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01/03: gnu: r-minimal, r-with-tests: Use G-expressions.
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From: |
guix-commits |
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Subject: |
01/03: gnu: r-minimal, r-with-tests: Use G-expressions. |
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Date: |
Tue, 30 Jan 2024 09:17:01 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit afe677a623f3ede51f3bb9be121de3d8ff0ea36e
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Jan 30 12:51:40 2024 +0100
gnu: r-minimal, r-with-tests: Use G-expressions.
* gnu/packages/statistics.scm (r-minimal, r-with-tests)[arguments]: Use
G-expressions.
Change-Id: I241297444cdb261dfc9901efd73c436a7ccf0acf
---
gnu/packages/statistics.scm | 363 ++++++++++++++++++++++----------------------
1 file changed, 181 insertions(+), 182 deletions(-)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bd47b7af60..e1c3aec0cb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -228,157 +228,157 @@ This package also provides @command{xls2csv} to export
Excel files to CSV.")
"0aj51j34q2b28y28xvlf0dwdj8vpnhjwpvqf7xm05s7fq857dxdk"))))
(build-system gnu-build-system)
(arguments
- `(#:disallowed-references (,tzdata-for-tests)
- #:make-flags
- (list (string-append "LDFLAGS=-Wl,-rpath="
- (assoc-ref %outputs "out")
- "/lib/R/lib")
- ;; This affects the embedded timestamp of only the core packages.
- "PKG_BUILT_STAMP=1970-01-01")
- #:phases
- (modify-phases %standard-phases
- (add-before 'configure 'do-not-compress-serialized-files
- (lambda* (#:key inputs #:allow-other-keys)
- ;; This ensures that Guix can detect embedded store references;
- ;; see bug #28157 for details.
- (substitute* "src/library/base/makebasedb.R"
- (("compress = TRUE") "compress = FALSE"))))
- (add-before 'configure 'patch-coreutils-paths
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((uname-bin (search-input-file inputs "/bin/uname"))
- (rm-bin (search-input-file inputs "/bin/rm")))
- (substitute* "src/scripts/R.sh.in"
- (("uname") uname-bin))
- (substitute* "src/unix/sys-std.c"
- (("rm -Rf ") (string-append rm-bin " -Rf ")))
- (substitute* "src/library/parallel/R/detectCores.R"
- (("'grep")
- (string-append "'"
- (search-input-file inputs "/bin/grep")))
- (("\\| wc -l")
- (string-append "| "
- (search-input-file inputs "/bin/wc")
- " -l"))))))
- (add-after 'unpack 'patch-tests
- (lambda _
- ;; This is needed because R is run during the check phase and
- ;; /bin/sh doesn't exist in the build container.
- (substitute* "src/unix/sys-unix.c"
- (("\"/bin/sh\"")
- (string-append "\"" (which "sh") "\"")))
- ;; This test fails because line numbers are off by two.
- (substitute* "tests/reg-packages.R"
- (("8 <= print" m) (string-append "## " m)))))
- (add-after 'unpack 'build-reproducibly
- (lambda _
- ;; The documentation contains time stamps to demonstrate
- ;; documentation generation in different phases.
- (substitute* "src/library/tools/man/Rd2HTML.Rd"
- (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
- "(removed for reproducibility)"))
-
- ;; Remove timestamp from tracing environment. This fixes
- ;; reproducibility of "methods.rd{b,x}".
- (substitute* "src/library/methods/R/trace.R"
- (("dateCreated = Sys.time\\(\\)")
- "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz =
\"UTC\")"))
-
- ;; Ensure that gzipped files are reproducible.
- (substitute* '("src/library/grDevices/Makefile.in"
- "doc/manual/Makefile.in")
- (("R_GZIPCMD\\)" line)
- (string-append line " -n")))
-
- ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
- ;; queries the mtime of a given file and records it in an object.
- ;; This is acceptable at runtime to detect stale source files,
- ;; but it destroys reproducibility at build time.
-
- ;; Similarly, the "srcfilecopy" procedure records the current
- ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
- (substitute* "src/library/base/R/srcfile.R"
- (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
- (string-append "timestamp <- \
+ (list
+ #:disallowed-references `(,tzdata-for-tests)
+ #:make-flags
+ #~(list (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib/R/lib")
+ ;; This affects the embedded timestamp of only the core packages.
