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Summary: Review Request: pypop - Python for Population Genomics
https://bugzilla.redhat.com/show_bug.cgi?id=464460
Summary: Review Request: pypop - Python for Population Genomics Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: alexl@users.sourceforge.net QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, fedora-package-review@redhat.com Estimated Hours: 0.0 Classification: Fedora
Spec URL: http://alexlan.fedorapeople.org/reviews/pypop.spec SRPM URL: http://alexlan.fedorapeople.org/reviews/pypop-0.7.0-1.fc8.src.rpm Description: PyPop is a bioinformatics framework for performing population genomics analysis, particularly on large-scale multilocus genotype data.
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https://bugzilla.redhat.com/show_bug.cgi?id=464460
Alex Lancaster alexl@users.sourceforge.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Group|fedora_contrib |
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--- Comment #1 from Alex Lancaster alexl@users.sourceforge.net 2008-09-29 04:59:55 EDT --- Note that rpmlint reports a bogus (in this context) error:
rpmlint pypop-0.7.0-1.fc8.i386.rpm pypop.i386: E: explicit-lib-dependency libxslt-python 1 packages and 0 specfiles checked; 1 errors, 0 warnings
The libxslt-python Requires is unavoidable because it is needed at runtime and isn't a C library and the automatic provides won't automatically pull in python libraries.
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--- Comment #2 from Alex Lancaster alexl@users.sourceforge.net 2008-09-29 05:09:03 EDT --- koji scratch build on F-8 is here:
https://koji.fedoraproject.org/koji/taskinfo?taskID=849331
and rawhide one is here:
https://koji.fedoraproject.org/koji/taskinfo?taskID=849349
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Pierre-YvesChibon pingou@pingoured.fr changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |pingou@pingoured.fr AssignedTo|nobody@fedoraproject.org |pingou@pingoured.fr Flag| |fedora-review?
--- Comment #3 from Pierre-YvesChibon pingou@pingoured.fr 2008-09-29 12:56:38 EDT --- Could you add to the reviews some example of input file and output file so that I can check that I obtain similar results while running the program here.
I take the review.
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https://bugzilla.redhat.com/show_bug.cgi?id=464460
--- Comment #4 from Alex Lancaster alexl@users.sourceforge.net 2008-09-29 18:54:14 EDT --- Created an attachment (id=318020) --> (https://bugzilla.redhat.com/attachment.cgi?id=318020) sample.ini (configuration file)
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--- Comment #5 from Alex Lancaster alexl@users.sourceforge.net 2008-09-29 18:54:54 EDT --- Created an attachment (id=318021) --> (https://bugzilla.redhat.com/attachment.cgi?id=318021) sample.pop (population file)
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--- Comment #6 from Alex Lancaster alexl@users.sourceforge.net 2008-09-29 18:57:35 EDT --- Created an attachment (id=318022) --> (https://bugzilla.redhat.com/attachment.cgi?id=318022) sample-out.txt (output file that should be generated)
I've attached 2 input files and sample-out.txt, the output file, which should be generated upon running pypop like this:
pypop -c sample.ini sample.pop
There may be minor differences with the exact numbers depending on your platform (e.g. i386 vs x86_64) and because the Monte Carlo algorithm uses a random number so a strict diff may produce differences.
