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Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.8.1-1.fc21.src.rpm Description: MDAnalysis is a python framework to analyze molecular dynamics trajectories generated by CHARMM, NAMD, LAMMPS, or Gromacs. It is mainly useful for geometric analyses, as there is no implemented potential model. It is inspired by the Schulten Group's MDtools for python, and the source for the DCD reading code is derived from VMD. MDAnalysis isGPL licensed, except for the dcd reading code (UIUC Open Source Licence) which comes from VMD (and is GPL-compatible). Gromacs trajectories are utilizing the Gromacs libxdrfile library (GPL). MDAnalysis exposes trajectory data transparently as NumPy arrays and as such it is easily extensible. Fedora Account System Username: rathann
Hi Dominik. Building this package none test is performed: ... Ran 0 tests in 0.757s
Sorry it took me so long to update. Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.9.2-2.fc21.src.rpm * Fri May 08 2015 Dominik Mierzejewski <rpm> 0.9.2-2 - call the testsuite per upstream docs * Wed May 06 2015 Dominik Mierzejewski <rpm> 0.9.2-1 - update to 0.9.2 - update upstream URL - drop obsolete patch - fix testsuite invocation koji scratch build: https://koji.fedoraproject.org/koji/taskinfo?taskID=9689982
- Please, fix non-standard-executable-perm errors. See rpmlint output. - libxdrfile (packaged in Fedora) is provided originally by the Gromacs developers under the GNU Lesser General Public License version 3. While under development together with the MDAnalysis code, the library was enhanced to provide xtc/trr frame indexing and seeking. This derivative version of the library, named libxdrfile2, is now provided under the GNU General Public License version 2. No Bundled Libraries guidelines are not applied. Please, package MDAnMDAnalysis-0.9.2/src/xdrfile/AUTHORS and MDAnMDAnalysis-0.9.2/src/xdrfile/README. - You could create a -doc sub-package for HTML documentation. - Please, write a comment to document multiple license. - This software is not compatible with Python3 yet. Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - Permissions on files are set properly. Note: See rpmlint output See: http://fedoraproject.org/wiki/Packaging/Guidelines#FilePermissions ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "BSD (3 clause)", "GPL (v2 or later)", "Unknown or generated". 167 files have unknown license. Detailed output of licensecheck in /home/sagitter/1189015-python-MDAnalysis/licensecheck.txt [!]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. [x]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [-]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [x]: Useful -debuginfo package or justification otherwise. [x]: Package is not known to require an ExcludeArch tag. [!]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 61440 bytes in 4 files. [!]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local Python: [x]: Python eggs must not download any dependencies during the build process. [-]: A package which is used by another package via an egg interface should provide egg info. [x]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Binary eggs must be removed in %prep ===== SHOULD items ===== Generic: [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [ ]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [x]: Rpmlint is run on debuginfo package(s). Note: No rpmlint messages. [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: python-MDAnalysis-0.9.2-2.fc23.x86_64.rpm python-MDAnalysis-0.9.2-2.fc23.src.rpm python-MDAnalysis.x86_64: E: explicit-lib-dependency python-matplotlib python-MDAnalysis.x86_64: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.x86_64: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.x86_64: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.x86_64: W: spelling-error %description -l en_US libxdrfile -> fiberfill python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/distances.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/xdrfile/_libxdrfile2.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/_transformations.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/KDTree/_CKDTree.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/parallel/distances.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/qcprot.so 0775L python-MDAnalysis.src: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.src: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.src: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.src: W: spelling-error %description -l en_US libxdrfile -> fiberfill 2 packages and 0 specfiles checked; 9 errors, 8 warnings. Rpmlint (debuginfo) ------------------- Checking: python-MDAnalysis-debuginfo-0.9.2-2.fc23.x86_64.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings. Rpmlint (installed packages) ---------------------------- python-MDAnalysis.x86_64: E: explicit-lib-dependency python-matplotlib python-MDAnalysis.x86_64: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.x86_64: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.x86_64: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.x86_64: W: spelling-error %description -l en_US libxdrfile -> fiberfill python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/distances.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/xdrfile/_libxdrfile2.