+ "PKG_BUILT_STAMP=1970-01-01")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'configure 'do-not-compress-serialized-files
+ (lambda _
+ ;; This ensures that Guix can detect embedded store references;
+ ;; see bug #28157 for details.
+ (substitute* "src/library/base/makebasedb.R"
+ (("compress = TRUE") "compress = FALSE"))))
+ (add-before 'configure 'patch-coreutils-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((uname-bin (search-input-file inputs "/bin/uname"))
+ (rm-bin (search-input-file inputs "/bin/rm")))
+ (substitute* "src/scripts/R.sh.in"
+ (("uname") uname-bin))
+ (substitute* "src/unix/sys-std.c"
+ (("rm -Rf ") (string-append rm-bin " -Rf ")))
+ (substitute* "src/library/parallel/R/detectCores.R"
+ (("'grep")
+ (string-append "'"
+ (search-input-file inputs "/bin/grep")))
+ (("\\| wc -l")
+ (string-append "| "
+ (search-input-file inputs "/bin/wc")
+ " -l"))))))
+ (add-after 'unpack 'patch-tests
+ (lambda _
+ ;; This is needed because R is run during the check phase and
+ ;; /bin/sh doesn't exist in the build container.
+ (substitute* "src/unix/sys-unix.c"
+ (("\"/bin/sh\"")
+ (string-append "\"" (which "sh") "\"")))
+ ;; This test fails because line numbers are off by two.
+ (substitute* "tests/reg-packages.R"
+ (("8 <= print" m) (string-append "## " m)))))
+ (add-after 'unpack 'build-reproducibly
+ (lambda _
+ ;; The documentation contains time stamps to demonstrate
+ ;; documentation generation in different phases.
+ (substitute* "src/library/tools/man/Rd2HTML.Rd"
+ (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
+ "(removed for reproducibility)"))
+
+ ;; Remove timestamp from tracing environment. This fixes
+ ;; reproducibility of "methods.rd{b,x}".
+ (substitute* "src/library/methods/R/trace.R"
+ (("dateCreated = Sys.time\\(\\)")
+ "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz =
\"UTC\")"))
+
+ ;; Ensure that gzipped files are reproducible.
+ (substitute* '("src/library/grDevices/Makefile.in"
+ "doc/manual/Makefile.in")
+ (("R_GZIPCMD\\)" line)
+ (string-append line " -n")))
+
+ ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
+ ;; queries the mtime of a given file and records it in an object.
+ ;; This is acceptable at runtime to detect stale source files,
+ ;; but it destroys reproducibility at build time.
+
+ ;; Similarly, the "srcfilecopy" procedure records the current
+ ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
+ (substitute* "src/library/base/R/srcfile.R"
+ (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
+ (string-append "timestamp <- \
as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
} else { " time "}, origin=\"1970-01-01\")\n")))
- ;; This library is installed using "install_package_description",
- ;; so we need to pass the "builtStamp" argument.
- (substitute* "src/library/tools/Makefile.in"
- (("(install_package_description\\(.*\"')\\)\"" line prefix)
- (string-append prefix ", builtStamp='1970-01-01')\"")))
-
- (substitute* "src/library/Recommended/Makefile.in"
- (("INSTALL_OPTS =" m)
- (string-append m " --built-timestamp=1970-01-01" m)))
-
- ;; R bundles an older version of help2man, which does not respect
- ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
- ;; because that breaks a test.
- (with-fluids ((%default-port-encoding "ISO-8859-1"))
- (substitute* "tools/help2man.pl"
- (("my \\$date = strftime \"%B %Y\", localtime" line)
- (string-append line " 1"))))
-
- ;; The "References" section of this file when converted to
- ;; package.rds is sometimes stored with a newline, sometimes with
- ;; a space. We avoid this problem by removing the line break
- ;; that is suspected to be the culprit.
