From unknown Sun Jun 22 00:58:20 2025 X-Loop: help-debbugs@gnu.org Subject: bug#42956: python-rpy2 fails to build Resent-From: bonfacemunyoki@gmail.com (Bonface M. K.) Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 20 Aug 2020 14:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 42956 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 42956@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15979345263355 (code B ref -1); Thu, 20 Aug 2020 14:43:02 +0000 Received: (at submit) by debbugs.gnu.org; 20 Aug 2020 14:42:06 +0000 Received: from localhost ([127.0.0.1]:43362 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k8llP-0000rg-O7 for submit@debbugs.gnu.org; Thu, 20 Aug 2020 10:42:06 -0400 Received: from lists.gnu.org ([209.51.188.17]:50268) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k8llO-0000rY-Hr for submit@debbugs.gnu.org; Thu, 20 Aug 2020 10:41:59 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55912) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1k8llO-0005WD-A3 for bug-guix@gnu.org; Thu, 20 Aug 2020 10:41:58 -0400 Received: from mail-wm1-x336.google.com ([2a00:1450:4864:20::336]:54103) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1k8llM-0002hC-1D for bug-guix@gnu.org; Thu, 20 Aug 2020 10:41:58 -0400 Received: by mail-wm1-x336.google.com with SMTP id u18so1832627wmc.3 for ; Thu, 20 Aug 2020 07:41:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:user-agent:mime-version; bh=hv1p7EZwV0CQ4StR6wlJCcrqM7sxwTxW7HLjkJaKTFo=; b=qkmRw2G7GOHYQJHPmR0XNwHX8FrfAJSnIPjnLp0Tb3ZvFHFfpY/Vxa7SapgV8SVdfD urFSrIHeqYSHA0kCPfRUs/SYUnpJukzN/2qYJwcNqtiPeypT/KO4Z75y4FJRV9GNWJ4S r3ptLJfTsQVeLRP4o8B/b5RBDETCbFojrDf+mpe1Ic/Mv9/WX+zUpYKAivt+9yjVNMzp TOwnyi/2qKRlrhgzKy7Sjjd/ErcOx3XQrVGMFu2oIwrJIS/t1VOlO8kQWclp9pf11Z5a sB7ZZRDEe2t6l2zNIVunFLsVstjP78+q7KJnmaKi9IQ0RFBzQpKEqEM/zB8oNJtplNvc VBSQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version; bh=hv1p7EZwV0CQ4StR6wlJCcrqM7sxwTxW7HLjkJaKTFo=; b=obpePXQPt+EGecUuNQPt7cTycWBV82XCr2eZOA0yuosfjwGr+leQvVF0W/F/KeXgHW W/fHTHzxxy9IztfhcMazGMPqu9V0Tsfy9U9KxJ8t1wy2sFC/zM0s3/yL+JUvnuQ8gRui WiPXtPTgyDdOtPzmO5L/c5bbX76TkjOexHv58jSSwaObuSCham7Z4w4U86KVyGpk6zqo UEP6asOyKEHFBG2vPUQxurBC1goynY7MNmq2XzL1ZCkA3gyQIYmDUk7s4GN5lIyVGQIN OAsXSPqGCf+7D+z9XDYTTKfvLt4m/jpyTaqI3zSOwDJenaSQFjc5HZswLK4ZyzCifwv1 G0nA== X-Gm-Message-State: AOAM530K4tW88E8uj3k6uBX4blouQWFZYhvFFxi/Es+LmalrNl84DMcb lkLAV21DBn2GOyFclqxwDEa5yjO/kfc= X-Google-Smtp-Source: ABdhPJycCTjb5bp9zLuf8TW6v58y4SQRnACCiBHpVqWc5+fJ91TRo9ILwwV7Yz6BQEro9nyg1KX1Ng== X-Received: by 2002:a05:600c:2907:: with SMTP id i7mr3612224wmd.182.1597934512858; Thu, 20 Aug 2020 07:41:52 -0700 (PDT) Received: from susa ([41.80.78.132]) by smtp.gmail.com with ESMTPSA id p22sm4320989wmc.38.2020.08.20.07.41.51 for (version=TLS1_2 cipher=ECDHE-ECDSA-CHACHA20-POLY1305 bits=256/256); Thu, 20 Aug 2020 07:41:52 -0700 (PDT) From: bonfacemunyoki@gmail.com (Bonface M. K.) Date: Thu, 20 Aug 2020 17:41:49 +0300 Message-ID: <86a6ypwf9u.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2a00:1450:4864:20::336; envelope-from=bonfacemunyoki@gmail.com; helo=mail-wm1-x336.