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https://bugzilla.redhat.com/show_bug.cgi?id=804125
--- Comment #3 from Gianluca Sforna <giallu(a)gmail.com> 2012-04-13 11:45:55 EDT ---
(In reply to comment #2)
Perhaps spell cheminformatics out to chemical informatics (perhaps
even
information science).
used chemical informatics, despite I'm not really used to call it that way.
> rdkit.x86_64: W: shared-lib-calls-exit /usr/lib64/libSmilesParse.so.1.2011.12.1
exit(a)GLIBC_2.2.5
> rdkit.x86_64: W: shared-lib-calls-exit /usr/lib64/libSLNParse.so.1.2011.12.1
exit(a)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.
Already did it in the past, but it seems that comes from some code
auto-generated during build. I will try to further investigate if you think
this is a blocker
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.
Fixed
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
.
> 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.
So, sping is some (dead) 3rd party code that should be eventually splitted. For
now, I think I will just remove it since it is used to draw chemical structures
when the default backend (cairo) is not available.
/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
Fixed.
Updated package with new upstream release at:
http://giallu.fedorapeople.org/rdkit-2012.03-1.fc16.src.rpm
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