- (substitute* "src/library/methods/DESCRIPTION.in"
- (("\\(2008\\)\n") "(2008) ")
- ((" ``Software") "``Software")
- (("Data Analysis:.") "Data Analysis:\n")
- (("Programming with R") " Programming with R"))
- (substitute* "src/library/tools/DESCRIPTION.in"
- (("codetools, methods, xml2, curl, commonmark, knitr, xfun,
mathjaxr")
- "codetools, methods, xml2, curl, commonmark,
+ ;; This library is installed using "install_package_description",
+ ;; so we need to pass the "builtStamp" argument.
+ (substitute* "src/library/tools/Makefile.in"
+ (("(install_package_description\\(.*\"')\\)\"" line prefix)
+ (string-append prefix ", builtStamp='1970-01-01')\"")))
+
+ (substitute* "src/library/Recommended/Makefile.in"
+ (("INSTALL_OPTS =" m)
+ (string-append m " --built-timestamp=1970-01-01" m)))
+
+ ;; R bundles an older version of help2man, which does not respect
+ ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
+ ;; because that breaks a test.
+ (with-fluids ((%default-port-encoding "ISO-8859-1"))
+ (substitute* "tools/help2man.pl"
+ (("my \\$date = strftime \"%B %Y\", localtime" line)
+ (string-append line " 1"))))
+
+ ;; The "References" section of this file when converted to
+ ;; package.rds is sometimes stored with a newline, sometimes with
+ ;; a space. We avoid this problem by removing the line break
+ ;; that is suspected to be the culprit.
+ (substitute* "src/library/methods/DESCRIPTION.in"
+ (("\\(2008\\)\n") "(2008) ")
+ ((" ``Software") "``Software")
+ (("Data Analysis:.") "Data Analysis:\n")
+ (("Programming with R") " Programming with R"))
+ (substitute* "src/library/tools/DESCRIPTION.in"
+ (("codetools, methods, xml2, curl, commonmark, knitr, xfun,
mathjaxr")
+ "codetools, methods, xml2, curl, commonmark,
knitr, xfun, mathjaxr"))))
- (add-before 'build 'set-locales
- (lambda _
- (setlocale LC_ALL "C")
- (setenv "LC_ALL" "C")))
- (add-before 'configure 'set-default-pager
- ;; Set default pager to "cat", because otherwise it is "false",
- ;; making "help()" print nothing at all.
- (lambda _ (setenv "PAGER" "cat")))
- (add-before 'configure 'set-timezone
- ;; Some tests require the timezone to be set. However, the
- ;; timezone may not just be "UTC", or else a brittle regression
- ;; test in reg-tests-1d will fail.
- ;; We also need TZ during the configure step.
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "TZ" "UTC+1")
- (setenv "TZDIR"
- (search-input-directory inputs
- "share/zoneinfo"))))
- (add-before 'check 'set-home
- ;; Some tests require that HOME be set.
- (lambda _ (setenv "HOME" "/tmp")))
- (add-after 'build 'make-info
- (lambda _ (invoke "make" "info")))
- (add-after 'build 'install-info
- (lambda _ (invoke "make" "install-info"))))
+ (add-before 'build 'set-locales
+ (lambda _
+ (setlocale LC_ALL "C")
+ (setenv "LC_ALL" "C")))
+ (add-before 'configure 'set-default-pager
+ ;; Set default pager to "cat", because otherwise it is "false",
+ ;; making "help()" print nothing at all.
+ (lambda _ (setenv "PAGER" "cat")))
+ (add-before 'configure 'set-timezone
+ ;; Some tests require the timezone to be set. However, the
+ ;; timezone may not just be "UTC", or else a brittle regression
+ ;; test in reg-tests-1d will fail.
+ ;; We also need TZ during the configure step.
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "TZ" "UTC+1")
+ (setenv "TZDIR"
+ (search-input-directory inputs
+ "share/zoneinfo"))))
+ (add-before 'check 'set-home
+ ;; Some tests require that HOME be set.
+ (lambda _ (setenv "HOME" "/tmp")))
+ (add-after 'build 'make-info
+ (lambda _ (invoke "make" "info")))
+ (add-after 'build 'install-info
+ (lambda _ (invoke "make" "install-info"))))
#:configure-flags
- `(;; We build the recommended packages here, because they are needed in
- ;; order to run the test suite. We disable them in the r-minimal
- ;; package.
