[Bug 447559] New: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

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comments should be made in the comments box of this bug report.

https://bugzilla.redhat.com/show_bug.cgi?id=447559

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes
                    that annotate a group of genes with a significant p-
                    value
           Product: Fedora
           Version: rawhide
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: medium
          Priority: medium
         Component: Package Review
        AssignedTo: [e-mail]
        ReportedBy: [e-mail]
         QAContact: [e-mail]
                CC: [e-mail],[e-mail]

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....
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)

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

[e-mail] changed:

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         AssignedTo|[e-mail]    |[e-mail]
             Status|NEW                         |ASSIGNED
               Flag|                            |fedora-review?

------- Additional Comments From [e-mail]  2008-05-21 07:56 EST -------

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.

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

------- Additional Comments From [e-mail]  2008-05-21 08:39 EST -------
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....

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

------- Additional Comments From [e-mail]  2008-05-21 08:45 EST -------
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).

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

------- Additional Comments From [e-mail]  2008-05-21 08:48 EST -------
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)

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

[e-mail] changed:

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               Flag|fedora-review?              |fedora-review+

------- Additional Comments From [e-mail]  2008-05-21 09:43 EST -------
APPROVED.

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

[e-mail] changed:

What    |Removed                     |Added
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               Flag|                            |fedora-cvs?

------- Additional Comments From [e-mail]  2008-05-21 18:33 EST -------
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

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

[e-mail] changed:

What    |Removed                     |Added
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               Flag|fedora-cvs?                 |fedora-cvs+

------- Additional Comments From [e-mail]  2008-05-22 14:40 EST -------
cvs done.

[Bug 447559] Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug report.

Summary: Review Request: perl-GO-TermFinder - Identify GO nodes that annotate a group of genes with a significant p-value

https://bugzilla.redhat.com/show_bug.cgi?id=447559

[e-mail] changed:

What    |Removed                     |Added
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             Status|ASSIGNED                    |CLOSED
         Resolution|                            |NEXTRELEASE

------- Additional Comments From [e-mail]  2008-06-04 08:39 EST -------
Pushed to updates/ and epel-testing. Thank you.