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

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=804125
Bug 804125 depends on bug 1293160, which changed state.

Bug 1293160 Summary: Re-enable building on armv7hl
https://bugzilla.redhat.com/show_bug.cgi?id=1293160

   What|Removed |Added

 Status|NEW |CLOSED
 Resolution|--- |NOTABUG



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

[bugzilla]

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



--- Comment #85 from Fedora Update System  ---
rdkit-2016.03.2-6.fc23 has been pushed to the Fedora 23 stable repository. If
problems still persist, please make note of it in this bug report.

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

[bugzilla]

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



--- Comment #84 from Fedora Update System  ---
rdkit-2016.03.2-6.fc24 has been pushed to the Fedora 24 stable repository. If
problems still persist, please make note of it in this bug report.

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

[bugzilla]

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



--- Comment #83 from Fedora Update System  ---
rdkit-2016.03.2-6.fc25 has been pushed to the Fedora 25 stable repository. If
problems still persist, please make note of it in this bug report.

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

[bugzilla]

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

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA
Last Closed||2016-08-31 12:29:43



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

[bugzilla]

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



--- Comment #82 from Fedora Update System  ---
rdkit-2016.03.2-6.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-2016-0a6d8b86c1

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

[bugzilla]

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



--- Comment #81 from Fedora Update System  ---
rdkit-2016.03.2-6.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-2016-1903e53093

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

[bugzilla]

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

Fedora Update System  changed:

   What|Removed |Added

 Status|MODIFIED|ON_QA



--- Comment #80 from Fedora Update System  ---
rdkit-2016.03.2-6.fc25 has been pushed to the Fedora 25 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-f9a7c78c30

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

[bugzilla]

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



--- Comment #79 from Fedora Update System  ---
rdkit-2016.03.2-6.fc23 has been submitted as an update to Fedora 23.
https://bodhi.fedoraproject.org/updates/FEDORA-2016-1903e53093

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

[bugzilla]

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



--- Comment #78 from Fedora Update System  ---
rdkit-2016.03.2-6.fc24 has been submitted as an update to Fedora 24.
https://bodhi.fedoraproject.org/updates/FEDORA-2016-0a6d8b86c1

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

[bugzilla]

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



--- Comment #77 from Fedora Update System  ---
rdkit-2016.03.2-6.fc25 has been submitted as an update to Fedora 25.
https://bodhi.fedoraproject.org/updates/FEDORA-2016-f9a7c78c30

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

[bugzilla]

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

Fedora Update System  changed:

   What|Removed |Added

 Status|ASSIGNED|MODIFIED



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

[bugzilla]

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



--- Comment #76 from Jon Ciesla  ---
Package request has been approved:
https://admin.fedoraproject.org/pkgdb/package/rpms/rdkit

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

[bugzilla]

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

Antonio Trande  changed:

   What|Removed |Added

  Flags|fedora-review?  |fedora-review+



--- Comment #75 from Antonio Trande  ---
(In reply to Gianluca Sforna from comment #74)
> (In reply to Antonio Trande from comment #72)
> > *
> 
> > 
> > - This package can't be built on epel7-pcc64le because of missing
> >   'pandoc' package.
> 
> Looks like there is a bug for this:
> https://bugzilla.redhat.com/show_bug.cgi?id=1293160

In this case, pcc64le should be excluded if you want build on epel7 already
now.

Review completed, package approved for Fedora and epel7.
If someone wishes point out something else, please do it.

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

[bugzilla]

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

Gianluca Sforna  changed:

   What|Removed |Added

 Depends On||1293160



--- Comment #74 from Gianluca Sforna  ---
(In reply to Antonio Trande from comment #72)
> *
> cp -a python2 python3
> find python3 -name '*.py' | xargs sed -i '1s|^#!.*|#!%{__python3}|'
> find python2 -name '*.py' | xargs sed -i '1s|^#!.*|#!%{__python2}|'
> 
> # fix tests scripts for python3 runtime
> find python3 -name 'test_list.py' | xargs sed -i 's/"python"/"python3"/g'
> sed -i.orig 's/python/python3/g' python3/Projects/DbCLI/TestDbCLI.py
> *

Correct, but it hurts only space requirements on builders, I'd rather not add
more stuff to an already busy spec file.


> 
> - Fix this typo
> 
> -D PYTHON_EXECUTABLE:FILEPATH=%{__python3} \
> %ifarch {%arm}<
> -D RDK_OPTIMIZE_NATIVE:BOOL=OFF \

Done

> 
> - This package can't be built on epel7-pcc64le because of missing
>   'pandoc' package.

Looks like there is a bug for this:
https://bugzilla.redhat.com/show_bug.cgi?id=1293160


> 
> - epel6: "cc1plus: error: unrecognized command line option "-mpopcnt""
I will not build for anyway EPEL6 due to boost requirements

Stuff in the list looks very minor, but if you like I will post a -7
spec.package. How close do you think we are to a positive review?


Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1293160
[Bug 1293160] Re-enable building on armv7hl
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[Bug 804125] Review Request: rdkit - A toolkit for cheminformatics and machine learning

[bugzilla]

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



--- Comment #73 from Antonio Trande  ---
> - These are commands for Python3 builds but are not conditionalized

Sorry, i meant without conditional macro.

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

[bugzilla]

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



--- Comment #72 from Antonio Trande  ---
Package Review
==

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed

- These are commands for Python3 builds but are not conditionalized

*
cp -a python2 python3
find python3 -name '*.py' | xargs sed -i '1s|^#!.*|#!%{__python3}|'
find python2 -name '*.py' | xargs sed -i '1s|^#!.*|#!%{__python2}|'

# fix tests scripts for python3 runtime
find python3 -name 'test_list.py' | xargs sed -i 's/"python"/"python3"/g'
sed -i.orig 's/python/python3/g' python3/Projects/DbCLI/TestDbCLI.py
*

- Fix this typo

-D PYTHON_EXECUTABLE:FILEPATH=%{__python3} \
%ifarch {%arm}<
-D RDK_OPTIMIZE_NATIVE:BOOL=OFF \

- This package can't be built on epel7-pcc64le because of missing
  'pandoc' package.