- "--with-cairo"
- "--with-blas=-lopenblas"
- "--with-libpng"
- "--with-jpeglib"
- "--with-libtiff"
- "--with-ICU"
- "--with-tcltk"
- ,(string-append "--with-tcl-config="
- (assoc-ref %build-inputs "tcl")
+ #~(list
+ ;; We build the recommended packages here, because they are needed in
+ ;; order to run the test suite. We disable them in the r-minimal
+ ;; package.
+ "--with-cairo"
+ "--with-blas=-lopenblas"
+ "--with-libpng"
+ "--with-jpeglib"
+ "--with-libtiff"
+ "--with-ICU"
+ "--with-tcltk"
+ (string-append "--with-tcl-config="
+ #$(this-package-input "tcl")
"/lib/tclConfig.sh")
- ,(string-append "--with-tk-config="
- (assoc-ref %build-inputs "tk")
+ (string-append "--with-tk-config="
+ #$(this-package-input "tk")
"/lib/tkConfig.sh")
- "--enable-R-shlib"
- "--enable-BLAS-shlib"
- "--with-system-tre")))
+ "--enable-R-shlib"
+ "--enable-BLAS-shlib"
+ "--with-system-tre")))
;; R has some support for Java. When the JDK is available at configure
;; time environment variables pointing to the JDK will be recorded under
;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
@@ -443,45 +443,44 @@ available, greatly increasing its breadth and scope.")
(package (inherit r-with-tests)
(name "r-minimal")
(arguments
- `(#:tests? #f
- ,@(substitute-keyword-arguments (package-arguments r-with-tests)
- ((#:disallowed-references refs '())
- (cons perl refs))
- ((#:configure-flags flags)
- ;; Do not build the recommended packages. The build system creates
- ;; random temporary directories and embeds their names in some
- ;; package files. We build these packages with the r-build-system
- ;; instead.
- `(cons "--without-recommended-packages" ,flags))
- ((#:phases phases '%standard-phases)
- `(modify-phases ,phases
- (add-after 'install 'remove-extraneous-references
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (substitute* (string-append out "/lib/R/etc/Makeconf")
- (("^# configure.*")
- "# Removed to avoid extraneous references\n"))
- (substitute* (string-append out "/lib/R/bin/libtool")
- (((string-append
- "(-L)?("
- (format #false
- "~a/[^-]+-(~{~a~^|~})-[^/]+"
- (%store-directory)
- '("bzip2"
- "file"
- "glibc-utf8-locales"
- "graphite2"
- "libselinux"
- "libsepol"
- "perl"
- "texinfo"
- "texlive-bin"
- "util-macros"
- "xz"))
- "|"
- (format #false "~a/[^-]+-glibc-[^-]+-static"
- (%store-directory))
- ")/lib")) ""))))))))))))
+ (substitute-keyword-arguments (package-arguments r-with-tests)
+ ((#:tests? #f #f) #f)
+ ((#:disallowed-references refs '())
+ (cons perl refs))
+ ((#:configure-flags flags)
+ ;; Do not build the recommended packages. The build system creates
+ ;; random temporary directories and embeds their names in some
+ ;; package files. We build these packages with the r-build-system
+ ;; instead.
+ #~(cons "--without-recommended-packages" #$flags))
+ ((#:phases phases '%standard-phases)
+ #~(modify-phases #$phases
+ (add-after 'install 'remove-extraneous-references
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* (string-append #$output "/lib/R/etc/Makeconf")
+ (("^# configure.*")
+ "# Removed to avoid extraneous references\n"))
+ (substitute* (string-append #$output "/lib/R/bin/libtool")
+ (((string-append
+ "(-L)?("
+ (format #false
+ "~a/[^-]+-(~{~a~^|~})-[^/]+"
+ (%store-directory)
+ '("bzip2"
+ "file"
+ "glibc-utf8-locales"
+ "graphite2"
+ "libselinux"
+ "libsepol"
+ "perl"
+ "texinfo"
+ "texlive-bin"
+ "util-macros"
+ "xz"))
+ "|"
+ (format #false "~a/[^-]+-glibc-[^-]+-static"
+ (%store-directory))
+ ")/lib")) ""))))))))))
(define-public rmath-standalone
(package (inherit r-minimal)