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gnu: python-rpy2: Update to 3.3.5.

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* gnu/packages/statistics.scm (python-rpy2): Update to 3.3.5.
[source]: Add patches to fix test failures.
[arguments]: Adjust custom 'check phase.
This commit is contained in:
Efraim Flashner 2020-08-23 11:02:11 +03:00
parent d0fc1e832c
commit 24cc25be89
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1 changed files with 78 additions and 67 deletions
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@ -5683,76 +5683,87 @@ to any arbitrary string. In this case, it is up to you to set valid values.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public python-rpy2 (define-public python-rpy2
;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because (package
;; it fixes a regression when using ggplot 3.2.0. (name "python-rpy2")
(let ((changeset "19868a8") (version "3.3.5")
(revision "1")) (source
(package (origin
(name "python-rpy2") (method url-fetch)
(version (git-version "3.0.4" revision changeset)) (uri (pypi-uri "rpy2" version))
(source (sha256
(origin (base32
(method hg-fetch) "1bs36rds5fq8821l5q85q2b25161rs9ppw5c26x0hjwj487gpcfj"))
(uri (hg-reference ;; These patches should be removed with the next release.
(url "https://bitbucket.org/rpy2/rpy2") (patches
(changeset changeset))) (list
(file-name (git-file-name name version)) (origin
(sha256 (method url-fetch)
(base32 (uri "https://github.com/rpy2/rpy2/commit/04c57598f00145d868ea8da31ac1b1e7c49f7570.patch")
"1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk")))) (file-name "python-rpy2-fix-test-failure.patch")
(build-system python-build-system) (sha256
(arguments (base32
'(#:modules ((ice-9 ftw) "1lqd3yxjfx1rxrybcmnapy0r6ambg9myrb98q4nlfhpxanwfdbbh")))
(srfi srfi-1) (origin
(srfi srfi-26) (method url-fetch)
(guix build utils) (uri "https://github.com/rpy2/rpy2/commit/685f67d0a6b47ea80e718116a10755019446aef7.patch")
(guix build python-build-system)) (file-name "python-rpy2-r-console-test-fix.patch")
#:phases (sha256
(modify-phases %standard-phases (base32
(replace 'check "18wpvfaa4c13d44cb4sw88c3c7403xdy5m8h82wfq8fjmcq3cmzn")))))))
(lambda* (#:key outputs inputs #:allow-other-keys) (build-system python-build-system)
(let ((cwd (getcwd))) (arguments
(setenv "TZ" "UTC") '(#:modules ((ice-9 ftw)
(setenv "PYTHONPATH" (srfi srfi-1)
(string-append cwd "/build/" (srfi srfi-26)
(find (cut string-prefix? "lib" <>) (guix build utils)
(scandir (string-append cwd "/build"))) (guix build python-build-system))
":" #:phases
(getenv "PYTHONPATH")))) (modify-phases %standard-phases
(invoke "pytest" "-v" "rpy/tests/")))))) (replace 'check
(propagated-inputs (lambda* (#:key outputs inputs #:allow-other-keys)
`(("python-cffi" ,python-cffi) (let ((cwd (getcwd)))
("python-six" ,python-six) (setenv "TZ" "UTC")
("python-jinja2" ,python-jinja2) (setenv "PYTHONPATH"
("python-numpy" ,python-numpy) (string-append cwd "/build/"
("python-pandas" ,python-pandas) (find (cut string-prefix? "lib" <>)
("python-pytz" ,python-pytz) (scandir (string-append cwd "/build")))
("python-ipython" ,python-ipython) ":"
("python-tzlocal" ,python-tzlocal))) (getenv "PYTHONPATH"))))
(inputs ;; test_vector_complex has issues when run in our environment.
`(("readline" ,readline) (invoke "pytest" "-v" "rpy2/tests/" "-k" "not test_vector_complex"))))))
("icu4c" ,icu4c) (propagated-inputs
("pcre" ,pcre) `(("python-cffi" ,python-cffi)
("r-minimal" ,r-minimal) ("python-six" ,python-six)
("r-survival" ,r-survival) ("python-jinja2" ,python-jinja2)
("r-ggplot2" ,r-ggplot2) ("python-numpy" ,python-numpy)
("r-rsqlite" ,r-rsqlite) ("python-pandas" ,python-pandas)
("r-dplyr" ,r-dplyr) ("python-pytz" ,python-pytz)
("r-dbplyr" ,r-dbplyr) ("python-ipython" ,python-ipython)
("python-numpy" ,python-numpy))) ("python-tzlocal" ,python-tzlocal)))
(native-inputs (inputs
`(("zlib" ,zlib) `(("readline" ,readline)
("python-pytest" ,python-pytest))) ("icu4c" ,icu4c)
(home-page "https://rpy2.github.io") ("pcre" ,pcre)
(synopsis "Python interface to the R language") ("r-minimal" ,r-minimal)
(description "rpy2 is a redesign and rewrite of rpy. It is providing a ("r-survival" ,r-survival)
("r-ggplot2" ,r-ggplot2)
("r-rsqlite" ,r-rsqlite)
("r-dplyr" ,r-dplyr)
("r-dbplyr" ,r-dbplyr)
("python-numpy" ,python-numpy)))
(native-inputs
`(("zlib" ,zlib)
("python-pytest" ,python-pytest)))
(home-page "https://rpy2.github.io")
(synopsis "Python interface to the R language")
(description "rpy2 is a redesign and rewrite of rpy. It is providing a
low-level interface to R from Python, a proposed high-level interface, low-level interface to R from Python, a proposed high-level interface,
including wrappers to graphical libraries, as well as R-like structures and including wrappers to graphical libraries, as well as R-like structures and
functions.") functions.")
;; Any of these licenses can be picked for the R interface. The whole ;; Any of these licenses can be picked for the R interface. The whole
;; project is released under GPLv2+ according to the license declaration ;; project is released under GPLv2+ according to the license declaration
;; in "setup.py". ;; in "setup.py".
(license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))) (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
(define-public java-jdistlib (define-public java-jdistlib
(package (package