- epel6: "cc1plus: error: unrecognized command line option "-mpopcnt""


= 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]: ldconfig called in %post and %postun if required.
[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: "Unknown or generated", "MIT/X11 (BSD like)", "BSL (v1.0)",
 "BSL", "BSD (3 clause)", "BSD (2 clause)". 2251 files have unknown
 license. Detailed output of licensecheck in
 /home/sagitter/rpmbuild/SRPMS/rdkit/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[x]: Package must own all directories that it creates.
 Note: Directories without known owners: /usr/lib64/cmake
[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.
[x]: 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 153600 bytes in 2 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 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]: 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 

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

[bugzilla]

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



--- Comment #71 from Rex Dieter  ---
A strong and not-so-humble suggestion (for reviewer and non-reviewer commenters
mostly): please focus on strict review blockers (those documented in package
review guidelines.  One specific item: rpmlint warnings are not blockers

Polish and nice-to-have stuff can certainly be added later (which is more
easily done with better collaboration after package is imported).

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

[bugzilla]

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



--- Comment #70 from Gianluca Sforna  ---
I used the suggestion from 
https://fedoraproject.org/wiki/Common_Rpmlint_issues#unused-direct-shlib-dependency

and added the linker flag in:
> https://giallu.fedorapeople.org/rdkit.spec
> https://giallu.fedorapeople.org/rdkit-2016.03.2-6.fc23.src.rpm

Antonio, please test it and let me know if it works

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

[bugzilla]

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



--- Comment #69 from Paul Emsley  ---
(In reply to Gianluca Sforna from comment #68)
> Another iteration at:
> https://giallu.fedorapeople.org/rdkit.spec
> https://giallu.fedorapeople.org/rdkit-2016.03.2-5.fc23.src.rpm
> 
> The "unused-direct-shlib-dependency" rpmlint issues seems to be rawhide
> specific, as my F24 mock build does not exhibit the same behavior. 

That's curious. Perhaps add to your CMakeLists.txt:

set (CMAKE_SHARED_LINKER_FLAGS "-Wl,--as-needed")

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

[bugzilla]

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



--- Comment #68 from Gianluca Sforna  ---
Another iteration at:
https://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2016.03.2-5.fc23.src.rpm

I fixed the rpath for the cartridge and the removed the fmcs script as
suggested in comment #66, the wrong-script-interpreter is also fixed for
fcms.py

The "unused-direct-shlib-dependency" rpmlint issues seems to be rawhide
specific, as my F24 mock build does not exhibit the same behavior. I will need
to investigate where this come from, please let me know if you consider this
blocking for the review.

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

[bugzilla]

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



--- Comment #67 from Antonio Trande  ---
Package Review
==

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed

Issues
==

- Remove rpath contained in /usr/lib64/pgsql/rdkit.so

- Fix wrong-script-interpreter and unused-direct-shlib-dependency
  warnings (see rpmlint output).

- Two tests are failed on my PC, i have disabled all tests for the reviewing

>Start   8: pyFPB
> 8: Test command: /usr/bin/python2 
> "/builddir/build/BUILD/rdkit-Release_2016_03_2/python2/Code/DataStructs/Wrap/testFPB.py"
> 8: Test timeout computed to be: 9.99988e+06
> 8: .
>  8/103 Test   #8: pyFPB ***Exception: Illegal  
> 0.32 sec

- The package does not build on epel because of issue reported in comment #61.

= MUST items =

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[!]: Rpath absent or only used for internal libs.
 Note: See rpmlint output
[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]: ldconfig called in %post and %postun if required.
[x]: Package does not contain any libtool archives (.la)

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: "Unknown or generated", "MIT/X11 (BSD like)", "BSL (v1.0)",
 "BSL", "BSD (3 clause)", "BSD (2 clause)". 2251 files have unknown
 license. Detailed output of licensecheck in
 /home/sagitter/rpmbuild/SRPMS/rdkit/licensecheck.txt
[x]: License file installed when any subpackage combination is installed.
[x]: Package must own all directories that it creates.
 Note: Directories without known owners: /usr/lib64/cmake
[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.
[x]: 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.
[-]: 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 153600 bytes in 2 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 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]: 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 

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

[bugzilla]

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



--- Comment #66 from Paul Emsley  ---
(In reply to Gianluca Sforna from comment #65)

> > 
> > Skip the test?
> 
> yep, I did it and prepared a new package

Good stuff.

> 
> https://giallu.fedorapeople.org/rdkit.spec
> https://giallu.fedorapeople.org/rdkit-2016.03.2-4.fc23.src.rpm
> 
> scratch build far rawhide:
> http://koji.fedoraproject.org/koji/taskinfo?taskID=15242505

You have put an executable script fmcs in
/usr/lib64/python2.7/site-packages/rdkit/Chem/fmcs.  I don't think that it
belongs there. RDKit users shouldn't have to add
/usr/lib64/python2.7/site-packages/rdkit/Chem/fmcs to their path to find it. In
fact, as it's just a shim I don't think it need to be packaged at all and RDKit
users can get to fmcs funcions via

>>> from RDKit.Chem import fmcs

or so?  (And that will use fmcs.py, not fmcs.)

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

[bugzilla]

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



--- Comment #65 from Gianluca Sforna  ---
(In reply to Paul Emsley from comment #64)
> I'd say that it is (very) esoteric.  Are you sure that you need to run the
> testPgSQL test?  It seems to me more of a test of your database
> configuration skills than of RDKit features. 

rdkit ships a PgSQL cartridge to store molecules in the DB. I think the idea is
to test those functions in the context of the DB server.

> 
> Skip the test?

yep, I did it and prepared a new package

https://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2016.03.2-4.fc23.src.rpm

scratch build far rawhide:
http://koji.fedoraproject.org/koji/taskinfo?taskID=15242505

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

[bugzilla]

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



--- Comment #64 from Paul Emsley  ---
(In reply to Gianluca Sforna from comment #63)

> does anyone know if it is
> possible to use pg_regress on the buildsystem chroot?

I do not know if it's possible.  It doesn't seem like a popular thing to want
to do.
I'd say that it is (very) esoteric.  Are you sure that you need to run the
testPgSQL test?  It seems to me more of a test of your database configuration
skills than of RDKit features. 

