java-cisd-base): Likewise. (java-cisd-args4j): Likewise. (java-cisd-jhdf5): Likewise. (java-native-access): Likewise. (java-native-access-platform): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise.
2021-07-24gnu: Use 'search-input-file' when looking for executables.Ludovic Courtès
* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when looking for executables. * gnu/packages/audio.scm (ableton-link): Likewise. * gnu/packages/benchmark.scm (fio): Likewise. * gnu/packages/bioinformatics.scm (roary): Likewise. (ngless): Likewise. * gnu/packages/boost.scm (boost-for-irods): Likewise. * gnu/packages/bootloaders.scm (grub): Likewise. (grub-efi): Likewise. * gnu/packages/chemistry.scm (inchi): Likewise. * gnu/packages/dictionaries.scm (ding): Likewise. * gnu/packages/dlang.scm (ldc): Likewise. * gnu/packages/education.scm (childsplay): Likewise. * gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise. (emacs-haskell-mode): Likewise. (emacs-auctex): Likewise. (emacs-ggtags): Likewise. (emacs-graphviz-dot-mode): Likewise. (emacs-flycheck-grammalecte): Likewise. (emacs-counsel-notmuch): Likewise. (emacspeak): Likewise. (emacs-exwm): Likewise. (emacs-exwm-x): Likewise. (emacs-treemacs): Likewise. (emacs-telega): Likewise. (emacs-exiftool): Likewise. * gnu/packages/emulators.scm (higan): Likewise. * gnu/packages/engineering.scm (freehdl): Likewise. (librepcb): Likewise. * gnu/packages/entr.scm (entr): Likewise. * gnu/packages/file-systems.scm (libeatmydata): Likewise. (xfstests): Likewise. (mergerfs): Likewise. (mergerfs-tools): Likewise. * gnu/packages/finance.scm (monero-gui): Likewise. * gnu/packages/flashing-tools.scm (flashrom): Likewise. * gnu/packages/fontutils.scm (fontforge): Likewise. * gnu/packages/game-development.scm (python2-renpy): Likewise. * gnu/packages/games.scm (opensurge): Likewise. (xboard): Likewise. (hyperrogue): Likewise. (flare-game): Likewise. (chessx): Likewise. * gnu/packages/geo.scm (grass): Likewise. * gnu/packages/glib.scm (glib): Likewise. * gnu/packages/gnome.scm (mm-common): Likewise. (network-manager-openvpn): Likewise. (network-manager-vpnc): Likewise. (network-manager-openconnect): Likewise. (apostrophe): Likewise. * gnu/packages/gnupg.scm (pius): Likewise. (jetring): Likewise. * gnu/packages/gnuzilla.scm (icedove): Likewise. * gnu/packages/golang.scm (go-1.4): Likewise. * gnu/packages/graphviz.scm (xdot): Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise. * gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise. * gnu/packages/ibus.scm (ibus): Likewise. * gnu/packages/image.scm (phockup): Likewise. * gnu/packages/irc.scm (quassel): Likewise. * gnu/packages/java.scm (drip): Likewise. (ant-bootstrap): Likewise. (tla2tools): Likewise. * gnu/packages/julia.scm (julia): Likewise. * gnu/packages/less.scm (lesspipe): Likewise. * gnu/packages/libreoffice.scm (libreoffice): Likewise. * gnu/packages/linux.scm (fuse): Likewise. (lm-sensors): Likewise. (bluez): Likewise. (fakeroot): Likewise. (inputattach): Likewise. * gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise. * gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise. * gnu/packages/lua.scm (fennel): Likewise. * gnu/packages/lxde.scm (spacefm): Likewise. * gnu/packages/mail.scm (public-inbox): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise. (maxima): Likewise. (frama-c): Likewise. * gnu/packages/messaging.scm (libgadu): Likewise. * gnu/packages/music.scm (denemo): Likewise. (curseradio): Likewise. * gnu/packages/netpbm.scm (netpbm): Likewise. * gnu/packages/networking.scm (blueman): Likewise. (squid): Likewise. (aircrack-ng): Likewise. * gnu/packages/node.scm (node): Likewise. (node-llparse-frontend-bootstrap): Likewise. (node-llparse-bootstrap): Likewise. (llhttp-bootstrap): Likewise. (node-lts): Likewise. * gnu/packages/ocaml.scm (ocaml-4.11): Likewise. (opam): Likewise. (ocaml-graph): Likewise. * gnu/packages/orpheus.scm (orpheus): Likewise. * gnu/packages/password-utils.scm (password-store): Likewise. * gnu/packages/python.scm (pypy3): Likewise. * gnu/packages/qt.scm (qt5ct): Likewise. * gnu/packages/radio.scm (libosmo-dsp): Likewise. * gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise. * gnu/packages/rust.scm (rust-1.30): Likewise. * gnu/packages/screen.scm (byobu): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/suckless.scm (surf): Likewise. * gnu/packages/syndication.scm (gfeeds): Likewise. * gnu/packages/telephony.scm (mumble): Likewise. * gnu/packages/terminals.scm (alacritty): Likewise. * gnu/packages/tex.scm (texlive-bin): Likewise. * gnu/packages/uml.scm (plantuml): Likewise. * gnu/packages/version-control.scm (python-git-multimail): Likewise. (gitolite): Likewise. (hg-commitsigs): Likewise. (git-when-merged): Likewise. (git-imerge): Likewise. (gita): Likewise. * gnu/packages/video.scm (you-get): Likewise. * gnu/packages/vim.scm (eovim): Likewise. * gnu/packages/virtualization.scm (qemu): Likewise. (virt-manager): Likewise. (criu): Likewise. * gnu/packages/vpn.scm (strongswan): Likewise. (xl2tpd): Likewise. * gnu/packages/wm.scm (i3lock-fancy): Likewise. * gnu/packages/wxwidgets.scm (python-wxpython): Likewise. (python2-wxpython): Likewise. * gnu/packages/xdisorg.scm (autorandr): Likewise. * gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise. (v86d): Likewise. (mkfontdir): Likewise. (xpra): Likewise.
2021-07-24gnu: Use 'search-input-file' when looking for *.so and *.a.Ludovic Courtès
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use 'search-input-file' when looking for *.a and *.so. * gnu/packages/emulators.scm (dolphin-emu): Likewise. * gnu/packages/engineering.scm (lepton-eda): Likewise. (pcb): Likewise. * gnu/packages/golang.scm (go-1.4): Likewise. (go-1.14): Likewise. * gnu/packages/haskell.scm (ghc-7): Likewise. * gnu/packages/irods.scm (irods): Likewise. * gnu/packages/language.scm (python2-tegaki-pygtk): Likewise. * gnu/packages/lisp-xyz.scm (sbcl-lzlib): Likewise. (sbcl-cl-gobject-introspection): Likewise. (sbcl-cl-ana): Likewise. (sbcl-cl-libuv): Likewise. (sbcl-cl-async): Likewise. (sbcl-mcclim): Likewise. (sbcl-zstd): Likewise. (sbcl-cl-opengl): Likewise. (sbcl-lev): Likewise. (sbcl-cl-glfw3): Likewise. * gnu/packages/machine-learning.scm (tensorflow): Likewise. * gnu/packages/messaging.scm (utox): Likewise. * gnu/packages/mpi.scm (java-openmpi): Likewise. * gnu/packages/music.scm (jack-select): Likewise. * gnu/packages/pascal.scm (fpc): Likewise. * gnu/packages/python-crypto.scm (python-libnacl): Likewise. * gnu/packages/python-xyz.scm (python-cairocffi): Likewise. (python-pyev): Likewise. (python-pytidylib): Likewise. * gnu/packages/radio.scm (unixcw): Likewise. * gnu/packages/rust.scm (rust-1.32): Likewise. * gnu/packages/security-token.scm (opensc): Likewise. (python-pyscard): Likewise. * gnu/packages/selinux.scm (python-setools): Likewise. * gnu/packages/spice.scm (libcacard): Likewise. * gnu/packages/telephony.scm (libtgvoip): Likewise.
