Spec URL: http://verdurin.fedorapeople.org/reviews/bowtie/bowtie.spec SRPM URL: http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.5-2.fc13.src.rpm Description: Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
There are some problems that still need to be fixed, such as the fact that the CFLAGS are hard-coded in the Makefile. I've mentioned this to upstream and asked that they amend the Makefile so as to allow command-line overriding of the CFLAGS. There's been no response yet. Here's the rpmlint output: bowtie.src: W: spelling-error Summary(en_US) ultrafast -> ultra fast, ultra-fast, ultrafilter bowtie.src: W: spelling-error %description -l en_US ultrafast -> ultra fast, ultra-fast, ultrafilter bowtie.src: W: spelling-error %description -l en_US Langmead -> Lang mead, Lang-mead, Langmuir bowtie.src: W: spelling-error %description -l en_US Ultrafast -> Ultra fast, Ultra-fast, Ultrafilter bowtie.x86_64: W: spelling-error Summary(en_US) ultrafast -> ultra fast, ultra-fast, ultrafilter bowtie.x86_64: W: spelling-error %description -l en_US ultrafast -> ultra fast, ultra-fast, ultrafilter bowtie.x86_64: W: spelling-error %description -l en_US Langmead -> Lang mead, Lang-mead, Langmuir bowtie.x86_64: W: spelling-error %description -l en_US Ultrafast -> Ultra fast, Ultra-fast, Ultrafilter bowtie.x86_64: W: no-manual-page-for-binary bowtie bowtie.x86_64: W: no-manual-page-for-binary bowtie-inspect bowtie.x86_64: W: no-manual-page-for-binary bowtie-build bowtie.x86_64: W: spelling-error Summary(en_US) ultrafast -> ultra fast, ultra-fast, ultrafilter bowtie.x86_64: W: spelling-error %description -l en_US ultrafast -> ultra fast, ultra-fast, ultrafilter bowtie.x86_64: W: spelling-error %description -l en_US Langmead -> Lang mead, Lang-mead, Langmuir bowtie.x86_64: W: spelling-error %description -l en_US Ultrafast -> Ultra fast, Ultra-fast, Ultrafilter bowtie.x86_64: W: no-manual-page-for-binary bowtie bowtie.x86_64: W: no-manual-page-for-binary bowtie-inspect bowtie.x86_64: W: no-manual-page-for-binary bowtie-build bowtie-debuginfo.x86_64: E: debuginfo-without-sources bowtie-debuginfo.x86_64: E: debuginfo-without-sources
- Hmm, there are no CFLAGS defintions in the Makefile... How about: make %{?_smp_mflags} -p EXTRA_FLAGS="%{optflags}" Then the debuginfo-without-sources error is gone and the rest should be ignorable. - When you don't want to build this for EL5, you can delete quite a lot of stuff: See: bug #603233 comment 11
Yes, you're right - I meant to say 'compilation flags'. Have applied your suggested fix: http://verdurin.fedorapeople.org/reviews/bowtie/bowtie.spec http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.5-3.fc13.src.rpm I do want to build for EL5 - would you suggest conditionals? Personally I would prefer to keep it as is, to improve readability.
New version with latest upstream release: http://verdurin.fedorapeople.org/reviews/bowtie/bowtie.spec http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.7-1.fc13.src.rpm There's a new rpmlint error: bowtie.x86_64: E: script-without-shebang /usr/share/bowtie/scripts/gen_dnamasks2colormask.pl This text file has executable bits set or is located in a path dedicated for executables, but lacks a shebang and cannot thus be executed. If the file is meant to be an executable script, add the shebang, otherwise remove the executable bits or move the file elsewhere. I've contacted the authors to clarify the status of this file.
Upstream says that the shebang will be included in the next release.
Please make sure that the component is set correctly so that that reviewer will see this bug. I have fixed it.
Brennan, thanks for catching that. There hasn't been an upstream release since 0.12.7, so the issue with /usr/share/bowtie/scripts/gen_dnamasks2colormask.pl remains.
Other than trivial spelling errors, rpmlint gives: bowtie.x86_64: E: script-without-shebang /usr/share/bowtie/scripts/gen_dnamasks2colormask.pl This text file has executable bits set or is located in a path dedicated for executables, but lacks a shebang and cannot thus be executed. If the file is meant to be an executable script, add the shebang, otherwise remove the executable bits or move the file elsewhere. Patch for this, and drop the patch when upstream fixes it. bowtie.x86_64: W: no-manual-page-for-binary bowtie Each executable in standard binary directories should have a man page. bowtie.x86_64: W: no-manual-page-for-binary bowtie-inspect Each executable in standard binary directories should have a man page. bowtie.x86_64: W: no-manual-page-for-binary bowtie-build Each executable in standard binary directories should have a man page. No man pages exist, unfortunately, but you might suggest that upstream create some. Otherwise: Good: - rpmlint checks return: - package meets naming guidelines - package meets packaging guidelines - license ( ) OK, text in %doc, matches source - spec file legible, in am. english - source matches upstream - package compiles on devel (x86) - no missing BR - no unnecessary BR - no locales - not relocatable - owns all directories that it creates - no duplicate files - permissions ok - %clean ok - macro use consistent - code, not content - no need for -docs - nothing in %doc affects runtime - no need for .desktop file To fix: Patch for shebang. Include the doc/ dir in %doc. Mock build in progress for BR check.
Mock build was good, so it's just the two issues above.
Many thanks for taking a look - I was beginning to give up hope... New version that should address those problems is up at: http://verdurin.fedorapeople.org/reviews/bowtie/bowtie.spec http://verdurin.fedorapeople.org/reviews/bowtie/bowtie-0.12.7-2.fc14.src.rpm
Anytime. Much better, APPROVED. If you're feeling particularly grateful: https://bugzilla.redhat.com/buglist.cgi?emailreporter1=1&classification=Fedora&emailtype1=exact&query_format=advanced&bug_status=NEW&bug_status=ASSIGNED&bug_status=MODIFIED&bug_status=ON_DEV&bug_status=ON_QA&bug_status=VERIFIED&bug_status=RELEASE_PENDING&bug_status=POST&email1=limb%40jcomserv.net&component=Package%20Review&product=Fedora Or: http://fedoraproject.org/PackageReviewStatus/NEW.html :)
New Package SCM Request ======================= Package Name: bowtie Short Description: An ultrafast, memory-efficient short read aligner Owners: verdurin Branches: f14 f15 el5 el6 InitialCC:
Git done (by process-git-requests).
bowtie-0.12.7-2.el6 has been submitted as an update for Fedora EPEL 6. https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.el6
bowtie-0.12.7-2.el5 has been submitted as an update for Fedora EPEL 5. https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.el5
bowtie-0.12.7-2.fc15 has been submitted as an update for Fedora 15. https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.fc15
bowtie-0.12.7-2.fc14 has been submitted as an update for Fedora 14. https://admin.fedoraproject.org/updates/bowtie-0.12.7-2.fc14
bowtie-0.12.7-2.el5 has been pushed to the Fedora EPEL 5 testing repository.
bowtie-0.12.7-2.fc15 has been pushed to the Fedora 15 stable repository.
bowtie-0.12.7-2.fc14 has been pushed to the Fedora 14 stable repository.
bowtie-0.12.7-2.el5 has been pushed to the Fedora EPEL 5 stable repository.
bowtie-0.12.7-2.el6 has been pushed to the Fedora EPEL 6 stable repository.