From cda20190bccf9bd55c264b1084eab8b6499c15cc Mon Sep 17 00:00:00 2001 From: Navid Afkhami Date: Sat, 2 Sep 2023 21:56:44 +0000 Subject: gnu: Add r-interactivedisplay. * gnu/packages/bioconductor.scm (r-interactivedisplay): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 85 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c913232680..e5e9c80291 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -51,6 +51,7 @@ #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages java) + #:use-module (gnu packages javascript) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -7734,6 +7735,90 @@ of other R packages who wish to make use of HTSlib.") microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplay + (package + (name "r-interactivedisplay") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplay" version)) + (sha256 + (base32 + "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl")) + (snippet + '(for-each delete-file + '("inst/www/js/jquery.js" + "inst/www/js/jquery.min.js" + "inst/www/js/jquery.dataTables.min.js"))))) + (properties `((upstream-name . "interactiveDisplay"))) + (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery-1.8.2") + "inst/www/js/jquery.js") + (,(assoc-ref inputs "js-jquery-1.9.1") + "inst/www/js/jquery.min.js") + (,(search-input-file inputs + "/share/javascript/jquery.dataTables.min.js") + "inst/www/js/jquery.dataTables.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets)))))))) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-biocmanager + r-category + r-dt + r-ggplot2 + r-gridsvg + r-interactivedisplaybase + r-plyr + r-rcolorbrewer + r-reshape2 + r-shiny + r-zlibbioc + r-xml)) + (native-inputs + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-datatables" ,js-datatables) + ("js-jquery-1.8.2" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.8.2.js") + (sha256 + (base32 + "0nikk2clbnyi02k0brvhbd8m43lfh4l1zrya35jya9sy6wb9b9ng")))) + ("js-jquery-1.9.1" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.9.1.js") + (sha256 + (base32 + "0h4dk67yc9d0kadqxb6b33585f3x3559p6qmp70l00qwq030vn3v")))))) + (home-page "https://bioconductor.org/packages/interactiveDisplay") + (synopsis "Package for Shiny web displays of Bioconductor objects") + (description + "This package offers interactive Shiny displays for Bioconductor +objects. In addition, this package empowers users to develop engaging +visualizations and interfaces for working with Bioconductor data.") + (license license:artistic2.0))) + (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") -- cgit v1.2.3 urses.scm, gnu/packages/networking.scm, gnu/packages/nickle.scm, gnu/packages/openbox.scm, gnu/packages/pdf.scm, gnu/packages/perl-check.scm, gnu/packages/perl.scm, gnu/packages/python-compression.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/python-xyz.scm, gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/ruby.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/ssh.scm, gnu/packages/suckless.scm, gnu/packages/tbb.scm, gnu/packages/telephony.scm, gnu/packages/text-editors.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/vim.scm, gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm, gnu/packages/xfce.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm, gnu/services/certbot.scm, gnu/services/desktop.scm, gnu/services/version-control.scm, gnu/services/web.scm, guix/import/hackage.scm, guix/licenses.scm: Likewise. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> nikita 2020-05-10gnu: emacs: Remove unneeded import....This is a followup to ef0cb0dd1d05efcfd3dba082a126eb75e8443485. Suggested by Jack Hill <jackhill@jackhill.us>. * gnu/packages/emacs.scm: Remove unneeded (ice-9 match) import. Ludovic Courtès 2020-05-06Merge branch 'master' into core-updatesMarius Bakke 2020-05-05gnu: emacs-next: Upgrade to 27.0.91....* gnu/packages/emacs.scm (emacs-next): Upgrade to 27.0.91. [inputs]: Remove imagemagick. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Jack Hill 2020-04-30Merge branch 'master' into core-updates... Conflicts: gnu/local.mk gnu/packages/backup.scm gnu/packages/emacs-xyz.scm gnu/packages/guile.scm gnu/packages/lisp.scm gnu/packages/openldap.scm gnu/packages/package-management.scm gnu/packages/web.scm gnu/packages/xorg.scm Marius Bakke 2020-04-28gnu: Add emacs-wide-int....* gnu/packages/emacs.scm (emacs-wide-int): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Diego Nicola Barbato 2020-03-30Merge branch 'master' into core-updates... Conflicts: gnu/packages/admin.scm gnu/packages/commencement.scm gnu/packages/guile.scm gnu/packages/linux.scm gnu/packages/package-management.scm gnu/packages/pulseaudio.scm gnu/packages/web.scm Marius Bakke 2020-03-29gnu: emacs-next: Add harfbuzz (text shaping engine) to inputs....* gnu/packages/emacs.scm (emacs-next)[inputs]: Add harfbuzz. [arguments]: Enable harfbuzz in #:configure-flags. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Alexey Abramov 2020-03-28Update email address and Savannah handle for Amin Bandali....* .mailmap, gnu/local.mk, gnu/packages/emacs-xyz.scm, gnu/packages/emacs.scm, gnu/packages/fonts.scm, gnu/packages/fpga.scm, gnu/packages/lean.scm, gnu/packages/maths.scm, gnu/packages/pulseaudio.scm: Update my email address. * build-aux/git-authenticate.scm: Update my Savannah handle. Amin Bandali 2020-03-27gnu: emacs: Fix format strings for compatibility with Guile 3....* gnu/packages/emacs.scm (emacs)[arguments]: In the 'patch-program-file-names' and 'install-site-start' phases, specify port in the calls to FORMAT. Marius Bakke 2020-03-27Merge branch 'master' into core-updates... Conflicts: gnu/packages/icu4c.scm gnu/packages/man.scm gnu/packages/python-xyz.scm guix/scripts/environment.scm guix/scripts/pack.scm guix/scripts/package.scm guix/scripts/pull.scm guix/store.scm Marius Bakke 2020-03-22gnu: emacs: Patch references to /bin/sh....When attempting to run ert-runner in the build side environment where /bin/sh doesn't exist as part of the emacs-elpy test suite, Emacs was throwing the error "Searching for program: No such file or directory, /bin/sh". This is because the default shell when SHELL is not set was "/bin/sh", as can be seen in callproc.c: sh = getenv ("SHELL"); Vshell_file_name = build_string (sh ? sh : "/bin/sh"); Thus, patch the occurrences of "/bin/sh" in the source files of Emacs to refer to their correct store location. * gnu/packages/emacs.scm (emacs)[phases]{patch-program-file-names}: Add phase. Maxim Cournoyer 2020-03-22gnu: emacs-minimal: Install the custom site-start file....This makes the EMACS-MINIMAL package more generally useful, by adding support to load autoload definitions. Note that this doesn't negatively impact the performance of the emacs-build-system, because at that time the --quick option is used, which disables loading site-start.el (which is the one calling GUIX-EMACS-AUTOLOAD-PACKAGES). * gnu/packages/emacs.scm (emacs-minimal)[phases]: Do not delete the 'install-site-start phase. [inputs]: Add the emacs/guix-emacs.el auxiliary file. Maxim Cournoyer 2020-03-22gnu: emacs: Re-indent....