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2018-02-03Merge branch 'master' into core-updatesMark H Weaver
2018-02-02gnu: Add fann.Mark Meyer
* gnu/packages/machine-learning.scm (fann): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2018-01-11Merge branch 'master' into core-updatesLeo Famulari
2018-01-10gnu: libsvm: Update to 3.22.Tobias Geerinckx-Rice
* gnu/packages/machine-learning.scm (libsvm): Update to 3.22. [source]: Use upstream tarball instead of a git snapshot.
2017-12-31Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner
2017-12-24gnu, doc: Use HTTPS for cran.r-project.org home pages.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm) (r-maldiquant, r-gprofiler)[home-page]: Use HTTPS. * gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape) (r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle) (r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim) (r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken) (r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise. * gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab) [home-page]: Likewise. * gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise. * gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign) (r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability) (r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr) (r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports) (r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops) (r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options) (r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel) (r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3) (r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots) (r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools) (r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp) (r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn) (r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]: Likewise. * gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]: Likewise. * doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
2017-12-19gnu: Remove redundant cmake libdir configure flags.Efraim Flashner
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove CMAKE_INSTALL_LIBDIR flag. * gnu/packages/calendar.scm (libical): Same. * gnu/packages/engineering.scm (kicad): Same. * gnu/packages/games.scm (openrct2, mgba): Same. * gnu/packages/gl.scm (virtualgl): Same. * gnu/packages/image-processing.scm (mia): Same. * gnu/packages/linux.scm (rdma-core): Same. * gnu/packages/machine-learning.scm (dlib): Same. * gnu/packages/maths.scm (lapack, superlu, z3): Same. * gnu/packages/password-utils.scm (keepassxc): Same. * gnu/packages/photo.scm (darktable): Same. * gnu/packages/rdesktop.scm (freerdp): Same.
2017-12-14gnu: python-scikit-learn: Patch test non-determinism.Ben Woodcroft
* gnu/packages/patches/python-scikit-learn-fix-test-non-determinism.patch: New file. * gnu/packages/machine-learning.scm (python-scikit-learn)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
2017-12-04gnu: python-scikit-learn: Update to 0.19.1.Tobias Geerinckx-Rice
* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.19.1.
2017-11-17gnu: python-scikit-learn: Move from python.scm to machine-learning.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-scikit-learn, python2-scikit-learn): Move from here... * gnu/packages/machine-learning.scm: ...to here.
2017-09-24Merge branch 'master' into stagingMarius Bakke
2017-09-22gnu: r-adaptivesparsity: Add dependency on Armadillo.Ludovic Courtès
Fixes a link error whereby -larmadillo would not be found. * gnu/packages/machine-learning.scm (r-adaptivesparsity)[inputs]: New field.
2017-09-21Merge branch 'master' into stagingMarius Bakke
2017-09-21gnu: dlib: Update to 19.7.Marius Bakke
* gnu/packages/machine-learning.scm (dlib): Update to 19.7. [arguments]: Add #:configure-flags. Remove redundant CXXFLAGS from 'check' phase.
