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rstudio.scm
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;;;
;;; Copyright © 2019, 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This program is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; This program is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with this program. If not, see <http://www.gnu.org/licenses/>.
;; RStudio server and its dependencies. Only the first level of dependencies is
;; built from source right now. Also RStudio itself bundles a lot of external
;; libraries, some with custom modifications.
;;
;; An older version is available at
;; https://github.com/BIMSBbioinfo/guix-bimsb/blob/master/bimsb/packages/staging.scm
(define-module (guix-science packages rstudio)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system copy)
#:use-module (guix build-system ant)
#:use-module (guix build-system node)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages databases)
#:use-module (gnu packages file)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages node)
#:use-module (gnu packages qt)
#:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (guix-science packages rstudio-node))
(define-public mathjax
(package
(name "mathjax")
(version "2.7.9")
( source (origin
(method url-fetch)
(uri (string-append "https://github.com/mathjax/MathJax/archive/" version ".tar.gz"))
(sha256
(base32
"1pv51xiy31pbd3jhli2rrda07s9cl1rxa2lizzr4983xr1wp45n9"))))
(build-system copy-build-system)
(arguments
'(#:install-plan
'(("." "."))))
(synopsis "JavaScript display engine for mathematics")
(description
"MathJax is an open-source JavaScript display engine for LaTeX, MathML,
and AsciiMath notation that works in all modern browsers, with built-in support
for assistive technology like screen readers.")
(home-page "https://www.mathjax.org/")
(license license:asl2.0)))
(define-public js-panmirror
;; This is the latest commit of the branch mentioned in RStudio’s
;; dependencies/common/install-panmirror.
(let ((commit "01345470a8f80becb1e128be24f59d2c34fb3a85")
(revision "1"))
(package
(name "js-panmirror")
;; No releases, no versions, no tags.
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/quarto-dev/quarto.git")
(commit commit)))
(file-name (git-file-name "js-panmirror" version))
(sha256
(base32
"1ngg95lh4n6yri3p4v2qps3vglnwcp054a54336rps16yi7814rb"))
(patches (search-patches "js-panmirror-no-pinyin.patch"))))
(build-system node-build-system)
(arguments
(list
#:node node-lts
#:imported-modules `(,@%node-build-system-modules
(guix build union))
#:modules '((guix build node-build-system)
(guix build union)
(guix build utils)
(ice-9 ftw))
#:tests? #false
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "apps/panmirror")
;; There is a lot of duplication among the dependencies.
;; esbuild will inline each duplicate and so there will
;; be multiple instances of e.g. prosemirror-model
;; resulting in all sorts of runtime problems since
;; identical definitions don't share state. The ugly
;; solution is to copy all node_modules from NODE_PATH
;; and manually hoist nested dependencies.
(let ((local (string-append (getcwd) "/node_modules")))
;; Build an editable copy of all node_modules
;; directories.
(union-build local
(string-split (getenv "NODE_PATH") #\:)
#:symlink copy-file
#:create-all-directories? #t)
;; The contents of every nested node_modules directory
;; should be moved up to the top.
(with-directory-excursion local
(for-each make-file-writable (find-files "." ".*"))
(let ((package-names
(scandir "."
(lambda (file)
(not (member file (list "." "..")))))))
(for-each
(lambda (package-name)
(let ((name (string-append package-name "/node_modules")))
(when (file-exists? name)
(let ((dependencies
(scandir name
(lambda (file)
(and (not (member file (list "." "..")))
(eq? 'directory
(stat:type
(stat (string-append name "/" file)))))))))
;; Move the directory to the top level.
(for-each
(lambda (dir)
(let ((source (string-append name "/" dir))
(target (string-append local "/" dir)))
(copy-recursively source target)
(delete-file-recursively source)))
dependencies)))))
package-names)))
(setenv "NODE_PATH"
(string-append local ":../../packages")))))
(delete 'configure)
(replace 'build
(lambda _
(invoke "esbuild"
"--bundle"
"--minify"
"--outfile=dist/panmirror.js"
"--loader:.png=dataurl"
"--loader:.gif=dataurl"
;; RStudio expects Panmirror to be available in window.Panmirror,
;; esbuild’s global-name binds to <name>.default though, so we need the
;; footer option to get the object into the right shape.