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/_transformations.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/KDTree/_CKDTree.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/parallel/distances.so 0775L python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/core/qcprot.so 0775L 2 packages and 0 specfiles checked; 9 errors, 4 warnings. Requires -------- python-MDAnalysis (rpmlib, GLIBC filtered): libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libm.so.6()(64bit) libpthread.so.0()(64bit) libpython2.7.so.1.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) netcdf4-python numpy python(abi) python-GridDataFormats python-biopython python-matplotlib python-networkx rtld(GNU_HASH) scipy Provides -------- python-MDAnalysis: python-MDAnalysis python-MDAnalysis(x86-64) Unversioned so-files -------------------- python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/KDTree/_CKDTree.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/xdrfile/_libxdrfile2.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/core/_transformations.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/core/distances.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/core/parallel/distances.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/core/qcprot.so Source checksums ---------------- https://pypi.python.org/packages/source/M/MDAnalysis/MDAnalysis-0.9.2.tar.gz : CHECKSUM(SHA256) this package : 2632e77bd30f6a088d59b599bb16269bf5c6ad02559e45fb630a08190c611800 CHECKSUM(SHA256) upstream package : 2632e77bd30f6a088d59b599bb16269bf5c6ad02559e45fb630a08190c611800 https://pypi.python.org/packages/source/M/MDAnalysisTests/MDAnalysisTests-0.9.2.tar.gz : CHECKSUM(SHA256) this package : 3a7d9a544b6805af70b9a327dea2bf2b837f453c3ce9a40ad21a8fe173763ecb CHECKSUM(SHA256) upstream package : 3a7d9a544b6805af70b9a327dea2bf2b837f453c3ce9a40ad21a8fe173763ecb Generated by fedora-review 0.5.3 (bcf15e3) last change: 2015-05-04 Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1189015 Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, Generic, Shell-api, C/C++ Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP, Ruby Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6
Thanks for the review, Antonio. Regarding the bundled xdrfile2, I have opened a discussion[1] with xdrfile upstream to include MDAnalysis changes. At the moment, there are no consumers of xdrfile in Fedora as far as I can tell, so if upstream accepts the changes, I should be able to simply patch MDAnalysis to use system xdrfile. I'm not able to reproduce the rpmlint permission issues. Docs were not packaged, but I'll add them to a -doc subpackage. [1] https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2015-May/008300.html
Any news here?
No news on the xdrfile front, I'm afraid, though there have been some discussions about consolidating the work by different groups on xdrfile in one place. I'll post an updated spec+srpm shortly, as there were a couple of new releases in the meantime.
rathann's scratch build of python-MDAnalysis-0.13.0-1.fc23.src.rpm for f24 failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12902046
Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.13.0-1.fc23.src.rpm * Mon Feb 08 2016 Dominik Mierzejewski <rpm> 0.13.0-1 - update to 0.13.0 - fix running tests - add Provides for bundled xdrfile - docs not included and failing to build, so disable for now * Wed Oct 14 2015 Dominik Mierzejewski <rpm> 0.12.1-1 - update to 0.12.1 - drop obsolete patch - use the new mda_nosetests script for running tests * Mon May 18 2015 Dominik Mierzejewski <rpm> 0.9.2-4 - relax Improper Torsion topology test check on i686 * Mon May 11 2015 Dominik Mierzejewski <rpm> 0.9.2-3 - document licensing breakdown - package docs
(In reply to Upstream Release Monitoring from comment #7) > rathann's scratch build of python-MDAnalysis-0.13.0-1.fc23.src.rpm for f24 > failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12902046 @Dominik It's failed on rawhide.
Actually it hasn't, I cancelled that task. Anyway, I found a way to build the docs as part of the build process, so here's a new release: Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.13.0-2.fc23.src.rpm * Tue Feb 09 2016 Dominik Mierzejewski <rpm> 0.13.0-2 - build docs - new dependency: seaborn
rathann's scratch build of python-MDAnalysis-0.13.0-2.fc23.src.rpm for f24 failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12915373
rathann's scratch build of python-MDAnalysis-0.13.0-2.fc23.src.rpm for f24 failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12915395
rathann's scratch build of python-MDAnalysis-0.13.0-2.fc23.src.rpm for f24 failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12915640
Looks like three of the tests that should pass with known failure status are returning an error when running on rawhide. I've disabled them for now and filed a report upstream. The tests pass on f23, so it might be an incompatibility with one of the updated python packages in rawhide. The next scratch build should succeed.
rathann's scratch build of python-MDAnalysis-0.13.0-2.fc23.src.rpm for f24 failed http://koji.fedoraproject.org/koji/taskinfo?taskID=12917506
*sigh* Last build succeeded on x86 and failed on armv7hl due to test timeouts. Re-running on just armv7hl with increased timeout value...
