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gnu: ocaml: Update to 4.7.0. Update ocaml to the latest version and fixes dependent packages by updating them or by adding new inputs, such as ocaml-num and ocamlbuild, that were removed from the core ocaml package. Rename packages that cannot be built with the new compiler with an ocaml4.02 prefix. Add ocaml4.02 dependencies. * gnu/packages/ocaml.scm (ocaml): Update to 4.7.0. (ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir) (ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip) (ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest) (ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree) (ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned) (ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult) (ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner) (ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools) (ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log) (ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos) (ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf) (ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake) (ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis) (ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq) (ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format) (ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi) (ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages. (opam): Update to 2.0.0. (camlp4): Update to 4.07+1. (camlp5): Update to 7.06. (hevea): Update to 2.32. (coq)[inputs]: Add ocaml-num. (emacs-tuareg): Update to 2.2.0. (ocaml-menhir)[native-inputs]: Add ocamlbuild. (ocaml-lablgtk): Update to 2.18.6. (unison)[inputs]: Use ocaml-4.02. (ocaml-findlib): Update to 1.8.0. (ocaml-ounit)[native-inputs]: Add ocamlbuild. (ocamlmod): Update to 0.0.9. (ocaml-frontc)[arguments]: Use ocaml-4.02. (ocaml-qcheck)[native-inputs]: Add ocamlbuild. (ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild. (ocaml-stringext)[native-inputs]: Add ocamlbuild. (ocaml-bisect): Update to 1.3.1. (ocaml4.01-bisect): Downgrade to 1.3. (ocaml-bitstring): Update to 3.1.0. (ocaml-topkg)[native-inputs]: Add ocamlbuild. (ocaml-rresult)[native-inputs]: Add ocamlbuild. (ocaml-sqlite3)[native-inputs]: Add ocamlbuild. (ocaml-csv)[native-inputs]: Add ocamlbuild. (ocaml-mtime)[native-inputs]: Add ocamlbuild. (ocaml-cmdliner)[native-inputs]: Add ocamlbuild. (ocaml-fmt)[native-inputs]: Add ocamlbuild. (ocaml-astring)[native-inputs]: Add ocamlbuild. (ocaml-alcotest)[native-inputs]: Add ocamlbuild. (ocaml-ppx-tools)[native-inputs]: Add ocamlbuild. (ocaml-react)[native-inputs]: Add ocamlbuild. (ocaml-ssl)[arguments]: Return #t in phases. (ocaml-lwt): Update to 4.1.0. (ocaml-logs)[native-inputs]: Add ocamlbuild. (ocaml-fpath)[native-inputs]: Add ocamlbuild. (ocaml-bos)[native-inputs]: Add ocamlbuild. (ocaml-xmlm): Update to 1.3.0. (ocaml-ulex): Update to 1.2.0. (ocaml-uchar)[native-inputs]: Add ocamlbuild. (ocaml-uutf): Update to 1.0.1. (ocaml-jsonm): Update to 1.0.1. (ocaml-ocurl): Update to 0.8.2. (ocaml-base64)[native-inputs]: Add ocamlbuild. (ocamlify)[native-inputs]: Use ocaml-4.02. (omake): Update to 0.10.3. (ocaml-batteries): Update to 2.9.0. (ocaml-pcre)[native-inputs]: Add ocamlbuild. (ocaml-expect): Update 0.0.6. (ocaml4.02-fileutils): Update to 0.5.3. (ocaml-oasis): Update 0.4.11. (ocaml-js-build-tools)[native-inputs]: Add ocamlbuild. (ocaml-bin-prot): Rename to ocaml4.02-bin-prot. (ocaml-fieldslib): Rename to ocaml4.02-fieldslib. (ocaml-ppx-core): Rename to ocaml4.02-ppx-core. (ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp. (ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver. (ocaml-cppo): Update to 1.6.5. (ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving. (ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv. (ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test. (ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench. (ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare. (ocaml-sexplib): Rename to ocaml4.02-sexplib. (ocaml-typerep): Rename to ocaml4.02-typerep. (ocaml-variantslib): Rename to ocaml4.02-variantslib. (ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv. (ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv. (ocaml-ppx-here): Rename to ocaml4.02-ppx-here. (ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert. (ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate. (ocaml-ppx-let): Rename to ocaml4.02-ppx-let. (ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv. (ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value. (ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang. (ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot. (ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail. (ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf. (ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message. (ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv. (ocaml-re): Update to 1.8.0. (ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect. (ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane. (ocaml-core-kernel): Rename to ocaml4.02-core-kernel. (ocaml-async-kernel): Rename to ocaml4.02-async-kernel. (ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel. (ocaml-core): Rename to ocaml4.02-core. (ocaml-async-unix): Rename to ocaml4.02-async-unix. (ocaml-async-extra): Rename to ocaml4.02-async-extra. (ocaml-async): Rename to ocaml4.02-async. (ocaml-ocplib-endian)[native-inputs]: Update to 1.0. (ocaml-cstruct): Rename to ocaml4.02-cstruct. (ocaml-hex): Rename to ocaml4.02-hex. (ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm. (ocaml-uri): Rename to ocaml4.02-uri. (optcomp): Use ocaml-4.02. (ocaml-piqilib): Update to 0.6.14. (ocaml-uuidm)[native-inputs]: Add ocamlbuild. (ocaml-graph): Update to 1.8.8. (ocaml-piqi): Update to 0.7.6. (bap): Update to 1.3.0. (ocaml-camomile): Update to 1.0.1. (ocaml-jbuilder): Use ocaml-4.02. (ocaml-lambda-term): Update to 1.13. (ocaml-utop): Update to 2.2.0. (ocaml-integers)[native-inputs]: Add ocamlbuild. (ocaml-ctypes): Update to 0.14.0. (ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild. (ocaml-tsdl)[native-inputs]: Add ocamlbuild. * gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02. * gnu/packages/maths.scm (cubicle): Update to 1.1.2. * gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch: Update patch. * guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib) (package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.
3 years ago
gnu: Separate Python core packages from the rest. * 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.
3 years ago
gnu: All snippets report errors using exceptions, else return #t. * gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm, gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm, gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/fpga.scm, gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm, gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm, gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm, gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm, gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm, gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm, gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm, gnu/packages/pretty-print.scm, gnu/packages/profiling.scm, gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm, gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm, gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm, gnu/packages/scribus.scm, gnu/packages/sdl.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm, gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm, gnu/packages/terminals.scm, gnu/packages/texinfo.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/tls.scm, gnu/packages/unrtf.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: In all snippets, report errors using exceptions, or else return #t.
4 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu: Use 'modify-phases' syntax. * 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.
5 years ago
gnu, doc: Use HTTPS for cran.r-project.org home pages. * 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.
4 years ago
  1. ;;; GNU Guix --- Functional package management for GNU
  2. ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
  3. ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
  4. ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
  5. ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
  6. ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
  7. ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
  8. ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
  9. ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
  10. ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
  11. ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
  12. ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  13. ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
  14. ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
  15. ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
  16. ;;;
  17. ;;; This file is part of GNU Guix.
  18. ;;;
  19. ;;; GNU Guix is free software; you can redistribute it and/or modify it
  20. ;;; under the terms of the GNU General Public License as published by
  21. ;;; the Free Software Foundation; either version 3 of the License, or (at
  22. ;;; your option) any later version.
  23. ;;;
  24. ;;; GNU Guix is distributed in the hope that it will be useful, but
  25. ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  26. ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  27. ;;; GNU General Public License for more details.
  28. ;;;
  29. ;;; You should have received a copy of the GNU General Public License
  30. ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
  31. (define-module (gnu packages machine-learning)
  32. #:use-module ((guix licenses) #:prefix license:)
  33. #:use-module (guix packages)
  34. #:use-module (guix utils)
  35. #:use-module (guix download)
  36. #:use-module (guix svn-download)
  37. #:use-module (guix build-system asdf)
  38. #:use-module (guix build-system cmake)
  39. #:use-module (guix build-system gnu)
  40. #:use-module (guix build-system ocaml)
  41. #:use-module (guix build-system python)
  42. #:use-module (guix build-system r)
  43. #:use-module (guix git-download)
  44. #:use-module (gnu packages)
  45. #:use-module (gnu packages adns)
  46. #:use-module (gnu packages algebra)
  47. #:use-module (gnu packages audio)
  48. #:use-module (gnu packages autotools)
  49. #:use-module (gnu packages base)
  50. #:use-module (gnu packages bash)
  51. #:use-module (gnu packages boost)
  52. #:use-module (gnu packages check)
  53. #:use-module (gnu packages compression)
  54. #:use-module (gnu packages cran)
  55. #:use-module (gnu packages databases)
  56. #:use-module (gnu packages dejagnu)
  57. #:use-module (gnu packages gcc)
  58. #:use-module (gnu packages glib)
  59. #:use-module (gnu packages graphviz)
  60. #:use-module (gnu packages gstreamer)
  61. #:use-module (gnu packages image)
  62. #:use-module (gnu packages linux)
  63. #:use-module (gnu packages lisp-xyz)
  64. #:use-module (gnu packages maths)
  65. #:use-module (gnu packages mpi)
  66. #:use-module (gnu packages ocaml)
  67. #:use-module (gnu packages onc-rpc)
  68. #:use-module (gnu packages perl)
  69. #:use-module (gnu packages pkg-config)
  70. #:use-module (gnu packages protobuf)
  71. #:use-module (gnu packages python)
  72. #:use-module (gnu packages python-science)
  73. #:use-module (gnu packages python-web)
  74. #:use-module (gnu packages python-xyz)
  75. #:use-module (gnu packages rpc)
  76. #:use-module (gnu packages serialization)
  77. #:use-module (gnu packages sphinx)
  78. #:use-module (gnu packages statistics)
  79. #:use-module (gnu packages sqlite)
  80. #:use-module (gnu packages swig)
  81. #:use-module (gnu packages web)
  82. #:use-module (gnu packages xml)
  83. #:use-module (gnu packages xorg)
  84. #:use-module (ice-9 match))
  85. (define-public fann
  86. ;; The last release is >100 commits behind, so we package from git.
  87. (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
  88. (package
  89. (name "fann")
  90. (version (string-append "2.2.0-1." (string-take commit 8)))
  91. (source (origin
  92. (method git-fetch)
  93. (uri (git-reference
  94. (url "https://github.com/libfann/fann.git")
  95. (commit commit)))
  96. (file-name (string-append name "-" version "-checkout"))
  97. (sha256
  98. (base32
  99. "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
  100. (build-system cmake-build-system)
  101. (arguments
  102. `(#:phases
  103. (modify-phases %standard-phases
  104. (replace 'check
  105. (lambda* (#:key outputs #:allow-other-keys)
  106. (let* ((out (assoc-ref outputs "out")))
  107. (with-directory-excursion (string-append (getcwd) "/tests")
  108. (invoke "./fann_tests"))))))))
  109. (home-page "http://leenissen.dk/fann/wp/")
  110. (synopsis "Fast Artificial Neural Network")
  111. (description
  112. "FANN is a neural network library, which implements multilayer
  113. artificial neural networks in C with support for both fully connected and
  114. sparsely connected networks.")
  115. (license license:lgpl2.1))))
  116. (define-public libsvm
  117. (package
  118. (name "libsvm")
  119. (version "3.23")
  120. (source
  121. (origin
  122. (method url-fetch)
  123. (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
  124. name "-" version ".tar.gz"))
  125. (sha256
  126. (base32 "0jpaq0rr92x38p4nk3gjan79ip67m6p80anb28z1d8601miysyi5"))))
  127. (build-system gnu-build-system)
  128. (arguments
  129. `(#:tests? #f ; no "check" target
  130. #:phases (modify-phases %standard-phases
  131. (delete 'configure)
  132. (replace
  133. 'install ; no ‘install’ target
  134. (lambda* (#:key outputs #:allow-other-keys)
  135. (let* ((out (assoc-ref outputs "out"))
  136. (bin (string-append out "/bin/")))
  137. (mkdir-p bin)
  138. (for-each (lambda (file)
  139. (copy-file file (string-append bin file)))
  140. '("svm-train"
  141. "svm-predict"
  142. "svm-scale")))
  143. #t)))))
  144. (home-page "https://www.csie.ntu.edu.tw/~cjlin/libsvm/")
  145. (synopsis "Library for Support Vector Machines")
  146. (description
  147. "LIBSVM is a machine learning library for support vector
  148. classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
  149. distribution estimation (one-class SVM). It supports multi-class
  150. classification.")
