On Thu, Aug 20, 2020 at 05:41:49PM +0300, Bonface M. K. wrote:
>
> Hi all,
>
> When trying to build(I'm using guix on
> 19da9059212dd81265369340ff1377c62b0cd22e) the python-rpy2 package, I get
> the following error:
>
I've bumped python-rpy2 to 3.3.5 and it now builds. Go ahead and try it
now!
> --8<---------------cut here---------------start------------->8---
> /gnu/store/84k7z6r044sllh3y0y90vj9dw8fgc6vz-python-rpy2-3.0.4-1.19868a8/lib/python3.8/site-packages/rpy2/_rinterface_cffi_build.py
> to _rinterface_cffi_build.cpython-38.pyc
> running install_egg_info
> running egg_info
> creating rpy2.egg-info
> writing rpy2.egg-info/PKG-INFO
> writing dependency_links to rpy2.egg-info/dependency_links.txt
> writing requirements to rpy2.egg-info/requires.txt
> writing top-level names to rpy2.egg-info/top_level.txt
> writing manifest file 'rpy2.egg-info/SOURCES.txt'
> reading manifest file 'rpy2.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no files found matching 'README' anywhere in distribution
> warning: no previously-included files matching '*patch*' found anywhere in
> distribution
> warning: no previously-included files matching '*diff*' found anywhere in
> distribution
> warning: no previously-included files matching '.hg' found anywhere in
> distribution
> warning: no files found matching 'MANIFEST'
> warning: no files found matching 'README'
> warning: no files found matching '_rinterface_cffi_build'
> no previously-included directories found matching 'dist'
> warning: no files found matching 'doc/source/rpy2_logo.png'
> writing manifest file 'rpy2.egg-info/SOURCES.txt'
> Copying rpy2.egg-info to
> /gnu/store/84k7z6r044sllh3y0y90vj9dw8fgc6vz-python-rpy2-3.0.4-1.19868a8/lib/python3.8/site-packages/rpy2-3.1.0.dev0-py3.8.egg-info
> running install_scripts
> phase `install' succeeded after 0.7 seconds
> starting phase `wrap'
> find-files:
> /gnu/store/84k7z6r044sllh3y0y90vj9dw8fgc6vz-python-rpy2-3.0.4-1.19868a8/bin:
> No such file or directory
> find-files:
> /gnu/store/84k7z6r044sllh3y0y90vj9dw8fgc6vz-python-rpy2-3.0.4-1.19868a8/sbin:
> No such file or directory
> phase `wrap' succeeded after 0.0 seconds
> starting phase `check'
> ============================= test session starts
> ==============================
> platform linux -- Python 3.8.2, pytest-5.3.5, py-1.8.1, pluggy-0.13.1 --
> /gnu/store/wc4xh9wj49rlbyivxi4lsws6whhzx4ab-python-wrapper-3.8.2/bin/python
> cachedir: .pytest_cache
> hypothesis profile 'default' ->
> database=DirectoryBasedExampleDatabase('/tmp/guix-build-python-rpy2-3.0.4-1.19868a8.drv-0/source/.hypothesis/examples')
> rootdir: /tmp/guix-build-python-rpy2-3.0.4-1.19868a8.drv-0/source
> plugins: hypothesis-5.4.1
> collecting ... collected 614 items / 1 error / 613 selected
>
> ==================================== ERRORS
> ====================================
> ___________ ERROR collecting rpy/tests/robjects/lib/test_ggplot2.py
> ____________
> ImportError while importing test module
> '/tmp/guix-build-python-rpy2-3.0.4-1.19868a8.drv-0/source/rpy/tests/robjects/lib/test_ggplot2.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> rpy/tests/robjects/lib/test_ggplot2.py:7: in <module>
> from rpy2.robjects.lib import ggplot2
> build/lib/rpy2/robjects/lib/ggplot2.py:56: in <module>
> rlang = importr('rlang', on_conflict='warn')
> build/lib/rpy2/robjects/packages.py:486: in importr
> pack = InstalledSTPackage(env, name,
> build/lib/rpy2/robjects/packages.py:204: in __init__
> self.__fill_rpy2r__(on_conflict=on_conflict)
> build/lib/rpy2/robjects/packages.py:329: in __fill_rpy2r__
> (super(SignatureTranslatedPackage, self)
> build/lib/rpy2/robjects/packages.py:252: in __fill_rpy2r__
> raise LibraryError('The symbol ' + rname +
> E rpy2.robjects.packages.LibraryError: The symbol .env in the package
> "rlang" is conflicting with a Python object attribute
> =============================== warnings summary
> ===============================
> /gnu/store/xdbplmjmgsdz6wxr63mghkxjkmma44k0-python-nose-1.3.7/lib/python3.8/site-packages/nose/importer.py:12
>
> /gnu/store/xdbplmjmgsdz6wxr63mghkxjkmma44k0-python-nose-1.3.7/lib/python3.8/site-packages/nose/importer.py:12:
> DeprecationWarning: the imp module is deprecated in favour of importlib; see
> the module's documentation for alternative uses
> from imp import find_module, load_module, acquire_lock, release_lock
>
> build/lib/rpy2/robjects/pandas2ri.py:15
>
> /tmp/guix-build-python-rpy2-3.0.4-1.19868a8.drv-0/source/build/lib/rpy2/robjects/pandas2ri.py:15:
> FutureWarning: pandas.core.index is deprecated and will be removed in a
> future version. The public classes are available in the top-level namespace.
> from pandas.core.index import Index as PandasIndex
>
> /gnu/store/3bk454z353a42l1l4yaxa6lrl3dh24mv-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/mark/structures.py:323
>
> /gnu/store/3bk454z353a42l1l4yaxa6lrl3dh24mv-python-pytest-5.3.5/lib/python3.8/site-packages/_pytest/mark/structures.py:323:
> PytestUnknownMarkWarning: Unknown pytest.mark.lib_dplyr - is this a typo?
> You can register custom marks to avoid this warning - for details, see
> https://docs.pytest.org/en/latest/mark.html
> warnings.warn(
>
> -- Docs: https://docs.pytest.org/en/latest/warnings.html
> !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection
> !!!!!!!!!!!!!!!!!!!!
> ========================= 3 warnings, 1 error in 3.98s
> =========================
> command "pytest" "-v" "rpy/tests/" failed with status 2
> builder for
> `/gnu/store/isdcfnwdw5s3c9dqix7arhn5i4pr7rn9-python-rpy2-3.0.4-1.19868a8.drv'
> failed with exit code 1
> build of
> /gnu/store/isdcfnwdw5s3c9dqix7arhn5i4pr7rn9-python-rpy2-3.0.4-1.19868a8.drv
> failed
> View build log at
> '/var/log/guix/drvs/is/dcfnwdw5s3c9dqix7arhn5i4pr7rn9-python-rpy2-3.0.4-1.19868a8.drv.bz2'.
> guix build: error: build of
> `/gnu/store/isdcfnwdw5s3c9dqix7arhn5i4pr7rn9-python-rpy2-3.0.4-1.19868a8.drv'
> failed
> --8<---------------cut here---------------end--------------->8---
>
> --
> Bonface M. K. (https://www.bonfacemunyoki.com)
> One Divine Emacs To Rule Them All
> GPG key = D4F09EB110177E03C28E2FE1F5BBAE1E0392253F
>
>
>
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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