Bug 611873

Fedora Review R-Rsolid 2010-07-14

rpmlint output:

R-Rsolid.x86_64: W: spelling-error Summary(en_US) Quantile -> Quintile, Quartile, Quantize
R-Rsolid.x86_64: W: spelling-error %description -l en_US dinucleotide -> di nucleotide, di-nucleotide, nucleotide
R-Rsolid.x86_64: W: spelling-error %description -l en_US quantile -> quintile, quartile, quantize
R-Rsolid.x86_64: W: spelling-error %description -l en_US mis -> mus, mos, mid
R-Rsolid-devel.x86_64: W: only-non-binary-in-usr-lib
R-Rsolid-devel.x86_64: W: no-documentation
R-Rsolid.src: W: spelling-error Summary(en_US) Quantile -> Quintile, Quartile, Quantize
R-Rsolid.src: W: spelling-error %description -l en_US dinucleotide -> di nucleotide, di-nucleotide, nucleotide
R-Rsolid.src: W: spelling-error %description -l en_US quantile -> quintile, quartile, quantize
R-Rsolid.src: W: spelling-error %description -l en_US mis -> mus, mos, mid
R-Rsolid.src:4: W: mixed-use-of-spaces-and-tabs (spaces: line 4, tab: line 3)
4 packages and 0 specfiles checked; 0 errors, 11 warnings.

You should fix the "mixed-use-of-spaces-and-tabs" - the others looks
like noise.



+ Package named according to R packaging guidelines
+ Specfile named after package
+ Package license "Artistic 2.0" is a Fedora approved license

- I can not find any licensing information for this package, neither
  in the package source, nor on the upstream website. Could you please
  indicate your source for stating that this package is licensed under
  the "Artistic 2.0" license.

+ Specfile is written in legible English
+ Source matches upstream:

$ md5sum Rsolid_0.9-2.tar.gz srpm/Rsolid_0.9-2.tar.gz 
a86608e6c0599e3af9b8082c4e1d31bf  Rsolid_0.9-2.tar.gz
a86608e6c0599e3af9b8082c4e1d31bf  srpm/Rsolid_0.9-2.tar.gz

+ Package compiles

- BuildRequires tetex-latex is deprecated - tex(latex) should be used instead

- The package installs the /usr/lib64/R/library/Rsolid directory but
  does not own it

+ No duplicate files, and %files has %defattr
+ Specfile uses macros consistently
  (Though you could say --configure-args="--with-hdf5=%{_prefix}")

+ Package contains code
+ %doc is not runtime essential
+ Headers are in -devel
+ -devel depends on main with fully qualified version

- Package does not own others directories, but since it installs files
  in /usr/lib64/R/library it must have a Requires: R-core (see the
  template in the Fedora R packaging guidelines).

+ Installed files have valid UTF8 filenames.

- R modules packages no longer run scriptlets, so the Requires(post)
  and Requires(postun) should be removed.

Thanks for taking a look.  I already have a version that fixes the spec formatting issue - I'll add fixes for the other problems.

I too couldn't find licence information, so I contacted the upstream authors, who said it was Artistic.  To clear this up, I'll ask if they can include explicit information with the release.

If upstream could fix the license in the DESCRIPTION file the warning during the build would go away:

* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:

Some other minor comments - which are not really packaging guidelines violations:
 - You mix listing directories in %files with trailing slash and without.
 - You have different format on different changelog entries (with and without a -)

New version at:

http://verdurin.fedorapeople.org/reviews/R-Rsolid/R-Rsolid.spec

http://verdurin.fedorapeople.org/reviews/R-Rsolid/R-Rsolid-0.9.2-3.fc13.src.rpm

Upstream added a licensing clarification to the DESCRIPTION file, without changing the release number.  The rest of your comments should have been addresses - some of the R problems were because I relied on the r2spec package, which is clearly a little out of date.

I've also noted that it doesn't build on EPEL5, though I don't think that should hold out acceptance into Fedora.  I'll pursue that separately with the authors.