2017-09-20gnu: Use 'modify-phases' syntax.Kei Kebreau
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal, wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use 'modify-phases' syntax. * gnu/packages/algebra.scm (arb)[arguments]: Likewise. * gnu/packages/apr.scm (apr-util)[arguments]: Likewise. * gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano, lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound, zita-convolver, zita-alsa-pcmi)[arguments]: Likewise. * gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise. * gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express, flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise. * gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise. * gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise. * gnu/packages/compression.scm (sharutils)[arguments]: Likewise. * gnu/packages/conky.scm (conky)[arguments]: Likewise. * gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise. * gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise. * gnu/packages/display-managers.scm (slim)[arguments]: Likewise. * gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise. * gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise. * gnu/packages/engineering.scm (pcb)[arguments]: Likewise. * gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise. * gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise. * gnu/packages/fltk.scm (fltk)[arguments]: Likewise. * gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise. * gnu/packages/gd.scm (perl-gd)[arguments]: Likewise. * gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise. * gnu/packages/glib.scm (glibmm)[arguments]: Likewise. * gnu/packages/gl.scm (glew)[arguments]: Likewise. * gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs, libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise. * gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise. * gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise. * gnu/packages/graphics.scm (agg)[arguments]: Likewise. * gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present, python2-pycairo)[arguments]: Likewise. * gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise. * gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise. * gnu/packages/hugs.scm (hugs)[arguments]: Likewise. * gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal) [arguments]: Likewise. * gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise. * gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise. * gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static, lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools) [arguments]: Likewise. * gnu/packages/lisp.scm (ccl)[arguments]: Likewise. * gnu/packages/lout.scm (lout)[arguments]: Likewise. * gnu/packages/lua.scm (luajit)[arguments]: Likewise. * gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise. * gnu/packages/mail.scm (exim)[arguments]: Likewise. * gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise. * gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun) [arguments]: Likewise. * gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise. * gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise. * gnu/packages/music.scm (solfege)[arguments]: Likewise. * gnu/packages/noweb.scm (noweb)[arguments]: Likewise. * gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]: Likewise. * gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu, zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise. * gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]: Likewise. * gnu/packages/photo.scm (gphoto2)[arguments]: Likewise. * gnu/packages/popt.scm (popt)[arguments]: Likewise. * gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]: Likewise. * gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise. * gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy, python-sqlalchemy, python-docopt)[arguments]: Likewise. * gnu/packages/rdf.scm (lrdf)[arguments]: Likewise. * gnu/packages/regex.scm (tre)[arguments]: Likewise. * gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise. * gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise. * gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise. * gnu/packages/scheme.scm (racket)[arguments]: Likewise. * gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise. * gnu/packages/serveez.scm (serveez)[arguments]: Likewise. * gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise. * gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise. * gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise. * gnu/packages/tcl.scm (expect)[arguments]: Likewise. * gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise. * gnu/packages/textutils.scm (recode, libgtextutils)[arguments]: Likewise. * gnu/packages/time.scm (time)[arguments]: Likewise. * gnu/packages/tor.scm (privoxy)[arguments]: Likewise. * gnu/packages/uucp.scm (uucp)[arguments]: Likewise. * gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise. * gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise. * gnu/packages/web.scm (tinyproxy)[arguments]: Likewise. * gnu/packages/wicd.scm (wicd)[arguments]: Likewise. * gnu/packages/wm.scm (bspwm)[arguments]: Likewise. * gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise. * gnu/packages/xfce.scm (xfconf)[arguments]: Likewise. * gnu/packages/xfig.scm (transfig)[arguments]: Likewise. * gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-09-04gnu: Put autoconf-related phases immediately after the 'unpack phase.Kei Kebreau
* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases accordingly. * gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss, htslib-for-sambamba)[arguments]: Likewise. * gnu/packages/ci.scm (cuirass)[arguments]: Likewise. * gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise. * gnu/packages/cpp.scm (libzen)[arguments]: Likewise. * gnu/packages/crypto.scm (opendht)[arguments]: Likewise. * gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise. * gnu/packages/debug.scm (stress-make)[arguments]: Likewise. * gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]: Likewise. * gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise. * gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise. * gnu/packages/engineering.scm (gerbv)[arguments]: Likewise. * gnu/packages/erlang.scm (erlang)[arguments]: Likewise. * gnu/packages/ftp.scm (weex)[arguments]: Likewise. * gnu/packages/gnome.scm (dia)[arguments]: Likewise. * gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise. * gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise. * gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]: Likewise. * gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise. * gnu/packages/irc.scm (weechat)[arguments]: Likewise. * gnu/packages/java.scm (classpath-devel)[arguments]: Likewise. * gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise. * gnu/packages/libusb.scm (hidapi)[arguments]: Likewise. * gnu/packages/linux.scm (gpm)[arguments]: Likewise. * gnu/packages/logging.scm (glog)[arguments]: Likewise. * gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise. * gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp) [arguments]: Likewise. * gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]: Likewise. * gnu/packages/microcom.scm (microcom)[arguments]: Likewise. * gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise. * gnu/packages/parallel.scm (slurm)[arguments]: Likewise. * gnu/packages/pdf.scm (libharu)[arguments]: Likewise. * gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise. * gnu/packages/serialization.scm (msgpack)[arguments]: Likewise. * gnu/packages/shells.scm (scsh)[arguments]: Likewise. * gnu/packages/telephony.scm (libiax2)[arguments]: Likewise. * gnu/packages/textutils.scm (dotconf)[arguments]: Likewise. * gnu/packages/version-control.scm (findnewest)[arguments]: Likewise. * gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
2017-08-03gnu: Add missing references to (gnu packages cran).Ricardo Wurmus
This is a follow-up to commit a8cba9dd112528d67a946eee057c838221eb5249. Reported-by: Efraim Flashner <efraim@flashner.co.il>
2017-05-10gnu: Add ocaml4.01-mcl.Ben Woodcroft
* gnu/packages/machine-learning.scm (ocaml4.01-mcl): New variable.
2017-04-17gnu: Fix typos in descriptions.Tobias Geerinckx-Rice
* gnu/packages/admin.scm (di)[description]: Likewise. * gnu/packages/bioinformatics.scm (r-annotate)[description]: Likewise. * gnu/packages/datastructures.scm (sparsehash)[description]: Likewise. * gnu/packages/dns.scm (knot)[description]: Likewise. * gnu/packages/emacs.scm (emacs-idle-highlight)[synopsis, description]: Likewise. * gnu/packages/gnome.scm (libpeas)[description]: Likewise. * gnu/packages/gtk.scm (python2-pygtk)[description]: Likewise. * gnu/packages/kde-frameworks.scm (kactivities)[description]: Fix typo. * gnu/packages/libevent.scm (perl-anyevent)[description]: Likewise. * gnu/packages/machine-learning.scm (ghmm)[description]: Likewise. * gnu/packages/mail.scm (mlmmj)[description]: Likewise. * gnu/packages/maths.scm (vc)[description]: Likewise. * gnu/packages/music.scm (gx-super-fuzz-lv2)[description]: Likewise. * gnu/packages/networking.scm (nload)[description]: Likewise. * gnu/packages/python.scm (python-execnet)[description]: Likewise. * gnu/packages/terminals.scm (tilda)[description]: Likewise. * gnu/packages/python.scm (python-execnet, python-tables) (python2-coverage-test-runner, python2-rope)[description]: Likewise.
2017-03-17gnu: Add ocaml-mcl.Ben Woodcroft
* gnu/packages/machine-learning.scm (ocaml-mcl): New variable.
2017-03-17gnu: r: Rename to r-minimal.Ricardo Wurmus
* gnu/packages/statistics.scm (r): Rename to... (r-minimal): ...this new variable. (r-with-recommended-packages): Rename to... (r): ...this. * guix/build-system/r.scm (default-r): Reference r-minimal. * gnu/packages/emacs.scm (emacs-ess)[inputs], gnu/packages/machine-learning.scm (shogun)[inputs], gnu/packages/python.scm (python-rpy2)[inputs], gnu/packages/bioinformatics.scm (ribotaper)[inputs], (couger)[propagated-inputs], (roary)[inputs], (rsem)[inputs], (rcas-web)[inputs]: Change "r" to "r-minimal".
2017-03-17gnu: r-nnet: Move to set of recommended R packages.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-nnet): Move from here... * gnu/packages/statistics.scm (r-nnet): ...to here because the other recommended R packages are here.
