gnu: r-minimal, r-with-tests: Use G-expressions.
* gnu/packages/statistics.scm (r-minimal, r-with-tests)[arguments]: Use G-expressions. Change-Id: I241297444cdb261dfc9901efd73c436a7ccf0acfmaster
Ricardo Wurmus
parent
9f1ab898c3
commit
afe677a623
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@ -228,157 +228,157 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
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"0aj51j34q2b28y28xvlf0dwdj8vpnhjwpvqf7xm05s7fq857dxdk"))))
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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="
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(assoc-ref %outputs "out")
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"/lib/R/lib")
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;; This affects the embedded timestamp of only the core packages.
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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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;; This ensures that Guix can detect embedded store references;
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;; see bug #28157 for details.
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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 "'"
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(search-input-file inputs "/bin/grep")))
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(("\\| wc -l")
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(string-append "| "
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(search-input-file inputs "/bin/wc")
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" -l"))))))
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(add-after 'unpack 'patch-tests
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(lambda _
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;; This is needed because R is run during the check phase and
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;; /bin/sh doesn't exist in the build container.
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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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;; This test fails because line numbers are off by two.
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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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;; The documentation contains time stamps to demonstrate
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;; documentation generation in different phases.
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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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(list
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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=" #$output "/lib/R/lib")
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;; This affects the embedded timestamp of only the core packages.
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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 _
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;; This ensures that Guix can detect embedded store references;
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;; see bug #28157 for details.
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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 "'"
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(search-input-file inputs "/bin/grep")))
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(("\\| wc -l")
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(string-append "| "
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(search-input-file inputs "/bin/wc")
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" -l"))))))
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(add-after 'unpack 'patch-tests
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(lambda _
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;; This is needed because R is run during the check phase and
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;; /bin/sh doesn't exist in the build container.
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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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;; This test fails because line numbers are off by two.
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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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;; The documentation contains time stamps to demonstrate
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;; documentation generation in different phases.
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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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;; Remove timestamp from tracing environment. This fixes
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;; reproducibility of "methods.rd{b,x}".
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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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;; Remove timestamp from tracing environment. This fixes
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;; reproducibility of "methods.rd{b,x}".
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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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;; Ensure that gzipped files are reproducible.
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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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;; Ensure that gzipped files are reproducible.
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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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;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
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;; queries the mtime of a given file and records it in an object.
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;; This is acceptable at runtime to detect stale source files,
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;; but it destroys reproducibility at build time.
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;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
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;; queries the mtime of a given file and records it in an object.
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;; This is acceptable at runtime to detect stale source files,
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;; but it destroys reproducibility at build time.
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;; Similarly, the "srcfilecopy" procedure records the current
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;; time. We change both of them to respect SOURCE_DATE_EPOCH.
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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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;; Similarly, the "srcfilecopy" procedure records the current
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;; time. We change both of them to respect SOURCE_DATE_EPOCH.
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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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;; This library is installed using "install_package_description",
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;; so we need to pass the "builtStamp" argument.
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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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;; This library is installed using "install_package_description",
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;; so we need to pass the "builtStamp" argument.
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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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(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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(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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;; R bundles an older version of help2man, which does not respect
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;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
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;; because that breaks a test.
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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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;; R bundles an older version of help2man, which does not respect
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;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
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;; because that breaks a test.
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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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;; The "References" section of this file when converted to
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;; package.rds is sometimes stored with a newline, sometimes with
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;; a space. We avoid this problem by removing the line break
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;; that is suspected to be the culprit.
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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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;; The "References" section of this file when converted to
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;; package.rds is sometimes stored with a newline, sometimes with
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;; a space. We avoid this problem by removing the line break
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;; that is suspected to be the culprit.
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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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;; Set default pager to "cat", because otherwise it is "false",
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;; making "help()" print nothing at all.
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(lambda _ (setenv "PAGER" "cat")))
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(add-before 'configure 'set-timezone
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;; Some tests require the timezone to be set. However, the
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;; timezone may not just be "UTC", or else a brittle regression
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;; test in reg-tests-1d will fail.
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;; We also need TZ during the configure step.
