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