Subject: bug#42956: closed (Re: bug#42956: python-rpy2 fails to build)

From: [email-masked] (GNU bug Tracking System)
Date: Sun, 23 Aug 2020 08:19:01 +0000

Your bug report

#42956: python-rpy2 fails to build

which was filed against the guix package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

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42956: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=42956
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Subject: Re: bug#42956: python-rpy2 fails to build
From: Efraim Flashner <[email-masked]>
To: "Bonface M. K." <[email-masked]>
Cc: [email-masked]
Date: Sun, 23 Aug 2020 11:17:36 +0300
List-Id: <debbugs-submit.debbugs.gnu.org>

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   <[email-masked]>   אפרים פלשנר
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Subject: python-rpy2 fails to build
From: [email-masked] (Bonface M. K.)
To: [email-masked]
Date: Thu, 20 Aug 2020 17:41:49 +0300
List-Id: <debbugs-submit.debbugs.gnu.org>

Hi all,

When trying to build(I'm using guix on
19da9059212dd81265369340ff1377c62b0cd22e) the python-rpy2 package, I get
the following error:

--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