Skip the test?

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

[bugzilla]

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



--- Comment #63 from Gianluca Sforna  ---
Thanks Paul, I actually added ifdef on %arm to disable the RDK_OPTIMIZE_NATIVE
flag and managed to fix another issue with the postgresql cartridge build,
switching to cmake also for that one [1]

However, I have now a failing test for PostgreSQL, do anyone know if it is
possible to use pg_regress on the buildsystem chroot?

Latest spec/srpm:
https://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2016.03.2-3.fc23.src.rpm

[1] https://github.com/rdkit/rdkit/pull/1009

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

[bugzilla]

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

Paul Emsley  changed:

   What|Removed |Added

 CC||pems...@gmail.com



--- Comment #62 from Paul Emsley  ---

Here's a patch for arm:


--- CMakeLists.txt-orig2016-08-07 01:24:15.72000 +0100
+++ CMakeLists.txt2016-08-07 01:28:10.99700 +0100
@@ -42,7 +42,9 @@

 if(NOT MSVC)
   if(RDK_OPTIMIZE_NATIVE)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
+ IF(NOT ${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm") 
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
+ endif()
   endif()
 endif()

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

[bugzilla]

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



--- Comment #61 from Rex Dieter  ---
Failure was some custom/incompatible compiler flag apparently:

cc1plus: error: unrecognized command line option '-mpopcnt'

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

[bugzilla]

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



--- Comment #60 from Antonio Trande  ---
Still failed on arm:

http://koji.fedoraproject.org/koji/taskinfo?taskID=15129093

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

[bugzilla]

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



--- Comment #59 from Gianluca Sforna  ---
(In reply to Rex Dieter from comment #58)
> BuildRequires: texlive-collection-latexrecommended
> and maybe also:
> BuildRequires: texlive-collection-fontsrecommended
> as a starting point.

Thanks Rex, that's very useful to know!

New package uploaded, build tested in rawhide:

https://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2016.03.2-2.fc23.src.rpm

BTW, I assume we haven't the same texlive metapackages for EPEL?

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

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=804125
Bug 804125 depends on bug 1358725, which changed state.

Bug 1358725 Summary: Fix auto-pointer registration in Boost Python 1.60
https://bugzilla.redhat.com/show_bug.cgi?id=1358725

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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

[bugzilla]

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



--- Comment #58 from Rex Dieter  ---
I'd recommend trying:
BuildRequires: texlive-collection-latexrecommended
and maybe also:
BuildRequires: texlive-collection-fontsrecommended
as a starting point.

Then, for any missing latex package(s), you can add more:

BuildRequires: tex(missing_tex_package_name)
lines until it's happy.

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

[bugzilla]

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



--- Comment #57 from Gianluca Sforna  ---
(In reply to Igor Gnatenko from comment #56)
> 
> BuildRequires: /usr/bin/pdflatex

Yep, I tried it but just uncovered a whole lot of more missing texlive parts,
fonts and stuff...

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

[bugzilla]

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



--- Comment #56 from Igor Gnatenko  ---
(In reply to Gianluca Sforna from comment #55)
> ok, it seems rawhide has either a different split of the texlive packages or
> (more probably) the dependencies between them changed so I need to find out
> what I really need to BuildRequire for the documentation.

BuildRequires: /usr/bin/pdflatex

?

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

[bugzilla]

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



--- Comment #55 from Gianluca Sforna  ---
ok, it seems rawhide has either a different split of the texlive packages or
(more probably) the dependencies between them changed so I need to find out
what I really need to BuildRequire for the documentation.

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

[bugzilla]

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



--- Comment #54 from Antonio Trande  ---
Fedora rawhide-i386.

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

[bugzilla]

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



--- Comment #53 from Gianluca Sforna  ---
(In reply to Antonio Trande from comment #52)
> 
> Gianluca, 'pdflatex' is still a missing command.

In which distro/arch? As stated above, mock build is fine.

BTW, thanks a lot for prodding the boost maintainer into looking at the issue.

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

[bugzilla]

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



--- Comment #52 from Antonio Trande  ---
(In reply to Gianluca Sforna from comment #46)
> I prepared an updated spec/srpm for the latest version.
> 
> It builds in mock for F23, but fails its test suite in F24 (and probably
> rawhide) due to https://bugzilla.redhat.com/show_bug.cgi?id=1358725
> 
> https://giallu.fedorapeople.org/rdkit.spec
> https://giallu.fedorapeople.org/rdkit-2016.03.2-1.fc23.src.rpm

Gianluca, 'pdflatex' is still a missing command.

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

[bugzilla]

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

Antonio Trande  changed:

   What|Removed |Added

 Depends On||1358725




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1358725
[Bug 1358725] Fix auto-pointer registration in Boost Python 1.60
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[Bug 804125] Review Request: rdkit - A toolkit for cheminformatics and machine learning

[bugzilla]

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



--- Comment #51 from Gianluca Sforna  ---
So, I found 
https://fedorahosted.org/fpc/ticket/567
on the python3 on EPEL topic.

It seems the guidelines/tooling are not finalized, so I guess we can live with
the current state of the SPEC file, since right now I'm only building for
python2 in EPEL.

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

[bugzilla]

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



--- Comment #50 from Gianluca Sforna  ---
(In reply to Igor Gnatenko from comment #49)
> python3 packages
> should not have python3, but should have python%{python3_pkgversion} prefix
> and some other things you need to consider if you really want to build it
> for EPEL7.

I am playing catchup on the Python guidelines since the 2/3 split, have you got
any pointers to the changes needed for EPEL? I have several users of my COPR
build on EL7 and if possible I would like to support them with the same
package.

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

[bugzilla]

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



--- Comment #49 from Igor Gnatenko  ---
(In reply to Gianluca Sforna from comment #48)
> Update. Same package also builds in mock for EPEL 7
but it doesn't mean that it's properly packaged for EPEL7. python3 packages
should not have python3, but should have python%{python3_pkgversion} prefix and
some other things you need to consider if you really want to build it for
EPEL7.

