[Bug 630644] Review Request: perl-Bio-SamTools - Bio::SamTools Perl module

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

 



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=630644

--- Comment #10 from Petr Pisar <ppisar@xxxxxxxxxx> 2011-03-14 07:59:46 EDT ---
Source file is original. Ok.
Description verified from README.

License is GPL+ or Artistic 2.0 (LICENSE, lib/Bio/DB/Sam.pm).
FIX: Correct License tag to reflect Artistic license version. See
https://fedoraproject.org/wiki/Licensing:Main#Good_Licenses for license names.

TODO: Replace version string with %{version} macro in Source0. It will make
upgrades smoother.

TODO: Remove unused commented-out code from spec file.

TODO: You can remove BuildRoot definition and it's purge in %install section
and %clean section as this is obsolete in Fedora.

FIX: Remove samtools-devel from Requires. Or is there any reason?

TODO: Instead of depending on perl-bioperl, find requires modules as put them
into spec file in perl(MODULE_NAME) notation. This is preferred method in perl
packages as it allows moving modules between RPM packages.

TODO: BuildRequire perl(Exporter) (lib/Bio/DB/Sam/Constants.pm:69) as it can
dual-live in the future (http://search.cpan.org/~ferreira/Exporter/).
TODO: BuildRequire perl(File::Spec) (lib/Bio/DB/Sam/SamToGBrowse.pm:3) as it
can dual-live in the future (http://search.cpan.org/~smueller/PathTools/).
TODO: BuildRequire perl(File::Temp) (lib/Bio/DB/Sam/SamToGBrowse.pm) as it can
dual-live in the future (http://search.cpan.org/~tjenness/File-Temp/).
TODO: BuildRequire perl(Cwd) (lib/Bio/DB/Sam.pm:2078) as it can dual-live in
the futurue (http://search.cpan.org/~smueller/PathTools/).
TODO: BuildRequire perl(Test) for (t/01sam.t:18) as it can dual-live in the
future (http://search.cpan.org/~sburke/Test/).

All tests pass. Ok.

$ rpmlint perl-Bio-SamTools.spec ../SRPMS/perl-Bio-SamTools-1.21-3.fc14.src.rpm
../RPMS/x86_64/perl-Bio-SamTools-1.21-3.fc14.x86_64.rpm 
perl-Bio-SamTools.x86_64: E: devel-dependency samtools-devel
perl-Bio-SamTools.x86_64: W: no-manual-page-for-binary bamToGBrowse.pl
2 packages and 1 specfiles checked; 1 errors, 1 warnings.
FIX: Is the samtools-devel needed at run time?

$ rpm -q -lv -p ../RPMS/x86_64/perl-Bio-SamTools-1.21-3.fc14.x86_64.rpm 
-rwxr-xr-x    1 root    root                     1913 bÅe 14 11:26
/usr/bin/bamToGBrowse.pl
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/Bio
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam
-rw-r--r--    1 root    root                    11025 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm
-rw-r--r--    1 root    root                    17097 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/Alignment.pm
-rw-r--r--    1 root    root                      335 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/FetchIterator.pm
-rw-r--r--    1 root    root                     2499 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/Pileup.pm
-rw-r--r--    1 root    root                     1993 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/PileupWrapper.pm
-rw-r--r--    1 root    root                     4571 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/Query.pm
-rw-r--r--    1 root    root                      402 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/ReadIterator.pm
-rw-r--r--    1 root    root                     1026 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Bam/Target.pm
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Sam
-rw-r--r--    1 root    root                    73347 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Sam.pm
-rw-r--r--    1 root    root                     2358 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Sam/Constants.pm
-rw-r--r--    1 root    root                    11636 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Sam/SamToGBrowse.pm
-rw-r--r--    1 root    root                     2284 bÅe 14 11:26
/usr/lib64/perl5/Bio/DB/Sam/Segment.pm
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/auto/Bio
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/auto/Bio/DB
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/lib64/perl5/auto/Bio/DB/Sam
-rwxr-xr-x    1 root    root                   277096 bÅe 14 11:26
/usr/lib64/perl5/auto/Bio/DB/Sam/Sam.so
drwxr-xr-x    2 root    root                        0 bÅe 14 11:26
/usr/share/doc/perl-Bio-SamTools-1.21
-rw-r--r--    1 root    root                     4850 zÃÅ 21 20:39
/usr/share/doc/perl-Bio-SamTools-1.21/Changes
-rw-r--r--    1 root    root                     1156 zÃÅ 21 20:39
/usr/share/doc/perl-Bio-SamTools-1.21/DISCLAIMER
-rw-r--r--    1 root    root                    23937 zÃÅ 21 20:39
/usr/share/doc/perl-Bio-SamTools-1.21/LICENSE
-rw-r--r--    1 root    root                     1946 zÃÅ 21 20:39
/usr/share/doc/perl-Bio-SamTools-1.21/README
-rw-r--r--    1 root    root                     2492 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
-rw-r--r--    1 root    root                     7437 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
-rw-r--r--    1 root    root                     2908 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
-rw-r--r--    1 root    root                     2249 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
-rw-r--r--    1 root    root                     2917 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
-rw-r--r--    1 root    root                     1886 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
-rw-r--r--    1 root    root                    20019 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Sam.3pm.gz
-rw-r--r--    1 root    root                     2409 bÅe 14 11:26
/usr/share/man/man3/Bio::DB::Sam::Constants.3pm.gz
File permissions and layout are Ok.

