[Bug 630644] Review Request: perl-Bio-SamTools - Bio::SamTools Perl module
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Wed Mar 16 14:30:31 UTC 2011
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https://bugzilla.redhat.com/show_bug.cgi?id=630644
--- Comment #15 from Petr Pisar <ppisar at redhat.com> 2011-03-16 10:30:30 EDT ---
Standalone spec file and spec file in SRPM differ. I will use the standalone
one in this review.
Spec file changes:
--- perl-Bio-SamTools.spec 2011-03-13 02:06:15.000000000 +0100
+++ perl-Bio-SamTools.spec.1 2011-03-14 22:52:48.000000000 +0100
@@ -1,24 +1,28 @@
Name: perl-Bio-SamTools
-Version: 1.21
-Release: 3%{?dist}
+Version: 1.27
+Release: 1%{?dist}
Summary: Bio::SamTools Perl module
-License: GPL+ or Artistic
+License: Artistic 2.0
Group: Development/Libraries
URL: http://search.cpan.org/dist/Bio-SamTools/
-Source0:
http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.21.tar.gz
-#Patch0: %%{name}-%%{version}-includes.patch
+Source0:
http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-%{version}.tar.gz
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: perl >= 0:5.008
-#BuildRequires: perl(Bio::Root::Version) >= 1.005009001
-BuildRequires: perl-bioperl
-BuildRequires: perl(ExtUtils::CBuilder)
-BuildRequires: perl(Module::Build)
-BuildRequires: samtools-devel >= 0.1.8
-BuildRequires: zlib-devel
-#Requires: perl(Bio::Root::Version) >= 1.005009001
+BuildRequires: perl(Bio::PrimarySeq)
+BuildRequires: perl(Bio::SeqFeature::Lite)
+BuildRequires: perl(ExtUtils::CBuilder)
+BuildRequires: perl(ExtUtils::MakeMaker)
+BuildRequires: perl(Module::Build)
+BuildRequires: perl(Exporter)
+BuildRequires: perl(File::Spec)
+BuildRequires: perl(File::Temp)
+BuildRequires: perl(Cwd)
+BuildRequires: perl(Test)
+BuildRequires: samtools-devel >= 0.1.8
+BuildRequires: zlib-devel
+
Requires: perl-bioperl
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo
$version))
-Requires: samtools-devel >= 0.1.8
%{?perl_default_filter}
@@ -32,7 +36,6 @@
sed -i 's|= find_sam(|= ("%{_includedir}/samtools", "%{_libdir}"|' Build.PL
%build
-#export SAMTOOLS="/usr/include/samtools"
%{__perl} Build.PL installdirs=vendor optimize="$RPM_OPT_FLAGS"
./Build
@@ -60,6 +63,13 @@
%{_bindir}/bamToGBrowse.pl
%changelog
+* Mon Mar 14 2011 Adam Huffman <bloch at verdurin.com> - 1.27-1
+- new upstream version 1.27
+- remove unnecessary runtime samtools-devel R
+- more fine-grained module BR for bioperl and others
+- fix license
+- remove commented cruft
+
* Sun Mar 13 2011 Adam Huffman <bloch at verdurin.com> - 1.21-3
- better fix for samtools headers from Petr Pisar
Source file is original. Ok.
> 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.
>
-License: GPL+ or Artistic
+License: Artistic 2.0
FIX: The package is dual-licensed. User can select between GPL+ and Artistic
2.0. Please mention both licenses in the License tag.
> > 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?
Yes, it's needed for EPEL5. Then keeping the BuildRoot code makes sense if you
want one spec file for Fedora and EPEL.
Build time dependencies are Ok.
All tests pass. Ok.
> FIX: Remove samtools-devel from Requires. Or is there any reason?
-Requires: samtools-devel >= 0.1.8
Ok.
> FIX: Is the samtools-devel needed at run time?
$ rpmlint perl-Bio-SamTools.spec ../SRPMS/perl-Bio-SamTools-1.27-1.fc14.src.rpm
../RPMS/x86_64/perl-Bio-SamTools-*1.27-1.fc14.x86_64.rpm
perl-Bio-SamTools.x86_64: W: no-manual-page-for-binary bamToGBrowse.pl
3 packages and 1 specfiles checked; 0 errors, 1 warnings.
rpmlint Ok.
