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2021-07-20gnu: python-graph-tool: Sort inputs alphabetically.Efraim Flashner
* gnu/packages/graph.scm (python-graph-tool)[native-inputs]: Sort alphabetically. [inputs]: Same. [propagated-inputs]: Same.
2021-07-20gnu: python-graph-tool: Update to 2.43.Alexandre Hannud Abdo
* gnu/packages/graph.scm (python-graph-tool): Update to 2.43. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-06-29gnu: python2-plotly: Remove package.zimoun
* gnu/packages/graph.scm (python2-plotly): Remove variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-05-15gnu: Add python-graph-tool.Alexandre Hannud Abdo
* gnu/packages/graph.scm (python-graph-tool): New variable. Signed-off-by: Marius Bakke <marius@gnu.org>
2021-04-25gnu: Add python-louvain 0.15.Vinicius Monego
* gnu/packages/graph.scm (python-louvain): Rename variable to python-louvain-0.6. (python-louvain): New variable. * gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Use python-louvain-0.6. Co-authored-by: Leo Famulari <leo@famulari.name>
2021-03-04gnu: python-plotly: Allow test phase to be skipped.Efraim Flashner
* gnu/packages/graph.scm (python-plotly)[arguments]: Wrap custom 'check phase tests with test with tests? keyword.
2021-03-04gnu: python-plotly: Update to 4.14.3.Efraim Flashner
* gnu/packages/graph.scm (python-plotly): Update to 4.14.3. [propagated-inputs]: Remove python-decorator. Add python-ipython, python-pillow. Move python-ipywidgets, python-xarray ... [native-inputs]: ... to here.
2020-11-26gnu: igraph: Omit static library.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (igraph)[arguments]: Add "--disable-static" to #:configure-flags.
2020-11-26gnu: igraph: Update to 0.8.4.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (igraph): Update to 0.8.4.
2020-09-14gnu: r-rgraphviz: Move to (gnu packages bioconductor).zimoun
* gnu/packages/graph.scm (r-rgraphviz): Move from here... * gnu/packages/bioconductor.scm (r-rgraphviz): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-14gnu: r-rgraphviz: Build reproducibly.Ricardo Wurmus
Fixes <https://bugs.gnu.org/43398>. * gnu/packages/graph.scm (r-rgraphviz)[arguments]: Add phase "make-reproducible".
2020-09-11gnu: r-igraph: Move to (gnu packages cran).zimoun
* gnu/packages/graph.scm (r-igraph): Move from here... * gnu/packages/cran.scm (r-igraph): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11gnu: r-diffusionmap: Move to (gnu packages cran).zimoun
* gnu/packages/graph.scm (r-diffusionmap): Move from here... * gnu/packages/cran.scm (r-diffusionmap): ...to here. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-08-18gnu: python-igraph: Update to 0.8.2.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (python-igraph): Update to 0.8.2.
2020-08-18gnu: igraph: Update to 0.8.2.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (igraph): Update to 0.8.2.
2020-07-16gnu: Use HTTPS for igraph.org.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (igraph, r-igraph)[home-page]: Use HTTPS.
2020-07-12gnu: Remove ".git" from "https://github/…/….git".Ludovic Courtès
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.
2020-06-22gnu: python-plotly: Update to 4.8.1.Pierre Langlois
But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-13gnu: r-rgraphviz: Update to 2.32.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.32.0.
2020-03-30Merge branch 'master' into core-updatesMarius Bakke
Conflicts: gnu/packages/admin.scm gnu/packages/commencement.scm gnu/packages/guile.scm gnu/packages/linux.scm gnu/packages/package-management.scm gnu/packages/pulseaudio.scm gnu/packages/web.scm
2020-03-29gnu: igraph: Update to 0.8.1.Tobias Geerinckx-Rice
* gnu/packages/graph.scm (igraph): Update to 0.8.1.
2020-03-27gnu: mscgen: Fix build with gd >= 2.3.0.Marius Bakke
'gd' no longer provides 'libgd-config', so use 'pkg-config' instead. * gnu/packages/graph.scm (mscgen)[native-inputs]: Add PKG-CONFIG.