2017-02-25gnu: dlib: Update to 19.3.Marius Bakke
* gnu/packages/machine-learning.scm (dlib): Update to 19.3. [arguments]: Enable one more test.
2017-02-21gnu: dlib: Update to 19.2.Marius Bakke
* gnu/packages/machine-learning.scm (dlib): Update to 19.2. [arguments]: Enable previously failing tests. Fix truthiness of some phases. [source]: End snippet on #t.
2016-11-28gnu: Add r-kernlab.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-kernlab): New variable.
2016-10-04gnu: ghmm: Run tests after install.Ricardo Wurmus
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Move "check" phase after "install"; add phase "fix-PYTHONPATH".
2016-09-23gnu: randomjungle: Only build on x86_64 and i686.Ricardo Wurmus
* gnu/packages/machine-learning.scm (randomjungle)[supported-systems]: Only build on x86_64 and i686.
2016-09-13gnu: dlib: Disable failing tests.Marius Bakke
* gnu/packages/machine-learning.scm (dlib)[arguments]: Add phase 'disable-failing-tests' for tests that are known not to work in the current release. [inputs]: Add lapack. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-13gnu: dlib: Do not build dlib twice for tests.Marius Bakke
* gnu/packages/machine-learning.scm (dlib)[arguments]: Use makefile instead of cmake in check phase to prevent full rebuild. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-13gnu: dlib: Remove unused fftw from inputs.Marius Bakke
* gnu/packages/machine-learning.scm (dlib)[inputs]: Remove fftw. (define-module): Don't include algebra.scm. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-08-18gnu: Add dlib.Marius Bakke
* gnu/packages/machine-learning.scm (dlib): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-08-08gnu: Add mcl.Ben Woodcroft
* gnu/packages/machine-learning.scm (mcl): New variable.
2016-05-31gnu: Add ghmm.Ricardo Wurmus
* gnu/packages/machine-learning.scm (ghmm): New variable.
2016-05-25gnu: randomjungle: Add gfortran:lib to native-inputs.Efraim Flashner
* gnu/packages/machine-learning.scm (randomjungle)[native-inputs]: Add gfortran:lib.
2016-04-14gnu: Add r-nnet.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-nnet): New variable.
2015-12-21gnu: Add AdaptiveSparsity.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
2015-11-02gnu: shogun: Disable build on non-x86_64.Ricardo Wurmus
* gnu/packages/machine-learning.scm (shogun)[supported-systems]: Add field.
2015-08-14gnu: shogun: Move package to machine-learning.scm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (shogun): Move from here... * gnu/packages/machine-learning.scm (shogun): ...to here.
2015-06-25gnu: Replace versioned gfortran inputs with just "gfortran".Ricardo Wurmus
* gnu/packages/julia.scm (julia)[inputs]: Replace "gfortran-4.8" with "gfortran". * gnu/packages/machine-learning.scm (randomjungle)[native-inputs]: Likewise. * gnu/packages/maths.scm (arpack-ng, lapack, petsc, superlu) (superlu-dist, openblas, openspecfun, atlas)[inputs]: Likewise. (octave)[native-inputs]: Likewise. (gmsh)[propagated-inputs]: Likewise. * gnu/packages/mpi.scm (openmpi)[inputs]: Likewise. * gnu/packages/python.scm (python-numpy-bootstrap)[native-inputs]: Likewise. * gnu/packages/python.scm (python-scipy)[native-inputs]: Likewise. * gnu/packages/statistics.scm (r)[inputs]: Replace "gfortran-4.9" with "gfortran".
2015-06-12gnu: Add randomjungle.Ricardo Wurmus
* gnu/packages/machine-learning.scm (randomjungle): New variable.
2015-06-12gnu: Add python-libsvm.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-libsvm): New variable.
2015-06-12gnu: Add libsvm.Ricardo Wurmus
* gnu/packages/machine-learning.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.
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