[Bug 804125] Review Request: rdkit - A toolkit for cheminformatics and machine learning

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https://bugzilla.redhat.com/show_bug.cgi?id=804125

Jeroen van Meeuwen <kanarip at kanarip.com> changed:

           What    |Removed                     |Added
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                 CC|                            |kanarip at kanarip.com

--- Comment #2 from Jeroen van Meeuwen <kanarip at kanarip.com> 2012-03-28 06:37:09 EDT ---
Just an initial review, I've not yet reviewed .spec, dependencies,
sub-packaging or run-time yet.

> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/x86_64/rdkit-2011.12-1.fc16.x86_64.rpm
> rdkit.x86_64: W: spelling-error Summary(en_US) cheminformatics -> misinformation
> rdkit.x86_64: W: spelling-error %description -l en_US cheminformatics -> misinformation

Perhaps spell cheminformatics out to chemical informatics (perhaps even
information science).

> rdkit.x86_64: W: shared-lib-calls-exit /usr/lib64/libSmilesParse.so.1.2011.12.1 exit at GLIBC_2.2.5
> rdkit.x86_64: W: shared-lib-calls-exit /usr/lib64/libSLNParse.so.1.2011.12.1 exit at GLIBC_2.2.5

I'm not sure what you can do about these other then logging a ticket upstream
with the details on why this is bad.

> 1 packages and 0 specfiles checked; 0 errors, 4 warnings.
> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/x86_64/rdkit-devel-2011.12-1.fc16.x86_64.rpm
> rdkit-devel.x86_64: W: no-documentation
> 1 packages and 0 specfiles checked; 0 errors, 1 warnings.

This can be ignored.

> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/noarch/rdkit-doc-2011.12-1.fc16.noarch.rpm
> rdkit-doc.noarch: W: no-documentation
> 1 packages and 0 specfiles checked; 0 errors, 1 warnings.

This can be ignored.

> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/noarch/rdkit-extras-2011.12-1.fc16.noarch.rpm
> rdkit-extras.noarch: W: no-documentation

This can be ignored.

rdkit-extras.noarch: E: non-executable-script
/usr/share/RDKit/Contrib/M_Kossner/Frames.py 0644L /usr/bin/python
rdkit-extras.noarch: E: non-executable-script
/usr/share/RDKit/Projects/SDView4/SDView.py 0644L /usr/bin/env
1 packages and 0 specfiles checked; 2 errors, 1 warnings.

These you can correct with a simple snippet - either choose to make the files
executable (mind you: may trigger a "executable script in non-standard
location" type of warning or error), or remove the shebang (mind you: may
render the program disfunctional if it expects to be able to execute these
files through a shell-out).

An example of finding those files:

# Find files with a shebang that do not have executable permissions
for file in `find %{buildroot}/%{geminstdir} -type f ! -perm /a+x -name
"*.rb"`; do
    [ ! -z "`head -n 1 $file | grep \"^#!/\"`" ] && chmod -v 755 $file
done

> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/x86_64/python-rdkit-2011.12-1.fc16.x86_64.rpm
> python-rdkit.x86_64: W: no-documentation

This can be ignored.

> python-rdkit.x86_64: E: non-executable-script /usr/lib64/python2.7/site-packages/rdkit/sping/tests/testallps.py 0644L /usr/bin/env
> python-rdkit.x86_64: E: non-executable-script /usr/lib64/python2.7/site-packages/rdkit/utils/pydoc_local.py 0644L /usr/bin/env
> python-rdkit.x86_64: E: non-executable-script /usr/lib64/python2.7/site-packages/rdkit/sping/examples/formatted-strings.py 0644L /usr/bin/env

Same as aforementioned; two options; make files executable or remove shebang.

> python-rdkit.x86_64: E: incorrect-fsf-address /usr/lib64/python2.7/site-packages/rdkit/sping/WX/pidWX.py
> 1 packages and 0 specfiles checked; 4 errors, 1 warnings.

While an upstream bug, the fix is easy. The address should read:

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/x86_64/rdkit-postgresql-2011.12-1.fc16.x86_64.rpm
> rdkit-postgresql.x86_64: W: spelling-error %description -l en_US mol -> mewl, mil, mo
> rdkit-postgresql.x86_64: W: spelling-error %description -l en_US datatype -> data type, data-type, database
> rdkit-postgresql.x86_64: W: spelling-error %description -l en_US fp -> pf, f, p
> rdkit-postgresql.x86_64: W: spelling-error %description -l en_US tanimoto -> animator
> 1 packages and 0 specfiles checked; 0 errors, 4 warnings.
> [kanarip at albert SPECS]$ rpmlint /home/kanarip/devel/rpmbuild/RPMS/x86_64/rdkit-debuginfo-2011.12-1.fc16.x86_64.rpm
> rdkit-debuginfo.x86_64: W: spurious-executable-perm /usr/src/debug/RDKit_2011_12_1/Code/RDBoost/python_streambuf.h
> rdkit-debuginfo.x86_64: W: spurious-executable-perm /usr/src/debug/RDKit_2011_12_1/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp

Remove the executable permissions from these files please;

# Fix anything executable that does not have a shebang
for file in `find %{buildroot}/%{_prefix}/src -type f -perm /a+x`; do
    [ -z "`head -n 1 $file | grep \"^#!/\"`" ] && chmod -v 644 $file
done

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