2020-03-24gnu: r-igraph: Update to 1.2.5.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.5.
2020-03-04gnu: Update pypi.python.org home pages & use HTTPS.Tobias Geerinckx-Rice
* gnu/packages/check.scm (python-unittest2, python-pytest-localserver) (python-discover)[home-page]: Follow (HTTPS) redirections. * gnu/packages/fontutils.scm (python2-defcon)[home-page]: Likewise. * gnu/packages/glib.scm (python2-pygobject-2)[home-page]: Likewise. * gnu/packages/graph.scm (python-igraph)[home-page]: Likewise. * gnu/packages/graphviz.scm (xdot)[home-page]: Likewise. * gnu/packages/pdf.scm (python-poppler-qt5)[home-page]: Likewise. * gnu/packages/python-web.scm (python-zope-event, python-zope-testing) (python-zope-testrunner, python-zope-i18nmessageid, python-zope-schema) (python-zope-configuration, python-zope-proxy, python-zope-location) (python-zope-security))[home-page]: Likewise. * gnu/packages/python-xyz.scm (python-setuptools,python-six) (python2-dogtail, python2-enum, python-enum34, python-unidecode) (python-numpydoc, python-decorator, python-drmaa, python-pathlib2) (python-ly, python-msgpack, python-termcolor, python-colorama) (python-pluggy, python2-pathlib2, python-rfc3987)[home-page]: Likewise.
2020-02-24gnu: python-igraph: Update to 0.8.0.Ricardo Wurmus
* gnu/packages/graph.scm (python-igraph): Update to 0.8.0. [arguments]: Replace build phase; move check phase after install phase; pass "--use-pkg-config" to avoid rebuilding igraph. [propagated-inputs]: Add python-texttable. [native-inputs]: Add python-pytest.
2020-02-24gnu: igraph: Update to 0.8.0.Ricardo Wurmus
* gnu/packages/graph.scm (igraph): Update to 0.8.0.
2020-02-11gnu: Add mscgen.Alexander Krotov
* gnu/packages/graph.scm (mscgen): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-01-21gnu: Use HTTPS for bioconductor.org.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS. * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked, r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno, r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise. * gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
2019-12-15gnu: r-rgraphviz: Update to 2.30.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.30.0.
2019-12-04gnu: python-pandas: Move to (gnu packages python-science).Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pandas, python2-pandas): Move from here... * gnu/packages/python-science.scm (python-pandas, python2-pandas): ...to here. * gnu/packages/benchmark.scm, gnu/packages/databases.scm, gnu/packages/graph.scm, gnu/packages/parallel.scm, gnu/packages/serialization.scm: Import (gnu packages python-science).
2019-11-28gnu: r-igraph: Update to 1.2.4.2.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.4.2.
2019-10-20gnu: Remove more GCC < 7 workarounds.Marius Bakke
* gnu/packages/abiword.scm (abiword)[arguments]: Do not pass "-std=c++11" to the GCC command line. * gnu/packages/aidc.scm (zbar)[arguments]: Likewise. * gnu/packages/android.scm (android-libbase, android-libcutils, android-libziparchive, fastboot)[arguments]: Likewise. * gnu/packages/audio.scm (azr3, guitarix, suil)[arguments]: Likewise. * gnu/packages/bioinformatics.scm (bless)[arguments]: Likewise. * gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Likewise. * gnu/packages/code.scm (rtags)[arguments]: Likewise. * gnu/packages/coq.scm (coq-gappa)[arguments]: Likewise. * gnu/packages/emulators.scm (dolphin-emu)[arguments]: Likewise. * gnu/packages/engineering.scm (xyce-serial, xyce-parallel)[arguments]: Likewise. * gnu/packages/gnupg.scm (pinentry-qt)[arguments]: Likewise. * gnu/packages/gobby.scm (libnet6, obby)[arguments]: Likewise. * gnu/packages/graph.scm (python-faiss)[arguments]: Likewise. * gnu/packages/graphics.scm (povray)[arguments]: Likewise. * gnu/packages/image-processing.scm (opencv, itk-snap)[arguments]: Likewise. * gnu/packages/image.scm (freeimage)[arguments]: Likewise. * gnu/packages/kodi.scm (crossguid)[arguments]: Likewise. * gnu/packages/music.scm (amsynth, qmidiarp, qmidiroute, seq24)[arguments]: Likewise. * gnu/packages/pdf.scm (python-poppler-qt5)[arguments]: Likewise. * gnu/packages/sagemath.scm (lcalc)[arguments]: Likewise. * gnu/packages/video.scm (vlc, mlt, v4l-utils)[arguments]: Likewise.