rathann's scratch build of python-MDAnalysis-0.13.0-2.fc23.src.rpm for f24 completed http://koji.fedoraproject.org/koji/taskinfo?taskID=12918189
Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - Permissions on files are set properly. Note: See rpmlint output See: http://fedoraproject.org/wiki/Packaging/Guidelines#FilePermissions - doc/sphinx/source/logos is released under CC-BY-ND license. I guess -doc subpackage must contain an own License tag: License: CC-BY-ND and GPLv2+ - -doc subpackage does not provide its own doc files (LICENSE AUTHORS CHANGELOG README SUMMARY.txt) - The libxdr code for accessing Gromacs trajectories including our modifications is published under the Lesser GNU Public Licence (LGPL). LGPLv2 license is missing. - Package does not provide python2-MDAnalysis (see Provides list) Since, sooner or later, this software will support Python3, I think it's better to package a python2-MDAnalysis already now. http://fedoraproject.org/wiki/Packaging:Python#Example_common_spec_file - python_provide macro is missing - Please, fix non-standard-executable-perm and unused-direct-shlib-dependency errors (see rpmlint output) ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: Header files in -devel subpackage, if present. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [!]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "BSD (3 clause)", "GPL (v2 or later)", "Unknown or generated". 261 files have unknown license. Detailed output of licensecheck in /home/sagitter/FedoraReview/1189015-python-MDAnalysis/licensecheck.txt [!]: License file installed when any subpackage combination is installed. [x]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. [x]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [-]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [x]: Useful -debuginfo package or justification otherwise. [x]: Package is not known to require an ExcludeArch tag. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 71680 bytes in 4 files. [!]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local Python: [x]: Python eggs must not download any dependencies during the build process. [x]: A package which is used by another package via an egg interface should provide egg info. [!]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Binary eggs must be removed in %prep ===== SHOULD items ===== Generic: [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [x]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python- MDAnalysis-doc , python-MDAnalysis-debuginfo [ ]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [x]: Rpmlint is run on debuginfo package(s). Note: No rpmlint messages. [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: python-MDAnalysis-0.13.0-2.fc24.x86_64.rpm python-MDAnalysis-doc-0.13.0-2.fc24.noarch.rpm python-MDAnalysis-debuginfo-0.13.0-2.fc24.x86_64.rpm python-MDAnalysis-0.13.0-2.fc24.src.rpm python-MDAnalysis.x86_64: E: explicit-lib-dependency python-matplotlib python-MDAnalysis.x86_64: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.x86_64: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.x86_64: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.x86_64: W: spelling-error %description -l en_US libxdrfile -> fiberfill python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/xdrfile/_libxdrfile2.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so 775 python-MDAnalysis.src: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.src: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.src: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.src: W: spelling-error %description -l en_US libxdrfile -> fiberfill 4 packages and 0 specfiles checked; 8 errors, 12 warnings. Rpmlint (debuginfo) ------------------- Checking: python-MDAnalysis-debuginfo-0.13.0-2.fc24.x86_64.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings. Rpmlint (installed packages) ---------------------------- python-MDAnalysis.x86_64: E: explicit-lib-dependency python-matplotlib python-MDAnalysis.x86_64: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.x86_64: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.x86_64: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.x86_64: W: spelling-error %description -l en_US libxdrfile -> fiberfill python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so /lib64/libpthread.so.0 python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so /lib64/libpthread.so.0 python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so /lib64/libpthread.so.0 python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so /lib64/libpthread.so.0 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/xdrfile/_libxdrfile2.