GNU bug report logs - #42956
python-rpy2 fails to build

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: bonfacemunyoki <at> gmail.com (Bonface M. K.)
To: bug-guix <at> gnu.org
Subject: python-rpy2 fails to build
Date: Thu, 20 Aug 2020 17:41:49 +0300

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

Message #10 received at 42956-done <at> debbugs.gnu.org (full text, mbox):

From: Efraim Flashner <efraim <at> flashner.co.il>
To: "Bonface M. K." <bonfacemunyoki <at> gmail.com>
Cc: 42956-done <at> debbugs.gnu.org
Subject: Re: bug#42956: python-rpy2 fails to build
Date: Sun, 23 Aug 2020 11:17:36 +0300

[Message part 1 (text/plain, inline)]

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 <at> flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[signature.asc (application/pgp-signature, inline)]

Message #13 received at 42956-done <at> debbugs.gnu.org (full text, mbox):

From: bonfacemunyoki <at> gmail.com (Bonface M. K.)
To: Efraim Flashner <efraim <at> flashner.co.il>
Cc: 42956-done <at> debbugs.gnu.org
Subject: Re: bug#42956: python-rpy2 fails to build
Date: Sun, 23 Aug 2020 13:47:10 +0300

Efraim Flashner <efraim <at> flashner.co.il> writes:

> 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!
>

Thanks! It builds now. You should probably close the issue now :)

-- 
Bonface M. K. (https://www.bonfacemunyoki.com)
One Divine Emacs To Rule Them All
GPG key = D4F09EB110177E03C28E2FE1F5BBAE1E0392253F

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