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

[bugzilla]

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



--- Comment #48 from Gianluca Sforna  ---
Update. Same package also builds in mock for EPEL 7

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

[bugzilla]

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



--- Comment #47 from Igor Gnatenko  ---
> %if 0%{?rhel} && 0%{?rhel} <= 6
drop such things, you don't build this package for EL*

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

[bugzilla]

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



--- Comment #46 from Gianluca Sforna  ---
I prepared an updated spec/srpm for the latest version.

It builds in mock for F23, but fails its test suite in F24 (and probably
rawhide) due to https://bugzilla.redhat.com/show_bug.cgi?id=1358725

https://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2016.03.2-1.fc23.src.rpm

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

[bugzilla]

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



--- Comment #45 from Antonio Trande  ---
make -C _build/latex all-pdf
make[1]: Entering directory
'/builddir/build/BUILD/rdkit-Release_2015_09_2/python2/Docs/Book/_build/latex'
pdflatex  'RDKit.tex'
make[1]: pdflatex: Command not found
Makefile:66: recipe for target 'RDKit.pdf' failed

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

[bugzilla]

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



--- Comment #44 from Gianluca Sforna  ---
(In reply to Antonio Trande from comment #43)
> Is this package for epel too ?

Yes, or at least it was supposed to. Recent versions have made it more
difficult to do so (for instance, now some recent boost is needed) so I would
need to check status.

Last successful build for EPEL 7 was for 2015.09 release, see 
https://copr.fedorainfracloud.org/coprs/giallu/rdkit/package/rdkit/
for details

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

[bugzilla]

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



--- Comment #43 from Antonio Trande  ---
Hi Gianluca.

Is this package for epel too ?

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

[bugzilla]

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

Antonio Trande  changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
   Assignee|nob...@fedoraproject.org|anto.tra...@gmail.com
  Flags||fedora-review?



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

[bugzilla]

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

Germano Massullo  changed:

   What|Removed |Added

  Flags|fedora-review?  |



--- Comment #42 from Germano Massullo  ---
Grr the package was still flagged as "Package Under Review", so it did not show
up in the pending review lists.
I just fixed the flag

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

[bugzilla]

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

Gianluca Sforna  changed:

   What|Removed |Added

 Status|ASSIGNED|NEW
   Assignee|i...@cicku.me  |nob...@fedoraproject.org
  Flags|needinfo?(i...@cicku.me)   |



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

[bugzilla]

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



--- Comment #41 from Gianluca Sforna  ---
Ok, starting the stalled review procedure. Will reassign to nobody in a week or
so if we can't continue it.

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

[bugzilla]

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



--- Comment #40 from Gianluca Sforna  ---
Updated package and spec, the tests are now fixed:

https://giallu.fedorapeople.org/rdkit-2015.09.2-2.fc23.src.rpm

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

[bugzilla]

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



--- Comment #39 from Gianluca Sforna  ---
Whoa! that was a huge list, but I think I got it.

https://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2015.09.2-1.fc23.src.rpm

are the new SRPM and spec, updated to the latest release.

Tests works, but are still disabled because there is an upstream bug about
nested tests (they calls python2 explicitly, so they fails when using python3)
but I am working on that.

Other than this I think I addressed all the other remarks.

If you want to have a look at built packages, I have a COPR for this:

https://copr.fedoraproject.org/coprs/giallu/rdkit/build/140387/

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

[bugzilla]

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

Christopher Meng  changed:

   What|Removed |Added

  Flags|needinfo?(i...@cicku.me)   |



--- Comment #37 from Christopher Meng  ---
Package Review
==

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated



Issues:
===
- 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.
  Note: License file license.txt is marked as %doc instead of %license
  See:
  http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text


= 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]: ldconfig called in %post and %postun if required.
[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: "Unknown or generated", "MIT/X11 (BSD like)", "BSL (v1.0)",
 "BSL", "BSD (3 clause)", "BSD (2 clause)". 1049 files have unknown
 license. Detailed output of licensecheck:

See attachment.

[x]: License file installed when any subpackage combination is installed.
[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.
[x]: 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 133120 bytes in 3 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]: Rpmlint is run on all rpms the build produces.
 Note: There are rpmlint messages (see attachment).
[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]: 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.
[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:
[-]: Uses parallel make %{?_smp_mflags} macro.
[x]: Avoid bundling fonts 

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

[bugzilla]

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



--- Comment #38 from Christopher Meng  ---
Created attachment 1073997
  --> https://bugzilla.redhat.com/attachment.cgi?id=1073997=edit
licensecheck of rdkit

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

[bugzilla]

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

Gianluca Sforna  changed:

   What|Removed |Added

  Flags||needinfo?(i...@cicku.me)



--- Comment #36 from Gianluca Sforna  ---
Christopher, are you able to complete the review? 
I am running a COPR for this since some time, so I'd rather close this review
request if I'm not able to make it into proper repos after three years.

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

[bugzilla]

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



--- Comment #35 from Gianluca Sforna gia...@gmail.com ---
Newest update on:
http://giallu.fedorapeople.org/rdkit.spec
https://giallu.fedorapeople.org/rdkit-2015.03.1-2.fc21.src.rpm

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

[bugzilla]

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



--- Comment #34 from Gianluca Sforna gia...@gmail.com ---
Updated spec and srpm:
http://giallu.fedorapeople.org/rdkit-2015.03.1-1.fc21.src.rpm
http://giallu.fedorapeople.org/rdkit.spec

Added the ?_isa bit on subpackages, will fix the python stuff at next release.
However, the shlib warning is eluding me since a long time...

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

[bugzilla]

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

Christopher Meng i...@cicku.me changed:

   What|Removed |Added

 Blocks||100 (ML-SIG)



--- Comment #33 from Christopher Meng i...@cicku.me ---
Please patch all /usr/bin/env python to %{__python2}.

Please try to fix the W: unused-direct-shlib-dependency issues, you can take a
look at the common rpmlint page.

Please add the ?_isa bits macro for non-noarch subpackages:

http://fedoraproject.org/wiki/Packaging:Guidelines#Requiring_Base_Package


Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=100
[Bug 100] Machine Learning SIG - review tracker
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[Bug 804125] Review Request: rdkit - A toolkit for cheminformatics and machine learning

[bugzilla]

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



--- Comment #32 from Gianluca Sforna gia...@gmail.com ---
So the only real issue I see on the report is a directory not owned. I
corrected that in -3.

http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2014.03.1-3.fc20.src.rpm

Anything left?

