diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/statistics.scm | 363 |
1 files 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) |