  151. (license license:bsd-3)))
  152. (define-public python-libsvm
  153. (package (inherit libsvm)
  154. (name "python-libsvm")
  155. (build-system gnu-build-system)
  156. (arguments
  157. `(#:tests? #f ; no "check" target
  158. #:make-flags '("-C" "python")
  159. #:phases
  160. (modify-phases %standard-phases
  161. (delete 'configure)
  162. (replace
  163. 'install ; no ‘install’ target
  164. (lambda* (#:key inputs outputs #:allow-other-keys)
  165. (let ((site (string-append (assoc-ref outputs "out")
  166. "/lib/python"
  167. (string-take
  168. (string-take-right
  169. (assoc-ref inputs "python") 5) 3)
  170. "/site-packages/")))
  171. (substitute* "python/svm.py"
  172. (("../libsvm.so.2") "libsvm.so.2"))
  173. (mkdir-p site)
  174. (for-each (lambda (file)
  175. (copy-file file (string-append site (basename file))))
  176. (find-files "python" "\\.py"))
  177. (copy-file "libsvm.so.2"
  178. (string-append site "libsvm.so.2")))
  179. #t)))))
  180. (inputs
  181. `(("python" ,python)))
  182. (synopsis "Python bindings of libSVM")))
  183. (define-public ghmm
  184. ;; The latest release candidate is several years and a couple of fixes have
  185. ;; been published since. This is why we download the sources from the SVN
  186. ;; repository.
  187. (let ((svn-revision 2341))
  188. (package
  189. (name "ghmm")
  190. (version (string-append "0.9-rc3-0." (number->string svn-revision)))
  191. (source (origin
  192. (method svn-fetch)
  193. (uri (svn-reference
  194. (url "http://svn.code.sf.net/p/ghmm/code/trunk")
  195. (revision svn-revision)))
  196. (file-name (string-append name "-" version "-checkout"))
  197. (sha256
  198. (base32
  199. "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
  200. (build-system gnu-build-system)
  201. (arguments
  202. `(#:imported-modules (,@%gnu-build-system-modules
  203. (guix build python-build-system))
  204. #:modules ((guix build python-build-system)
  205. ,@%gnu-build-system-modules)
  206. #:phases
  207. (modify-phases %standard-phases
  208. (add-after 'unpack 'enter-dir
  209. (lambda _ (chdir "ghmm") #t))
  210. (delete 'check)
  211. (add-after 'install 'check
  212. (assoc-ref %standard-phases 'check))
  213. (add-before 'check 'fix-PYTHONPATH
  214. (lambda* (#:key inputs outputs #:allow-other-keys)
  215. (let ((python-version (python-version
  216. (assoc-ref inputs "python"))))
  217. (setenv "PYTHONPATH"
  218. (string-append (getenv "PYTHONPATH")
  219. ":" (assoc-ref outputs "out")
  220. "/lib/python" python-version
  221. "/site-packages")))
  222. #t))
  223. (add-after 'enter-dir 'fix-runpath
  224. (lambda* (#:key outputs #:allow-other-keys)
  225. (substitute* "ghmmwrapper/setup.py"
  226. (("^(.*)extra_compile_args = \\[" line indent)
  227. (string-append indent
  228. "extra_link_args = [\"-Wl,-rpath="
  229. (assoc-ref outputs "out") "/lib\"],\n"
  230. line
  231. "\"-Wl,-rpath="
  232. (assoc-ref outputs "out")
  233. "/lib\", ")))
  234. #t))
  235. (add-after 'enter-dir 'disable-broken-tests
  236. (lambda _
  237. (substitute* "tests/Makefile.am"
  238. ;; GHMM_SILENT_TESTS is assumed to be a command.
  239. (("TESTS_ENVIRONMENT.*") "")
  240. ;; Do not build broken tests.
  241. (("chmm .*") "")
  242. (("read_fa .*") "")
  243. (("mcmc .*") "")
  244. (("label_higher_order_test.*$")
  245. "label_higher_order_test\n"))
  246. ;; These Python unittests are broken as there is no gato.
  247. ;; See https://sourceforge.net/p/ghmm/support-requests/3/
  248. (substitute* "ghmmwrapper/ghmmunittests.py"
  249. (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
  250. line indent)
  251. (string-append indent
  252. "@unittest.skip(\"Disabled by Guix\")\n"
  253. line)))
  254. #t)))))
  255. (inputs
  256. `(("python" ,python-2) ; only Python 2 is supported
  257. ("libxml2" ,libxml2)))
  258. (native-inputs
  259. `(("pkg-config" ,pkg-config)
  260. ("dejagnu" ,dejagnu)
  261. ("swig" ,swig)
  262. ("autoconf" ,autoconf)
  263. ("automake" ,automake)
  264. ("libtool" ,libtool)))
  265. (home-page "http://ghmm.org")
  266. (synopsis "Hidden Markov Model library")
  267. (description
  268. "The General Hidden Markov Model library (GHMM) is a C library with
  269. additional Python bindings implementing a wide range of types of @dfn{Hidden
  270. Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
  271. training, HMM clustering, HMM mixtures.")
  272. (license license:lgpl2.0+))))
  273. (define-public mcl
  274. (package
  275. (name "mcl")
  276. (version "14.137")
  277. (source (origin
  278. (method url-fetch)
  279. (uri (string-append
  280. "http://micans.org/mcl/src/mcl-"
  281. (string-replace-substring version "." "-")
  282. ".tar.gz"))
  283. (sha256
  284. (base32
  285. "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
  286. (build-system gnu-build-system)
  287. (arguments
  288. `(#:configure-flags (list "--enable-blast")))
  289. (inputs
  290. `(("perl" ,perl)))
  291. (home-page "http://micans.org/mcl/")
  292. (synopsis "Clustering algorithm for graphs")
  293. (description
  294. "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
  295. fast and scalable unsupervised cluster algorithm for graphs (also known as
  296. networks) based on simulation of (stochastic) flow in graphs.")
  297. ;; In the LICENCE file and web page it says "The software is licensed
  298. ;; under the GNU General Public License, version 3.", but in several of
  299. ;; the source code files it suggests GPL3 or later.
  300. ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
  301. (license license:gpl3)))
  302. (define-public ocaml-mcl
  303. (package
  304. (name "ocaml-mcl")
  305. (version "12-068oasis4")
  306. (source
  307. (origin
  308. (method git-fetch)
  309. (uri (git-reference
  310. (url "https://github.com/fhcrc/mcl.git")
  311. (commit version)))
  312. (file-name (git-file-name name version))
  313. (sha256
  314. (base32
  315. "0009dc3h2jp3qg5val452wngpqnbfyhbcxylghq0mrjqxx0jdq5p"))))
  316. (build-system ocaml-build-system)
  317. (arguments
  318. `(#:phases
  319. (modify-phases %standard-phases
  320. (add-before 'configure 'patch-paths
  321. (lambda _
  322. (substitute* "configure"
  323. (("/bin/sh") (which "sh")))
  324. (substitute* "setup.ml"
  325. (("LDFLAGS=-fPIC")
  326. (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
  327. (("-std=c89") "-std=gnu99")
  328. ;; This is a mutable string, which is no longer supported. Use
  329. ;; a byte buffer instead.
  330. (("String.make \\(String.length s\\)")
  331. "Bytes.make (String.length s)")
  332. ;; These two belong together.
  333. (("OASISString.replace_chars")
  334. "Bytes.to_string (OASISString.replace_chars")
  335. ((" s;")
  336. " s);"))
  337. (substitute* "myocamlbuild.ml"
  338. (("std=c89") "std=gnu99"))
  339. ;; Since we build with a more recent OCaml, we have to use C99 or
  340. ;; later. This causes problems with the old C code.
  341. (substitute* "src/impala/matrix.c"
  342. (("restrict") "restrict_"))
  343. #t)))))
  344. (native-inputs
  345. `(("ocamlbuild" ,ocamlbuild)))
  346. (home-page "https://github.com/fhcrc/mcl")
  347. (synopsis "OCaml wrappers around MCL")
  348. (description
  349. "This package provides OCaml bindings for the MCL graph clustering
  350. algorithm.")
  351. (license license:gpl3)))
  352. (define-public randomjungle
  353. (package
  354. (name "randomjungle")
  355. (version "2.1.0")
  356. (source
  357. (origin
  358. (method url-fetch)
  359. (uri (string-append
  360. "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
  361. "/randomjungle/randomjungle-" version ".tar_.gz"))
  362. (patches (search-patches "randomjungle-disable-static-build.patch"))
  363. (sha256
  364. (base32
  365. "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
  366. (build-system gnu-build-system)
  367. (arguments
  368. `(#:configure-flags
  369. (list "--disable-static"
  370. (string-append "--with-boost="
  371. (assoc-ref %build-inputs "boost")))
  372. #:phases
  373. (modify-phases %standard-phases
  374. (add-before
  375. 'configure 'set-CXXFLAGS
  376. (lambda _
  377. (setenv "CXXFLAGS" "-fpermissive ")
  378. #t)))))
  379. (inputs
  380. `(("boost" ,boost)
  381. ("gsl" ,gsl)
  382. ("libxml2" ,libxml2)
  383. ("zlib" ,zlib)))
  384. (native-inputs
  385. `(("gfortran" ,gfortran)
  386. ("gfortran:lib" ,gfortran "lib")))
  387. ;; Non-portable assembly instructions are used so building fails on
  388. ;; platforms other than x86_64 or i686.
  389. (supported-systems '("x86_64-linux" "i686-linux"))
  390. (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
  391. (synopsis "Implementation of the Random Forests machine learning method")
  392. (description
  393. "Random Jungle is an implementation of Random Forests. It is supposed to
  394. analyse high dimensional data. In genetics, it can be used for analysing big
  395. Genome Wide Association (GWA) data. Random Forests is a powerful machine
  396. learning method. Most interesting features are variable selection, missing
  397. value imputation, classifier creation, generalization error estimation and
  398. sample proximities between pairs of cases.")
  399. (license license:gpl3+)))
  400. (define-public openfst
  401. (package
  402. (name "openfst")
  403. (version "1.7.2")
  404. (source (origin
  405. (method url-fetch)
  406. (uri (string-append "http://www.openfst.org/twiki/pub/FST/"
  407. "FstDownload/openfst-" version ".tar.gz"))
  408. (sha256
  409. (base32
  410. "0fqgk8195kz21is09gwzwnrg7fr9526bi9mh4apyskapz27pbhr1"))))
  411. (build-system gnu-build-system)
  412. (home-page "http://www.openfst.org")
  413. (synopsis "Library for weighted finite-state transducers")
  414. (description "OpenFst is a library for constructing, combining,
  415. optimizing, and searching weighted finite-state transducers (FSTs).")
