From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id YyrqHS2MPl9ESwAA0tVLHw (envelope-from ) for ; Thu, 20 Aug 2020 14:43:57 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id sLRPGS2MPl8mKAAAbx9fmQ (envelope-from ) for ; Thu, 20 Aug 2020 14:43:57 +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 E543C94062F for ; Thu, 20 Aug 2020 14:43:56 +0000 (UTC) Received: from localhost ([::1]:46332 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1k8lnH-0007CE-OY for larch@yhetil.org; Thu, 20 Aug 2020 10:43:55 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56106) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1k8lmS-0006SB-J5 for bug-guix@gnu.org; Thu, 20 Aug 2020 10:43:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:60052) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1k8lmQ-0002lb-9B for bug-guix@gnu.org; Thu, 20 Aug 2020 10:43:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1k8lmQ-0000tY-6p for bug-guix@gnu.org; Thu, 20 Aug 2020 10:43:02 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#42956: python-rpy2 fails to build Resent-From: bonfacemunyoki@gmail.com (Bonface M. K.) 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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 X-Spam-Score: -0.0 (/) X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=qkmRw2G7; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=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: 0.09 X-TUID: ntbeqEa3kivV 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