* gnu/packages/emacs.scm (emacs): Fix indentation. Maxim Cournoyer 2020-03-22gnu: emacs: Byte compile the site-lisp directory, without coupling....This re-instates what the previously reverted commit did, but without adding a dependency on the (guix build emacs-utils) module. * gnu/packages/emacs.scm (emacs)[phases]{install-site-start}: Define a EMACS-BYTE-COMPILE-DIRECTORY procedure, and use it. Maxim Cournoyer 2020-03-22Revert "gnu: emacs: Byte compile the site-lisp directory."...This reverts commit 4714d0fc1a96eb6d421b64b0b585fe8043dcd07b. Rational: Having to rebuild Emacs every time (guix build emacs-utils) changes is not great. Maxim Cournoyer 2020-03-04Merge branch 'master' into core-updatesMarius Bakke 2020-02-27gnu: emacs: Fix comment....* gnu/packages/emacs.scm (emacs): Fix comment. Maxim Cournoyer 2020-02-27gnu: emacs: Byte compile the site-lisp directory....* gnu/packages/emacs.scm (emacs): Use the (gnu build emacs-utils) module. Byte compile the site-lisp directory as part of the 'install-site-start' phase. (emacs-minimal, emacs-xwidgets, emacs-no-x, emacs-no-x-toolkit): Reset modules to those of the gnu-build-system. Maxim Cournoyer 2020-01-22gnu: Replace uses of 'libjpeg' with 'libjpeg-turbo'....* gnu/packages/abiword.scm (abiword)[inputs]: Change from LIBJPEG to LIBJPEG-TURBO. * gnu/packages/admin.scm (testdisk)[inputs]: Likewise. * gnu/packages/algebra.scm (giac)[inputs]: Likewise. * gnu/packages/animation.scm (synfig)[inputs]: Likewise. * gnu/packages/astronomy.scm (gnuastro, celestia)[inputs]: Likewise. * gnu/packages/cdrom.scm (dvdstyler)[inputs]: Likewise. * gnu/packages/cran.scm (r-jpeg, r-tiff, r-readbitmap)[inputs]: Likewise. * gnu/packages/cups.scm (cups-filters, hplip)[inputs]: Likewise. * gnu/packages/display-managers.scm (slim)[inputs]: Likewise. * gnu/packages/ebook.scm (fbreader)[inputs]: Likewise. * gnu/packages/emacs.scm (emacs)[inputs]: Likewise. * gnu/packages/enlightenment.scm (efl)[propagated-inputs]: Likewise. * gnu/packages/fltk.scm (fltk, ntk)[inputs]: Likewise. * gnu/packages/fontutils.scm (fontforge)[inputs]: Likewise. * gnu/packages/freedesktop.scm (weston)[inputs]: Likewise. * gnu/packages/game-development.scm (sfml, allegro, aseprite, python-pygame, eureka, ioquake3)[inputs]: Likewise. * gnu/packages/games.scm (adanaxisgpl, freedroidrpg, irrlicht, minetest, fizmo, supertuxkart, gzdoom, xmoto, xonotic)[inputs]: Likewise. * gnu/packages/gd.scm (gd, perl-gd)[inputs]: Likewise. * gnu/packages/ghostscript.scm (lcms)[inputs]: Likewise. (ghostscript)[inputs, native-inputs]: Likewise. * gnu/packages/gimp.scm (gegl, gimp)[inputs]: Likewise. * gnu/packages/gnome.scm (libgnomeui, eog, tracker-miners, gthumb)[inputs]: Likewise. * gnu/packages/gnunet.scm (libextractor)[inputs]: Likewise. * gnu/packages/gnustep.scm (windowmaker)[inputs]: Likewise. * gnu/packages/graphics.scm (blender, blender-2.79, openimageio, openscenegraph, openscenegraph-3.4, povray, fgallery)[inputs]: Likewise. * gnu/packages/graphviz.scm (graphviz)[inputs]: Likewise. * gnu/packages/gstreamer.scm (gst-plugins-good)[inputs]: Likewise. * gnu/packages/gtk.scm (gdk-pixbuf)[inputs]: Likewise. * gnu/packages/image-processing.scm (dcmtk, mia, vtk, opencv, vips, nip2, vxl, insight-toolkit)[inputs]: Likewise. * gnu/packages/image-viewers.scm (gpicview, luminance-hdr)[inputs]: Likewise. * gnu/packages/image.scm (jpegoptim, libtiff, leptonica, imlib2, freeimage, vigra, libwebp, libmng, jasper, steghide, jp2a)[inputs]: Likewise. * gnu/packages/imagemagick.scm (imagemagick, graphicsmagick)[inputs]: Likewise. * gnu/packages/java.scm (icedtea-6, icedtea-7, openjdk9, openjdk11, openjdk12)[inputs]: Likewise. * gnu/packages/kde-frameworks.scm (khtml)[inputs]: Likewise. * gnu/packages/kodi.scm (kodi)[inputs]: Likewise. * gnu/packages/machine-learning.scm (dlib, tensorflow)[inputs]: Likewise. * gnu/packages/mate.scm (atril, eom)[inputs]: Likewise. * gnu/packages/maths.scm (hdf4, hdf-java, hdf-eos2, netcdf)[inputs]: Likewise. * gnu/packages/netpbm.scm (netpbm)[inputs]: Likewise. * gnu/packages/pdf.scm (zathura-pdf-mupdf, podofo, mupdf, fbida)[inputs]: Likewise. * gnu/packages/photo.scm (libraw, libpano13, enblend-enfuse, darktable, hugin, rawtherapee)[inputs]: Likewise. * gnu/packages/prolog.scm (swi-prolog)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-hdf4, python-pillow)[inputs]: Likewise. * gnu/packages/qt.scm (qtbase, qtwebkit)[inputs]: Likewise. * gnu/packages/rdesktop.scm (freerdp)[inputs]: Likewise. * gnu/packages/scanner.scm (sane-backends, xsane)[inputs]: Likewise. * gnu/packages/scheme.scm (racket)[inputs]: Likewise. * gnu/packages/scribus.scm (scribus)[inputs]: Likewise. * gnu/packages/sdl.scm (sdl-image)[propagated-inputs]: Likewise. (guile-sdl)[native-inputs]: Likewise. * gnu/packages/spice.scm (spice-gtk)[inputs]: Likewise. * gnu/packages/statistics.scm (r-with-tests)[inputs]: Likewise. * gnu/packages/tcl.scm (perl-tk)[inputs]: Likewise. * gnu/packages/upnp.scm (readymedia)[inputs]: Likewise. * gnu/packages/video.scm (mplayer, mpv, v4l-utils, motion)[inputs]: Likewise. * gnu/packages/web-browsers.scm (dillo, links)[inputs]: Likewise. * gnu/packages/web.scm (netsurf)[inputs]: Likewise. * gnu/packages/webkit.scm (webkitgtk)[inputs]: Likewise. * gnu/packages/wine.scm (wine)[inputs]: Likewise. * gnu/packages/wv.scm (wv)[inputs]: Likewise. * gnu/packages/wxwidgets.scm (wxwidgets, wxwidgets-2)[inputs]: Likewise. * gnu/packages/xdisorg.scm (xscreensaver)[inputs]: Likewise. * gnu/packages/xfce.scm (tumbler)[inputs]: Likewise. * gnu/packages/xfig.scm (xfig, transfig)[inputs]: Likewise. * gnu/packages/xorg.scm (xpra)[inputs]: Likewise. Marius Bakke 2020-01-17Update email address for Amin Bandali....* .mailmap: Add name and email addresses for Amin Bandali. * gnu/local.mk, gnu/packages/emacs-xyz.scm, gnu/packages/emacs.scm, gnu/packages/fpga.scm, gnu/packages/lean.scm, gnu/packages/maths.scm: Update email address for Amin Bandali. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr> Amin Bandali 2019-12-23gnu: Add emacs-next....Add `emacs-next' for building latest Emacs from git. * gnu/packages/emacs.scm (emacs-next): New variable. (emacs): make the autoload deletion snippet not fail when eshell/esh-groups.el does not exist. This enables reuse of the entire snippet field of `emacs' for `emacs-next'. * gnu/packages/patches/emacs27-exec-path.patch: New file. * gnu/local.mk (dist_patch_DATA): Add the above patch file to it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Amin Bandali 2019-12-09gnu: emacs: Delete the subdirs.el file under the site-lisp directory....This fixes bug #38533 (see: https://bugs.gnu.org/38533). * gnu/packages/emacs.scm (emacs)[phases]{install-site-start}: Delete the subdirs.el file. Reported-by: Diego Nicola Barbato <dnbarbato@posteo.de> Maxim Cournoyer 2019-12-07gnu: emacs: Reorder EMACSLOADPATH search path specification....Move Guix profiles' site-lisp before Emacs' own in the search path specification, so that user installed packages can override Emacs' builtin versions. Fixes issue #38399 (see: https://bugs.gnu.org/38399). Reported-by: Diego Nicola Barbato <dnbarbato@posteo.de> * gnu/packages/emacs.scm (emacs): Move the Emacs builtin library directory suffix to the end of the search path. Maxim Cournoyer