  416. (license license:asl2.0)))
  417. (define-public shogun
  418. (package
  419. (name "shogun")
  420. (version "6.1.3")
  421. (source
  422. (origin
  423. (method url-fetch)
  424. (uri (string-append
  425. "ftp://shogun-toolbox.org/shogun/releases/"
  426. (version-major+minor version)
  427. "/sources/shogun-" version ".tar.bz2"))
  428. (sha256
  429. (base32
  430. "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
  431. (modules '((guix build utils)
  432. (ice-9 rdelim)))
  433. (snippet
  434. '(begin
  435. ;; Remove non-free sources and files referencing them
  436. (for-each delete-file
  437. (find-files "src/shogun/classifier/svm/"
  438. "SVMLight\\.(cpp|h)"))
  439. (for-each delete-file
  440. (find-files "examples/undocumented/libshogun/"
  441. (string-append
  442. "(classifier_.*svmlight.*|"
  443. "evaluation_cross_validation_locked_comparison).cpp")))
  444. ;; Remove non-free functions.
  445. (define (delete-ifdefs file)
  446. (with-atomic-file-replacement file
  447. (lambda (in out)
  448. (let loop ((line (read-line in 'concat))
  449. (skipping? #f))
  450. (if (eof-object? line)
  451. #t
  452. (let ((skip-next?
  453. (or (and skipping?
  454. (not (string-prefix?
  455. "#endif //USE_SVMLIGHT" line)))
  456. (string-prefix?
  457. "#ifdef USE_SVMLIGHT" line))))
  458. (when (or (not skipping?)
  459. (and skipping? (not skip-next?)))
  460. (display line out))
  461. (loop (read-line in 'concat) skip-next?)))))))
  462. (for-each delete-ifdefs
  463. (append
  464. (find-files "src/shogun/classifier/mkl"
  465. "^MKLClassification\\.cpp")
  466. (find-files "src/shogun/classifier/svm"
  467. "^SVMLightOneClass\\.(cpp|h)")
  468. (find-files "src/shogun/multiclass"
  469. "^ScatterSVM\\.(cpp|h)")
  470. (find-files "src/shogun/kernel/"
  471. "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
  472. (find-files "src/shogun/regression/svr"
  473. "^(MKLRegression|SVRLight)\\.(cpp|h)")
  474. (find-files "src/shogun/transfer/domain_adaptation"
  475. "^DomainAdaptationSVM\\.(cpp|h)")))
  476. #t))))
  477. (build-system cmake-build-system)
  478. (arguments
  479. '(#:tests? #f ;no check target
  480. #:phases
  481. (modify-phases %standard-phases
  482. (add-after 'unpack 'delete-broken-symlinks
  483. (lambda _
  484. (for-each delete-file '("applications/arts/data"
  485. "applications/asp/data"
  486. "applications/easysvm/data"
  487. "applications/msplicer/data"
  488. "applications/ocr/data"
  489. "examples/meta/data"
  490. "examples/undocumented/data"))
  491. #t))
  492. (add-after 'unpack 'change-R-target-path
  493. (lambda* (#:key outputs #:allow-other-keys)
  494. (substitute* '("src/interfaces/r/CMakeLists.txt"
  495. "examples/meta/r/CMakeLists.txt")
  496. (("\\$\\{R_COMPONENT_LIB_PATH\\}")
  497. (string-append (assoc-ref outputs "out")
  498. "/lib/R/library/")))
  499. #t))
  500. (add-after 'unpack 'fix-octave-modules
  501. (lambda* (#:key outputs #:allow-other-keys)
  502. (substitute* "src/interfaces/octave/CMakeLists.txt"
  503. (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
  504. "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
  505. ;; change target directory
  506. (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
  507. (string-append (assoc-ref outputs "out")
  508. "/share/octave/packages")))
  509. (substitute* '("src/interfaces/octave/swig_typemaps.i"
  510. "src/interfaces/octave/sg_print_functions.cpp")
  511. ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
  512. (("octave/config\\.h") "octave/octave-config.h")
  513. (("octave/oct-obj.h") "octave/ovl.h"))
  514. #t))
  515. (add-after 'unpack 'move-rxcpp
  516. (lambda* (#:key inputs #:allow-other-keys)
  517. (let ((rxcpp-dir "shogun/third-party/rxcpp"))
  518. (mkdir-p rxcpp-dir)
  519. (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
  520. #t)))
  521. (add-before 'build 'set-HOME
  522. ;; $HOME needs to be set at some point during the build phase
  523. (lambda _ (setenv "HOME" "/tmp") #t)))
  524. #:configure-flags
  525. (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
  526. "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
  527. "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
  528. ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
  529. ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
  530. ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
  531. ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
  532. "-DINTERFACE_OCTAVE=ON"
  533. "-DINTERFACE_PYTHON=ON"
  534. "-DINTERFACE_R=ON")))
  535. (inputs
  536. `(("python" ,python)
  537. ("numpy" ,python-numpy)
  538. ("r-minimal" ,r-minimal)
  539. ("octave" ,octave-cli)
  540. ("swig" ,swig)
  541. ("eigen" ,eigen)
  542. ("hdf5" ,hdf5)
  543. ("atlas" ,atlas)
  544. ("arpack" ,arpack-ng)
  545. ("lapack" ,lapack)
  546. ("glpk" ,glpk)
  547. ("libxml2" ,libxml2)
  548. ("lzo" ,lzo)
  549. ("zlib" ,zlib)))
  550. (native-inputs
  551. `(("pkg-config" ,pkg-config)
  552. ("rxcpp" ,rxcpp)))
  553. ;; Non-portable SSE instructions are used so building fails on platforms
  554. ;; other than x86_64.
  555. (supported-systems '("x86_64-linux"))
  556. (home-page "https://shogun-toolbox.org/")
  557. (synopsis "Machine learning toolbox")
  558. (description
  559. "The Shogun Machine learning toolbox provides a wide range of unified and
  560. efficient Machine Learning (ML) methods. The toolbox seamlessly
  561. combines multiple data representations, algorithm classes, and general purpose
  562. tools. This enables both rapid prototyping of data pipelines and extensibility
  563. in terms of new algorithms.")
  564. (license license:gpl3+)))
  565. (define-public rxcpp
  566. (package
  567. (name "rxcpp")
  568. (version "4.1.0")
  569. (source
  570. (origin
  571. (method git-fetch)
  572. (uri (git-reference
  573. (url "https://github.com/ReactiveX/RxCpp.git")
  574. (commit (string-append "v" version))))
  575. (sha256
  576. (base32 "1rdpa3jlc181jd08nk437aar085h28i45s6nzrv65apb3xyyz0ij"))
  577. (file-name (git-file-name name version))))
  578. (build-system cmake-build-system)
  579. (arguments
  580. `(#:phases
  581. (modify-phases %standard-phases
  582. (add-after 'unpack 'remove-werror
  583. (lambda _
  584. (substitute* (find-files ".")
  585. (("-Werror") ""))
  586. #t))
  587. (replace 'check
  588. (lambda _
  589. (invoke "ctest"))))))
  590. (native-inputs
  591. `(("catch" ,catch-framework)))
  592. (home-page "http://reactivex.io/")
  593. (synopsis "Reactive Extensions for C++")
  594. (description
  595. "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
  596. values-distributed-in-time. ReactiveX is a library for composing asynchronous
  597. and event-based programs by using observable sequences.
  598. It extends the observer pattern to support sequences of data and/or events and
  599. adds operators that allow you to compose sequences together declaratively while
  600. abstracting away concerns about things like low-level threading,
  601. synchronization, thread-safety, concurrent data structures, and non-blocking
  602. I/O.")
  603. (license license:asl2.0)))
  604. (define-public r-adaptivesparsity
  605. (package
  606. (name "r-adaptivesparsity")
  607. (version "1.6")
  608. (source (origin
  609. (method url-fetch)
  610. (uri (cran-uri "AdaptiveSparsity" version))
  611. (sha256
  612. (base32
  613. "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
  614. (properties
  615. `((upstream-name . "AdaptiveSparsity")))
  616. (build-system r-build-system)
  617. (arguments
  618. `(#:phases
  619. (modify-phases %standard-phases
  620. (add-after 'unpack 'link-against-armadillo
  621. (lambda _
  622. (substitute* "src/Makevars"
  623. (("PKG_LIBS=" prefix)
  624. (string-append prefix "-larmadillo"))))))))
  625. (propagated-inputs
  626. `(("r-mass" ,r-mass)
  627. ("r-matrix" ,r-matrix)
  628. ("r-rcpp" ,r-rcpp)
  629. ("r-rcpparmadillo" ,r-rcpparmadillo)))
  630. (inputs
  631. `(("armadillo" ,armadillo)))
  632. (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
  633. (synopsis "Adaptive sparsity models")
  634. (description
  635. "This package implements the Figueiredo machine learning algorithm for
  636. adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
  637. geometric models.")
  638. (license license:lgpl3+)))
  639. (define-public gemmlowp-for-tensorflow
  640. ;; The commit hash is taken from "tensorflow/workspace.bzl".
  641. (let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
  642. (revision "2"))
  643. (package
  644. (name "gemmlowp")
  645. (version (git-version "0" revision commit))
  646. (source (origin
  647. (method url-fetch)
  648. (uri (string-append "https://mirror.bazel.build/"
  649. "github.com/google/gemmlowp/archive/"
  650. commit ".zip"))
  651. (file-name (string-append "gemmlowp-" version ".zip"))
  652. (sha256
  653. (base32
  654. "0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
  655. (build-system cmake-build-system)
  656. (arguments
  657. `(#:configure-flags
  658. (list ,@(match (%current-system)
  659. ((or "x86_64-linux" "i686-linux")
  660. '("-DCMAKE_CXX_FLAGS=-msse2"))
  661. (_ '())))
  662. #:phases
  663. (modify-phases %standard-phases
  664. ;; This directory contains the CMakeLists.txt.
  665. (add-after 'unpack 'chdir
  666. (lambda _ (chdir "contrib") #t))
  667. ;; There is no install target
  668. (replace 'install
  669. (lambda* (#:key outputs #:allow-other-keys)
  670. (let* ((out (assoc-ref outputs "out"))
  671. (lib (string-append out "/lib/"))
  672. (inc (string-append out "/include/")))
  673. (install-file "../build/libeight_bit_int_gemm.so" lib)
  674. (for-each (lambda (dir)
  675. (let ((target (string-append inc "/" dir)))
  676. (mkdir-p target)
  677. (for-each (lambda (h)
  678. (install-file h target))
  679. (find-files (string-append "../" dir)
  680. "\\.h$"))))
  681. '("meta" "profiling" "public" "fixedpoint"
  682. "eight_bit_int_gemm" "internal"))
  683. #t))))))
  684. (native-inputs
  685. `(("unzip" ,unzip)))
  686. (home-page "https://github.com/google/gemmlowp")
  687. (synopsis "Small self-contained low-precision GEMM library")
  688. (description
  689. "This is a small self-contained low-precision @dfn{general matrix
  690. multiplication} (GEMM) library. It is not a full linear algebra library.
  691. Low-precision means that the input and output matrix entries are integers on
  692. at most 8 bits. To avoid overflow, results are internally accumulated on more
  693. than 8 bits, and at the end only some significant 8 bits are kept.")
  694. (license license:asl2.0))))
  695. (define-public dlib
  696. (package
  697. (name "dlib")
  698. (version "19.7")
  699. (source (origin
  700. (method url-fetch)
  701. (uri (string-append
  702. "http://dlib.net/files/dlib-" version ".tar.bz2"))
  703. (sha256
  704. (base32
  705. "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
  706. (modules '((guix build utils)))
  707. (snippet
  708. '(begin
  709. ;; Delete ~13MB of bundled dependencies.
  710. (delete-file-recursively "dlib/external")
  711. (delete-file-recursively "docs/dlib/external")
  712. #t))))
  713. (build-system cmake-build-system)
  714. (arguments
  715. `(#:phases
  716. (modify-phases %standard-phases
  717. (add-after 'unpack 'disable-asserts
  718. (lambda _
  719. ;; config.h recommends explicitly enabling or disabling asserts
  720. ;; when building as a shared library. By default neither is set.
  721. (substitute* "dlib/config.h"
  722. (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
  723. #t))
  724. (add-after 'disable-asserts 'disable-failing-tests
  725. (lambda _
  726. ;; One test times out on MIPS, so we need to disable it.
