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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.
2021-08-12Merge 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
2021-08-03gnu: texlive-latex-base: Propagate ‘texlive-latex-l3backend’Thiago Jung Bauermann
Some packages need files from ‘texlive-latex-l3backend’ – which is a supporting package of LaTeX3 – so propagate it from ‘texlive-latex-base’. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Remove ‘texlive-latex-l3backend’ from the texlive union. * gnu/packages/tex.scm (texlive-latex-base)[propagated-inputs]: Add ‘texlive-latex-l3backend’. (texlive-latex-xkeyval)[native-inputs]: Remove ‘texlive-latex-l3backend’. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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
2021-07-29gnu: r-matrixstats: Update to 0.60.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.60.0.
2021-07-29gnu: r-e1071: Update to 1.7-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-8.
2021-07-29gnu: r-with-tests: Add missing TeX Live packages.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Add texlive-grfext and texlive-latex-l3backend to the texlive union.
2021-07-28gnu: r-ranger: Update to 0.13.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ranger): Update to 0.13.1.
2021-07-28gnu: r-blob: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-blob): Update to 1.2.2.
2021-07-28gnu: r-rcpparmadillo: Update to 0.10.6.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.10.6.0.0.
2021-07-28gnu: r-readr: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-readr): Update to 2.0.0. [propagated-inputs]: Remove r-bh; add r-tzdb and r-vroom.
2021-07-28gnu: r-tibble: Update to 3.1.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 3.1.3.
2021-07-28gnu: r-pryr: Update to 0.1.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pryr): Update to 0.1.5. [propagated-inputs]: Add r-lobstr and r-rcpp. [native-inputs]: Remove r-rcpp.
2021-07-28gnu: r-stringi: Update to 1.7.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-stringi): Update to 1.7.3.
2021-07-28gnu: r-with-tests: Hardcode path to coreutils’ rmLars-Dominik Braun
When running R in a container like this guix environment --no-cwd -C --ad-hoc r-minimal -- Rscript -e 'Sys.timezone()' it would print an additional line sh: rm: command not found before exiting. * gnu/packages/statistics.scm (r-with-tests) [#:phases]: Add substitute* to patch call to `rm` and rename phase to reflect what it does now.
2021-08-24gnu: r-xml: Update to 3.99-0.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.7.
2021-08-24gnu: r-rsqlite: Update to 2.2.8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rsqlite): Update to 2.2.8.
2021-08-24gnu: r-rmarkdown: Update to 2.10.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.10.
2021-08-24gnu: r-readr: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-readr): Update to 2.0.1.
2021-08-24gnu: r-r6: Update to 2.5.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r6): Update to 2.5.1.
2021-08-24gnu: r-survival: Update to 3.2-12.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 3.2-12.
2021-08-24gnu: r-with-tests: Update to 4.1.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-with-tests): Update to 4.1.1.
2021-08-06gnu: Add r-datasaurus.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-datasaurus): New variable.
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-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".
2021-07-21gnu: Add r-glinternet.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-glinternet): New variable.
2021-07-21gnu: Add r-naniar.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-naniar): New variable.
2021-07-21gnu: Add r-norm.Lars-Dominik Braun
* gnu/packages/statistics.scm (r-norm): New variable.
2021-07-18Merge branch 'master' into core-updatesLudovic Courtès
2021-07-10gnu: r-car: Update to 3.0-11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-car): Update to 3.0-11.
2021-07-10gnu: r-lme4: Update to 1.1-27.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-27.1.
2021-07-10gnu: r-quantreg: Update to 5.86.Ricardo Wurmus
* gnu/packages/statistics.scm (r-quantreg): Update to 5.86.
2021-07-10gnu: r-plotly: Update to 4.9.4.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.9.4.1.
2021-07-10gnu: r-mvtnorm: Update to 1.1-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.1-2.
2021-07-10gnu: r-glmnet: Update to 4.1-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-glmnet): Update to 4.1-2.
2021-07-10gnu: r-rmarkdown: Update to 2.9.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.9.
2021-07-10gnu: r-devtools: Update to 2.4.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-devtools): Update to 2.4.2.
2021-07-10gnu: r-ade4: Update to 1.7-17.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-17. [propagated-inputs]: Remove r-progress.
2021-07-10gnu: r-dplyr: Update to 1.0.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dplyr): Update to 1.0.7.
2021-07-10gnu: r-testthat: Update to 3.0.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-testthat): Update to 3.0.4.
2021-07-10gnu: r-mime: Update to 0.11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mime): Update to 0.11.
2021-07-10gnu: r-ggplot2: Update to 3.3.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.5.
2021-07-10gnu: r-gtools: Update to 3.9.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtools): Update to 3.9.2. [arguments]: Remove.
2021-06-26gnu: python-rpy2: Update to 3.4.5.BonfaceKilz
* gnu/packages/statistics.scm (python-rpy2): Update to 3.4.5 [source]: Remove the patches. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-06Merge branch 'master' into core-updatesMarius Bakke
Conflicts: gnu/local.mk gnu/packages/algebra.scm gnu/packages/bioinformatics.scm gnu/packages/curl.scm gnu/packages/docbook.scm gnu/packages/emacs-xyz.scm gnu/packages/maths.scm gnu/packages/plotutils.scm gnu/packages/python-web.scm gnu/packages/python-xyz.scm gnu/packages/radio.scm gnu/packages/readline.scm gnu/packages/tls.scm gnu/packages/xml.scm gnu/packages/xorg.scm
2021-06-03gnu: r-with-tests: Use patched texlive-amsfonts.Lars-Dominik Braun
See commit 75af43162e58a0b3fdc804963809ecb801fb81b7. * gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Replace texlive-amsfonts with texlive-amsfonts/patched.
2021-06-02gnu: r-robustbase: Update to 0.93-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-8.
2021-06-02gnu: r-deoptimr: Update to 1.0-9.Ricardo Wurmus
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-9.
2021-06-02gnu: r-beeswarm: Update to 0.4.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-beeswarm): Update to 0.4.0.
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