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-rw-r--r--gnu/packages/statistics.scm80
1 files changed, 27 insertions, 53 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 133ce41c43..e02c342c6f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -102,7 +102,7 @@ be output in text, PostScript, PDF or HTML.")
(define-public r
(package
(name "r")
- (version "3.3.2")
+ (version "3.3.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@@ -110,7 +110,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
(base32
- "0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j"))))
+ "0v7wpj89b0i3ad3fi1wak5c93hywmbxv8sdnixhq8l17782nidss"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
@@ -131,8 +131,19 @@ be output in text, PostScript, PDF or HTML.")
(add-after 'unpack 'build-recommended-packages-reproducibly
(lambda _
(substitute* "src/library/Recommended/Makefile.in"
- (("INSTALL_OPTS =.*" line)
- (string-append line " --built-timestamp=1970-01-01")))
+ (("INSTALL_OPTS =(.*)" line rest )
+ (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01"
+ rest)))
+ ;; Ensure that gzipped files are reproducible
+ (substitute* '("src/library/grDevices/Makefile.in"
+ "doc/manual/Makefile.in")
+ (("R_GZIPCMD\\)" line)
+ (string-append line " -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')\"")))
#t))
(add-before 'configure 'set-default-pager
;; Set default pager to "cat", because otherwise it is "false",
@@ -159,11 +170,7 @@ be output in text, PostScript, PDF or HTML.")
"--with-ICU"
"--enable-R-shlib"
"--enable-BLAS-shlib"
- "--with-system-zlib"
- "--with-system-bzlib"
- "--with-system-pcre"
- "--with-system-tre"
- "--with-system-xz")))
+ "--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
@@ -346,24 +353,6 @@ functions of regression coefficients, and 'epredict' methods that handle
non-estimable cases correctly.")
(license license:gpl2+)))
-(define-public r-gtable
- (package
- (name "r-gtable")
- (version "0.1.2")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "gtable" version))
- (sha256
- (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
- (build-system r-build-system)
- (home-page "https://cran.r-project.org/web/packages/gtable")
- (synopsis "R library to arrange grobs in tables")
- (description
- "Gtable is a collection of tools to make it easier to work with
-\"tables\" of grobs.")
- (license license:gpl2+)))
-
(define-public r-pheatmap
(package
(name "r-pheatmap")
@@ -1068,22 +1057,6 @@ from knitr Rmarkdown.")
the execution time of R expressions.")
(license license:bsd-2)))
-(define-public r-codetools
- (package
- (name "r-codetools")
- (version "0.2-14")
- (source (origin
- (method url-fetch)
- (uri (cran-uri "codetools" version))
- (sha256
- (base32
- "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
- (build-system r-build-system)
- (home-page "https://cran.r-project.org/web/packages/codetools/index.html")
- (synopsis "Code analysis tools for R")
- (description "This package provides code analysis tools for R.")
- (license license:gpl3+)))
-
(define-public r-pryr
(package
(name "r-pryr")
@@ -1471,15 +1444,14 @@ building design matrices.")
(define-public python-statsmodels
(package
(name "python-statsmodels")
- (version "0.6.1")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
- (uri (string-append "https://pypi.python.org/packages/source/"
- "s/statsmodels/statsmodels-" version ".tar.gz"))
+ (uri (pypi-uri "statsmodels" version))
(sha256
(base32
- "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))
+ "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
(patches (search-patches "python-statsmodels-fix-tests.patch"))))
(build-system python-build-system)
(arguments
@@ -1491,7 +1463,9 @@ building design matrices.")
(lambda _
;; Set the matplotlib backend to Agg to avoid problems using the
;; GTK backend without a display.
- (substitute* (find-files "statsmodels/graphics/tests" "\\.py")
+ (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
+ '("statsmodels/tsa/vector_ar/tests/test_var.py"
+ "statsmodels/duration/tests/test_survfunc.py"))
(("import matplotlib\\.pyplot as plt" line)
(string-append "import matplotlib;matplotlib.use('Agg');"
line)))
@@ -2246,11 +2220,11 @@ variety of formats.")
"0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
(properties `((upstream-name . "gtable")))
(build-system r-build-system)
- (home-page "http://cran.r-project.org/web/packages/gtable")
- (synopsis "Arrange grobs in tables")
+ (home-page "https://cran.r-project.org/web/packages/gtable")
+ (synopsis "R library to arrange grobs in tables")
(description
- "This package provides tools to make it easier to work with tables of
-grobs.")
+ "Gtable is a collection of tools to make it easier to work with
+\"tables\" of grobs.")
(license license:gpl2+)))
(define-public r-gridextra
@@ -2568,7 +2542,7 @@ data.")
(base32
"0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
(build-system r-build-system)
- (home-page "http://cran.r-project.org/web/packages/codetools")
+ (home-page "https://cran.r-project.org/web/packages/codetools")
(synopsis "Code analysis tools for R")
(description "This package provides code analysis tools for R to check R
code for possible problems.")