"--global-name=_internalPanmirror"
"--footer:js=window.Panmirror=_internalPanmirror.default"
"--define:process.env.NODE_ENV=\"production\""
"--define:process.env.DEBUG=\"\""
"--define:process.env.TERM=\"\""
"--define:process.platform=\"\""
"--platform=browser"
"--main-fields=browser,module,main"
"--conditions=browser,module"
"--format=iife"
"src/index.ts")))
(replace 'install
(lambda _
(let ((target (string-append #$output "/share/javascript/panmirror")))
(install-file "dist/panmirror.js" target)
(install-file "dist/panmirror.css" target))))
(delete 'avoid-node-gyp-rebuild))))
(native-inputs
(list esbuild))
(inputs
(list node-biblatex-csl-converter-2.1.0
node-clipboard-2.0.11
node-diff-match-patch-1.0.5
node-fuse-js-6.6.2
node-jayson-4.1.0
node-js-yaml-4.1.0
node-lodash-debounce-4.0.8
node-lodash-orderby-4.6.0
node-lodash-uniqby-4.7.0
node-orderedmap-1.1.8
;; We cannot build node-jieba, which node-pinyin depends on. Instead, patch it out.
;;node-pinyin-2.11.2
node-prosemirror-changeset-2.2.1
node-prosemirror-commands-1.5.2
node-prosemirror-dev-tools-3.1.0
node-prosemirror-dropcursor-1.8.1
node-prosemirror-gapcursor-1.3.2
node-prosemirror-history-1.3.2
node-prosemirror-inputrules-1.2.1
node-prosemirror-keymap-1.2.2
node-prosemirror-model-1.19.2
node-prosemirror-schema-list-1.3.0
node-prosemirror-state-1.4.3
node-prosemirror-tables-1.3.2
node-prosemirror-transform-1.7.3
node-prosemirror-utils-0.9.6
node-prosemirror-view-1.31.5
node-react-18.2.0
node-react-dom-18.2.0
node-react-textarea-autosize-8.5.0
node-react-window-1.8.9
node-sentence-splitter-3.2.3
node-thenby-1.3.4
node-tlite-0.1.9
node-transliteration-2.3.5
node-typescript-4.9.5
node-use-debounce-9.0.4
node-vscode-languageserver-types-3.17.3
node-zenscroll-4.0.2
;; For core
node-markdown-it-13.0.1))
(home-page "https://rstudio.com/products/rstudio/#rstudio-server")
(synopsis "Integrated development environment (IDE) for R")
(description "RStudio is an integrated development environment (IDE) for the R
programming language. Some of its features include: Customizable workbench
with all of the tools required to work with R in one place (console, source,
plots, workspace, help, history, etc.); syntax highlighting editor with code
completion; execute code directly from the source editor (line, selection, or
file); full support for authoring Sweave and TeX documents. RStudio can also
be run as a server, enabling multiple users to access the RStudio IDE using a
web browser.")
(license license:agpl3))))
(define-public rstudio-server
;; Latest commit of the guix-science-v<version> branch.
(let ((commit "547dcf861cac0253a8abb52c135e44e02ba407a1"))
(package
(name "rstudio-server")
(version "2023.06.1+524")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/guix-science/rstudio.git")
(commit commit)))
(file-name (git-file-name "rstudio" version))
(sha256
(base32
"09ndvzdql6vyr2rcm979ibq5hwwzqzsw4fijf4vwcd77lvkvhwmr"))
(modules '((guix build utils)))
(snippet
'(for-each delete-file-recursively
;; de-blob: windows tools
'("dependencies/windows/tools"
;; auto-generated files
"src/cpp/session/include/session/SessionOptions.gen.hpp"
"src/cpp/server/include/server/ServerOptions.gen.hpp")))))
(build-system cmake-build-system)
(arguments
(list
#:out-of-source? #f ; required by 'make-writable
#:configure-flags
'(list
"-DRSTUDIO_TARGET=Server"
"-DCMAKE_BUILD_TYPE=Release"
"-DRSTUDIO_USE_SYSTEM_YAML_CPP=1"
"-DRSTUDIO_USE_SYSTEM_BOOST=1"
"-DRSTUDIO_USE_SYSTEM_SOCI=1"
"-DQUARTO_ENABLED=0"
;; auto-detection seems to be broken with boost 1.72
"-DRSTUDIO_BOOST_SIGNALS_VERSION=2")
#:tests? #f ; no tests exist
#:modules '((guix build cmake-build-system)
(guix build utils)
(ice-9 match))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'unpack-dictionary
(lambda* (#:key inputs native-inputs #:allow-other-keys)
(let ((dict-dir "dependencies/dictionaries"))
(mkdir dict-dir)
(invoke "unzip" "-qd" dict-dir (assoc-ref inputs "dict-source-tarball")))))
;; change the default paths for mathjax and pandoc and a hardcoded call to `which`
(add-after 'unpack 'patch-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Don't build panmirror. We already got it.