  727. ;; Others are flaky on some platforms.
  728. (let* ((system ,(or (%current-target-system)
  729. (%current-system)))
  730. (disabled-tests (cond
  731. ((string-prefix? "mips64" system)
  732. '("object_detector" ; timeout
  733. "data_io"))
  734. ((string-prefix? "armhf" system)
  735. '("learning_to_track"))
  736. ((string-prefix? "i686" system)
  737. '("optimization"))
  738. (else '()))))
  739. (for-each
  740. (lambda (test)
  741. (substitute* "dlib/test/makefile"
  742. (((string-append "SRC \\+= " test "\\.cpp")) "")))
  743. disabled-tests)
  744. #t)))
  745. (replace 'check
  746. (lambda _
  747. ;; No test target, so we build and run the unit tests here.
  748. (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
  749. (with-directory-excursion test-dir
  750. (invoke "make" "-j" (number->string (parallel-job-count)))
  751. (invoke "./dtest" "--runall"))
  752. #t)))
  753. (add-after 'install 'delete-static-library
  754. (lambda* (#:key outputs #:allow-other-keys)
  755. (delete-file (string-append (assoc-ref outputs "out")
  756. "/lib/libdlib.a"))
  757. #t)))))
  758. (native-inputs
  759. `(("pkg-config" ,pkg-config)
  760. ;; For tests.
  761. ("libnsl" ,libnsl)))
  762. (inputs
  763. `(("giflib" ,giflib)
  764. ("lapack" ,lapack)
  765. ("libjpeg" ,libjpeg)
  766. ("libpng" ,libpng)
  767. ("libx11" ,libx11)
  768. ("openblas" ,openblas)
  769. ("zlib" ,zlib)))
  770. (synopsis
  771. "Toolkit for making machine learning and data analysis applications in C++")
  772. (description
  773. "Dlib is a modern C++ toolkit containing machine learning algorithms and
  774. tools. It is used in both industry and academia in a wide range of domains
  775. including robotics, embedded devices, mobile phones, and large high performance
  776. computing environments.")
  777. (home-page "http://dlib.net")
  778. (license license:boost1.0)))
  779. (define-public python-scikit-learn
  780. (package
  781. (name "python-scikit-learn")
  782. (version "0.22.1")
  783. (source
  784. (origin
  785. (method git-fetch)
  786. (uri (git-reference
  787. (url "https://github.com/scikit-learn/scikit-learn.git")
  788. (commit version)))
  789. (file-name (git-file-name name version))
  790. (sha256
  791. (base32
  792. "1xqxv210gsmjw094vc5ghq2y9lmm74qkk22pq6flcjzj51b86jxf"))))
  793. (build-system python-build-system)
  794. (arguments
  795. `(#:phases
  796. (modify-phases %standard-phases
  797. (add-after 'build 'build-ext
  798. (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
  799. (replace 'check
  800. (lambda _
  801. ;; Restrict OpenBLAS threads to prevent segfaults while testing!
  802. (setenv "OPENBLAS_NUM_THREADS" "1")
  803. ;; Some tests require write access to $HOME.
  804. (setenv "HOME" "/tmp")
  805. (invoke "pytest" "sklearn" "-m" "not network")))
  806. (add-before 'reset-gzip-timestamps 'make-files-writable
  807. (lambda* (#:key outputs #:allow-other-keys)
  808. ;; Make sure .gz files are writable so that the
  809. ;; 'reset-gzip-timestamps' phase can do its work.
  810. (let ((out (assoc-ref outputs "out")))
  811. (for-each make-file-writable
  812. (find-files out "\\.gz$"))
  813. #t))))))
  814. (inputs
  815. `(("openblas" ,openblas)))
  816. (native-inputs
  817. `(("python-joblib" ,python-joblib)
  818. ("python-pytest" ,python-pytest)
  819. ("python-pandas" ,python-pandas) ;for tests
  820. ("python-cython" ,python-cython)))
  821. (propagated-inputs
  822. `(("python-numpy" ,python-numpy)
  823. ("python-scipy" ,python-scipy)))
  824. (home-page "https://scikit-learn.org/")
  825. (synopsis "Machine Learning in Python")
  826. (description
  827. "Scikit-learn provides simple and efficient tools for data mining and
  828. data analysis.")
  829. (properties `((python2-variant . ,(delay python2-scikit-learn))))
  830. (license license:bsd-3)))
  831. ;; scikit-learn 0.22 and later only supports Python 3, so we stick with
  832. ;; an older version here.
  833. (define-public python2-scikit-learn
  834. (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn))))
  835. (package
  836. (inherit base)
  837. (version "0.20.4")
  838. (source (origin
  839. (method git-fetch)
  840. (uri (git-reference
  841. (url "https://github.com/scikit-learn/scikit-learn.git")
  842. (commit version)))
  843. (file-name (git-file-name "python-scikit-learn" version))
  844. (sha256
  845. (base32
  846. "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))))))
  847. (define-public python-scikit-rebate
  848. (package
  849. (name "python-scikit-rebate")
  850. (version "0.6")
  851. (source (origin
  852. (method url-fetch)
  853. (uri (pypi-uri "skrebate" version))
  854. (sha256
  855. (base32
  856. "1h7qs9gjxpzqabzhb8rmpv3jpmi5iq41kqdibg48299h94iikiw7"))))
  857. (build-system python-build-system)
  858. ;; Pandas is only needed to run the tests.
  859. (native-inputs
  860. `(("python-pandas" ,python-pandas)))
  861. (propagated-inputs
  862. `(("python-numpy" ,python-numpy)
  863. ("python-scipy" ,python-scipy)
  864. ("python-scikit-learn" ,python-scikit-learn)
  865. ("python-joblib" ,python-joblib)))
  866. (home-page "https://epistasislab.github.io/scikit-rebate/")
  867. (synopsis "Relief-based feature selection algorithms for Python")
  868. (description "Scikit-rebate is a scikit-learn-compatible Python
  869. implementation of ReBATE, a suite of Relief-based feature selection algorithms
  870. for Machine Learning. These algorithms excel at identifying features that are
  871. predictive of the outcome in supervised learning problems, and are especially
  872. good at identifying feature interactions that are normally overlooked by
  873. standard feature selection algorithms.")
  874. (license license:expat)))
  875. (define-public python-autograd
  876. (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
  877. (revision "0")
  878. (version (git-version "0.0.0" revision commit)))
  879. (package
  880. (name "python-autograd")
  881. (home-page "https://github.com/HIPS/autograd")
  882. (source (origin
  883. (method git-fetch)
  884. (uri (git-reference
  885. (url home-page)
  886. (commit commit)))
  887. (sha256
  888. (base32
  889. "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
  890. (file-name (git-file-name name version))))
  891. (version version)
  892. (build-system python-build-system)
  893. (native-inputs
  894. `(("python-nose" ,python-nose)
  895. ("python-pytest" ,python-pytest)))
  896. (propagated-inputs
  897. `(("python-future" ,python-future)
  898. ("python-numpy" ,python-numpy)))
  899. (arguments
  900. `(#:phases (modify-phases %standard-phases
  901. (replace 'check
  902. (lambda _
  903. (invoke "py.test" "-v"))))))
  904. (synopsis "Efficiently computes derivatives of NumPy code")
  905. (description "Autograd can automatically differentiate native Python and
  906. NumPy code. It can handle a large subset of Python's features, including loops,
  907. ifs, recursion and closures, and it can even take derivatives of derivatives
  908. of derivatives. It supports reverse-mode differentiation
  909. (a.k.a. backpropagation), which means it can efficiently take gradients of
  910. scalar-valued functions with respect to array-valued arguments, as well as
  911. forward-mode differentiation, and the two can be composed arbitrarily. The
  912. main intended application of Autograd is gradient-based optimization.")
  913. (license license:expat))))
  914. (define-public python2-autograd
  915. (package-with-python2 python-autograd))
  916. (define-public lightgbm
  917. (package
  918. (name "lightgbm")
  919. (version "2.0.12")
  920. (source (origin
  921. (method url-fetch)
  922. (uri (string-append
  923. "https://github.com/Microsoft/LightGBM/archive/v"
  924. version ".tar.gz"))
  925. (sha256
  926. (base32
  927. "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
  928. (file-name (string-append name "-" version ".tar.gz"))))
  929. (native-inputs
  930. `(("python-pytest" ,python-pytest)
  931. ("python-nose" ,python-nose)))
  932. (inputs
  933. `(("openmpi" ,openmpi)))
  934. (propagated-inputs
  935. `(("python-numpy" ,python-numpy)
  936. ("python-scipy" ,python-scipy)))
  937. (arguments
  938. `(#:configure-flags
  939. '("-DUSE_MPI=ON")
  940. #:phases
  941. (modify-phases %standard-phases
  942. (replace 'check
  943. (lambda* (#:key outputs #:allow-other-keys)
  944. (with-directory-excursion ,(string-append "../LightGBM-" version)
  945. (invoke "pytest" "tests/c_api_test/test_.py")))))))
  946. (build-system cmake-build-system)
  947. (home-page "https://github.com/Microsoft/LightGBM")
  948. (synopsis "Gradient boosting framework based on decision tree algorithms")
  949. (description "LightGBM is a gradient boosting framework that uses tree
  950. based learning algorithms. It is designed to be distributed and efficient with
  951. the following advantages:
  952. @itemize
  953. @item Faster training speed and higher efficiency
  954. @item Lower memory usage
  955. @item Better accuracy
  956. @item Parallel and GPU learning supported (not enabled in this package)
  957. @item Capable of handling large-scale data
  958. @end itemize\n")
  959. (license license:expat)))
  960. (define-public vowpal-wabbit
  961. ;; Language bindings not included.
  962. (package
  963. (name "vowpal-wabbit")
  964. (version "8.5.0")
  965. (source (origin
  966. (method git-fetch)
  967. (uri (git-reference
  968. (url "https://github.com/JohnLangford/vowpal_wabbit")
  969. (commit version)))
  970. (sha256
  971. (base32
  972. "04bwzk6ifgnz3fmzid8b7avxf9n5pnx9xcjm61nkjng1vv0bpj8x"))
  973. (file-name (git-file-name name version))))
  974. (inputs
  975. `(("boost" ,boost)
  976. ("zlib" ,zlib)))
  977. (arguments
  978. `(#:configure-flags
  979. (list (string-append "--with-boost="
  980. (assoc-ref %build-inputs "boost")))
  981. #:phases
  982. (modify-phases %standard-phases
  983. (add-after 'unpack 'make-files-writable
  984. (lambda _
  985. (for-each make-file-writable (find-files "." ".*")) #t)))))
  986. (build-system gnu-build-system)
  987. (home-page "https://github.com/JohnLangford/vowpal_wabbit")
  988. (synopsis "Fast machine learning library for online learning")
  989. (description "Vowpal Wabbit is a machine learning system with techniques
  990. such as online, hashing, allreduce, reductions, learning2search, active, and
  991. interactive learning.")
  992. (license license:bsd-3)))
  993. (define-public python2-fastlmm
  994. (package
  995. (name "python2-fastlmm")
  996. (version "0.2.21")
  997. (source
  998. (origin
  999. (method url-fetch)
  1000. (uri (pypi-uri "fastlmm" version ".zip"))
  1001. (sha256
  1002. (base32
  1003. "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
  1004. (build-system python-build-system)
  1005. (arguments
  1006. `(#:tests? #f ; some test files are missing
  1007. #:python ,python-2)) ; only Python 2.7 is supported
  1008. (propagated-inputs
  1009. `(("python2-numpy" ,python2-numpy)
  1010. ("python2-scipy" ,python2-scipy)
  1011. ("python2-matplotlib" ,python2-matplotlib)
  1012. ("python2-pandas" ,python2-pandas)
  1013. ("python2-scikit-learn" ,python2-scikit-learn)
  1014. ("python2-pysnptools" ,python2-pysnptools)))
  1015. (native-inputs
  1016. `(("unzip" ,unzip)
  1017. ("python2-cython" ,python2-cython)
  1018. ("python2-mock" ,python2-mock)
  1019. ("python2-nose" ,python2-nose)))
  1020. (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
  1021. (synopsis "Perform genome-wide association studies on large data sets")
  1022. (description
  1023. "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
  1024. Models, is a program for performing both single-SNP and SNP-set genome-wide
  1025. association studies (GWAS) on extremely large data sets.")