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

[bugzilla]

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



--- Comment #30 from Gianluca Sforna gia...@gmail.com ---
Works on Koji.
http://koji.fedoraproject.org/koji/taskinfo?taskID=6862522

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

[bugzilla]

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



--- Comment #29 from Christopher Meng i...@cicku.me ---
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.9AZKoz
+ umask 022
+ cd /builddir/build/BUILD
+ cd rdkit-Release_2014_03_1
+ export RDBASE=/builddir/build/BUILD/rdkit-Release_2014_03_1
+ RDBASE=/builddir/build/BUILD/rdkit-Release_2014_03_1
+ export LD_LIBRARY_PATH=/builddir/build/BUILD/rdkit-Release_2014_03_1/lib
+ LD_LIBRARY_PATH=/builddir/build/BUILD/rdkit-Release_2014_03_1/lib
+ export PYTHONPATH=/builddir/build/BUILD/rdkit-Release_2014_03_1
+ PYTHONPATH=/builddir/build/BUILD/rdkit-Release_2014_03_1
+ make test
Running tests...
/usr/bin/ctest --force-new-ctest-process 
Test project /builddir/build/BUILD/rdkit-Release_2014_03_1
  Start  1: testInchi
 1/79 Test  #1: testInchi    Passed0.21 sec
  Start  2: testDict
 2/79 Test  #2: testDict .   Passed0.07 sec
  Start  3: testDataStructs
 3/79 Test  #3: testDataStructs ..   Passed0.08 sec
  Start  4: pyBV
 4/79 Test  #4: pyBV .   Passed3.81 sec
  Start  5: pyDiscreteValueVect
 5/79 Test  #5: pyDiscreteValueVect ..   Passed0.23 sec
  Start  6: pySparseIntVect
 6/79 Test  #6: pySparseIntVect ..   Passed0.22 sec
  Start  7: testTransforms
 7/79 Test  #7: testTransforms ...   Passed0.02 sec
  Start  8: testGrid
 8/79 Test  #8: testGrid .   Passed0.43 sec
  Start  9: testPyGeometry
 9/79 Test  #9: testPyGeometry ...   Passed0.25 sec
  Start 10: testMatrices
10/79 Test #10: testMatrices .   Passed0.01 sec
  Start 11: testAlignment
11/79 Test #11: testAlignment    Passed0.02 sec
  Start 12: pyAlignment
12/79 Test #12: pyAlignment ..   Passed0.28 sec
  Start 13: testOptimizer
13/79 Test #13: testOptimizer    Passed0.01 sec
  Start 14: testUFFForceField
14/79 Test #14: testUFFForceField ***Exception: Other  0.13 sec
  Start 15: testMMFFForceField
15/79 Test #15: testMMFFForceField ...***Exception: Other  0.29 sec
  Start 16: pyForceFieldConstraints
16/79 Test #16: pyForceFieldConstraints ..***Failed0.37 sec
  Start 17: testDistGeom
17/79 Test #17: testDistGeom .   Passed0.02 sec
  Start 18: pyDistGeom
18/79 Test #18: pyDistGeom ...   Passed0.21 sec
  Start 19: graphmolTest1
19/79 Test #19: graphmolTest1    Passed0.25 sec
  Start 20: graphmolcpTest
20/79 Test #20: graphmolcpTest ...   Passed0.05 sec
  Start 21: graphmolqueryTest
21/79 Test #21: graphmolqueryTest    Passed0.05 sec
  Start 22: graphmolMolOpsTest
22/79 Test #22: graphmolMolOpsTest ...   Passed3.35 sec
  Start 23: graphmoltestCanon
23/79 Test #23: graphmoltestCanon    Passed0.37 sec
  Start 24: graphmoltestChirality
24/79 Test #24: graphmoltestChirality    Passed0.23 sec
  Start 25: graphmoltestPickler
25/79 Test #25: graphmoltestPickler ..   Passed0.71 sec
  Start 26: graphmolIterTest
26/79 Test #26: graphmolIterTest .   Passed0.05 sec
  Start 27: testDepictor
27/79 Test #27: testDepictor .   Passed0.85 sec
  Start 28: pyDepictor
28/79 Test #28: pyDepictor ...   Passed0.73 sec
  Start 29: smiTest1
29/79 Test #29: smiTest1 .   Passed0.55 sec
  Start 30: smaTest1
30/79 Test #30: smaTest1 .   Passed2.69 sec
  Start 31: fileParsersTest1
31/79 Test #31: fileParsersTest1 .   Passed   13.93 sec
  Start 32: testMolSupplier
32/79 Test #32: testMolSupplier ..   Passed0.72 sec
  Start 33: testMolWriter
33/79 Test #33: testMolWriter    Passed0.71 sec
  Start 34: testTplParser
34/79 Test #34: testTplParser    Passed0.06 sec
  Start 35: testMol2ToMol
35/79 Test #35: testMol2ToMol    Passed0.11 sec
  Start 36: testSubstructMatch
36/79 Test #36: testSubstructMatch ...   Passed0.05 sec
  Start 37: testReaction
37/79 Test #37: testReaction .   Passed0.21 sec
  Start 38: pyChemReactions
38/79 Test #38: pyChemReactions ..   Passed0.26 sec
  Start 39: testChemTransforms
39/79 Test #39: testChemTransforms ...   Passed0.16 sec
  Start 40: testSubgraphs1
40/79 Test #40: testSubgraphs1 ...   Passed0.67 sec
  Start 41: testSubgraphs2
41/79 Test #41: testSubgraphs2 ...   Passed0.06 sec
  Start 42: 

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

[bugzilla]

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



--- Comment #28 from Gianluca Sforna gia...@gmail.com ---
And now it went final:

http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2014.03.1-1.fc20.src.rpm

Are there any more blockers? After two years I'd like push it to repos and move
on :)

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

[bugzilla]

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



--- Comment #27 from Gianluca Sforna gia...@gmail.com ---
I am not sure if rawhide was broken or the latest rdkit (currently in beta)
fixed the issue, but it works:

http://koji.fedoraproject.org/koji/taskinfo?taskID=6821330

Updated files:
http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2014.03.1beta1-1.fc20.src.rpm

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

[bugzilla]

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



--- Comment #26 from Christopher Meng cicku...@gmail.com ---
Rawhide build failed.