(substitute* "src/gwt/build.xml"
(("target name=\"panmirror\"" m)
(string-append m " if=\"false\"")))
(substitute* "src/cpp/session/CMakeLists.txt"
(("\\$\\{RSTUDIO_DEPENDENCIES_DIR\\}/mathjax-27")
(assoc-ref inputs "mathjax"))
(("set\\(RSTUDIO_DEPENDENCIES_PANDOC_DIR.*")
(string-append "set(RSTUDIO_DEPENDENCIES_PANDOC_DIR "
(assoc-ref inputs "pandoc") ")\n"))
(("DESTINATION \"\\$\\{RSTUDIO_INSTALL_BIN\\}/pandoc\"")
(string-append "DESTINATION \"" #$output "/share/pandoc\"")))
(install-file (search-input-file inputs "/include/catch2/catch.hpp")
"src/cpp/tests/cpp/tests/vendor/")
(substitute* "src/cpp/session/session-options.json"
(("resources/mathjax-27") (assoc-ref inputs "mathjax")))
(substitute* "src/cpp/session/include/session/SessionConstants.hpp"
;; XXX: It looks like there’s a bug in RStudio right now, which
;; appends the binary name “pandoc” to this path, if it is an
;; absolute path.
(("bin/pandoc") (string-append (assoc-ref inputs "pandoc") "/bin")))
(substitute* "src/cpp/core/r_util/REnvironmentPosix.cpp"
(("runCommand\\(\"which") (string-append "runCommand(\"" (assoc-ref inputs "which") "/bin/which")))
(substitute* "src/cpp/session/modules/clang/CodeCompletion.cpp"
(("/usr/bin/which") (string-append (assoc-ref inputs "which") "/bin/which")))
(substitute* '("src/cpp/session/SessionConsoleProcess.cpp" "src/cpp/session/modules/SessionTerminalShell.cpp")
(("/usr/bin/env") (string-append (assoc-ref inputs "coreutils") "/bin/env")))
(substitute* '("src/cpp/session/modules/SessionFiles.R")
(("\"zip\"") (string-append "\"" (assoc-ref inputs "zip") "/bin/zip\"")))
(substitute* '("src/cpp/session/modules/SessionFiles.cpp")
(("/usr/bin/unzip") (string-append (assoc-ref inputs "unzip") "/bin/unzip")))
(substitute* "src/cpp/core/system/Architecture.cpp"
(("/usr/bin/uname") (string-append (assoc-ref inputs "coreutils") "/bin/uname")))
(substitute* "src/cpp/session/SessionModuleContext.cpp"
(("cmd\\(\"file\"\\)") (string-append "cmd(\"" (assoc-ref inputs "file") "/bin/file\")")))
(substitute* "src/cpp/session/modules/SessionGit.cpp"
(("\"ssh-add") (string-append "\"" (assoc-ref inputs "openssh") "/bin/ssh-add"))
(("\"ssh-agent") (string-append "\"" (assoc-ref inputs "openssh") "/bin/ssh-agent")))
(substitute* "src/cpp/session/modules/SessionSVN.cpp"
(("\"patch\"") (string-append "\"" (assoc-ref inputs "patch") "/bin/patch\"")))))
(add-after 'unpack 'set-environment-variables
(lambda* (#:key inputs #:allow-other-keys)
(setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
;; set proper version information
(match (string-split #$version (char-set #\. #\+))
((major minor patch suffix)
(setenv "RSTUDIO_VERSION_MAJOR" major)
(setenv "RSTUDIO_VERSION_MINOR" minor)
(setenv "RSTUDIO_VERSION_PATCH" patch)
(setenv "RSTUDIO_VERSION_SUFFIX" (string-append "+" suffix))))
(setenv "PACKAGE_OS" "GNU Guix")))
;; Must be run after patch-source-shebangs, which changes
;; report-option.sh’s interpreter line.
(add-before 'configure 'generate-server-options
(lambda _
;; Generate *.gen.hpp files deleted by source snippet.
