upstream some packages

1 files changed, 1 insertions, 155 deletions

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)))))