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 #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. -- 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