  1026. (license license:asl2.0)))
  1027. ;; There have been no proper releases yet.
  1028. (define-public kaldi
  1029. (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
  1030. (revision "1"))
  1031. (package
  1032. (name "kaldi")
  1033. (version (git-version "0" revision commit))
  1034. (source (origin
  1035. (method git-fetch)
  1036. (uri (git-reference
  1037. (url "https://github.com/kaldi-asr/kaldi.git")
  1038. (commit commit)))
  1039. (file-name (git-file-name name version))
  1040. (sha256
  1041. (base32
  1042. "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
  1043. (build-system gnu-build-system)
  1044. (arguments
  1045. `(#:test-target "test"
  1046. #:phases
  1047. (modify-phases %standard-phases
  1048. (add-after 'unpack 'chdir
  1049. (lambda _ (chdir "src") #t))
  1050. (replace 'configure
  1051. (lambda* (#:key build system inputs outputs #:allow-other-keys)
  1052. (when (not (or (string-prefix? "x86_64" system)
  1053. (string-prefix? "i686" system)))
  1054. (substitute* "makefiles/linux_openblas.mk"
  1055. (("-msse -msse2") "")))
  1056. (substitute* "makefiles/default_rules.mk"
  1057. (("/bin/bash") (which "bash")))
  1058. (substitute* "Makefile"
  1059. (("ext_depend: check_portaudio")
  1060. "ext_depend:"))
  1061. (substitute* '("online/Makefile"
  1062. "onlinebin/Makefile"
  1063. "gst-plugin/Makefile")
  1064. (("../../tools/portaudio/install")
  1065. (assoc-ref inputs "portaudio")))
  1066. ;; This `configure' script doesn't support variables passed as
  1067. ;; arguments, nor does it support "prefix".
  1068. (let ((out (assoc-ref outputs "out"))
  1069. (openblas (assoc-ref inputs "openblas"))
  1070. (openfst (assoc-ref inputs "openfst")))
  1071. (substitute* "configure"
  1072. (("check_for_slow_expf;") "")
  1073. ;; This affects the RPATH and also serves as the installation
  1074. ;; directory.
  1075. (("KALDILIBDIR=`pwd`/lib")
  1076. (string-append "KALDILIBDIR=" out "/lib")))
  1077. (mkdir-p out) ; must exist
  1078. (setenv "CONFIG_SHELL" (which "bash"))
  1079. (setenv "OPENFST_VER" ,(package-version openfst))
  1080. (invoke "./configure"
  1081. "--use-cuda=no"
  1082. "--shared"
  1083. (string-append "--openblas-root=" openblas)
  1084. (string-append "--fst-root=" openfst)))))
  1085. (add-after 'build 'build-ext-and-gstreamer-plugin
  1086. (lambda _
  1087. (invoke "make" "-C" "online" "depend")
  1088. (invoke "make" "-C" "online")
  1089. (invoke "make" "-C" "onlinebin" "depend")
  1090. (invoke "make" "-C" "onlinebin")
  1091. (invoke "make" "-C" "gst-plugin" "depend")
  1092. (invoke "make" "-C" "gst-plugin")
  1093. #t))
  1094. ;; TODO: also install the executables.
  1095. (replace 'install
  1096. (lambda* (#:key outputs #:allow-other-keys)
  1097. (let* ((out (assoc-ref outputs "out"))
  1098. (inc (string-append out "/include"))
  1099. (lib (string-append out "/lib")))
  1100. (mkdir-p lib)
  1101. ;; The build phase installed symlinks to the actual
  1102. ;; libraries. Install the actual targets.
  1103. (for-each (lambda (file)
  1104. (let ((target (readlink file)))
  1105. (delete-file file)
  1106. (install-file target lib)))
  1107. (find-files lib "\\.so"))
  1108. ;; Install headers
  1109. (for-each (lambda (file)
  1110. (let ((target-dir (string-append inc "/" (dirname file))))
  1111. (install-file file target-dir)))
  1112. (find-files "." "\\.h"))
  1113. (install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
  1114. (string-append lib "/gstreamer-1.0"))
  1115. #t))))))
  1116. (inputs
  1117. `(("alsa-lib" ,alsa-lib)
  1118. ("gfortran" ,gfortran "lib")
  1119. ("glib" ,glib)
  1120. ("gstreamer" ,gstreamer)
  1121. ("jack" ,jack-1)
  1122. ("openblas" ,openblas)
  1123. ("openfst" ,openfst)
  1124. ("portaudio" ,portaudio)
  1125. ("python" ,python)))
  1126. (native-inputs
  1127. `(("glib" ,glib "bin") ; glib-genmarshal
  1128. ("grep" ,grep)
  1129. ("sed" ,sed)
  1130. ("pkg-config" ,pkg-config)
  1131. ("which" ,which)))
  1132. (home-page "https://kaldi-asr.org/")
  1133. (synopsis "Speech recognition toolkit")
  1134. (description "Kaldi is an extensible toolkit for speech recognition
  1135. written in C++.")
  1136. (license license:asl2.0))))
  1137. (define-public gst-kaldi-nnet2-online
  1138. (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
  1139. (revision "1"))
  1140. (package
  1141. (name "gst-kaldi-nnet2-online")
  1142. (version (git-version "0" revision commit))
  1143. (source (origin
  1144. (method git-fetch)
  1145. (uri (git-reference
  1146. (url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
  1147. (commit commit)))
  1148. (file-name (git-file-name name version))
  1149. (sha256
  1150. (base32
  1151. "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
  1152. (build-system gnu-build-system)
  1153. (arguments
  1154. `(#:tests? #f ; there are none
  1155. #:make-flags
  1156. (list (string-append "SHELL="
  1157. (assoc-ref %build-inputs "bash") "/bin/bash")
  1158. (string-append "KALDI_ROOT="
  1159. (assoc-ref %build-inputs "kaldi-src"))
  1160. (string-append "KALDILIBDIR="
  1161. (assoc-ref %build-inputs "kaldi") "/lib")
  1162. "KALDI_FLAVOR=dynamic")
  1163. #:phases
  1164. (modify-phases %standard-phases
  1165. (add-after 'unpack 'chdir
  1166. (lambda _ (chdir "src") #t))
  1167. (replace 'configure
  1168. (lambda* (#:key inputs #:allow-other-keys)
  1169. (let ((glib (assoc-ref inputs "glib")))
  1170. (setenv "CXXFLAGS" "-fPIC")
  1171. (setenv "CPLUS_INCLUDE_PATH"
  1172. (string-append glib "/include/glib-2.0:"
  1173. glib "/lib/glib-2.0/include:"
  1174. (assoc-ref inputs "gstreamer")
  1175. "/include/gstreamer-1.0")))
  1176. (substitute* "Makefile"
  1177. (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
  1178. (("\\$\\(error Cannot find") "#"))
  1179. #t))
  1180. (add-before 'build 'build-depend
  1181. (lambda* (#:key make-flags #:allow-other-keys)
  1182. (apply invoke "make" "depend" make-flags)))
  1183. (replace 'install
  1184. (lambda* (#:key outputs #:allow-other-keys)
  1185. (let* ((out (assoc-ref outputs "out"))
  1186. (lib (string-append out "/lib/gstreamer-1.0")))
  1187. (install-file "libgstkaldinnet2onlinedecoder.so" lib)
  1188. #t))))))
  1189. (inputs
  1190. `(("glib" ,glib)
  1191. ("gstreamer" ,gstreamer)
  1192. ("jansson" ,jansson)
  1193. ("openfst" ,openfst)
  1194. ("kaldi" ,kaldi)))
  1195. (native-inputs
  1196. `(("bash" ,bash)
  1197. ("glib:bin" ,glib "bin") ; glib-genmarshal
  1198. ("kaldi-src" ,(package-source kaldi))
  1199. ("pkg-config" ,pkg-config)))
  1200. (home-page "https://kaldi-asr.org/")
  1201. (synopsis "Gstreamer plugin for decoding speech")
  1202. (description "This package provides a GStreamer plugin that wraps
  1203. Kaldi's @code{SingleUtteranceNnet2Decoder}. It requires iVector-adapted DNN
  1204. acoustic models. The iVectors are adapted to the current audio stream
  1205. automatically.")
  1206. (license license:asl2.0))))
  1207. (define-public kaldi-gstreamer-server
  1208. (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
  1209. (revision "1"))
  1210. (package
  1211. (name "kaldi-gstreamer-server")
  1212. (version (git-version "0" revision commit))
  1213. (source (origin
  1214. (method git-fetch)
  1215. (uri (git-reference
  1216. (url "https://github.com/alumae/kaldi-gstreamer-server.git")
  1217. (commit commit)))
  1218. (file-name (git-file-name name version))
  1219. (sha256
  1220. (base32
  1221. "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
  1222. (build-system gnu-build-system)
  1223. (arguments
  1224. `(#:tests? #f ; there are no tests that can be run automatically
  1225. #:modules ((guix build utils)
  1226. (guix build gnu-build-system)
  1227. (srfi srfi-26))
  1228. #:phases
  1229. (modify-phases %standard-phases
  1230. (delete 'configure)
  1231. (replace 'build
  1232. (lambda* (#:key outputs #:allow-other-keys)
  1233. ;; Disable hash randomization to ensure the generated .pycs
  1234. ;; are reproducible.
  1235. (setenv "PYTHONHASHSEED" "0")
  1236. (with-directory-excursion "kaldigstserver"
  1237. (for-each (lambda (file)
  1238. (apply invoke
  1239. `("python"
  1240. "-m" "compileall"
  1241. "-f" ; force rebuild
  1242. ,file)))
  1243. (find-files "." "\\.py$")))
  1244. #t))
  1245. (replace 'install
  1246. (lambda* (#:key inputs outputs #:allow-other-keys)
  1247. (let* ((out (assoc-ref outputs "out"))
  1248. (bin (string-append out "/bin"))
  1249. (share (string-append out "/share/kaldi-gstreamer-server/")))
  1250. ;; Install Python files
  1251. (with-directory-excursion "kaldigstserver"
  1252. (for-each (cut install-file <> share)
  1253. (find-files "." ".*")))
  1254. ;; Install sample configuration files
  1255. (for-each (cut install-file <> share)
  1256. (find-files "." "\\.yaml"))
  1257. ;; Install executables
  1258. (mkdir-p bin)
  1259. (let* ((server (string-append bin "/kaldi-gst-server"))
  1260. (client (string-append bin "/kaldi-gst-client"))
  1261. (worker (string-append bin "/kaldi-gst-worker"))
  1262. (PYTHONPATH (getenv "PYTHONPATH"))
  1263. (GST_PLUGIN_PATH (string-append
  1264. (assoc-ref inputs "gst-kaldi-nnet2-online")
  1265. "/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
  1266. (wrap (lambda (wrapper what)
  1267. (with-output-to-file wrapper
  1268. (lambda _
  1269. (format #t
  1270. "#!~a
  1271. export PYTHONPATH=~a
  1272. export GST_PLUGIN_PATH=~a
  1273. exec ~a ~a/~a \"$@\"~%"
  1274. (which "bash") PYTHONPATH GST_PLUGIN_PATH
  1275. (which "python") share what)))
  1276. (chmod wrapper #o555))))
  1277. (for-each wrap
  1278. (list server client worker)
  1279. (list "master_server.py"
  1280. "client.py"
  1281. "worker.py")))
  1282. #t))))))
  1283. (inputs
  1284. `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
  1285. ("python2" ,python-2)
  1286. ("python2-futures" ,python2-futures)
  1287. ("python2-pygobject" ,python2-pygobject)
  1288. ("python2-pyyaml" ,python2-pyyaml)
  1289. ("python2-tornado" ,python2-tornado)
  1290. ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
  1291. (home-page "https://github.com/alumae/kaldi-gstreamer-server")
  1292. (synopsis "Real-time full-duplex speech recognition server")
  1293. (description "This is a real-time full-duplex speech recognition server,
  1294. based on the Kaldi toolkit and the GStreamer framework and implemented in
  1295. Python.")
  1296. (license license:bsd-2))))
  1297. ;; Note that Tensorflow includes a "third_party" directory, which seems to not
  1298. ;; only contain modified subsets of upstream library source code, but also
  1299. ;; adapter headers provided by Google (such as the fft.h header, which is not
  1300. ;; part of the upstream project code). The Tensorflow code includes headers
  1301. ;; from the "third_party" directory. It does not look like we can replace
  1302. ;; these headers with unmodified upstream files, so we keep them.
