| Age | Commit message (Expand) | Author |
|---|
| 2021-10-12 | Merge remote-tracking branch 'origin/master' into core-updates-frozen. | Mathieu Othacehe |
| 2021-10-12 | gnu: clipper: Disable non-deterministic test....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>
| Felix Gruber |
| 2021-10-08 | gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-chipseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: pigx-bsseq: Remove dependency on pandoc-citeproc....* 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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: ngless: Fix build....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.
| Lars-Dominik Braun |
| 2021-10-08 | gnu: Update Haskell ecosystem....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>
| Lars-Dominik Braun |
| 2021-09-29 | gnu: pigx-chipseq: Update to 0.0.53....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
| Ricardo Wurmus |
| 2021-09-22 | gnu: Update some packages using old JavaScript minifier....* 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>
| Charles |
| 2021-09-20 | gnu: Add r-presto....* gnu/packages/bioinformatics.scm (r-presto): New variable.
| zimoun |
| 2021-09-13 | gnu: discrover: Update package name in texlive-union....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
| Ricardo Wurmus |
| 2021-09-07 | Merge branch 'master' into core-updates-frozen | Ludovic Courtès |
| 2021-09-06 | gnu: Use the non-deprecated TeX packages....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.
| Ludovic Courtès |
| 2021-09-06 | gnu: Add megadepth....* gnu/packages/bioinformatics.scm (megadepth): New variable.
| Ricardo Wurmus |
| 2021-09-06 | gnu: Replace PYTHONPATH with GUIX_PYTHONPATH....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>
| Felix Gruber |
| 2021-09-01 | gnu: Add r-catch....* gnu/packages/bioinformatics.scm (r-catch): New variable.
| Ricardo Wurmus |
| 2021-08-31 | gnu: Add scregseg....* gnu/packages/bioinformatics.scm (scregseg): New variable.
| Ricardo Wurmus |
| 2021-08-31 | gnu: python-strawc: Propagate pybind11....* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus |
| 2021-08-31 | gnu: python-scanpy: Propagate sinfo....* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus |
| 2021-08-12 | Merge branch 'master' into core-updates-frozen... 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
| Marius Bakke |
| 2021-07-29 | Merge branch 'master' into core-updates-frozen... 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
| Marius Bakke |
| 2021-08-30 | gnu: Add python-coolbox....* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
| Ricardo Wurmus |
| 2021-08-30 | gnu: python-scanpy: Update to 1.8.1....* 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.
| Ricardo Wurmus |
| 2021-08-30 | gnu: Add python-dna-features-viewer....* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
| Ricardo Wurmus |
| 2021-08-30 | gnu: Add python-pybbi....* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
| Ricardo Wurmus |
| 2021-08-27 | gnu: Add python-strawc....* gnu/packages/bioinformatics.scm (python-strawc): New variable.
| Ricardo Wurmus |
| 2021-08-27 | gnu: Add r-cytonorm....* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
| Ricardo Wurmus |
| 2021-08-25 | gnu: Add ivar....* gnu/packages/bioinformatics.scm (ivar): New variable.
| Ricardo Wurmus |
| 2021-08-20 | gnu: fastp: Update to 0.20.1....* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
| Ricardo Wurmus |
| 2021-08-11 | gnu: pigx-rnaseq: Update to 0.0.18....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
| Ricardo Wurmus |
| 2021-08-13 | gnu: pigx-rnaseq: Update to 0.0.19....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
| Ricardo Wurmus |
| 2021-08-05 | gnu: pigx-sars-cov2-ww: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
| Ricardo Wurmus |
| 2021-08-03 | gnu: Add r-spectre....* gnu/packages/bioinformatics.scm (r-spectre): New variable.
| Ricardo Wurmus |
| 2021-07-26 | gnu: Add seqan 3....* 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.
| Ricardo Wurmus |
| 2021-07-26 | gnu: Add segemehl....* gnu/packages/bioinformatics.scm (segemehl): New variable.
| Ricardo Wurmus |
| 2021-07-24 | gnu: Use 'search-input-directory' and 'search-input-file' where appropriate....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.
| Ludovic Courtès |
| 2021-07-24 | gnu: Use 'search-input-file' when looking for .jar files....* 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.
| Ludovic Courtès |
| 2021-07-24 | gnu: Use 'search-input-file' when looking for executables....* 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.
| Ludovic Courtès |
| 2021-07-24 | gnu: Use 'search-input-file' when looking for *.so and *.a....* 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.
| Ludovic Courtès |
| 2021-07-24 | gnu: Use 'search-input-directory' when looking for C/C++ library headers....* 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.
| Ludovic Courtès |
| 2021-07-24 | gnu: Use 'search-input-directory' for the Eigen header directory....* 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.
| Ludovic Courtès |
| 2021-07-24 | gnu: Use 'search-input-directory' when looking for tzdata....* 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".
| Ludovic Courtès |
| 2021-07-22 | gnu: python-pysam: Make the check phase honor the tests? argument....* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
| Efraim Flashner |
| 2021-07-22 | gnu: python-pysam: Update to 0.16.0.1....* 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.
| Efraim Flashner |
| 2021-07-22 | gnu: Add htslib-1.10....* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
| Efraim Flashner |
| 2021-07-22 | gnu: python-biopython: Update to 1.73....* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
| Efraim Flashner |
| 2021-07-21 | gnu: Add r-battenberg....* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
| Lars-Dominik Braun |
| 2021-07-21 | gnu: Add r-ascat....* gnu/packages/bioinformatics.scm (r-ascat): New variable.
| Lars-Dominik Braun |