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

[bugzilla]

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



--- Comment #25 from Gianluca Sforna gia...@gmail.com ---
(In reply to Christopher Meng from comment #24)
 1. F20+ has solved this bug, you can drop these:
 
 # we don't want to provide private python extension libs, snippet from:
 # http://fedoraproject.org/wiki/Packaging:AutoProvidesAndRequiresFiltering
 %{?filter_setup:
 %filter_provides_in %{python_sitearch}/.*\.so$ 
 %filter_setup
 }

great. Removed


 
 2. %package devel
 Summary:Development files for %{name}
 Group:  Development/Libraries
 Requires:   %{name}%{?_isa} = %{version}-%{release}
 Requires:   cmake
 Requires:   python2-devel
 Requires:   boost-devel
 
 %{?_isa} should be used for all Requires.

Are you sure? The relevant page does not mention it at all
https://fedoraproject.org/wiki/Packaging:Guidelines#Requiring_Base_Package

 
 3. A software suite for chemical informatics, computational chemistry, 
 and predictive modeling
 
 Missing a dot.
 

Fixed

 4. %{python_sitearch} -- %{python2_sitearch}

Fixed

 
 5. All Group tags can be dropped.

Fixed

 
 6. Project has moved to github, with a new version:
 
 https://github.com/rdkit/rdkit/releases

Changed

Updated spec and srpm:
http://giallu.fedorapeople.org/rdkit-2013.09.2-1.fc20.src.rpm
http://giallu.fedorapeople.org/rdkit.spec

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

[bugzilla]

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



--- Comment #24 from Christopher Meng cicku...@gmail.com ---
1. F20+ has solved this bug, you can drop these:

# we don't want to provide private python extension libs, snippet from:
# http://fedoraproject.org/wiki/Packaging:AutoProvidesAndRequiresFiltering
%{?filter_setup:
%filter_provides_in %{python_sitearch}/.*\.so$ 
%filter_setup
}

2. %package devel
Summary:Development files for %{name}
Group:  Development/Libraries
Requires:   %{name}%{?_isa} = %{version}-%{release}
Requires:   cmake
Requires:   python2-devel
Requires:   boost-devel

%{?_isa} should be used for all Requires.

3. A software suite for chemical informatics, computational chemistry, 
and predictive modeling

Missing a dot.

4. %{python_sitearch} -- %{python2_sitearch}

5. All Group tags can be dropped.

6. Project has moved to github, with a new version:

https://github.com/rdkit/rdkit/releases

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

[bugzilla]

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



--- Comment #23 from Gianluca Sforna gia...@gmail.com ---
I had a todo item for that. Done in:

http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2013.09.1-2.fc20.src.rpm

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

[bugzilla]

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

Christopher Meng cicku...@gmail.com changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
   Assignee|nob...@fedoraproject.org|cicku...@gmail.com
  Flags||fedora-review?



--- Comment #22 from Christopher Meng cicku...@gmail.com ---
I think package's cmake files should be put under %{_libdir}/cmake/, it
shouldn't be stored directly under libdir.

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

[bugzilla]

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



--- Comment #18 from Gianluca Sforna gia...@gmail.com ---
my FAS username is giallu. Is this a new requirement or what?

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

[bugzilla]

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



--- Comment #19 from Michael Schwendt bugs.mich...@gmx.net ---
It's no so new anymore and the default if you fill out the fedora-review form:

https://bugzilla.redhat.com/enter_bug.cgi?product=Fedoraformat=fedora-review
https://fedoraproject.org/wiki/New_package_process_for_existing_contributors

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

[bugzilla]

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



--- Comment #20 from Gianluca Sforna gia...@gmail.com ---
Thanks Michael, I hope the new field was added after March 2012 when I opened
this, so at least I have some kind of excuse :)

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

[bugzilla]

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



--- Comment #21 from Michael Schwendt bugs.mich...@gmx.net ---
;)  Several tickets from Sep 2012 contain it.

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

[bugzilla]

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



--- Comment #16 from Gianluca Sforna gia...@gmail.com ---
(In reply to Christopher Meng from comment #14)
 Also %{docdir}/README should be changed to %{_pkgdocdir}/README
 

done


 Then, cmake has %cmake macro, you should rpm -E %cmake and find if the macro
 can replace 6 lines of options.

done

 
 Next, Remove rm -rf %{buildroot} in %install

done

 
 Last, are these %{_libdir}/*.cmake needed?

they are useful if you want to build programs using the rdkit libraries. As the
comment says, I am not sure that is a good place for them but inherited it from
upstream so I left them there for now.

Also, I updated the package to latest upstream release, which is supposed to
work with pillow. A rawhide mock build passes so I assume we are ok.

http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2013.06.1-2.fc19.src.rpm

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

[bugzilla]

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



--- Comment #17 from Christopher Meng cicku...@gmail.com ---
OK.

What's your FAS username?(Please include this in every review request.)

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

[bugzilla]

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

--- Comment #15 from Mario Blättermann mario.blaetterm...@gmail.com ---
python-imaging is needed to run the tests. This package is deprecated and now
virtually provided by python-pillow [1]. Make sure it works with Pillow. There
are sometimes small corrections needed to the Python file headers [2].

[1] http://fedoraproject.org/wiki/Features/Pillow
[2] http://fedoraproject.org/wiki/Features/Pillow#How_To_Test

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

[bugzilla]

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

--- Comment #13 from Gianluca Sforna gia...@gmail.com ---
http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2013.06.1-1.fc19.src.rpm

Updated to latest release, includes suggestions from Christopher

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

[bugzilla]

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

--- Comment #14 from Christopher Meng cicku...@gmail.com ---
Hi,

First, becasue F20 will use unversioned docdir name, in your global field you
should modify

%global docdir  %{_docdir}/%{name}-%{version}

Also %{docdir}/README should be changed to %{_pkgdocdir}/README

Then, cmake has %cmake macro, you should rpm -E %cmake and find if the macro
can replace 6 lines of options.