2021-07-24gnu: Use 'search-input-directory' when looking for C/C++ library headers.Ludovic Courtès
* gnu/packages/arcan.scm (arcan)[arguments]: Use 'search-input-directory' for "include/libdrm" and "include/apr-1". * gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish. * gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers. * gnu/packages/cedille.scm (cedille): Likewise for IAL headers. * gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx headers. * gnu/packages/cups.scm (hplip): Likewise for libusb headers. * gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers. * gnu/packages/game-development.scm (python2-renpy): Likewise for fribidi headers. * gnu/packages/games.scm (pokerth): Likewise for libircclient. * gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile. * gnu/packages/hurd.scm (hurd): Likewise for libtirpc. * gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for libcxx, catch2, and nlohmann-json-cpp. * gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's errno.h. * gnu/packages/kde-pim.scm (kdepim-runtime): Use 'search-input-directory' for "include/KF5". (kmessagelib): Likewise. * gnu/packages/kde.scm (kdeconnect): Likewise. * gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc. * gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband". * gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h" and "aspell.h". * gnu/packages/radio.scm (dream): Use 'search-input-file' and 'search-input-directory' for pulseaudio, sndfile, etc. * gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and libaudit. * gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for libcxx. * gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5". * gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest". (libopenshot): Likewise for "include/UnitTest++". * gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for protobuf file.
2021-07-24gnu: Use 'search-input-directory' for the Eigen header directory.Ludovic Courtès
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use 'search-input-directory' when searching for Eigen headers. * gnu/packages/bioinformatics.scm (nanopolish): Likewise. * gnu/packages/machine-learning.scm (tensorflow): Likewise.
2021-07-24gnu: Use 'search-input-directory' when looking for tzdata.Ludovic Courtès
* gnu/packages/backup.scm (duplicity)[arguments]: Use 'search-input-directory' for "share/zoneinfo". * gnu/packages/bioinformatics.scm (pigx-rnaseq): Likewise. (pigx-bsseq): Likewise. * gnu/packages/calcurse.scm (calcurse): Likewise. * gnu/packages/calendar.scm (date): Likewise. * gnu/packages/compression.scm (lhasa): Likewise. * gnu/packages/cran.scm (r-rstan): Likewise. * gnu/packages/django.scm (python-django): Likewise. * gnu/packages/dlang.scm (ldc-bootstrap): Likewise. * gnu/packages/finance.scm (ledger): Likewise. * gnu/packages/glib.scm (glib): Likewise. * gnu/packages/golang.scm (go-1.4): Likewise. (go-1.14): Likewise. * gnu/packages/kde-frameworks.scm (kcalendarcore): Likewise. (kdelibs4support): Likewise. * gnu/packages/kodi.scm (kodi): Likewise. * gnu/packages/mail.scm (mu): Likewise. * gnu/packages/perl.scm (perl-libtime-parsedate): Likewise. * gnu/packages/python-xyz.scm (python-robotframework): Likewise. (python-dparse): Likewise. * gnu/packages/rrdtool.scm (rrdtool): Likewise. * gnu/packages/statistics.scm (r-with-tests): Likewise. * gnu/packages/vim.scm (vim): Likewise. * gnu/packages/virtualization.scm (ganeti): Likewise. * gnu/packages/vpn.scm (strongswan): Likewise. * gnu/packages/xfce.scm (xfce4-panel): Likewise. * gnu/packages/mate.scm (libmateweather): Use 'search-input-file' for "share/zoneinfo/zone.tab".
2021-07-22gnu: python-pysam: Make the check phase honor the tests? argument.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f.
2021-07-22gnu: python-pysam: Update to 0.16.0.1.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Replace htslib-1.9 with 1.10. [native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10, bcftools-1.9 with 1.10. (bcftools-1.9): Replace with bcftools-1.10. [native-inputs]: Replace htslib-1.9 with 1.10. (samtools-1.9): Replace with samtools-1.10. [inputs]: Replace htslib-1.9 with 1.10.
2021-07-22gnu: Add htslib-1.10.Efraim Flashner
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22gnu: python-biopython: Update to 1.73.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
2021-07-21gnu: Add r-battenberg.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21gnu: Add r-ascat.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-28 20:27:19 +0000