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 #12 from Adam Huffman <bloch@xxxxxxxxxxxx> 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 and %clean section as this is obsolete in Fedora.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 bÅe 14 11:26 > /usr/bin/bamToGBrowse.pl > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/Bio > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam > -rw-r--r-- 1 root root 11025 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm > -rw-r--r-- 1 root root 17097 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/Alignment.pm > -rw-r--r-- 1 root root 335 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/FetchIterator.pm > -rw-r--r-- 1 root root 2499 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/Pileup.pm > -rw-r--r-- 1 root root 1993 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/PileupWrapper.pm > -rw-r--r-- 1 root root 4571 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/Query.pm > -rw-r--r-- 1 root root 402 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/ReadIterator.pm > -rw-r--r-- 1 root root 1026 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Bam/Target.pm > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Sam > -rw-r--r-- 1 root root 73347 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Sam.pm > -rw-r--r-- 1 root root 2358 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Sam/Constants.pm > -rw-r--r-- 1 root root 11636 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Sam/SamToGBrowse.pm > -rw-r--r-- 1 root root 2284 bÅe 14 11:26 > /usr/lib64/perl5/Bio/DB/Sam/Segment.pm > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/auto/Bio > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/auto/Bio/DB > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/lib64/perl5/auto/Bio/DB/Sam > -rwxr-xr-x 1 root root 277096 bÅe 14 11:26 > /usr/lib64/perl5/auto/Bio/DB/Sam/Sam.so > drwxr-xr-x 2 root root 0 bÅe 14 11:26 > /usr/share/doc/perl-Bio-SamTools-1.21 > -rw-r--r-- 1 root root 4850 zÃÅ 21 20:39 > /usr/share/doc/perl-Bio-SamTools-1.21/Changes > -rw-r--r-- 1 root root 1156 zÃÅ 21 20:39 > /usr/share/doc/perl-Bio-SamTools-1.21/DISCLAIMER > -rw-r--r-- 1 root root 23937 zÃÅ 21 20:39 > /usr/share/doc/perl-Bio-SamTools-1.21/LICENSE > -rw-r--r-- 1 root root 1946 zÃÅ 21 20:39 > /usr/share/doc/perl-Bio-SamTools-1.21/README > -rw-r--r-- 1 root root 2492 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz > -rw-r--r-- 1 root root 7437 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz > -rw-r--r-- 1 root root 2908 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz > -rw-r--r-- 1 root root 2249 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz > -rw-r--r-- 1 root root 2917 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz > -rw-r--r-- 1 root root 1886 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz > -rw-r--r-- 1 root root 20019 bÅe 14 11:26 > /usr/share/man/man3/Bio::DB::Sam.3pm.gz > -rw-r--r-- 1 root root 2409 bÅe 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. -- 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. _______________________________________________ package-review mailing list package-review@xxxxxxxxxxxxxxxxxxxxxxx https://admin.fedoraproject.org/mailman/listinfo/package-review