  1303. (define-public tensorflow
  1304. (package
  1305. (name "tensorflow")
  1306. (version "1.9.0")
  1307. (source
  1308. (origin
  1309. (method git-fetch)
  1310. (uri (git-reference
  1311. (url "https://github.com/tensorflow/tensorflow.git")
  1312. (commit (string-append "v" version))))
  1313. (file-name (string-append "tensorflow-" version "-checkout"))
  1314. (sha256
  1315. (base32
  1316. "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
  1317. (build-system cmake-build-system)
  1318. (arguments
  1319. `(#:tests? #f ; no "check" target
  1320. #:build-type "Release"
  1321. #:configure-flags
  1322. (let ((protobuf (assoc-ref %build-inputs "protobuf"))
  1323. (protobuf:native (assoc-ref %build-inputs "protobuf:native"))
  1324. (jsoncpp (assoc-ref %build-inputs "jsoncpp"))
  1325. (snappy (assoc-ref %build-inputs "snappy"))
  1326. (sqlite (assoc-ref %build-inputs "sqlite")))
  1327. (list
  1328. ;; Use protobuf from Guix
  1329. (string-append "-Dprotobuf_STATIC_LIBRARIES="
  1330. protobuf "/lib/libprotobuf.so")
  1331. (string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
  1332. protobuf:native "/bin/protoc")
  1333. ;; Use snappy from Guix
  1334. (string-append "-Dsnappy_STATIC_LIBRARIES="
  1335. snappy "/lib/libsnappy.so")
  1336. ;; Yes, this is not actually the include directory but a prefix...
  1337. (string-append "-Dsnappy_INCLUDE_DIR=" snappy)
  1338. ;; Use jsoncpp from Guix
  1339. (string-append "-Djsoncpp_STATIC_LIBRARIES="
  1340. jsoncpp "/lib/libjsoncpp.so")
  1341. ;; Yes, this is not actually the include directory but a prefix...
  1342. (string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
  1343. ;; Use sqlite from Guix
  1344. (string-append "-Dsqlite_STATIC_LIBRARIES="
  1345. sqlite "/lib/libsqlite.a")
  1346. ;; Use system libraries wherever possible. Currently, this
  1347. ;; only affects zlib.
  1348. "-Dsystemlib_ALL=ON"
  1349. "-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
  1350. "-Dtensorflow_BUILD_SHARED_LIB=ON"
  1351. "-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
  1352. "-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
  1353. "-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
  1354. #:make-flags
  1355. (list "CC=gcc")
  1356. #:modules ((ice-9 ftw)
  1357. (guix build utils)
  1358. (guix build cmake-build-system))
  1359. #:phases
  1360. (modify-phases %standard-phases
  1361. (add-after 'unpack 'set-source-file-times-to-1980
  1362. ;; At the end of the tf_python_build_pip_package target, a ZIP
  1363. ;; archive should be generated via bdist_wheel, but it fails with
  1364. ;; "ZIP does not support timestamps before 1980". Luckily,
  1365. ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
  1366. ;; 1980.
  1367. (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
  1368. ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
  1369. (add-after 'unpack 'python3.7-compatibility
  1370. (lambda _
  1371. (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
  1372. "tensorflow/python/lib/core/ndarray_tensor.cc"
  1373. "tensorflow/python/lib/core/py_func.cc")
  1374. (("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
  1375. (substitute* "tensorflow/c/eager/c_api.h"
  1376. (("unsigned char async")
  1377. "unsigned char is_async"))
  1378. ;; Remove dependency on tensorboard, a complicated but probably
  1379. ;; optional package.
  1380. (substitute* "tensorflow/tools/pip_package/setup.py"
  1381. ((".*'tensorboard >.*") ""))
  1382. #t))
  1383. (add-after 'python3.7-compatibility 'chdir
  1384. (lambda _ (chdir "tensorflow/contrib/cmake") #t))
  1385. (add-after 'chdir 'disable-downloads
  1386. (lambda* (#:key inputs #:allow-other-keys)
  1387. (substitute* (find-files "external" "\\.cmake$")
  1388. (("GIT_REPOSITORY.*") "")
  1389. (("GIT_TAG.*") "")
  1390. (("PREFIX ")
  1391. "DOWNLOAD_COMMAND \"\"\nPREFIX "))
  1392. ;; Use packages from Guix
  1393. (let ((grpc (assoc-ref inputs "grpc")))
  1394. (substitute* "CMakeLists.txt"
  1395. ;; Sqlite
  1396. (("include\\(sqlite\\)") "")
  1397. (("\\$\\{sqlite_STATIC_LIBRARIES\\}")
  1398. (string-append (assoc-ref inputs "sqlite")
  1399. "/lib/libsqlite3.so"))
  1400. (("sqlite_copy_headers_to_destination") "")
  1401. ;; PNG
  1402. (("include\\(png\\)") "")
  1403. (("\\$\\{png_STATIC_LIBRARIES\\}")
  1404. (string-append (assoc-ref inputs "libpng")
  1405. "/lib/libpng16.so"))
  1406. (("png_copy_headers_to_destination") "")
  1407. ;; JPEG
  1408. (("include\\(jpeg\\)") "")
  1409. (("\\$\\{jpeg_STATIC_LIBRARIES\\}")
  1410. (string-append (assoc-ref inputs "libjpeg")
  1411. "/lib/libjpeg.so"))
  1412. (("jpeg_copy_headers_to_destination") "")
  1413. ;; GIF
  1414. (("include\\(gif\\)") "")
  1415. (("\\$\\{gif_STATIC_LIBRARIES\\}")
  1416. (string-append (assoc-ref inputs "giflib")
  1417. "/lib/libgif.so"))
  1418. (("gif_copy_headers_to_destination") "")
  1419. ;; lmdb
  1420. (("include\\(lmdb\\)") "")
  1421. (("\\$\\{lmdb_STATIC_LIBRARIES\\}")
  1422. (string-append (assoc-ref inputs "lmdb")
  1423. "/lib/liblmdb.so"))
  1424. (("lmdb_copy_headers_to_destination") "")
  1425. ;; Protobuf
  1426. (("include\\(protobuf\\)") "")
  1427. (("protobuf_copy_headers_to_destination") "")
  1428. (("^ +protobuf") "")
  1429. ;; gRPC
  1430. (("include\\(grpc\\)")
  1431. "find_package(grpc REQUIRED NAMES gRPC)")
  1432. (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
  1433. ;; Eigen
  1434. (("include\\(eigen\\)")
  1435. (string-append "find_package(eigen REQUIRED NAMES Eigen3)
  1436. set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
  1437. (assoc-ref inputs "eigen") "/include/eigen3)"))
  1438. (("^ +eigen") "")
  1439. ;; snappy
  1440. (("include\\(snappy\\)")
  1441. "add_definitions(-DTF_USE_SNAPPY)")
  1442. (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
  1443. ;; jsoncpp
  1444. (("include\\(jsoncpp\\)") "")
  1445. (("^ +jsoncpp") ""))
  1446. (substitute* "tf_core_framework.cmake"
  1447. ((" grpc") "")
  1448. (("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
  1449. (which "grpc_cpp_plugin"))
  1450. ;; Link with gRPC libraries
  1451. (("add_library\\(tf_protos_cc.*" m)
  1452. (string-append m
  1453. (format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
  1454. ~a/lib/libgrpc++_unsecure.a \
  1455. ~a/lib/libgrpc_unsecure.a \
  1456. ~a/lib/libaddress_sorting.a \
  1457. ~a/lib/libgpr.a \
  1458. ~a//lib/libcares.so
  1459. )\n"
  1460. grpc grpc grpc grpc
  1461. (assoc-ref inputs "c-ares"))))))
  1462. (substitute* "tf_tools.cmake"
  1463. (("add_dependencies\\(\\$\\{proto_text.*") ""))
  1464. ;; Remove dependency on bundled grpc
  1465. (substitute* "tf_core_distributed_runtime.cmake"
  1466. (("tf_core_cpu grpc") "tf_core_cpu"))
  1467. ;; This directory is a dependency of many targets.
  1468. (mkdir-p "protobuf")
  1469. #t))
  1470. (add-after 'configure 'unpack-third-party-sources
  1471. (lambda* (#:key inputs #:allow-other-keys)
  1472. ;; This is needed to configure bundled packages properly.
  1473. (setenv "CONFIG_SHELL" (which "bash"))
  1474. (for-each
  1475. (lambda (name)
  1476. (let* ((what (assoc-ref inputs (string-append name "-src")))
  1477. (name* (string-map (lambda (c)
  1478. (if (char=? c #\-)
  1479. #\_ c)) name))
  1480. (where (string-append "../build/" name* "/src/" name*)))
  1481. (cond
  1482. ((string-suffix? ".zip" what)
  1483. (mkdir-p where)
  1484. (with-directory-excursion where
  1485. (invoke "unzip" what)))
  1486. ((string-suffix? ".tar.gz" what)
  1487. (mkdir-p where)
  1488. (invoke "tar" "xf" what
  1489. "-C" where "--strip-components=1"))
  1490. (else
  1491. (let ((parent (dirname where)))
  1492. (mkdir-p parent)
  1493. (with-directory-excursion parent
  1494. (when (file-exists? name*)
  1495. (delete-file-recursively name*))
  1496. (copy-recursively what name*)
  1497. (map make-file-writable
  1498. (find-files name* ".*"))))))))
  1499. (list "boringssl"
  1500. "cub"
  1501. "double-conversion"
  1502. "farmhash"
  1503. "fft2d"
  1504. "highwayhash"
  1505. "nsync"
  1506. "re2"))
  1507. (rename-file "../build/cub/src/cub/cub-1.8.0/"
  1508. "../build/cub/src/cub/cub/")
  1509. #t))
  1510. (add-after 'unpack 'fix-python-build
  1511. (lambda* (#:key inputs outputs #:allow-other-keys)
  1512. (mkdir-p "protobuf-src")
  1513. (invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
  1514. "-C" "protobuf-src" "--strip-components=1")
  1515. (mkdir-p "eigen-src")
  1516. (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
  1517. "-C" "eigen-src" "--strip-components=1")
  1518. (substitute* "tensorflow/contrib/cmake/tf_python.cmake"
  1519. ;; Ensure that all Python dependencies can be found at build time.
  1520. (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
  1521. (string-append m ":" (getenv "PYTHONPATH")))
  1522. ;; Take protobuf source files from our source package.
  1523. (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
  1524. (string-append (getcwd) "/protobuf-src/src/google")))
  1525. (substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
  1526. "tensorflow/contrib/cmake/tf_python.cmake")
  1527. ;; Take Eigen source files from our source package.
