[Bug 630644] Review Request: perl-Bio-SamTools - Bio::SamTools Perl module
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Mon Mar 14 11:59:49 UTC 2011
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https://bugzilla.redhat.com/show_bug.cgi?id=630644
--- Comment #10 from Petr Pisar <ppisar at redhat.com> 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and %clean section as this is obsolete in Fedora.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 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.
$ 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.
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