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001, WEIRD_PORT=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.1 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) 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 from rpy2.robjects.lib import ggplot2 build/lib/rpy2/robjects/lib/ggplot2.py:56: in 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 From unknown Sun Jun 22 00:58:20 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: bonfacemunyoki@gmail.com (Bonface M. K.) Subject: bug#42956: closed (Re: bug#42956: python-rpy2 fails to build) Message-ID: References: <20200823081736.GA1058@E5400> <86a6ypwf9u.fsf@gmail.com> X-Gnu-PR-Message: they-closed 42956 X-Gnu-PR-Package: guix Reply-To: 42956@debbugs.gnu.org Date: Sun, 23 Aug 2020 08:19:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1598170741-15391-1" This is a multi-part message in MIME format... ------------=_1598170741-15391-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" 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@debbugs.gnu.org. --=20 42956: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D42956 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1598170741-15391-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 To: "Bonface M. K." Subject: Re: bug#42956: python-rpy2 fails to build 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-Debbugs-Envelope-To: 42956-done Cc: 42956-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --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-- ------------=_1598170741-15391-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 20 Aug 2020 14:42:06 +0000 Received: from localhost ([127.0.0.1]:43362 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k8llP-0000rg-O7 for submit@debbugs.gnu.org; Thu, 20 Aug 2020 10:42:06 -0400 Received: from lists.gnu.org ([209.51.188.17]:50268) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k8llO-0000rY-Hr for submit@debbugs.gnu.org; Thu, 20 Aug 2020 10:41:59 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55912) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1k8llO-0005WD-A3 for bug-guix@gnu.org; Thu, 20 Aug 2020 10:41:58 -0400 Received: from mail-wm1-x336.google.com ([2a00:1450:4864:20::336]:54103) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1k8llM-0002hC-1D for bug-guix@gnu.org; Thu, 20 Aug 2020 10:41:58 -0400 Received: by mail-wm1-x336.google.com with SMTP id u18so1832627wmc.3 for ; Thu, 20 Aug 2020 07:41:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:user-agent:mime-version; bh=hv1p7EZwV0CQ4StR6wlJCcrqM7sxwTxW7HLjkJaKTFo=; b=qkmRw2G7GOHYQJHPmR0XNwHX8FrfAJSnIPjnLp0Tb3ZvFHFfpY/Vxa7SapgV8SVdfD urFSrIHeqYSHA0kCPfRUs/SYUnpJukzN/2qYJwcNqtiPeypT/KO4Z75y4FJRV9GNWJ4S r3ptLJfTsQVeLRP4o8B/b5RBDETCbFojrDf+mpe1Ic/Mv9/WX+zUpYKAivt+9yjVNMzp TOwnyi/2qKRlrhgzKy7Sjjd/ErcOx3XQrVGMFu2oIwrJIS/t1VOlO8kQWclp9pf11Z5a sB7ZZRDEe2t6l2zNIVunFLsVstjP78+q7KJnmaKi9IQ0RFBzQpKEqEM/zB8oNJtplNvc VBSQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version; bh=hv1p7EZwV0CQ4StR6wlJCcrqM7sxwTxW7HLjkJaKTFo=; b=obpePXQPt+EGecUuNQPt7cTycWBV82XCr2eZOA0yuosfjwGr+leQvVF0W/F/KeXgHW W/fHTHzxxy9IztfhcMazGMPqu9V0Tsfy9U9KxJ8t1wy2sFC/zM0s3/yL+JUvnuQ8gRui WiPXtPTgyDdOtPzmO5L/c5bbX76TkjOexHv58jSSwaObuSCham7Z4w4U86KVyGpk6zqo UEP6asOyKEHFBG2vPUQxurBC1goynY7MNmq2XzL1ZCkA3gyQIYmDUk7s4GN5lIyVGQIN OAsXSPqGCf+7D+z9XDYTTKfvLt4m/jpyTaqI3zSOwDJenaSQFjc5HZswLK4ZyzCifwv1 G0nA== X-Gm-Message-State: AOAM530K4tW88E8uj3k6uBX4blouQWFZYhvFFxi/Es+LmalrNl84DMcb lkLAV21DBn2GOyFclqxwDEa5yjO/kfc= X-Google-Smtp-Source: ABdhPJycCTjb5bp9zLuf8TW6v58y4SQRnACCiBHpVqWc5+fJ91TRo9ILwwV7Yz6BQEro9nyg1KX1Ng== X-Received: by 2002:a05:600c:2907:: with SMTP id i7mr3612224wmd.182.1597934512858; Thu, 20 Aug 2020 07:41:52 -0700 (PDT) Received: from susa ([41.80.78.132]) by smtp.gmail.com with ESMTPSA id p22sm4320989wmc.38.2020.08.20.07.41.51 for (version=TLS1_2 cipher=ECDHE-ECDSA-CHACHA20-POLY1305 bits=256/256); Thu, 20 Aug 2020 07:41:52 -0700 (PDT) From: bonfacemunyoki@gmail.com (Bonface M. K.) To: bug-guix@gnu.org Subject: python-rpy2 fails to build Date: Thu, 20 Aug 2020 17:41:49 +0300 Message-ID: <86a6ypwf9u.