From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id yI7uN4AmQl9nPAAA0tVLHw (envelope-from ) for ; Sun, 23 Aug 2020 08:19:12 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id rO+YM4AmQl93BAAA1q6Kng (envelope-from ) for ; Sun, 23 Aug 2020 08:19:12 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 051C69400EF for ; Sun, 23 Aug 2020 08:19:11 +0000 (UTC) Received: from localhost ([::1]:48108 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1k9lDZ-0002zD-30 for larch@yhetil.org; Sun, 23 Aug 2020 04:19:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:46886) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1k9lDS-0002yh-2Z for bug-guix@gnu.org; Sun, 23 Aug 2020 04:19:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40481) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1k9lDR-0000a7-Q7 for bug-guix@gnu.org; Sun, 23 Aug 2020 04:19:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1k9lDR-00040L-Mo for bug-guix@gnu.org; Sun, 23 Aug 2020 04:19:01 -0400 Subject: bug#42956: python-rpy2 fails to build Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-To: bug-guix@gnu.org Resent-Date: Sun, 23 Aug 2020 08:19:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: cc-closed 42956 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: "Bonface M. K." Mail-Followup-To: 42956@debbugs.gnu.org, efraim@flashner.co.il, bonfacemunyoki@gmail.com Received: via spool by 42956-done@debbugs.gnu.org id=D42956.159817070515336 (code D ref 42956); Sun, 23 Aug 2020 08:19:01 +0000 Received: (at 42956-done) by debbugs.gnu.org; 23 Aug 2020 08:18:25 +0000 Received: from localhost ([127.0.0.1]:52025 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k9lCn-0003zF-5I for submit@debbugs.gnu.org; Sun, 23 Aug 2020 04:18:25 -0400 Received: from flashner.co.il ([178.62.234.194]:32882) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k9lCh-0003yw-Hu for 42956-done@debbugs.gnu.org; Sun, 23 Aug 2020 04:18:20 -0400 Received: from localhost (unknown [31.210.181.177]) by flashner.co.il (Postfix) with ESMTPSA id 8ED0B40041; Sun, 23 Aug 2020 08:18:09 +0000 (UTC) Date: Sun, 23 Aug 2020 11:17:36 +0300 From: Efraim Flashner Message-ID: <20200823081736.GA1058@E5400> References: <86a6ypwf9u.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="sm4nu43k4a2Rpi4c" Content-Disposition: inline In-Reply-To: <86a6ypwf9u.fsf@gmail.com> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: 42956-done@debbugs.gnu.org Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Spam-Score: -2.61 X-TUID: 8xv/Zeph0q0P --sm4nu43k4a2Rpi4c Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Thu, Aug 20, 2020 at 05:41:49PM +0300, Bonface M. K. wrote: >=20 > Hi all, >=20 > When trying to build(I'm using guix on > 19da9059212dd81265369340ff1377c62b0cd22e) the python-rpy2 package, I get > the following error: >=20 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/l= ib/python3.8/site-packages/rpy2/_rinterface_cffi_build.py to _rinterface_cf= fi_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 i= n distribution > warning: no previously-included files matching '*diff*' found anywhere in= distribution > warning: no previously-included files matching '.hg' found anywhere in di= stribution > 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-pyth= on-rpy2-3.0.4-1.19868a8/lib/python3.8/site-packages/rpy2-3.1.0.dev0-py3.8.e= gg-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' > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D test session starts =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > 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=3DDirectoryBasedExampleDatabase(= '/tmp/guix-build-python-rpy2-3.0.4-1.19868a8.drv-0/source/.hypothesis/examp= les') > 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 >=20 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ERRORS =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D > ___________ 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 > from rpy2.robjects.lib import ggplot2 > build/lib/rpy2/robjects/lib/ggplot2.py:56: in > rlang =3D importr('rlang', on_conflict=3D'warn') > build/lib/rpy2/robjects/packages.py:486: in importr > pack =3D InstalledSTPackage(env, name, > build/lib/rpy2/robjects/packages.py:204: in __init__ > self.__fill_rpy2r__(on_conflict=3Don_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 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D warnings summary =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > /gnu/store/xdbplmjmgsdz6wxr63mghkxjkmma44k0-python-nose-1.3.7/lib/python3= =2E8/site-packages/nose/importer.py:12 > /gnu/store/xdbplmjmgsdz6wxr63mghkxjkmma44k0-python-nose-1.3.7/lib/pytho= n3.8/site-packages/nose/importer.py:12: DeprecationWarning: the imp module = is deprecated in favour of importlib; see the module's documentation for al= ternative uses > from imp import find_module, load_module, acquire_lock, release_lock >=20 > 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 a= nd will be removed in a future version. The public classes are available i= n the top-level namespace. > from pandas.core.index import Index as PandasIndex >=20 > /gnu/store/3bk454z353a42l1l4yaxa6lrl3dh24mv-python-pytest-5.3.5/lib/pytho= n3.8/site-packages/_pytest/mark/structures.py:323 > /gnu/store/3bk454z353a42l1l4yaxa6lrl3dh24mv-python-pytest-5.3.5/lib/pyt= hon3.8/site-packages/_pytest/mark/structures.py:323: PytestUnknownMarkWarni= ng: Unknown pytest.mark.lib_dplyr - is this a typo? You can register custo= m marks to avoid this warning - for details, see https://docs.pytest.org/en= /latest/mark.html > warnings.warn( >=20 > -- Docs: https://docs.pytest.org/en/latest/warnings.html > !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!= !!!!!!! > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D 3 warnings, 1 error in 3.98s =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > 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-p= ython-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--- >=20 > --=20 > Bonface M. K. (https://www.bonfacemunyoki.com) > One Divine Emacs To Rule Them All > GPG key =3D D4F09EB110177E03C28E2FE1F5BBAE1E0392253F >=20 >=20 >=20 --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --sm4nu43k4a2Rpi4c Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAl9CJiAACgkQQarn3Mo9 g1Fy5A//RozkCatRJ0mUxc64cLibAwVjcz8Tod/5UyT8w0zBJ5oY0/a62Tr80pEa rXgnS6eQIeGtLxVuw9tFLPxXSG71tEdRWdypaQYAcbykRtJSKO4NEnDtY8bbZutw /rXzU8Zas+5pt/6OSwJznpCVfIUPje+nALTIxCWWc9jcQ0CLGcJetdtT6B/15aWJ BmsKVOyxiJVi1tsqtX1/lKz6+6lhPwXtYqdGlFOq/RAFh+cnh5av207hRss6Xjbd sUS3a7G3nK+5icp/SBKXpCFhwCJzEa9wF9CsBI/UboLvQAAbAzFClxzdIt6nfZ+W gEnl2qO+i0nGr4JonVcwdMNlxU0AH0BBADN1rS2R2eiL40iBr3nAVme/X2sgmBT5 2xieWL4wCjGcGuad1ZVq2FHXk5MH1EfvuYem6IfjzimN5WwV3qKr4DG4mHki0lPd /hqC4F21kzddCVKTcdzHWS/v+cEiqJF7t6aehRNuubPccVM6WgOMXgUTPVhi+ehj /7SZgzkoxOtoOUXHq8zOYJ4rYzpYxNe6JcP87pmuu2+JFmXcs+AxOCpJO+o9W8M6 bh06FWEcLljiTepNCWDRifQwDXrokVMyunFZcXevbwNfs1q0rLPXJACiocC8qNlp EnPww22kPRVvgcnRhr5u2YAFwZOqDdVXP+c2/wS1VInaDBiQqlI= =89ky -----END PGP SIGNATURE----- --sm4nu43k4a2Rpi4c--