[Bug 1189015] Review Request: python-MDAnalysis - Analyze and manipulate molecular dynamics trajectories

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https://bugzilla.redhat.com/show_bug.cgi?id=1189015



--- Comment #27 from Antonio Trande <anto.trande@xxxxxxxxx> ---
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
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/qcprot.so
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/coordinates/xdrfile
775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/selections 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/topology 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/coordinates/xdrfile
775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/coordinates/pdb 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/numpy/lib 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_static 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/visualization 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/topology 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_images 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/lib 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/selections 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/analysis 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/lib 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/core 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/selections
775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/visualization 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/lib 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/analysis 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/analysis/hbonds 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/core 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/numpy 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/topology/tpr 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/visualization
775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/core 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/coordinates 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_sources/documentation_pages/coordinates
775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/_modules/MDAnalysis/topology 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/coordinates 775
python-MDAnalysis-doc.noarch: E: non-standard-dir-perm
/usr/share/doc/python-MDAnalysis-doc/documentation_pages/analysis 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
python-MDAnalysis.src:113: W: rpm-buildroot-usage %build
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

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