  1528. (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
  1529. (string-append (getcwd) "/eigen-src/"))
  1530. ;; Take Eigen headers from our own package.
  1531. (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
  1532. (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
  1533. ;; Correct the RUNPATH of ops libraries generated for Python.
  1534. ;; TODO: this doesn't work :(
  1535. ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
  1536. ;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
  1537. ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
  1538. ;; error: depends on 'libpywrap_tensorflow_internal.so', which
  1539. ;; cannot be found in RUNPATH ...
  1540. (substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
  1541. (("set_target_properties.*")
  1542. (string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
  1543. COMPILE_FLAGS ${target_compile_flags} \
  1544. INSTALL_RPATH_USE_LINK_PATH TRUE \
  1545. INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
  1546. #t))
  1547. (add-after 'build 'build-pip-package
  1548. (lambda* (#:key outputs #:allow-other-keys)
  1549. (setenv "LDFLAGS"
  1550. (string-append "-Wl,-rpath="
  1551. (assoc-ref outputs "out") "/lib"))
  1552. (invoke "make" "tf_python_build_pip_package")
  1553. #t))
  1554. (add-after 'build-pip-package 'install-python
  1555. (lambda* (#:key outputs #:allow-other-keys)
  1556. (let ((out (assoc-ref outputs "out"))
  1557. (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))))
  1558. (invoke "python" "-m" "pip" "install" wheel
  1559. (string-append "--prefix=" out))
  1560. ;; XXX: broken RUNPATH, see fix-python-build phase.
  1561. (delete-file
  1562. (string-append
  1563. out "/lib/python3.7/site-packages/tensorflow/contrib/"
  1564. "seq2seq/python/ops/lib_beam_search_ops.so"))
  1565. #t))))))
  1566. (native-inputs
  1567. `(("pkg-config" ,pkg-config)
  1568. ("protobuf:native" ,protobuf-3.6) ; protoc
  1569. ("protobuf:src" ,(package-source protobuf-3.6))
  1570. ("eigen:src" ,(package-source eigen-for-tensorflow))
  1571. ;; install_pip_packages.sh wants setuptools 39.1.0 specifically.
  1572. ("python-setuptools" ,python-setuptools-for-tensorflow)
  1573. ;; The commit hashes and URLs for third-party source code are taken
  1574. ;; from "tensorflow/workspace.bzl".
  1575. ("boringssl-src"
  1576. ,(let ((commit "ee7aa02")
  1577. (revision "1"))
  1578. (origin
  1579. (method git-fetch)
  1580. (uri (git-reference
  1581. (url "https://boringssl.googlesource.com/boringssl")
  1582. (commit commit)))
  1583. (file-name (string-append "boringssl-0-" revision
  1584. (string-take commit 7)
  1585. "-checkout"))
  1586. (sha256
  1587. (base32
  1588. "1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
  1589. ("cub-src"
  1590. ,(let ((version "1.8.0"))
  1591. (origin
  1592. (method url-fetch)
  1593. (uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
  1594. "cub/archive/" version ".zip"))
  1595. (file-name (string-append "cub-" version ".zip"))
  1596. (sha256
  1597. (base32
  1598. "1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
  1599. ("double-conversion-src"
  1600. ,(let ((commit "5664746")
  1601. (revision "1"))
  1602. (origin
  1603. (method git-fetch)
  1604. (uri (git-reference
  1605. (url "https://github.com/google/double-conversion.git")
  1606. (commit commit)))
  1607. (file-name
  1608. (git-file-name "double-conversion"
  1609. (string-append "0-" revision "."
  1610. (string-take commit 7))))
  1611. (sha256
  1612. (base32
  1613. "1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
  1614. ("farmhash-src"
  1615. ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
  1616. (origin
  1617. (method url-fetch)
  1618. (uri (string-append
  1619. "https://mirror.bazel.build/github.com/google/farmhash/archive/"
  1620. commit ".tar.gz"))
  1621. (file-name (string-append "farmhash-0-" (string-take commit 7)
  1622. ".tar.gz"))
  1623. (sha256
  1624. (base32
  1625. "185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
  1626. ;; The license notice on the home page at
  1627. ;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
  1628. ;; Copyright Takuya OOURA, 1996-2001
  1629. ;;
  1630. ;; You may use, copy, modify and distribute this code for any purpose
  1631. ;; (include commercial use) and without fee. Please refer to this
  1632. ;; package when you modify this code.
  1633. ;;
  1634. ;; We take the identical tarball from the Bazel mirror, because the URL
  1635. ;; at the home page is not versioned and might change.
  1636. ("fft2d-src"
  1637. ,(origin
  1638. (method url-fetch)
  1639. (uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
  1640. (file-name "fft2d.tar.gz")
  1641. (sha256
  1642. (base32
  1643. "15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
  1644. ("highwayhash-src"
  1645. ,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
  1646. (revision "1"))
  1647. (origin
  1648. (method git-fetch)
  1649. (uri (git-reference
  1650. (url "https://github.com/google/highwayhash.git")
  1651. (commit commit)))
  1652. (file-name (string-append "highwayhash-0-" revision
  1653. (string-take commit 7)
  1654. "-checkout"))
  1655. (sha256
  1656. (base32
  1657. "154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
  1658. ("nsync-src"
  1659. ,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
  1660. (revision "1"))
  1661. (origin
  1662. (method url-fetch)
  1663. (uri (string-append "https://mirror.bazel.build/"
  1664. "github.com/google/nsync/archive/"
  1665. version ".tar.gz"))
  1666. (file-name (string-append "nsync-0." revision
  1667. "-" (string-take version 7)
  1668. ".tar.gz"))
  1669. (sha256
  1670. (base32
  1671. "0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
  1672. ("re2-src"
  1673. ,(let ((commit "e7efc48")
  1674. (revision "1"))
  1675. (origin
  1676. (method git-fetch)
  1677. (uri (git-reference
  1678. (url "https://github.com/google/re2")
  1679. (commit commit)))
  1680. (file-name (string-append "re2-0-" revision
  1681. (string-take commit 7)
  1682. "-checkout"))
  1683. (sha256
  1684. (base32
  1685. "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
  1686. ("googletest" ,googletest)
  1687. ("swig" ,swig)
  1688. ("unzip" ,unzip)))
  1689. (propagated-inputs
  1690. `(("python-absl-py" ,python-absl-py)
  1691. ("python-astor" ,python-astor)
  1692. ("python-gast" ,python-gast)
  1693. ("python-grpcio" ,python-grpcio)
  1694. ("python-numpy" ,python-numpy)
  1695. ("python-protobuf" ,python-protobuf-3.6)
  1696. ("python-six" ,python-six)
  1697. ("python-termcolo" ,python-termcolor)
  1698. ("python-wheel" ,python-wheel)))
  1699. (inputs
  1700. `(("c-ares" ,c-ares)
  1701. ("eigen" ,eigen-for-tensorflow)
  1702. ("gemmlowp" ,gemmlowp-for-tensorflow)
  1703. ("lmdb" ,lmdb)
  1704. ("libjpeg" ,libjpeg)
  1705. ("libpng" ,libpng)
  1706. ("giflib" ,giflib)
  1707. ("grpc" ,grpc-1.16.1 "static")
  1708. ("grpc:bin" ,grpc-1.16.1)
  1709. ("jsoncpp" ,jsoncpp-for-tensorflow)
  1710. ("snappy" ,snappy)
  1711. ("sqlite" ,sqlite)
  1712. ("protobuf" ,protobuf-3.6)
  1713. ("python" ,python-wrapper)
  1714. ("zlib" ,zlib)))
  1715. (home-page "https://tensorflow.org")
  1716. (synopsis "Machine learning framework")
  1717. (description
  1718. "TensorFlow is a flexible platform for building and training machine
  1719. learning models. It provides a library for high performance numerical
  1720. computation and includes high level Python APIs, including both a sequential
  1721. API for beginners that allows users to build models quickly by plugging
  1722. together building blocks and a subclassing API with an imperative style for
  1723. advanced research.")
  1724. (license license:asl2.0)))
  1725. (define-public python-iml
  1726. (package
  1727. (name "python-iml")
  1728. (version "0.6.2")
  1729. (source
  1730. (origin
  1731. (method url-fetch)
  1732. (uri (pypi-uri "iml" version))
  1733. (sha256
  1734. (base32
  1735. "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
  1736. (build-system python-build-system)
  1737. (propagated-inputs
  1738. `(("ipython" ,python-ipython)
  1739. ("nose" ,python-nose)
  1740. ("numpy" ,python-numpy)
  1741. ("pandas" ,python-pandas)
  1742. ("scipy" ,python-scipy)))
  1743. (home-page "http://github.com/interpretable-ml/iml")
  1744. (synopsis "Interpretable Machine Learning (iML) package")
  1745. (description "Interpretable ML (iML) is a set of data type objects,
  1746. visualizations, and interfaces that can be used by any method designed to
  1747. explain the predictions of machine learning models (or really the output of
  1748. any function). It currently contains the interface and IO code from the Shap
  1749. project, and it will potentially also do the same for the Lime project.")
  1750. (license license:expat)))
  1751. (define-public python-keras-applications
  1752. (package
  1753. (name "python-keras-applications")
  1754. (version "1.0.8")
  1755. (source
  1756. (origin
  1757. (method url-fetch)
  1758. (uri (pypi-uri "Keras_Applications" version))
  1759. (sha256
  1760. (base32
  1761. "1rcz31ca4axa6kzhjx4lwqxbg4wvlljkj8qj9a7p9sfd5fhzjyam"))))
  1762. (build-system python-build-system)
  1763. ;; The tests require Keras, but this package is needed to build Keras.
  1764. (arguments '(#:tests? #f))
  1765. (propagated-inputs
  1766. `(("python-h5py" ,python-h5py)
  1767. ("python-numpy" ,python-numpy)))
  1768. (native-inputs
  1769. `(("python-pytest" ,python-pytest)
  1770. ("python-pytest-cov" ,python-pytest-cov)
  1771. ("python-pytest-pep8" ,python-pytest-pep8)
  1772. ("python-pytest-xdist" ,python-pytest-xdist)))
  1773. (home-page "https://github.com/keras-team/keras-applications")
  1774. (synopsis "Reference implementations of popular deep learning models")
  1775. (description
  1776. "This package provides reference implementations of popular deep learning
  1777. models for use with the Keras deep learning framework.")
  1778. (license license:expat)))
  1779. (define-public python-keras-preprocessing
  1780. (package
  1781. (name "python-keras-preprocessing")
  1782. (version "1.1.0")
  1783. (source
  1784. (origin
  1785. (method url-fetch)
  1786. (uri (pypi-uri "Keras_Preprocessing" version))
  1787. (sha256
  1788. (base32
  1789. "1r98nm4k1svsqjyaqkfk23i31bl1kcfcyp7094yyj3c43phfp3as"))))
  1790. (build-system python-build-system)
  1791. (propagated-inputs
  1792. `(("python-numpy" ,python-numpy)
  1793. ("python-six" ,python-six)))
  1794. (native-inputs
  1795. `(("python-pandas" ,python-pandas)
  1796. ("python-pillow" ,python-pillow)
  1797. ("python-pytest" ,python-pytest)
  1798. ("python-pytest-cov" ,python-pytest-cov)
  1799. ("python-pytest-xdist" ,python-pytest-xdist)
  1800. ("tensorflow" ,tensorflow)))
  1801. (home-page "https://github.com/keras-team/keras-preprocessing/")
  1802. (synopsis "Data preprocessing and augmentation for deep learning models")
  1803. (description
  1804. "Keras Preprocessing is the data preprocessing and data augmentation
  1805. module of the Keras deep learning library. It provides utilities for working
  1806. with image data, text data, and sequence data.")