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so 775 python-MDAnalysis.x86_64: E: non-standard-executable-perm /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so 775 3 packages and 0 specfiles checked; 8 errors, 12 warnings. Requires -------- python-MDAnalysis (rpmlib, GLIBC filtered): libc.so.6()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libpthread.so.0()(64bit) libpython2.7.so.1.0()(64bit) netcdf4-python numpy python(abi) python-GridDataFormats python-biopython python-matplotlib python-networkx python-seaborn rtld(GNU_HASH) scipy python-MDAnalysis-debuginfo (rpmlib, GLIBC filtered): python-MDAnalysis-doc (rpmlib, GLIBC filtered): Provides -------- python-MDAnalysis: bundled(xdrfile) python-MDAnalysis python-MDAnalysis(x86-64) python-MDAnalysis-debuginfo: python-MDAnalysis-debuginfo python-MDAnalysis-debuginfo(x86-64) python-MDAnalysis-doc: python-MDAnalysis-doc Unversioned so-files -------------------- python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/xdrfile/_libxdrfile2.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so Source checksums ---------------- https://pypi.python.org/packages/source/M/MDAnalysis/MDAnalysis-0.13.0.tar.gz : CHECKSUM(SHA256) this package : bdf5a15842bd4e4635fcb60297978252c55c5828c9b7003d810c9e19a4fffbe6 CHECKSUM(SHA256) upstream package : bdf5a15842bd4e4635fcb60297978252c55c5828c9b7003d810c9e19a4fffbe6 https://pypi.python.org/packages/source/M/MDAnalysisTests/MDAnalysisTests-0.13.0.tar.gz : CHECKSUM(SHA256) this package : 852d5c24c018f093c3b4cdc5046df50ac48e157df94481299ff21687bacabab9 CHECKSUM(SHA256) upstream package : 852d5c24c018f093c3b4cdc5046df50ac48e157df94481299ff21687bacabab9 Generated by fedora-review 0.6.0 (7737a2a) last change: 2015-11-26 Command line :./try-fedora-review -m fedora-rawhide-x86_64 -b 1189015 Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, Generic, Shell-api, C/C++ Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP, Ruby Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6
(In reply to Antonio Trande from comment #18) > Package Review > ============== > > Legend: > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated > [ ] = Manual review needed > > > Issues: > ======= > - Permissions on files are set properly. > Note: See rpmlint output > See: http://fedoraproject.org/wiki/Packaging/Guidelines#FilePermissions Fixed the permissions. > - doc/sphinx/source/logos is released under CC-BY-ND license. > I guess -doc subpackage must contain an own License tag: > License: CC-BY-ND and GPLv2+ Why? These two licenses are already in the main package license list. > - -doc subpackage does not provide its own doc files > (LICENSE AUTHORS CHANGELOG README SUMMARY.txt) Should it? > - The libxdr code for accessing Gromacs trajectories including our > modifications is published under the Lesser GNU Public Licence > (LGPL). > LGPLv2 license is missing. I can't find any file stating the above. Please tell me where you found this information, exactly. > - Package does not provide python2-MDAnalysis (see Provides list) > Since, sooner or later, this software will support Python3, I think it's > better to package a python2-MDAnalysis already now. > http://fedoraproject.org/wiki/Packaging:Python#Example_common_spec_file > - python_provide macro is missing Done. > - Please, fix non-standard-executable-perm and unused-direct-shlib-dependency > errors (see rpmlint output) Fixed the 775 permissions. [...] > Rpmlint (installed packages) > ---------------------------- > python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency > /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so > /lib64/libpthread.so.0 > python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency > /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so > /lib64/libpthread.so.0 > python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency > /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so > /lib64/libpthread.so.0 > python-MDAnalysis.x86_64: W: unused-direct-shlib-dependency > /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so > /lib64/libpthread.so.0 The -pthread option in gcc command used to compile these comes from python distutils and I'm not sure it's safe to drop it, considering our python interpreter is built with thread support. Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.13.0-3.fc23.src.rpm * Fri Feb 12 2016 Dominik Mierzejewski <rpm> 0.13.0-3 - backport a fix for failing tests on f24 (due to numpy 1.11 changes) - install LICENSE with the doc subpackage as well - move building of docs to the build section - use some python-related convenience macros
(In reply to Dominik 'Rathann' Mierzejewski from comment #19) > (In reply to Antonio Trande from comment #18) > > Package Review > > ============== > > > > Legend: > > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated > > [ ] = Manual review needed > > > > > > Issues: > > > - doc/sphinx/source/logos is released under CC-BY-ND license. > > I guess -doc subpackage must contain an own License tag: > > License: CC-BY-ND and GPLv2+ > > Why? These two licenses are already in the main package license list. In the -doc package there is not any files distributed under BSD or MIT or NCSA license. Therefore, license have to be specified. > > > - -doc subpackage does not provide its own doc files > > (LICENSE AUTHORS CHANGELOG README SUMMARY.txt) > > Should it? They may contain unspecified informations in the documentation files; of course, we can also omit them even if -doc is a stand-alone package. > > > - The libxdr code for accessing Gromacs trajectories including our > > modifications is published under the Lesser GNU Public Licence > > (LGPL). > > LGPLv2 license is missing. > > I can't find any file stating the above. Please tell me where you found this > information, exactly. MDAnalysis/coordinates/xdrfile/src
