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https://gitlab.univ-nantes.fr/glicid-public/guix-glicid.git
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using @@ to export already defined r-with-tests
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commit
3340a680ab
1 changed files with 3 additions and 167 deletions
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@ -1,169 +1,5 @@
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(define-module (glicid packages r)
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#:use-module (guix build-system gnu)
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#:use-module (guix download)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bash)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages curl)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages icu4c)
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#:use-module (gnu packages image)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages pcre)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages tcl)
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#:use-module (gnu packages tex)
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#:use-module (gnu packages texinfo)
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#:use-module (gnu packages xorg)
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#:use-module (glicid packages gcc)
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#:use-module (guix build-system gnu)
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)
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(define-module (glicid packages r))
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; stolen from r-with-tests @ (gnu packages statistics
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(define-public R
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(package
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(name "R")
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(version "4.3.1")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://cran/src/base/R-"
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(version-major version) "/R-"
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version ".tar.gz"))
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(sha256
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(base32
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"16dswjcymzr2mj1vjwqdyjaa9d4isa1p6c9viihnyg02y4jbzl4d"))))
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(build-system gnu-build-system)
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(arguments
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`(#:disallowed-references (,tzdata-for-tests)
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#:make-flags
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(list (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib/R/lib")
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"PKG_BUILT_STAMP=1970-01-01")
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#:phases
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(modify-phases %standard-phases
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(add-before 'configure 'do-not-compress-serialized-files
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "src/library/base/makebasedb.R"
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(("compress = TRUE") "compress = FALSE"))))
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(add-before 'configure 'patch-coreutils-paths
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((uname-bin (search-input-file inputs "/bin/uname"))
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(rm-bin (search-input-file inputs "/bin/rm")))
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(substitute* "src/scripts/R.sh.in"
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(("uname") uname-bin))
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(substitute* "src/unix/sys-std.c"
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(("rm -Rf ") (string-append rm-bin " -Rf ")))
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(substitute* "src/library/parallel/R/detectCores.R"
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(("'grep")
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(string-append "'" (search-input-file inputs "/bin/grep")))
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(("\\| wc -l")
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(string-append "| " (search-input-file inputs "/bin/wc") " -l"))))))
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(add-after 'unpack 'patch-tests
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(lambda _
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(substitute* "src/unix/sys-unix.c"
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(("\"/bin/sh\"")
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(string-append "\"" (which "sh") "\"")))
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(substitute* "tests/reg-packages.R"
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(("8 <= print" m) (string-append "## " m)))))
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(add-after 'unpack 'build-reproducibly
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(lambda _
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(substitute* "src/library/tools/man/Rd2HTML.Rd"
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(("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
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"(removed for reproducibility)"))
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(substitute* "src/library/methods/R/trace.R"
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(("dateCreated = Sys.time\\(\\)")
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"dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
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(substitute* '("src/library/grDevices/Makefile.in"
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"doc/manual/Makefile.in")
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(("R_GZIPCMD\\)" line)
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(string-append line " -n")))
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(substitute* "src/library/base/R/srcfile.R"
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(("timestamp <- (timestamp.*|file.mtime.*)" _ time)
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(string-append "timestamp <- \
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as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
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as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
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} else { " time "}, origin=\"1970-01-01\")\n")))
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(substitute* "src/library/tools/Makefile.in"
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(("(install_package_description\\(.*\"')\\)\"" line prefix)
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(string-append prefix ", builtStamp='1970-01-01')\"")))
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(define-public R (@@ (gnu packages statistics) r-with-tests))
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(substitute* "src/library/Recommended/Makefile.in"
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(("INSTALL_OPTS =" m)
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(string-append m " --built-timestamp=1970-01-01" m)))
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(with-fluids ((%default-port-encoding "ISO-8859-1"))
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(substitute* "tools/help2man.pl"
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(("my \\$date = strftime \"%B %Y\", localtime" line)
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(string-append line " 1"))))
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(substitute* "src/library/methods/DESCRIPTION.in"
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(("\\(2008\\)\n") "(2008) ")
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((" ``Software") "``Software")
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(("Data Analysis:.") "Data Analysis:\n")
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(("Programming with R") " Programming with R"))
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(substitute* "src/library/tools/DESCRIPTION.in"
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(("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr")
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"codetools, methods, xml2, curl, commonmark,
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knitr, xfun, mathjaxr"))))
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(add-before 'build 'set-locales
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(lambda _
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(setlocale LC_ALL "C")
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(setenv "LC_ALL" "C")))
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(add-before 'configure 'set-default-pager
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(lambda _ (setenv "PAGER" "cat")))
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(add-before 'configure 'set-timezone
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "TZ" "UTC+1")
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(setenv "TZDIR"
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(search-input-directory inputs
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"share/zoneinfo"))))
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(add-before 'check 'set-home
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(lambda _ (setenv "HOME" "/tmp")))
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(add-after 'build 'make-info
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(lambda _ (invoke "make" "info")))
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(add-after 'build 'install-info
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(lambda _ (invoke "make" "install-info"))))
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#:configure-flags
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`(
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"--with-cairo"
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"--with-blas=-lopenblas"
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"--with-libpng"
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"--with-jpeglib"
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"--with-libtiff"
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"--with-ICU"
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"--with-tcltk"
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,(string-append "--with-tcl-config="
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(assoc-ref %build-inputs "tcl")
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"/lib/tclConfig.sh")
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,(string-append "--with-tk-config="
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(assoc-ref %build-inputs "tk")
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"/lib/tkConfig.sh")
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"--enable-R-shlib"
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"--enable-BLAS-shlib"
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"--with-system-tre")))
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(native-inputs
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(list bzip2 perl pkg-config texinfo
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(texlive-updmap.cfg
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(list texlive-fancyvrb texlive-inconsolata texlive-upquote texlive-xkeyval))
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tzdata-for-tests xz))
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(inputs
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(list coreutils curl openblas gfortran grep icu4c libjpeg-turbo libpng libtiff libxt
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pango pcre2 readline tcl tk which zlib bash-minimal))
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(native-search-paths
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(list (search-path-specification
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(variable "R_LIBS_SITE")
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(files (list "site-library/")))))
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(home-page "https://www.r-project.org/")
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(synopsis "Environment for statistical computing and graphics")
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(description
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"R is a language and environment for statistical computing and graphics.
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It provides a variety of statistical techniques, such as linear and nonlinear
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modeling, classical statistical tests, time-series analysis, classification
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and clustering. It also provides robust support for producing
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publication-quality data plots. A large amount of 3rd-party packages are
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available, greatly increasing its breadth and scope.")
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(license license:gpl3+)))
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R
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