Next, Remove rm -rf %{buildroot} in %install

Last, are these %{_libdir}/*.cmake needed?

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

[bugzilla]

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

Christopher Meng cicku...@gmail.com changed:

   What|Removed |Added

 CC||cicku...@gmail.com

--- Comment #12 from Christopher Meng cicku...@gmail.com ---
1. No need for BuildRoot tag.

2. Remove the commented lines of snapshot Source0.

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

[bugzilla]

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

--- Comment #11 from Gianluca Sforna gia...@gmail.com ---
(In reply to Jason Tibbitts from comment #10)
 cal 2012 tells me  that October 21st 2012 was a Sunday, not a Wednesday.
Fixed

 
 One new non-executable-script complaint:
 
   python-rdkit.x86_64: E: non-executable-script
/usr/lib64/python2.7/site-packages/rdkit/Chem/MCS.py 0644L /usr/bin/env
 
 and one old one:
 
   python-rdkit.x86_64: E: non-executable-script
/usr/lib64/python2.7/site-packages/rdkit/utils/pydoc_local.py 0644L
/usr/bin/env
 
 Not sure what you want to do with those.

The first one is really a python module, so I removed the shebang.
The second I am not sure, asked upstream.

 
 Still some spurious-executable-perm complaints in the debuginfo package. 
 Why would cpp and header files be executable in the source tree?

not intentional I guess, reported upstream

 
 Could you comment on the purpose of these?  Would it not be better for these
 to be packaged as documentation?  Actually, that pretty much goes for the
 rest of the stuff in rdkit-extras; at least the Contrib stuff doesn't seem
 to be terribly useful just sitting under /usr/share.
 
   rdkit-extras.noarch: W: devel-file-in-non-devel-package
 /usr/share/RDKit/Contrib/PBF/PBFRDKit.h
   rdkit-extras.noarch: W: devel-file-in-non-devel-package
 /usr/share/RDKit/Contrib/PBF/demo.cpp
   rdkit-extras.noarch: W: devel-file-in-non-devel-package
 /usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp
 

The extras are examples of actual rdkit usage. I am not sure where it is best
to put them in the filesystem, but if consensus is they should go in docs I can
surely move them.


 Can you comment on the stuff in the External directory?  I just want to make
 sure none of it is bundled external code.
 
 Also on the subject of the External directory, some of it is differently
 licensed (cmim is GPL, pymol is Pymol, whatever that is).  Can you be
 certain that none of that is included in the final package?  If not, the
 License: tag will need modification.

That is supposed to contain glue code to USE external code. For instance, inchi
is pulled as a dep and linked as usual.
pymol is code from upstream, I asked to put there a proper license.
I also asked upstream about cmim, it seems from the build logs it is using just
a couple modules from that, maybe it can be replaced or disabled.


 
 Why do all of the libraries seem to carry a 1beta1 when this is versioned
 as a post-release package?

not sure why it was there, but the suffix looks correct in the latest package


 
 I kind of wish the masses if library files all carried a some sort of
 libRD prefix, because there are so many of them and they appear to be
 rather generically named, especially libhc.so. 

Yeah, I can propose upstream to add a prefix on all, nice to see no conflicts
were found though.


http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2013.03.2-1.fc18.src.rpm

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

[bugzilla]

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

Gianluca Sforna gia...@gmail.com changed:

   What|Removed |Added

  Flags|needinfo?(gia...@gmail.com) |

--- Comment #9 from Gianluca Sforna gia...@gmail.com ---
I removed and checked automatic runtime requirements for -devel but they did
not include python2-devel or boost, so I kept those.

All the other suggestions are now in the package:

http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2013.03-2.fc18.src.rpm

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

[bugzilla]

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

--- Comment #10 from Jason Tibbitts ti...@math.uh.edu ---
So, after a fashion, this does build for me and I'll toss out a few random
comments.  Without any way to test this I'm just sort of poking about, but I
guess it can't hurt.

rpmlint has just a few complaints that weren't mentioned earlier:

  rdkit.src: E: specfile-error warning: bogus date in %changelog:
   Wed Oct 21 2012 Gianluca Sforna gia...@gmail.com - 2012.09-1
cal 2012 tells me  that October 21st 2012 was a Sunday, not a Wednesday.

One new non-executable-script complaint:

  python-rdkit.x86_64: E: non-executable-script
   /usr/lib64/python2.7/site-packages/rdkit/Chem/MCS.py 0644L /usr/bin/env

and one old one:

  python-rdkit.x86_64: E: non-executable-script
   /usr/lib64/python2.7/site-packages/rdkit/utils/pydoc_local.py 0644L
   /usr/bin/env

Not sure what you want to do with those.

Still some spurious-executable-perm complaints in the debuginfo package.  Why
would cpp and header files be executable in the source tree?

  rdkit-debuginfo.x86_64: W: spurious-executable-perm
   /usr/src/debug/RDKit_2013_03_1/External/INCHI-API/inchi.cpp
  rdkit-debuginfo.x86_64: W: spurious-executable-perm
   /usr/src/debug/RDKit_2013_03_1/External/INCHI-API/Wrap/pyInchi.cpp
  rdkit-debuginfo.x86_64: W: spurious-executable-perm
   /usr/src/debug/RDKit_2013_03_1/External/INCHI-API/inchi.h

Could you comment on the purpose of these?  Would it not be better for these to
be packaged as documentation?  Actually, that pretty much goes for the rest of
the stuff in rdkit-extras; at least the Contrib stuff doesn't seem to be
terribly useful just sitting under /usr/share.

  rdkit-extras.noarch: W: devel-file-in-non-devel-package
/usr/share/RDKit/Contrib/PBF/PBFRDKit.h
  rdkit-extras.noarch: W: devel-file-in-non-devel-package
/usr/share/RDKit/Contrib/PBF/demo.cpp
  rdkit-extras.noarch: W: devel-file-in-non-devel-package
/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp

Can you comment on the stuff in the External directory?  I just want to make
sure none of it is bundled external code.

Also on the subject of the External directory, some of it is differently
licensed (cmim is GPL, pymol is Pymol, whatever that is).  Can you be certain
that none of that is included in the final package?  If not, the License: tag
will need modification.