2019-09-14gnu: r-diffusionmap: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.2.0.
2019-06-17gnu: Add rw.Andreas Enge
* gnu/packages/graph.scm (rw): New variable.
2019-06-17gnu: edge-addition-planarity-suite: Move to the (gnu packages graph) module.Andreas Enge
* gnu/packages/maths.scm (edge-addition-planarity-suite): Move from here... * gnu/packages/maths.scm (edge-addition-planarity-suite): ...to here.
2019-05-16gnu: Add python-leidenalg.Ricardo Wurmus
* gnu/packages/graph.scm (python-leidenalg): New variable.
2019-05-06gnu: r-rgraphviz: Update to 2.28.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.28.0.
2019-04-24gnu: r-igraph: Update to 1.2.4.1.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.4.1.
2019-04-02gnu: Add python-louvain.Ricardo Wurmus
* gnu/packages/graph.scm (python-louvain): New variable.
2019-03-29gnu: python-faiss: Fix building on non-Intel architectures.Efraim Flashner
* gnu/packages/graph.scm (python-faiss)[arguments]: Adjust custom 'build-swig phase to change build flags for different archictures.
2019-03-29gnu: faiss: Fix building on non-Intel architectures.Efraim Flashner
* gnu/packages/graph.scm (faiss)[source]: Add snippet to wrap Intel specific headers. [arguments]: Adjust custom 'prepare-build phase to adjust compile flags for different architectures.
2019-03-29gnu: Add python-faiss.Ricardo Wurmus
* gnu/packages/graph.scm (python-faiss): New variable.
2019-03-29gnu: Add faiss.Ricardo Wurmus
* gnu/packages/graph.scm (faiss): New variable.
2019-03-07gnu: r-igraph: Update to 1.2.4.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.4.
2019-01-15gnu: Separate Python core packages from the rest.Ricardo Wurmus
* gnu/packages/python.scm: Move hundreds of package definitions from here... * gnu/packages/python-xyz.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/benchmark.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/calendar.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/cluster.scm, gnu/packages/compression.scm, gnu/packages/connman.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/direct-connect.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/docker.scm, gnu/packages/ebook.scm, gnu/packages/elf.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/finance.scm, gnu/packages/fltk.scm, gnu/packages/fontutils.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/geo.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/ham-radio.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/kde-frameworks.scm, gnu/packages/key-mon.scm, gnu/packages/libffi.scm, gnu/packages/libreoffice.scm, gnu/packages/libusb.scm, gnu/packages/lirc.scm, gnu/packages/logging.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/mate.scm, gnu/packages/maths.scm, gnu/packages/medical.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/nutrition.scm, gnu/packages/openldap.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/photo.scm, gnu/packages/polkit.scm, gnu/packages/protobuf.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/qt.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm, gnu/packages/search.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/simulation.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wicd.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: Update module references.
2018-11-07gnu: r-rgraphviz: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.26.0.
2018-10-05gnu: python-plotly: Add python-pandas to inputs.Ricardo Wurmus
* gnu/packages/graph.scm (python-plotly)[propagated-inputs]: Add python-pandas.
2018-09-06Add missing use-modules clause.Ricardo Wurmus
This is a follow-up to commit 5dfe491290b14a1ee7efd70f9cd083969c24e1c2. Sorry! * gnu/packages/bioinformatics.scm, gnu/packages/graph.scm: Use (gnu packages bioconductor).
2018-09-05gnu: r-igraph: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.2.
2018-09-05gnu: r-diffusionmap: Update to 1.1-0.1.Ricardo Wurmus
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.1-0.1.
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