Package: guix;
Reported by: bonfacemunyoki <at> gmail.com (Bonface M. K.)
Date: Thu, 20 Aug 2020 14:43:02 UTC
Severity: normal
Done: Efraim Flashner <efraim <at> flashner.co.il>
Bug is archived. No further changes may be made.
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From: help-debbugs <at> gnu.org (GNU bug Tracking System) To: bonfacemunyoki <at> gmail.com (Bonface M. K.) Subject: bug#42956: closed (Re: bug#42956: python-rpy2 fails to build) Date: Sun, 23 Aug 2020 08:19:01 +0000
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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 42956 <at> debbugs.gnu.org. -- 42956: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=42956 GNU Bug Tracking System Contact help-debbugs <at> gnu.org with problems
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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 3 (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)]
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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 +0300Hi 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
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