(In reply to Antonio Trande from comment #20) > (In reply to Dominik 'Rathann' Mierzejewski from comment #19) > > (In reply to Antonio Trande from comment #18) > > > Package Review > > > ============== > > > > > > Legend: > > > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated > > > [ ] = Manual review needed > > > > > > > > > Issues: > > > > > - doc/sphinx/source/logos is released under CC-BY-ND license. > > > I guess -doc subpackage must contain an own License tag: > > > License: CC-BY-ND and GPLv2+ > > > > Why? These two licenses are already in the main package license list. > > In the -doc package there is not any files distributed under BSD or MIT or > NCSA license. Therefore, license have to be specified. Alright, I'll correct the license field there, then. > > > - -doc subpackage does not provide its own doc files > > > (LICENSE AUTHORS CHANGELOG README SUMMARY.txt) > > > > Should it? > > They may contain unspecified informations in the documentation files; of > course, we can also omit them even if -doc is a stand-alone package. It can be installed independently of the main package, but I don't see the point in duplicating those files in it. > > > - The libxdr code for accessing Gromacs trajectories including our > > > modifications is published under the Lesser GNU Public Licence > > > (LGPL). > > > LGPLv2 license is missing. > > > > I can't find any file stating the above. Please tell me where you found this > > information, exactly. > > MDAnalysis/coordinates/xdrfile/src That directory contains just one file: dcd.c, which says this at the top: /* MDAnalysis --- http://mdanalysis.googlecode.com Copyright (c) 2006-2011 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein, and contributors (see website for details) Released under the GNU Public Licence, v2 or any higher version Please cite your use of MDAnalysis in published work: N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, in press. */ Please point me to the exact file where you found the LGPLv2 reference.
This is from source archive on https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.13.0-3.fc23.src.rpm ************************************************************** $ ll MDAnalysis/coordinates/xdrfile/src total 420 -rw-rw-r--. 1 sagitter sagitter 1699 Jan 12 12:46 AUTHORS -rw-rw-r--. 1 sagitter sagitter 18092 Jan 12 12:46 COPYING -rw-rw-r--. 1 sagitter sagitter 387 Jan 12 12:46 __init___py -rw-rw-r--. 1 sagitter sagitter 23630 Jan 12 12:46 libxdrfile2.i -rw-rw-r--. 1 sagitter sagitter 17489 Jan 15 23:40 libxdrfile2.py -rw-rw-r--. 1 sagitter sagitter 156988 Jan 12 12:46 libxdrfile2_wrap.c -rw-rw-r--. 1 sagitter sagitter 359 Jan 12 12:46 NEWS -rw-rw-r--. 1 sagitter sagitter 56208 Jan 12 12:46 numpy.i -rw-rw-r--. 1 sagitter sagitter 1554 Jan 12 12:46 README -rw-rw-r--. 1 sagitter sagitter 1899 Jan 12 12:46 setup_py -rw-rw-r--. 1 sagitter sagitter 64192 Jan 12 12:46 xdrfile.c -rw-rw-r--. 1 sagitter sagitter 23296 Jan 12 12:46 xdrfile.h -rw-rw-r--. 1 sagitter sagitter 16943 Jan 12 12:46 xdrfile_trr.c -rw-rw-r--. 1 sagitter sagitter 2333 Jan 12 12:46 xdrfile_trr.h -rw-rw-r--. 1 sagitter sagitter 6400 Jan 12 12:46 xdrfile_xtc.c -rw-rw-r--. 1 sagitter sagitter 2447 Jan 12 12:46 xdrfile_xtc.h [sagitter@localhost MDAnalysis-0.13.0]$ cat MDAnalysis/coordinates/xdrfile/src/README libxdrfile2 ============= This library allows to read GROMACS trr and xtc files and also to convert from one format to another. libxdrfile2 is a derivative of the `libxdrfile library`_ written by the Gromacs developers. For MDAnalysis we added Python bindings (generated with SWIG_). For libxdrfile2 we added new indexing and seeking capabilities to the library. .. _`libxdr library`: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library .. _SWIG: http://www.swig.org/ Licensing ========= libxdrfile is provided by the Gromacs developers under the GNU Lesser General Public License version 3. While under development together with the MDAnalysis code, the library was enhanced to provide xtc/trr frame indexing and seeking. This derivative version of the library, named libxdrfile2, is now provided under the GNU General Public License version 2. Read the AUTHORS and COPYING files for details. Python bindings =============== Although the whole ``xdrfile`` package is distributed together with `MDAnalysis <http://mdanalysis.googlecode.com>` it is also possible to use it as a stand-alone library. Build the library from the src directory:: mv xdrfile/setup_py setup.py mv xdrfile/__init___py xdrfile/__init__.py swig -python xdrfile/libxdrfile2.i # or copy libxdrfile2.py to xdrfile/ python setup.py build --build-lib=. (This does an in-place build but you can also do a normal ``python setup.py install``.) Note that in order to import the module you will have to do: from xdrfile import libxdrfile2 ************************************************************************ However, the derivated library on MDAnalysis is released under GPLv2. Okay, no LGPL is necessary.