$ rpm -q -lv -p ../RPMS/x86_64/perl-Bio-SamTools-1.27-1.fc14.x86_64.rpm
-rwxr-xr-x 1 root root 1913 bře 16 15:03
/usr/bin/bamToGBrowse.pl
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/Bio
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/Bio/DB
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam
-rw-r--r-- 1 root root 11125 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm
-rw-r--r-- 1 root root 17097 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Alignment.pm
-rw-r--r-- 1 root root 335 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/FetchIterator.pm
-rw-r--r-- 1 root root 2499 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Pileup.pm
-rw-r--r-- 1 root root 1993 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/PileupWrapper.pm
-rw-r--r-- 1 root root 4596 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Query.pm
-rw-r--r-- 1 root root 402 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/ReadIterator.pm
-rw-r--r-- 1 root root 1046 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Target.pm
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Sam
-rw-r--r-- 1 root root 73642 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Sam.pm
-rw-r--r-- 1 root root 2358 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Sam/Constants.pm
-rw-r--r-- 1 root root 12201 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Sam/SamToGBrowse.pm
-rw-r--r-- 1 root root 2284 bře 16 15:03
/usr/lib64/perl5/Bio/DB/Sam/Segment.pm
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/auto/Bio
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/auto/Bio/DB
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/lib64/perl5/auto/Bio/DB/Sam
-rwxr-xr-x 1 root root 278152 bře 16 15:03
/usr/lib64/perl5/auto/Bio/DB/Sam/Sam.so
drwxr-xr-x 2 root root 0 bře 16 15:03
/usr/share/doc/perl-Bio-SamTools-1.27
-rw-r--r-- 1 root root 5766 pro 20 21:32
/usr/share/doc/perl-Bio-SamTools-1.27/Changes
-rw-r--r-- 1 root root 1156 pro 20 21:32
/usr/share/doc/perl-Bio-SamTools-1.27/DISCLAIMER
-rw-r--r-- 1 root root 23937 pro 20 21:32
/usr/share/doc/perl-Bio-SamTools-1.27/LICENSE
-rw-r--r-- 1 root root 1946 pro 20 21:32
/usr/share/doc/perl-Bio-SamTools-1.27/README
-rw-r--r-- 1 root root 2491 bře 16 15:03
/usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
-rw-r--r-- 1 root root 7437 bře 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
-rw-r--r-- 1 root root 2908 bře 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
-rw-r--r-- 1 root root 2249 bře 16 15:03
/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
-rw-r--r-- 1 root root 2917 bře 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
-rw-r--r-- 1 root root 1886 bře 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
-rw-r--r-- 1 root root 20078 bře 16 15:03
/usr/share/man/man3/Bio::DB::Sam.3pm.gz
-rw-r--r-- 1 root root 2409 bře 16 15:03
/usr/share/man/man3/Bio::DB::Sam::Constants.3pm.gz
File layout and permission are Ok.
$ rpm -q --requires -p ../RPMS/x86_64/perl-Bio-SamTools-1.27-1.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 /usr/bin/perl
FIX: Is the dependency on perl-bioperl required? In other words, is explicit
`Requires: perl-bioperl' statement in spec file needed? Does this package use
some scripts or data files directly from perl-bioperl? Or are autodiscovered
perl() dependencies, that are part of perl-bioperl, sufficient?. If the later
is true, remove the Requires statement from spec file.
$ rpm -q --provides -p ../RPMS/x86_64/perl-Bio-SamTools-1.27-1.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) = 1.27
1 perl-Bio-SamTools(x86-64) = 1.27-1.fc14
1 perl-Bio-SamTools = 1.27-1.fc14
1 perl(Bio::SeqFeature::Coverage)
Binary provides Ok.
$ resolvedeps-f16 ../RPMS/x86_64/perl-Bio-SamTools-1.27-1.fc14.x86_64.rpm
Binary dependencies resolvable. Ok.
Package builds in F16
(http://koji.fedoraproject.org/koji/taskinfo?taskID=2917368). Ok.
Otherwise package is in line with Fedora and perl packaging guidelines.
Please correct all `FIX' prefixed issues and submit new spec file.
Resolution: Package NOT approved.
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