$ rpm -q --requires -p ../RPMS/x86_64/perl-Bio-SamTools-1.21-3.fc14.x86_64.rpm
|sort | uniq -c
      1 libc.so.6(GLIBC_2.2.5)(64bit)  
      1 libc.so.6(GLIBC_2.3.4)(64bit)  
      1 libc.so.6(GLIBC_2.3)(64bit)  
      1 libc.so.6(GLIBC_2.4)(64bit)  
      1 libc.so.6(GLIBC_2.7)(64bit)  
      1 libc.so.6()(64bit)  
      1 libgcc_s.so.1(GCC_3.0)(64bit)  
      1 libgcc_s.so.1(GCC_3.3.1)(64bit)  
      1 libgcc_s.so.1()(64bit)  
      1 libz.so.1(ZLIB_1.2.2)(64bit)  
      1 libz.so.1(ZLIB_1.2.3.3)(64bit)  
      1 libz.so.1()(64bit)  
      1 perl(base)  
      1 perl(Bio::DB::Bam::Alignment)  
      1 perl(Bio::DB::Bam::AlignWrapper)  
      1 perl(Bio::DB::Bam::FetchIterator)  
      1 perl(Bio::DB::Bam::PileupWrapper)  
      1 perl(Bio::DB::Bam::Query)  
      1 perl(Bio::DB::Bam::ReadIterator)  
      1 perl(Bio::DB::Bam::Target)  
      1 perl(Bio::DB::Sam)  
      1 perl(Bio::DB::Sam::Constants)  
      1 perl(Bio::DB::Sam::SamToGBrowse)  
      1 perl(Bio::DB::Sam::Segment)  
      1 perl-bioperl  
      1 perl(Bio::PrimarySeq)  
      1 perl(Bio::SeqFeature::Lite)  
      1 perl(Carp)  
      1 perl(constant)  
      1 perl(Cwd)  
      1 perl(Exporter)  
      1 perl(File::Basename)  
      1 perl(File::Spec)  
      1 perl(File::Temp)  
      1 perl(:MODULE_COMPAT_5.12.3)  
      1 perl(strict)  
      1 perl(warnings)  
      1 rpmlib(CompressedFileNames) <= 3.0.4-1
      1 rpmlib(FileDigests) <= 4.6.0-1
      1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
      1 rpmlib(PayloadIsXz) <= 5.2-1
      2 rpmlib(VersionedDependencies) <= 3.0.3-1
      1 rtld(GNU_HASH)  
      1 samtools-devel >= 0.1.8
      1 /usr/bin/perl  
Here you can see some perl-bioperl modules discovered by rpmbuild you can put
into spec files as BuildRequires instead of perl-bioperl. Please be aware this
is just informative. There can be other not discovered dependencies.

$ rpm -q --provides -p ../RPMS/x86_64/perl-Bio-SamTools-1.21-3.fc14.x86_64.rpm
|sort | uniq -c 
      1 perl(Bio::DB::Bam)  
      1 perl(Bio::DB::Bam::Alignment)  
      1 perl(Bio::DB::Bam::AlignWrapper)  
      1 perl(Bio::DB::Bam::FetchIterator)  
      1 perl(Bio::DB::Bam::Pileup)  
      1 perl(Bio::DB::Bam::PileupWrapper)  
      1 perl(Bio::DB::Bam::Query)  
      1 perl(Bio::DB::Bam::ReadIterator)  
      1 perl(Bio::DB::Bam::SplitAlignmentPart)  
      1 perl(Bio::DB::Bam::Target)  
      1 perl(Bio::DB::Sam::Constants)  
      1 perl(Bio::DB::Sam::Fai)  
      1 perl(Bio::DB::Sam::SamToGBrowse)  
      1 perl(Bio::DB::Sam::Segment)  
      1 perl(Bio::DB::Sam::Segment::Iterator)  
      1 perl(Bio::DB::Sam) = 1.21
      1 perl-Bio-SamTools(x86-64) = 1.21-3.fc14
      1 perl-Bio-SamTools = 1.21-3.fc14
      1 perl(Bio::SeqFeature::Coverage)  
Binary provides are Ok.

$ resolvedeps-f16 ../RPMS/x86_64/perl-Bio-SamTools-1.21-3.fc14.x86_64.rpm 
Binary dependencies resolvable. Ok.

Package builds in F16
(http://koji.fedoraproject.org/koji/taskinfo?taskID=2910808). Ok.

Otherwise package is in line with Fedora and perl packaging guide lines.

TODO: Consider upgrading the package to latest upstream version (1.27
currently).


Please correct all `FIX' prefixed issues, consider fixing all `TODO' items and
provide new spec file.

Resolution: Package NOT approved.

-- 
Configure bugmail: https://bugzilla.redhat.com/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are on the CC list for the bug.
--
Fedora Extras Perl SIG
http://www.fedoraproject.org/wiki/Extras/SIGs/Perl
perl-devel mailing list
perl-devel@xxxxxxxxxxxxxxxxxxxxxxx
https://admin.fedoraproject.org/mailman/listinfo/perl-devel



[Index of Archives]     [Fedora Announce]     [Fedora Kernel]     [Fedora Testing]     [Fedora Legacy Announce]     [Fedora PHP Devel]     [Kernel Devel]     [Fedora Legacy]     [Fedora Maintainers]     [Fedora Desktop]     [PAM]     [Red Hat Development]     [Big List of Linux Books]     [Gimp]     [Yosemite Information]
  Powered by Linux