[Bug 630644] Review Request: perl-Bio-SamTools - Bio::SamTools Perl module
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Mon Mar 14 22:05:51 UTC 2011
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https://bugzilla.redhat.com/show_bug.cgi?id=630644
--- Comment #12 from Adam Huffman <bloch at verdurin.com> 2011-03-14 18:05:49 EDT ---
(In reply to comment #10)
> 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.
>
Done.
> TODO: Replace version string with %{version} macro in Source0. It will make
> upgrades smoother.
>
Done, though some people seem to prefer using the numbers for easier
downloading - a matter of preference, I suppose.
> TODO: Remove unused commented-out code from spec file.
>
Done.
> TODO: You can remove BuildRoot definition and it's purge in %install section
> and %clean section as this is obsolete in Fedora.
>
I'm hoping to build for EPEL5 - isn't this still needed there?
> FIX: Remove samtools-devel from Requires. Or is there any reason?
>
Done - will do more testing on this to make it's not needed.
> 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.
>
Done. I looked through the source and couldn't find anything beyond what's
listed below.
> 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/).
>
Done.
> 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?
>
See above - removed.
> $ rpm -q -lv -p ../RPMS/x86_64/perl-Bio-SamTools-1.21-3.fc14.x86_64.rpm
> -rwxr-xr-x 1 root root 1913 bře 14 11:26
> /usr/bin/bamToGBrowse.pl
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/Bio
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/Bio/DB
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam
> -rw-r--r-- 1 root root 11025 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm
> -rw-r--r-- 1 root root 17097 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/Alignment.pm
> -rw-r--r-- 1 root root 335 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/FetchIterator.pm
> -rw-r--r-- 1 root root 2499 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/Pileup.pm
> -rw-r--r-- 1 root root 1993 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/PileupWrapper.pm
> -rw-r--r-- 1 root root 4571 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/Query.pm
> -rw-r--r-- 1 root root 402 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/ReadIterator.pm
> -rw-r--r-- 1 root root 1026 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Bam/Target.pm
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Sam
> -rw-r--r-- 1 root root 73347 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Sam.pm
> -rw-r--r-- 1 root root 2358 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Sam/Constants.pm
> -rw-r--r-- 1 root root 11636 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Sam/SamToGBrowse.pm
> -rw-r--r-- 1 root root 2284 bře 14 11:26
> /usr/lib64/perl5/Bio/DB/Sam/Segment.pm
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/auto/Bio
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/auto/Bio/DB
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/lib64/perl5/auto/Bio/DB/Sam
> -rwxr-xr-x 1 root root 277096 bře 14 11:26
> /usr/lib64/perl5/auto/Bio/DB/Sam/Sam.so
> drwxr-xr-x 2 root root 0 bře 14 11:26
> /usr/share/doc/perl-Bio-SamTools-1.21
> -rw-r--r-- 1 root root 4850 zář 21 20:39
> /usr/share/doc/perl-Bio-SamTools-1.21/Changes
> -rw-r--r-- 1 root root 1156 zář 21 20:39
> /usr/share/doc/perl-Bio-SamTools-1.21/DISCLAIMER
> -rw-r--r-- 1 root root 23937 zář 21 20:39
> /usr/share/doc/perl-Bio-SamTools-1.21/LICENSE
> -rw-r--r-- 1 root root 1946 zář 21 20:39
> /usr/share/doc/perl-Bio-SamTools-1.21/README
> -rw-r--r-- 1 root root 2492 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
> -rw-r--r-- 1 root root 7437 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
> -rw-r--r-- 1 root root 2908 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
> -rw-r--r-- 1 root root 2249 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
> -rw-r--r-- 1 root root 2917 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
> -rw-r--r-- 1 root root 1886 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
> -rw-r--r-- 1 root root 20019 bře 14 11:26
> /usr/share/man/man3/Bio::DB::Sam.3pm.gz
> -rw-r--r-- 1 root root 2409 bře 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.
>
See above - I've manually checked for other bioperl module 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).
>
Done.
>
> Please correct all `FIX' prefixed issues, consider fixing all `TODO' items and
> provide new spec file.
>
Spec:
http://verdurin.fedorapeople.org/reviews/perl-Bio-SamTools/perl-Bio-SamTools.spec
SRPM:
http://verdurin.fedorapeople.org/reviews/perl-Bio-SamTools/perl-Bio-SamTools-1.27-1.fc16.src.rpm
> Resolution: Package NOT approved.
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