Is this package ready ?
Sorry, I was on vacation. Are there any outstanding issues that need to be resolved? Upstream released 0.14.0 in the meantime so I'll post an updated srpm in the next couple of days.
It looks like numpy 1.11.0 in rawhide breaks MDAnalysis 0.14.0 due to clash with python-tempdir. Stay tuned.
Ok, upstream has fixed it and the testsuite passes now. Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.14.0-1.fc23.src.rpm * Fri Mar 11 2016 Dominik Mierzejewski <rpm> 0.14.0-1 - update to 0.14.0 - don't build docs for now, upstream published them in a zip file - drop obsolete patch - fix tests with numpy 1.11 - fix license field for docs subpackage - install LICENSE with the doc subpackage as well - move building of docs to the build section - use some python-related convenience macros
Is this package even for EPEL? Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - I guess python2-MDAnalysis sub-package have to be made even if python3 is not supported yet. ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: Header files in -devel subpackage, if present. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "BSD (3 clause)", "BSD (2 clause)", "Unknown or generated". 241 files have unknown license. Detailed output of licensecheck in /home/sagitter/FedoraReview/1189015-python-MDAnalysis/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [x]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. [-]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [-]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [x]: Useful -debuginfo package or justification otherwise. [x]: Package is not known to require an ExcludeArch tag. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 81920 bytes in 4 files. [x]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local Python: [x]: Python eggs must not download any dependencies during the build process. [x]: A package which is used by another package via an egg interface should provide egg info. [?]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Binary eggs must be removed in %prep ===== SHOULD items ===== Generic: [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [-]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in python- MDAnalysis-doc , python-MDAnalysis-debuginfo [ ]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [x]: Rpmlint is run on debuginfo package(s). Note: No rpmlint messages. [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: python-MDAnalysis-0.14.0-1.fc25.x86_64.rpm python-MDAnalysis-doc-0.14.0-1.fc25.noarch.rpm python-MDAnalysis-debuginfo-0.14.0-1.fc25.x86_64.rpm python-MDAnalysis-0.14.0-1.fc25.src.rpm python-MDAnalysis.x86_64: E: explicit-lib-dependency python-matplotlib python-MDAnalysis.x86_64: W: spelling-error %description -l en_US isGPL -> Ispell python-MDAnalysis.x86_64: W: spelling-error %description -l en_US dcd -> dc, dd, did python-MDAnalysis.x86_64: W: spelling-error %description -l en_US Gromacs -> Groomsman python-MDAnalysis.x86_64: W: spelling-error %description -l en_US libxdrfile -> fiberfill python-MDAnalysis.x86_64: W: private-shared-object-provides /usr/lib64/python2.7/site-packages/MDAnalysis/lib/formats/libmdaxdr.so libmdaxdr.so()(64bit) python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so python-MDAnalysis.x86_64: W: no-soname /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so 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PYTHONPATH=%{buildroot}%{python2_sitelib}:%{buildroot}%{python2_sitearch}:$PWD \ python-MDAnalysis.src: W: invalid-url Source2: https://github.com/MDAnalysis/mdanalysis/releases/download/release-0.14.0/Documentation.zip HTTP Error 403: Forbidden 4 packages and 0 specfiles checked; 36 errors, 15 warnings. Rpmlint (debuginfo) ------------------- Checking: python-MDAnalysis-debuginfo-0.14.0-1.fc25.x86_64.