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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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;; Some tests require that HOME be set.
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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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(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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;; Set default pager to "cat", because otherwise it is "false",
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;; making "help()" print nothing at all.
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(lambda _ (setenv "PAGER" "cat")))
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(add-before 'configure 'set-timezone
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;; Some tests require the timezone to be set. However, the
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;; timezone may not just be "UTC", or else a brittle regression
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;; test in reg-tests-1d will fail.
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;; We also need TZ during the configure step.
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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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;; Some tests require that HOME be set.
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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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`(;; We build the recommended packages here, because they are needed in
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;; order to run the test suite. We disable them in the r-minimal
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;; package.
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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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#~(list
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;; We build the recommended packages here, because they are needed in
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;; order to run the test suite. We disable them in the r-minimal
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;; package.
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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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#$(this-package-input "tcl")
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"/lib/tclConfig.sh")
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,(string-append "--with-tk-config="
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(assoc-ref %build-inputs "tk")
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(string-append "--with-tk-config="
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#$(this-package-input "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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"--enable-R-shlib"
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"--enable-BLAS-shlib"
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"--with-system-tre")))
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;; R has some support for Java. When the JDK is available at configure
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;; time environment variables pointing to the JDK will be recorded under
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;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
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@ -443,45 +443,44 @@ available, greatly increasing its breadth and scope.")
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(package (inherit r-with-tests)
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(name "r-minimal")
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(arguments
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`(#:tests? #f
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,@(substitute-keyword-arguments (package-arguments r-with-tests)
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((#:disallowed-references refs '())
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(cons perl refs))
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((#:configure-flags flags)
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;; Do not build the recommended packages. The build system creates
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;; random temporary directories and embeds their names in some
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;; package files. We build these packages with the r-build-system
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;; instead.
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`(cons "--without-recommended-packages" ,flags))
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((#:phases phases '%standard-phases)
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`(modify-phases ,phases
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(add-after 'install 'remove-extraneous-references
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(substitute* (string-append out "/lib/R/etc/Makeconf")
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(("^# configure.*")
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"# Removed to avoid extraneous references\n"))
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(substitute* (string-append out "/lib/R/bin/libtool")
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(((string-append
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"(-L)?("
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(format #false
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"~a/[^-]+-(~{~a~^|~})-[^/]+"
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(%store-directory)
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'("bzip2"
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"file"
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"glibc-utf8-locales"
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"graphite2"
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"libselinux"
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"libsepol"
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"perl"
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"texinfo"
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"texlive-bin"
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"util-macros"
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"xz"))
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"|"
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(format #false "~a/[^-]+-glibc-[^-]+-static"
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(%store-directory))
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")/lib")) ""))))))))))))
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(substitute-keyword-arguments (package-arguments r-with-tests)
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((#:tests? #f #f) #f)
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((#:disallowed-references refs '())
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(cons perl refs))
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((#:configure-flags flags)
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;; Do not build the recommended packages. The build system creates
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;; random temporary directories and embeds their names in some
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;; package files. We build these packages with the r-build-system
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;; instead.
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#~(cons "--without-recommended-packages" #$flags))
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((#:phases phases '%standard-phases)
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#~(modify-phases #$phases
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(add-after 'install 'remove-extraneous-references
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(substitute* (string-append #$output "/lib/R/etc/Makeconf")
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(("^# configure.*")
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"# Removed to avoid extraneous references\n"))
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(substitute* (string-append #$output "/lib/R/bin/libtool")
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(((string-append
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"(-L)?("
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(format #false
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"~a/[^-]+-(~{~a~^|~})-[^/]+"
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(%store-directory)
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'("bzip2"
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"file"
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"glibc-utf8-locales"
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"graphite2"
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"libselinux"
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"libsepol"
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"perl"
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"texinfo"
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"texlive-bin"
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"util-macros"
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"xz"))
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"|"
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(format #false "~a/[^-]+-glibc-[^-]+-static"
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(%store-directory))
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")/lib")) ""))))))))))
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(define-public rmath-standalone
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(package (inherit r-minimal)
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Reference in New Issue