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2a00:1450:4864:20::336; envelope-from=bonfacemunyoki@gmail.com; helo=mail-wm1-x336.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001, WEIRD_PORT=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.1 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) 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 from rpy2.robjects.lib import ggplot2 build/lib/rpy2/robjects/lib/ggplot2.py:56: in 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 ------------=_1598170741-15391-1-- From unknown Sun Jun 22 00:58:20 2025 X-Loop: help-debbugs@gnu.org Subject: bug#42956: python-rpy2 fails to build Resent-From: bonfacemunyoki@gmail.com (Bonface M. K.) Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Sun, 23 Aug 2020 10:48:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 42956 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Efraim Flashner Cc: 42956-done@debbugs.gnu.org Received: via spool by 42956-done@debbugs.gnu.org id=D42956.159817964229817 (code D ref 42956); Sun, 23 Aug 2020 10:48:02 +0000 Received: (at 42956-done) by debbugs.gnu.org; 23 Aug 2020 10:47:22 +0000 Received: from localhost ([127.0.0.1]:52157 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k9nWz-0007kr-Qq for submit@debbugs.gnu.org; Sun, 23 Aug 2020 06:47:22 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:54660) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k9nWy-0007ke-EV for 42956-done@debbugs.gnu.org; Sun, 23 Aug 2020 06:47:20 -0400 Received: by mail-wm1-f54.google.com with SMTP id 83so5710324wme.4 for <42956-done@debbugs.gnu.org>; Sun, 23 Aug 2020 03:47:20 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=EUpBauMKZX6emhB7Wgezeph8KJAXxJuEtawck8RTgHc=; b=DlHgOyCWX1ap6Yh7I0/BptxThOpEwtMqxtwc7p28qA8QJSU5Awszag/1aq/h6EJ6jX prIg6J4cVX5cM8lcOFFSlyBIx+PbfE2orEa9XSc7ojYpxg1ahfVBujPyngeJN2x6YQjL /y4fFvmtqDBR0OUwXCH8nD4DWpdRHg/c5YZVcFm2fYpqME6VPwugf+AzwyyupXsi0OU6 lS0IgmUjJPHYyg5Zrzd+Zi5bPmbzlsrHyqnbf7ziY1Lr/DteRL/PLF993PjR0z5Diojf GlvtvGgnHcP4gfF9GOZ9XwS/N18SbWG8Z0xVYZxHBqn3Zs5Hd4XAT1lhm+Pz/9JVPwb9 OsVg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=EUpBauMKZX6emhB7Wgezeph8KJAXxJuEtawck8RTgHc=; b=tnTW5g2H8ZIchQOAR/FWhnwG3ZllLhunx6gRfmIMYguW9Zc1r4Jrhud3dRJng6W8pz v32qYju64c58wqZdXQ77LZpZ2TotfPDdPknvFwNgz5fOc+PQGgV5zzUobbYzZIHk8Zir agEEVIMq/ex/qybP/V43Odcghi0cOo/l1VVv2EN7OuhUQynhCf0F6iUH87KWCn/Tq4YE gOspZEcNgivn/NaUvmIB64aj1qE265VWMrb4b9QuG9q1RRHKHfkFPBz/4IkHtcfENzAh iezQnC3j8dtVxn3tyHqWgg2copETpXBlC9IScBLDCUWVrTvvN5shcDL4GDNJNdx4eyGn 2Kng== X-Gm-Message-State: AOAM5322wBrtZNh2E7Mq9nAd+iS/B0H6cjq31Lx0gvZ2IAhoWn0ZauTv 9gxzaU+uqGm3sLu9kiRKenU+s0GEZfE= X-Google-Smtp-Source: ABdhPJz5sLNETjF6zgviVPWmdcRH+woQii9oC2lTQ8Um08qYO/fBU/n6yWQOVM/xmuPNKCDQ9HdTIA== X-Received: by 2002:a1c:9883:: with SMTP id a125mr1090499wme.133.1598179634264; Sun, 23 Aug 2020 03:47:14 -0700 (PDT) Received: from susa ([41.80.205.124]) by smtp.gmail.com with ESMTPSA id s12sm3535514wmj.26.2020.08.23.03.47.12 (version=TLS1_2 cipher=ECDHE-ECDSA-CHACHA20-POLY1305 bits=256/256); Sun, 23 Aug 2020 03:47:13 -0700 (PDT) From: bonfacemunyoki@gmail.com (Bonface M. K.) References: <86a6ypwf9u.fsf@gmail.com> <20200823081736.GA1058@E5400> Date: Sun, 23 Aug 2020 13:47:10 +0300 In-Reply-To: <20200823081736.GA1058@E5400> (Efraim Flashner's message of "Sun, 23 Aug 2020 11:17:36 +0300") Message-ID: <86y2m5vdu9.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Efraim Flashner 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