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings. Rpmlint (installed packages) ---------------------------- rpmlint does not work on rawhide. Requires -------- python-MDAnalysis (rpmlib, GLIBC filtered): libc.so.6()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libpthread.so.0()(64bit) libpython2.7.so.1.0()(64bit) netcdf4-python numpy python(abi) python-GridDataFormats python-biopython python-matplotlib python-networkx python-seaborn rtld(GNU_HASH) scipy python-MDAnalysis-debuginfo (rpmlib, GLIBC filtered): python-MDAnalysis-doc (rpmlib, GLIBC filtered): Provides -------- python-MDAnalysis: bundled(xdrfile) libmdaxdr.so()(64bit) python-MDAnalysis python-MDAnalysis(x86-64) python-MDAnalysis-debuginfo: python-MDAnalysis-debuginfo python-MDAnalysis-debuginfo(x86-64) python-MDAnalysis-doc: python-MDAnalysis-doc Unversioned so-files -------------------- python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/_dcdmodule.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/coordinates/dcdtimeseries.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/_transformations.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/c_distances_openmp.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/formats/cython_util.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/formats/libmdaxdr.so python-MDAnalysis: /usr/lib64/python2.7/site-packages/MDAnalysis/lib/qcprot.so Source checksums ---------------- https://github.com/MDAnalysis/mdanalysis/releases/download/release-0.14.0/Documentation.zip : CHECKSUM(SHA256) this package : 7be9ee1c53ebfd62e88190130de5e4ff3eb3fc1631b56c270bb3afa1bd726618 CHECKSUM(SHA256) upstream package : 7be9ee1c53ebfd62e88190130de5e4ff3eb3fc1631b56c270bb3afa1bd726618 https://pypi.python.org/packages/source/M/MDAnalysis/MDAnalysis-0.14.0.tar.gz : CHECKSUM(SHA256) this package : 3006cc0479b63e31ce6681f4db1f4e94f786aef2ec431670bc10f715c6dfec05 CHECKSUM(SHA256) upstream package : 3006cc0479b63e31ce6681f4db1f4e94f786aef2ec431670bc10f715c6dfec05 https://pypi.python.org/packages/source/M/MDAnalysisTests/MDAnalysisTests-0.14.0.tar.gz : CHECKSUM(SHA256) this package : 11fb626a362016ebd1b52e9b15df253ebdc9960d13cd331732ed732ba0b4c8b9 CHECKSUM(SHA256) upstream package : 11fb626a362016ebd1b52e9b15df253ebdc9960d13cd331732ed732ba0b4c8b9 Generated by fedora-review 0.6.0 (7737a2a) last change: 2015-11-26 Command line :./try-fedora-review -m fedora-rawhide-x86_64 -b 1189015 Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, Generic, Shell-api, C/C++ Disabled plugins: Java, SugarActivity, fonts, Haskell, Ocaml, Perl, R, PHP, Ruby Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6
PLease, fix all 'non-standard-dir-perm' warnings.
Spec URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis.spec SRPM URL: https://rathann.fedorapeople.org/review/python-MDAnalysis/python-MDAnalysis-0.14.0-2.fc23.src.rpm * Tue Mar 15 2016 Dominik Mierzejewski <rpm> 0.14.0-2 - fix non-standard-dir-perm in doc subpackage - move python2 build to python2-MDAnalysis subpackage - exclude private libmdaxdr.so from Provides: EPEL branches are not planned at the moment, but that may change in the future.
Package approved.
Package request has been approved: https://admin.fedoraproject.org/pkgdb/package/python-MDAnalysis
python-MDAnalysis-0.14.0-2.fc23 has been submitted as an update to Fedora 23. https://bodhi.fedoraproject.org/updates/FEDORA-2016-208b886ecc
python-MDAnalysis-0.14.0-2.fc24 has been submitted as an update to Fedora 24. https://bodhi.fedoraproject.org/updates/FEDORA-2016-0cfcd23be2
python-MDAnalysis-0.14.0-2.fc24 has been pushed to the Fedora 24 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-0cfcd23be2
python-MDAnalysis-0.14.0-2.fc23 has been pushed to the Fedora 23 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-208b886ecc
python-MDAnalysis-0.14.0-2.fc24 has been pushed to the Fedora 24 stable repository. If problems still persist, please make note of it in this bug report.
python-MDAnalysis-0.14.0-2.fc23 has been pushed to the Fedora 23 stable repository. If problems still persist, please make note of it in this bug report.