Spec URL: http://pilot.genomicscenter.nl/genomics/SPECS/perl-GO-TermFinder.spec SRPM URL: http://pilot.genomicscenter.nl/genomics/el5/SRPMS/perl-GO-TermFinder-0.82-1.el5.src.rpm Description: This package is intended to provide a method whereby the P-values of a set of GO annotations can be determined for a set of genes, based on the number of genes that exist in the particular genome (or in a selected background distribution from the genome), and their annotation, and the frequency with which the GO nodes are annotated across the provided set of genes. The P-value is simply calculated using the hypergeometric distribution as the probability of x or more out of n genes having a given annotation, given that G of N have that annotation in the genome in general. We chose the hypergeometric distribution (sampling without replacement) since it is more accurate, though slower to calculate, than the binomial distribution (sampling with replacement). Additional Information: This is my first perl package ;-) - Targeted for EL-5, F-8, F-9 and rawhide. See also koji scratch builds: - http://koji.fedoraproject.org/koji/taskinfo?taskID=620022 (dist-f8-updates-candidate) - http://koji.fedoraproject.org/koji/taskinfo?taskID=620032 (dist-f9-updates-candidate) - http://koji.fedoraproject.org/koji/taskinfo?taskID=620080 (dist-f10)
Review: + package builds in mock. Koji build => http://koji.fedoraproject.org/koji/taskinfo?taskID=622400 + rpmlint is silent for SRPM and for RPM. + source files match upstream url ffebb282cdd3d8dbd5819d57d2c20d37 GO-TermFinder-0.82.tar.gz + package meets naming and packaging guidelines. + specfile is properly named, is cleanly written + Spec file is written in American English. + Spec file is legible. + dist tag is present. + build root is correct. + license is open source-compatible. + License text is included in package. + %doc is present. + BuildRequires are proper. + %clean is present. + package installed properly. + Macro use appears rather consistent. + Package contains code, not content. + no headers or static libraries. + no .pc file present. + no -devel subpackage + no .la files. + no translations are available + Does owns the directories it creates. + no scriptlets present. + no duplicates in %files. + file permissions are appropriate. + make test gave All tests successful. Files=5, Tests=8101, 28 wallclock secs (27.44 cusr + 0.35 csys = 27.79 CPU) + Package perl-GO-TermFinder-0.82-1.fc10 => Provides: Native.so perl(GO::AnnotatedGene) = 0.11 perl(GO::Annotation) = 0.11 perl(GO::AnnotationProvider) = 0.12 perl(GO::AnnotationProvider::AnnotationParser) = 0.15 perl(GO::Node) = 0.16 perl(GO::OntologyProvider) = 0.12 perl(GO::OntologyProvider::OboParser) = 0.01 perl(GO::OntologyProvider::OntologyParser) = 0.15 perl(GO::Reference) = 0.1 perl(GO::TermFinder) = 0.82 perl(GO::TermFinder::Native) perl(GO::TermFinder::Native::Distributions) perl(GO::TermFinder::Nativec) perl(GO::TermFinderReport::Html) = 0.12 perl(GO::TermFinderReport::Text) = 0.10 perl(GO::Utils::File) = 0.12 perl(GO::Utils::General) = 0.11 perl(GO::View) = 0.15 perl(GO::View::GD) = 0.11 Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libm.so.6 libm.so.6(GLIBC_2.0) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(GLIBCXX_3.4) perl(:MODULE_COMPAT_5.10.0) perl(CGI) perl(CGI) perl(DynaLoader) perl(Exporter) perl(GD) perl(GD) perl(GO::AnnotationProvider) perl(GO::Node) perl(GO::OntologyProvider) perl(GO::TermFinder::Native) perl(GO::View::GD) perl(GraphViz) perl(GraphViz) perl(IO::File) perl(Storable) perl(Storable) perl(base) perl(diagnostics) perl(strict) perl(vars) perl(warnings) rtld(GNU_HASH) SHOULD: Add perl(GD), perl(GraphViz) as BR. Check build.log which said Warning: prerequisite GD 0 not found. Warning: prerequisite GraphViz 0 not found.
Added suggested BuildRequires: SPEC: http://pilot.genomicscenter.nl/genomics/SPECS/perl-GO-TermFinder.spec SRPM: http://pilot.genomicscenter.nl/genomics/el5/SRPMS/perl-GO-TermFinder-0.82-2.el5.src.rpm
Since perl(GraphViz) is a Build Requirement now, the EL-5 branch for this package will need to wait for perl-GraphViz to be branched for EL-5 (contacted maintainer -cweyl- already - the package builds clean for EL-5, so I've requested he branches for EL-5).
Koji scratch builds for perl-GO-TermFinder-0.82-2: - http://koji.fedoraproject.org/koji/taskinfo?taskID=622505 (dist-f8-updates-candidate) - http://koji.fedoraproject.org/koji/taskinfo?taskID=622496 (dist-f9-updates-candidate) - http://koji.fedoraproject.org/koji/taskinfo?taskID=622517 (dist-f10)
APPROVED.
New Package CVS Request ======================= Package Name: perl-GO-TermFinder Short Description: Identify GO nodes that annotate a group of genes with a significant p-value Owners: kanarip Branches: F-8 F-9 EL-5 InitialCC: perl-sig Cvsextras Commits: yes
cvs done.
Pushed to updates/ and epel-testing. Thank you.