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

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https://bugzilla.redhat.com/show_bug.cgi?id=630644

--- Comment #15 from Petr Pisar <ppisar@xxxxxxxxxx> 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@xxxxxxxxxxxx> - 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@xxxxxxxxxxxx> - 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 bÅe 16 15:03
/usr/bin/bamToGBrowse.pl
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/Bio
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam
-rw-r--r--    1 root    root                    11125 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm
-rw-r--r--    1 root    root                    17097 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Alignment.pm
-rw-r--r--    1 root    root                      335 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/FetchIterator.pm
-rw-r--r--    1 root    root                     2499 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Pileup.pm
-rw-r--r--    1 root    root                     1993 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/PileupWrapper.pm
-rw-r--r--    1 root    root                     4596 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Query.pm
-rw-r--r--    1 root    root                      402 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/ReadIterator.pm
-rw-r--r--    1 root    root                     1046 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Bam/Target.pm
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Sam
-rw-r--r--    1 root    root                    73642 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Sam.pm
-rw-r--r--    1 root    root                     2358 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Sam/Constants.pm
-rw-r--r--    1 root    root                    12201 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Sam/SamToGBrowse.pm
-rw-r--r--    1 root    root                     2284 bÅe 16 15:03
/usr/lib64/perl5/Bio/DB/Sam/Segment.pm
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/auto/Bio
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/auto/Bio/DB
drwxr-xr-x    2 root    root                        0 bÅe 16 15:03
/usr/lib64/perl5/auto/Bio/DB/Sam
-rwxr-xr-x    1 root    root                   278152 bÅe 16 15:03
/usr/lib64/perl5/auto/Bio/DB/Sam/Sam.so
drwxr-xr-x    2 root    root                        0 bÅe 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 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
-rw-r--r--    1 root    root                     7437 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
-rw-r--r--    1 root    root                     2908 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
-rw-r--r--    1 root    root                     2249 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
-rw-r--r--    1 root    root                     2917 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
-rw-r--r--    1 root    root                     1886 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
-rw-r--r--    1 root    root                    20078 bÅe 16 15:03
/usr/share/man/man3/Bio::DB::Sam.3pm.gz
-rw-r--r--    1 root    root                     2409 bÅe 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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