(with-directory-excursion "src/cpp"
(invoke "./generate-options.R"))))
(add-after 'install 'install-panmirror
(lambda* (#:key inputs #:allow-other-keys)
(let ((panmirror (string-append (assoc-ref inputs "js-panmirror")
"/share/javascript/panmirror")))
(copy-recursively panmirror
(string-append #$output "/www/js/panmirror"))))))))
(native-inputs
`(("unzip" ,unzip)
("catch2" ,catch2)
;; gwt-components are built using ant
("ant" ,ant)
("jdk" ,openjdk11 "jdk")
;; Copied to output
("js-panmirror" ,js-panmirror)
;; For src/cpp/generate-options.R
("r-jsonlite" ,r-jsonlite)
("r-stringi" ,r-stringi)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("jq" ,jq)))
(inputs
`(("boost" ,boost)
("zlib" ,zlib)
("linux-pam" ,linux-pam)
("yaml-cpp" ,yaml-cpp)
("r-minimal" ,r-minimal)
("openssl" ,openssl)
;; for libuuid
("util-linux" ,util-linux "lib")
("pandoc" ,pandoc)
("which" ,which)
("mathjax" ,mathjax) ; XXX: not sure this is the correct version, but
; any 2.7 patch release should work, right?
;; for `env`
("coreutils" ,coreutils)
;; File panel -> More -> Export
("zip" ,zip)
;; File panel -> Upload -> Upload zip file
("unzip" ,unzip)
;; For database support, uses only client library.
("postgresql" ,postgresql)
("sqlite" ,sqlite)
("soci" ,soci)
;; For `file` utility, binary file detection
("file" ,file)
;; For `patch` utility, apply SVN patches
("patch" ,patch)
;; For `ssh-add`/`ssh-agent`
("openssh" ,openssh)
;; External resources.
("dict-source-tarball"
,(origin
(method url-fetch)
(uri "https://s3.amazonaws.com/rstudio-buildtools/dictionaries/core-dictionaries.zip")
(sha256
(base32
"153lg3ai97qzbqp6zjg10dh3sfvz80v42cjw45zwz7gv1risjha3"))))))
(home-page "https://rstudio.com/products/rstudio/#rstudio-server")
(synopsis "Integrated development environment (IDE) for R")
(description "RStudio is an integrated development environment (IDE) for the R
programming language. Some of its features include: Customizable workbench
with all of the tools required to work with R in one place (console, source,
plots, workspace, help, history, etc.); syntax highlighting editor with code
completion; execute code directly from the source editor (line, selection, or
file); full support for authoring Sweave and TeX documents. RStudio can also
be run as a server, enabling multiple users to access the RStudio IDE using a
web browser.")
(license license:agpl3))))
(define-public rstudio-server-multi-version
(package
(inherit rstudio-server)
(name "rstudio-server-multi-version")
(source
(origin
(inherit (package-source rstudio-server))
(patches
(append
(origin-patches (package-source rstudio-server))
(search-patches
"patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch"
"patches/rstudio-server-multi-version/0002-sessionProcessConfig-Configure-R-version-from-active.patch"
"patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch"
"patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch"
"patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch"
"patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch"
"patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch")))))
(description "This fork of RStudio allows users to switch to
different versions of R from the toolbar or project settings. R
versions can be recorded in @file{/etc/rstudio/r-versions} and in the
user's @file{~/.local/share/rstudio/r-versions}.")))
(define-public rstudio
(package (inherit rstudio-server)
(name "rstudio")
(arguments
(substitute-keyword-arguments (package-arguments rstudio-server)
((#:configure-flags flags)
#~(list "-DRSTUDIO_TARGET=Desktop"
"-DCMAKE_BUILD_TYPE=Release"
"-DRSTUDIO_USE_SYSTEM_YAML_CPP=1"
"-DRSTUDIO_USE_SYSTEM_BOOST=1"
"-DRSTUDIO_USE_SYSTEM_SOCI=1"
"-DQUARTO_ENABLED=0"
;; auto-detection seems to be broken with boost 1.72
"-DRSTUDIO_BOOST_SIGNALS_VERSION=2"
(string-append "-DQT_QMAKE_EXECUTABLE="
#$(this-package-input "qtbase")
"/bin/qmake")))
((#:phases phases)
#~(modify-phases #$phases
(add-after 'install 'wrap-program
(lambda* (#:key inputs #:allow-other-keys)
(let ((bin (string-append #$output "/bin"))
(qtwebengine-path (string-append
#$(this-package-input "qtwebengine")
"/lib/qt5/libexec/QtWebEngineProcess")))
(wrap-program (string-append bin "/rstudio")
`("QTWEBENGINEPROCESS_PATH" ":" = (,qtwebengine-path))))))))))
(inputs
(modify-inputs (package-inputs rstudio-server)
(prepend qtbase-5
qtdeclarative-5
qtlocation
qtsvg-5
qtsensors-5
qtxmlpatterns
qtwebchannel-5
qtwebengine-5)))
(synopsis "Integrated development environment (IDE) for R (desktop version)")))