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-rw-r--r--gn/packages/python24.scm32
-rw-r--r--gn/packages/statistics.scm156
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)))))