There is a new warning in rpmlint:

R-Rsolid-devel.x86_64: W: only-non-binary-in-usr-lib
There are only non binary files in /usr/lib so they should be in /usr/share.

on which I'd welcome guidance.

New rpmlint output:

R-Rsolid.src: W: spelling-error Summary(en_US) Quantile -> Quintile, Quartile, Quantize
R-Rsolid.src: W: spelling-error %description -l en_US dinucleotide -> di nucleotide, di-nucleotide, nucleotide
R-Rsolid.src: W: spelling-error %description -l en_US quantile -> quintile, quartile, quantize
R-Rsolid.src: W: spelling-error %description -l en_US mis -> mus, mos, mid
R-Rsolid.x86_64: W: spelling-error Summary(en_US) Quantile -> Quintile, Quartile, Quantize
R-Rsolid.x86_64: W: spelling-error %description -l en_US dinucleotide -> di nucleotide, di-nucleotide, nucleotide
R-Rsolid.x86_64: W: spelling-error %description -l en_US quantile -> quintile, quartile, quantize
R-Rsolid.x86_64: W: spelling-error %description -l en_US mis -> mus, mos, mid
R-Rsolid-devel.x86_64: W: only-non-binary-in-usr-lib
R-Rsolid-devel.x86_64: W: no-documentation
4 packages and 0 specfiles checked; 0 errors, 10 warnings.

Same as before except that the "mixed-use-of-spaces-and-tabs" is no longer there. The remaining warnings can be ignored. (The "only-non-binary-in-usr-lib" is not new - it was there before too.)


+ New source states the license in the DESCRIPTION file
+ New source matches upstream:

$ md5sum srpm/Rsolid_0.9-2.tar.gz Rsolid_0.9-2.tar.gz 
4a619392ad87865bc4f4c1588199f75a  srpm/Rsolid_0.9-2.tar.gz
4a619392ad87865bc4f4c1588199f75a  Rsolid_0.9-2.tar.gz

+ BuildRequires are now good
+ Package now owns directories it creates

- New specfile lists some files more than once. Warnings during rpmbuild:

warning: File listed twice: /usr/lib64/R/library/Rsolid/DESCRIPTION
warning: File listed twice: /usr/lib64/R/library/Rsolid/html
warning: File listed twice: /usr/lib64/R/library/Rsolid/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/Rsolid/html/Rsolid.html

This is a better %files section:

%files
%defattr(-, root, root, -)
%dir %{_libdir}/R/library/%{packname}
%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
%doc %{_libdir}/R/library/%{packname}/html
%{_libdir}/R/library/%{packname}/INDEX
%{_libdir}/R/library/%{packname}/Meta
%{_libdir}/R/library/%{packname}/R
%{_libdir}/R/library/%{packname}/data
%{_libdir}/R/library/%{packname}/help
%{_libdir}/R/library/%{packname}/libs

+ Package now properly depend on packages owning directories where files are
  installed
+ The relic Requires for the no longer existing scriptlets have been removed

That was roughly how I had the %files section before but you pointed out that it didn't then own the directory /usr/lib64/R/library/Rsolid.

How about adding extra %exclude entries for those duplicate files instead?

I added the

%dir %{_libdir}/R/library/%{packname}

which adds the directory without its contents.

Using %exclude in the way you propose won't work. An %excluded file will not be made part of the package no matter how many times you list it.

Okay, new version at:

http://verdurin.fedorapeople.org/reviews/R-Rsolid/R-Rsolid.spec

http://verdurin.fedorapeople.org/reviews/R-Rsolid/R-Rsolid-0.9.2-4.fc13.src.rpm

The documentation on %exclude that I could find was confusing, and I suppose it shows.

Package approved.

Package Change Request
======================
Package Name: R-Rsolid
Short Description: Quantile normalization and base calling for second generation sequencing data
New Branches:  F-12 F-13 EL-5 EL-6
Owners: verdurin
InitialCC:

You seem to have added a "Package Change Request" when you meant to do a "New Package CVS Request" ? :) This confuses the tool we use to process these. ;) 

Processed manually, cvs done.

The package has been built long ago - someone forgot to close the review request.