  1807. (license license:expat)))
  1808. (define-public python-keras
  1809. (package
  1810. (name "python-keras")
  1811. (version "2.2.4")
  1812. (source
  1813. (origin
  1814. (method url-fetch)
  1815. (uri (pypi-uri "Keras" version))
  1816. (patches (search-patches "python-keras-integration-test.patch"))
  1817. (sha256
  1818. (base32
  1819. "1j8bsqzh49vjdxy6l1k4iwax5vpjzniynyd041xjavdzvfii1dlh"))))
  1820. (build-system python-build-system)
  1821. (arguments
  1822. `(#:phases
  1823. (modify-phases %standard-phases
  1824. (add-after 'unpack 'remove-tests-for-unavailable-features
  1825. (lambda _
  1826. (delete-file "keras/backend/theano_backend.py")
  1827. (delete-file "keras/backend/cntk_backend.py")
  1828. (delete-file "tests/keras/backend/backend_test.py")
  1829. ;; FIXME: This doesn't work because Tensorflow is missing the
  1830. ;; coder ops library.
  1831. (delete-file "tests/keras/test_callbacks.py")
  1832. #t))
  1833. (replace 'check
  1834. (lambda _
  1835. ;; These tests attempt to download data files from the internet.
  1836. (delete-file "tests/integration_tests/test_datasets.py")
  1837. (delete-file "tests/integration_tests/imagenet_utils_test.py")
  1838. (setenv "PYTHONPATH"
  1839. (string-append (getcwd) "/build/lib:"
  1840. (getenv "PYTHONPATH")))
  1841. (invoke "py.test" "-v"
  1842. "-p" "no:cacheprovider"
  1843. "--ignore" "keras/utils"))))))
  1844. (propagated-inputs
  1845. `(("python-h5py" ,python-h5py)
  1846. ("python-keras-applications" ,python-keras-applications)
  1847. ("python-keras-preprocessing" ,python-keras-preprocessing)
  1848. ("python-numpy" ,python-numpy)
  1849. ("python-pydot" ,python-pydot)
  1850. ("python-pyyaml" ,python-pyyaml)
  1851. ("python-scipy" ,python-scipy)
  1852. ("python-six" ,python-six)
  1853. ("tensorflow" ,tensorflow)
  1854. ("graphviz" ,graphviz)))
  1855. (native-inputs
  1856. `(("python-pandas" ,python-pandas)
  1857. ("python-pytest" ,python-pytest)
  1858. ("python-pytest-cov" ,python-pytest-cov)
  1859. ("python-pytest-pep8" ,python-pytest-pep8)
  1860. ("python-pytest-timeout" ,python-pytest-timeout)
  1861. ("python-pytest-xdist" ,python-pytest-xdist)
  1862. ("python-sphinx" ,python-sphinx)
  1863. ("python-requests" ,python-requests)))
  1864. (home-page "https://github.com/keras-team/keras")
  1865. (synopsis "High-level deep learning framework")
  1866. (description "Keras is a high-level neural networks API, written in Python
  1867. and capable of running on top of TensorFlow. It was developed with a focus on
  1868. enabling fast experimentation. Use Keras if you need a deep learning library
  1869. that:
  1870. @itemize
  1871. @item Allows for easy and fast prototyping (through user friendliness,
  1872. modularity, and extensibility).
  1873. @item Supports both convolutional networks and recurrent networks, as well as
  1874. combinations of the two.
  1875. @item Runs seamlessly on CPU and GPU.
  1876. @end itemize\n")
  1877. (license license:expat)))
  1878. (define-public sbcl-cl-libsvm-format
  1879. (let ((commit "3300f84fd8d9f5beafc114f543f9d83417c742fb")
  1880. (revision "0"))
  1881. (package
  1882. (name "sbcl-cl-libsvm-format")
  1883. (version (git-version "0.1.0" revision commit))
  1884. (source
  1885. (origin
  1886. (method git-fetch)
  1887. (uri (git-reference
  1888. (url "https://github.com/masatoi/cl-libsvm-format.git")
  1889. (commit commit)))
  1890. (file-name (git-file-name name version))
  1891. (sha256
  1892. (base32
  1893. "0284aj84xszhkhlivaigf9qj855fxad3mzmv3zfr0qzb5k0nzwrg"))))
  1894. (build-system asdf-build-system/sbcl)
  1895. (native-inputs
  1896. `(("prove" ,sbcl-prove)
  1897. ("prove-asdf" ,sbcl-prove-asdf)))
  1898. (inputs
  1899. `(("alexandria" ,sbcl-alexandria)))
  1900. (synopsis "LibSVM data format reader for Common Lisp")
  1901. (description
  1902. "This Common Lisp library provides a fast reader for data in LibSVM
  1903. format.")
  1904. (home-page "https://github.com/masatoi/cl-libsvm-format")
  1905. (license license:expat))))
  1906. (define-public cl-libsvm-format
  1907. (sbcl-package->cl-source-package sbcl-cl-libsvm-format))
  1908. (define-public ecl-cl-libsvm-format
  1909. (sbcl-package->ecl-package sbcl-cl-libsvm-format))
  1910. (define-public sbcl-cl-online-learning
  1911. (let ((commit "fc7a34f4f161cd1c7dd747d2ed8f698947781423")
  1912. (revision "0"))
  1913. (package
  1914. (name "sbcl-cl-online-learning")
  1915. (version (git-version "0.5" revision commit))
  1916. (source
  1917. (origin
  1918. (method git-fetch)
  1919. (uri (git-reference
  1920. (url "https://github.com/masatoi/cl-online-learning.git")
  1921. (commit commit)))
  1922. (file-name (git-file-name name version))
  1923. (sha256
  1924. (base32
  1925. "14x95rlg80ay5hv645ki57pqvy12v28hz4k1w0f6bsfi2rmpxchq"))))
  1926. (build-system asdf-build-system/sbcl)
  1927. (native-inputs
  1928. `(("prove" ,sbcl-prove)
  1929. ("prove-asdf" ,sbcl-prove-asdf)))
  1930. (inputs
  1931. `(("cl-libsvm-format" ,sbcl-cl-libsvm-format)
  1932. ("cl-store" ,sbcl-cl-store)))
  1933. (arguments
  1934. `(;; FIXME: Tests pass but then the check phase crashes
  1935. #:tests? #f))
  1936. (synopsis "Online Machine Learning for Common Lisp")
  1937. (description
  1938. "This library contains a collection of machine learning algorithms for
  1939. online linear classification written in Common Lisp.")
  1940. (home-page "https://github.com/masatoi/cl-online-learning")
  1941. (license license:expat))))
  1942. (define-public cl-online-learning
  1943. (sbcl-package->cl-source-package sbcl-cl-online-learning))
  1944. (define-public ecl-cl-online-learning
  1945. (sbcl-package->ecl-package sbcl-cl-online-learning))
  1946. (define-public sbcl-cl-random-forest
  1947. (let ((commit "85fbdd4596d40e824f70f1b7cf239cf544e49d51")
  1948. (revision "0"))
  1949. (package
  1950. (name "sbcl-cl-random-forest")
  1951. (version (git-version "0.1" revision commit))
  1952. (source
  1953. (origin
  1954. (method git-fetch)
  1955. (uri (git-reference
  1956. (url "https://github.com/masatoi/cl-random-forest.git")
  1957. (commit commit)))
  1958. (file-name (git-file-name name version))
  1959. (sha256
  1960. (base32
  1961. "097xv60i1ndz68sg9p4pc7c5gvyp9i1xgw966b4wwfq3x6hbz421"))))
  1962. (build-system asdf-build-system/sbcl)
  1963. (native-inputs
  1964. `(("prove" ,sbcl-prove)
  1965. ("prove-asdf" ,sbcl-prove-asdf)
  1966. ("trivial-garbage" ,sbcl-trivial-garbage)))
  1967. (inputs
  1968. `(("alexandria" ,sbcl-alexandria)
  1969. ("cl-libsvm-format" ,sbcl-cl-libsvm-format)
  1970. ("cl-online-learning" ,sbcl-cl-online-learning)
  1971. ("lparallel" ,sbcl-lparallel)))
  1972. (arguments
  1973. `(;; The tests download data from the Internet
  1974. #:tests? #f
  1975. #:phases
  1976. (modify-phases %standard-phases
  1977. (add-after 'unpack 'add-sb-cltl2-dependency
  1978. (lambda _
  1979. ;; sb-cltl2 is required by lparallel when using sbcl, but it is
  1980. ;; not loaded automatically.
  1981. (substitute* "cl-random-forest.asd"
  1982. (("\\(in-package :cl-user\\)")
  1983. "(in-package :cl-user) #+sbcl (require :sb-cltl2)"))
  1984. #t)))))
  1985. (synopsis "Random Forest and Global Refinement for Common Lisp")
  1986. (description
  1987. "CL-random-forest is an implementation of Random Forest for multiclass
  1988. classification and univariate regression written in Common Lisp. It also
  1989. includes an implementation of Global Refinement of Random Forest.")
  1990. (home-page "https://github.com/masatoi/cl-random-forest")
  1991. (license license:expat))))
  1992. (define-public cl-random-forest
  1993. (sbcl-package->cl-source-package sbcl-cl-random-forest))
  1994. (define-public ecl-cl-random-forest
  1995. (sbcl-package->ecl-package sbcl-cl-random-forest))
  1996. (define-public gloo
  1997. (let ((version "0.0.0") ; no proper version tag
  1998. (commit "ca528e32fea9ca8f2b16053cff17160290fc84ce")
  1999. (revision "0"))
  2000. (package
  2001. (name "gloo")
  2002. (version (git-version version revision commit))
  2003. (source
  2004. (origin
  2005. (method git-fetch)
  2006. (uri (git-reference
  2007. (url "https://github.com/facebookincubator/gloo.git")
  2008. (commit commit)))
  2009. (file-name (git-file-name name version))
  2010. (sha256
  2011. (base32
  2012. "1q9f80zy75f6njrzrqkmhc0g3qxs4gskr7ns2jdqanxa2ww7a99w"))))
  2013. (build-system cmake-build-system)
  2014. (native-inputs
  2015. `(("googletest" ,googletest)))
  2016. (arguments
  2017. `(#:configure-flags '("-DBUILD_TEST=1")
  2018. #:phases
  2019. (modify-phases %standard-phases
  2020. (replace 'check
  2021. (lambda _
  2022. (invoke "make" "gloo_test")
  2023. #t)))))
  2024. (synopsis "Collective communications library")
  2025. (description
  2026. "Gloo is a collective communications library. It comes with a
  2027. number of collective algorithms useful for machine learning applications.
  2028. These include a barrier, broadcast, and allreduce.")
  2029. (home-page "https://github.com/facebookincubator/gloo")
  2030. (license license:bsd-3))))
  2031. (define-public python-umap-learn
  2032. (package
  2033. (name "python-umap-learn")
  2034. (version "0.3.10")
  2035. (source
  2036. (origin
  2037. (method url-fetch)
  2038. (uri (pypi-uri "umap-learn" version))
  2039. (sha256
  2040. (base32
  2041. "02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1"))))
  2042. (build-system python-build-system)
  2043. (native-inputs
  2044. `(("python-joblib" ,python-joblib)
  2045. ("python-nose" ,python-nose)))
  2046. (propagated-inputs
  2047. `(("python-numba" ,python-numba)
  2048. ("python-numpy" ,python-numpy)
  2049. ("python-scikit-learn" ,python-scikit-learn)
  2050. ("python-scipy" ,python-scipy)))
  2051. (home-page "https://github.com/lmcinnes/umap")
  2052. (synopsis
  2053. "Uniform Manifold Approximation and Projection")
  2054. (description
  2055. "Uniform Manifold Approximation and Projection is a dimension reduction
  2056. technique that can be used for visualisation similarly to t-SNE, but also for
  2057. general non-linear dimension reduction.")
  2058. (license license:bsd-3)))