Why do all of the libraries seem to carry a 1beta1 when this is versioned as
a post-release package?

I kind of wish the masses if library files all carried a some sort of libRD
prefix, because there are so many of them and they appear to be rather
generically named, especially libhc.so.  I did look for conflicts, though,
and didn't find any outside of an instance of libhc in an obscure project at
http://code.google.com/p/isdp/, and that library doesn't appear to have come
from the source anyway.  So I don't think there's any blocker here, but it's
something to be aware of.

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

[bugzilla]

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

--- Comment #8 from Gianluca Sforna gia...@gmail.com ---
I'm here, trying to sort upstream's SVN-git migration. Will update the spec
asap.

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

[bugzilla]

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

Jason Tibbitts ti...@math.uh.edu changed:

   What|Removed |Added

 CC||gia...@gmail.com
  Flags||needinfo?(gia...@gmail.com)

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

[bugzilla]

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

Mario Blättermann mario.blaetterm...@gmail.com changed:

   What|Removed |Added

 CC||mario.blaetterm...@gmail.co
   ||m

--- Comment #7 from Mario Blättermann mario.blaetterm...@gmail.com ---
Just a few initial comments:

BuildRequires:  python-devel

This is deprecated, you have to require python2-devel:
https://fedoraproject.org/wiki/Packaging:Python#BuildRequires


Regarding the runtime requirements of the subpackages, first have a look what
rpm pulls automatically before adding some things there by hand. I'm quite sure
that the -devel package will get the python2-devel dependency anyway.


Requires: %{name} = %{version}-%{release}
For arch-dependent packages, we need a fully versioned dependency:
Requires: %{name}%{?_isa} = %{version}-%{release}


Don't mix %{buildroot} and $RPM_BUILD_ROOT in the same spec file.


%defattr(-,root,root,-)
This line is obsolete, even for EPEL-5 packages, although rpmlint doesn't say
so.


Please remove unneeded parts from the file header (the line regarding
python_sitelib).

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

[bugzilla]

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

--- Comment #6 from Gianluca Sforna gia...@gmail.com ---
Another upstream release:
http://giallu.fedorapeople.org/rdkit.spec
http://giallu.fedorapeople.org/rdkit-2013.03-1.fc18.src.rpm

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

[bugzilla]

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

--- Comment #5 from Gianluca Sforna gia...@gmail.com ---
Updated again:
http://giallu.fedorapeople.org/rdkit-2012.12-1.fc18.src.rpm
http://giallu.fedorapeople.org/rdkit.spec

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

[bugzilla]

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

--- Comment #4 from Gianluca Sforna gia...@gmail.com ---
Updated package:
http://giallu.fedorapeople.org/rdkit-2012.06-1.fc17.src.rpm

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

[bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.


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

--- Comment #3 from Gianluca Sforna gia...@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@GLIBC_2.2.5
  rdkit.x86_64: W: shared-lib-calls-exit 
  /usr/lib64/libSLNParse.so.1.2011.12.1 exit@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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[Bug 804125] Review Request: rdkit - A toolkit for cheminformatics and machine learning

[bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.


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

Jeroen van Meeuwen kana...@kanarip.com changed:

   What|Removed |Added

 CC||kana...@kanarip.com

--- Comment #2 from Jeroen van Meeuwen kana...@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@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@GLIBC_2.2.5
 rdkit.x86_64: W: shared-lib-calls-exit /usr/lib64/libSLNParse.so.1.2011.12.1 
 exit@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@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@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@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@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@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@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 

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

[bugzilla]

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comments should be made in the comments box of this bug.


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

--- Comment #1 from Gianluca Sforna gia...@gmail.com 2012-03-16 13:06:45 EDT 
---
rpmlint output

$ rpmlint /var/lib/mock/fedora-16-i386/result/*.rpm
python-rdkit.i686: W: no-documentation
python-rdkit.i686: E: non-executable-script
/usr/lib/python2.7/site-packages/rdkit/sping/tests/testallps.py 0644L
/usr/bin/env
python-rdkit.i686: E: non-executable-script
/usr/lib/python2.7/site-packages/rdkit/utils/pydoc_local.py 0644L /usr/bin/env
python-rdkit.i686: E: non-executable-script
/usr/lib/python2.7/site-packages/rdkit/sping/examples/formatted-strings.py
0644L /usr/bin/env
python-rdkit.i686: E: incorrect-fsf-address
/usr/lib/python2.7/site-packages/rdkit/sping/WX/pidWX.py
rdkit.i686: W: spelling-error Summary(en_US) cheminformatics - misinformation
rdkit.i686: W: spelling-error %description -l en_US cheminformatics -
misinformation
rdkit.i686: W: shared-lib-calls-exit /usr/lib/libSLNParse.so.1.2011.12.1
exit@GLIBC_2.0
rdkit.i686: W: shared-lib-calls-exit /usr/lib/libSmilesParse.so.1.2011.12.1
exit@GLIBC_2.0
rdkit.src: W: spelling-error Summary(en_US) cheminformatics - misinformation
rdkit.src: W: spelling-error %description -l en_US cheminformatics -
misinformation
rdkit.src: W: invalid-url Source0:
http://rdkit.googlecode.com/files/RDKit_2011_12_1.tgz HTTP Error 404: Not Found
rdkit-debuginfo.i686: W: spurious-executable-perm
/usr/src/debug/RDKit_2011_12_1/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp
rdkit-debuginfo.i686: W: spurious-executable-perm
/usr/src/debug/RDKit_2011_12_1/Code/RDBoost/python_streambuf.h
rdkit-devel.i686: W: no-documentation
rdkit-doc.noarch: W: no-documentation
rdkit-extras.noarch: W: no-documentation
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
rdkit-postgresql.i686: W: spelling-error %description -l en_US mol - mewl,
mil, mo
rdkit-postgresql.i686: W: spelling-error %description -l en_US datatype - data
type, data-type, database
rdkit-postgresql.i686: W: spelling-error %description -l en_US fp - pf, f, p
rdkit-postgresql.i686: W: spelling-error %description -l en_US tanimoto -
animator
8 packages and 0 specfiles checked; 6 errors, 17 warnings.

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