diff options
| -rw-r--r-- | gn/packages/python24.scm | 32 | ||||
| -rw-r--r-- | gn/packages/statistics.scm | 156 |
2 files changed, 1 insertions, 187 deletions
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm index 8edb1be..19cedb9 100644 --- a/gn/packages/python24.scm +++ b/gn/packages/python24.scm @@ -7,13 +7,11 @@ #:use-module (guix build-system python) #:use-module (gn packages databases) #:use-module (gn packages python) - #:use-module (gn packages statistics) #:use-module (past packages python) #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages maths) #:use-module (gnu packages python-xyz) - #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (srfi srfi-1)) @@ -454,33 +452,3 @@ for Python. The design goals are: @item Compatibility with MySQL-3.23 and later @end itemize") (license license:gpl2+))) - -(define-public python24-rpy2 - (package - (inherit python-rpy2) - (name "python24-rpy2") - (version "2.0.8") - (source - (origin - (method url-fetch) - (uri (pypi-uri "rpy2" version)) - (sha256 - (base32 - "0g6vmv4pxc9bwb756z1vfdlzviib84afjmp4l5cw22x8qqvw1s9s")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2.4 - #:use-setuptools? #f - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "rpy" - ;(invoke "python" "tests.py") - (invoke "python" "tests_rpy_classic.py"))))))) - (inputs `()) - (propagated-inputs - `(("python-numpy" ,python24-numpy-1.2) - ("r-minimal" ,r-minimal-2) - ("r-survival" ,r-2-survival))))) diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index e0377be..d91a053 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -13,9 +13,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) - #:use-module (gnu packages statistics) - #:use-module (gnu packages texinfo) - #:use-module (srfi srfi-1)) + #:use-module (gnu packages statistics)) (define-public r-hmisc-3 (package @@ -151,155 +149,3 @@ traits (CTL). The additional correlation information obtained can be combined with QTL information to perform de novo reconstruction of interaction networks.") (license license:gpl3))) - -;; r-with-tests is private so we inherit from r-minimal. -(define r-with-tests-2 - (package - (inherit r-minimal) - (name "r-with-tests") - (version "2.15.3") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://cran/src/base" - "/R-" (version-major version) - "/R-" version ".tar.gz")) - (sha256 - (base32 - "1mjmq95s5nrwppbzic6lzanjq65j3sxg85l1q09c0fxdin7s70y5")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file "NEWS.pdf") - #t)))) - (arguments - (substitute-keyword-arguments (package-arguments r-minimal) - ((#:tests? _ #t) #t) - ((#:configure-flags cf) - `(cons* "--with-system-zlib" - "--with-system-bzlib" - "--with-system-pcre" - (delete "--without-recommended-packages" ,cf))) - ((#:phases phases) - `(modify-phases ,phases - ;; We can only use some of 'build-reproducibly with this older version. - (replace '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")))) - #t)))))) - (native-inputs - `(("texinfo" ,texinfo-4) - ,@(alist-delete "texinfo" (package-native-inputs r-minimal)))) - (properties '((release-date "2013-03-01"))))) - -(define-public r-minimal-2 - (package - (inherit r-with-tests-2) - (name "r-minimal") - (arguments - (substitute-keyword-arguments (package-arguments r-with-tests-2) - ((#:tests? _ #f) #f) - ((#: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)))))) - -(define-public r-2-lattice - (package - (inherit r-lattice) - (name "r-lattice") - (version "0.20-31") - (source - (origin - (method url-fetch) - (uri (cran-uri "lattice" version)) - (sha256 - (base32 - "1b3m3rg1zd8ssk5jjswk5y93js89vh6939kfajh6i6wphndxigb1")))) - (build-system r-build-system) - (arguments - `(#:r ,r-minimal-2)))) - -(define-public r-2-matrix - (package - (inherit r-matrix) - (name "r-matrix") - (version "1.2-0") - (source - (origin - (method url-fetch) - (uri (cran-uri "Matrix" version)) - (sha256 - (base32 - "0ywz213p6cpwnklxd81hzdyxjzagaj6cn32ycc5rcnhxy30d7kk5")))) - (arguments - `(#:r ,r-minimal-2)) - (propagated-inputs - `(("r-lattice" ,r-2-lattice))))) - -(define-public r-2-survival - (package - (inherit r-survival) - (name "r-survival") - (version "2.41-3") - (source - (origin - (method url-fetch) - (uri (cran-uri "survival" version)) - (sha256 - (base32 - "07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk")))) - (arguments - `(#:r ,r-minimal-2)) - (propagated-inputs - `(("r-matrix" ,r-2-matrix))))) |