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Alex Lancaster alexl@users.sourceforge.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED
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--- Comment #7 from Pierre-YvesChibon pingou@pingoured.fr 2008-09-30 03:40:15 EDT --- Package Review ==============
Key: - = N/A x = Check ! = Problem ? = Not evaluated
=== REQUIRED ITEMS === [x] Package is named according to the Package Naming Guidelines. [x] Spec file name must match the base package %{name}, in the format %{name}.spec. [x] Package meets the Packaging Guidelines. [x] Package successfully compiles and builds into binary rpms on at least one supported architecture. Tested on: F9/x86_64 [x] Rpmlint output: pypop.x86_64: E: explicit-lib-dependency libxslt-python [x] Package is not relocatable. [x] Buildroot is correct (%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)) [x] Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x] License field in the package spec file matches the actual license. License type:GPLv2+ [x] If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %doc. [x] Spec file is legible and written in American English. [x] Sources used to build the package matches the upstream source, as provided in the spec URL. SHA1SUM of package: 80637be9cca104b8ab0fe538674858eff00a99ee SHA1SUM of upstream: 80637be9cca104b8ab0fe538674858eff00a99ee [x] Package is not known to require ExcludeArch [x] All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. [-] The spec file handles locales properly. [-] ldconfig called in %post and %postun if required. [x] Package must own all directories that it creates. [x] Package requires other packages for directories it uses. [x] Package does not contain duplicates in %files. [x] Permissions on files are set properly. [x] Package has a %clean section, which contains rm -rf %{buildroot}. [x] Package consistently uses macros. [x] Package contains code, or permissable content. [-] Large documentation files are in a -doc subpackage, if required. [x] Package uses nothing in %doc for runtime. [-] Header files in -devel subpackage, if present. [-] Static libraries in -devel subpackage, if present. [-] Package requires pkgconfig, if .pc files are present. [-] Development .so files in -devel subpackage, if present. [-] Fully versioned dependency in subpackages, if present. [x] Package does not contain any libtool archives (.la). [-] Package contains a properly installed %{name}.desktop file if it is a GUI application. -> No GUI at the moment but that will be something to add when the GUI will be available [x] Package does not own files or directories owned by other packages.
=== SUGGESTED ITEMS === [x] Latest version is packaged. [x] Package does not include license text files separate from upstream. [-] Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x] Reviewer should test that the package builds in mock. Tested on: Koji F8 and Rawhide [x] Package should compile and build into binary rpms on all supported architectures. Tested on: Koji F8 and Rawhide [x] Package functions as described (according to comment #14 and #16). [-] Scriptlets must be sane, if used. [-] The placement of pkgconfig(.pc) files is correct. [-] File based requires are sane.
=== Issues === 1- Please consider using %defattr(-,root,root,-) instead of %defattr(-,root,root). You can fix that at commit time
=== Suggestions === 1- It might be nice to add a link on the page http://www.pypop.org/ to the sources.
PACKAGE APPROVED
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Pierre-YvesChibon pingou@pingoured.fr changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-review? |fedora-review+
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Alex Lancaster alexl@users.sourceforge.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag| |fedora-cvs?
--- Comment #8 from Alex Lancaster alexl@users.sourceforge.net 2008-09-30 04:06:09 EDT --- New Package CVS Request ======================= Package Name: pypop Short Description: Python for population genomics Owners: alexlan Branches: F-8 F-9 InitialCC:
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--- Comment #9 from Huzaifa S. Sidhpurwala huzaifas@redhat.com 2008-09-30 05:43:46 EDT --- cvs done
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Huzaifa S. Sidhpurwala huzaifas@redhat.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs? |fedora-cvs+
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--- Comment #10 from Fedora Update System updates@fedoraproject.org 2008-09-30 06:44:01 EDT --- pypop-0.7.0-2.fc9 has been submitted as an update for Fedora 9. http://admin.fedoraproject.org/updates/pypop-0.7.0-2.fc9
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--- Comment #11 from Fedora Update System updates@fedoraproject.org 2008-09-30 06:47:05 EDT --- pypop-0.7.0-2.fc8 has been submitted as an update for Fedora 8. http://admin.fedoraproject.org/updates/pypop-0.7.0-2.fc8
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Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |ON_QA
--- Comment #12 from Fedora Update System updates@fedoraproject.org 2008-10-01 02:40:02 EDT --- pypop-0.7.0-2.fc9 has been pushed to the Fedora 9 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update pypop'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F9/FEDORA-2008-8487
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--- Comment #13 from Fedora Update System updates@fedoraproject.org 2008-10-01 02:41:31 EDT --- pypop-0.7.0-2.fc8 has been pushed to the Fedora 8 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update pypop'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F8/FEDORA-2008-8497
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--- Comment #14 from Fedora Update System updates@fedoraproject.org 2008-10-09 17:27:44 EDT --- pypop-0.7.0-2.fc9 has been pushed to the Fedora 9 stable repository. If problems still persist, please make note of it in this bug report.
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Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution| |NEXTRELEASE
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--- Comment #15 from Fedora Update System updates@fedoraproject.org 2008-10-09 17:33:57 EDT --- pypop-0.7.0-2.fc8 has been pushed to the Fedora 8 stable repository. If problems still persist, please make note of it in this bug report.
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Alex Lancaster alexl@users.sourceforge.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs+ |fedora-cvs?
--- Comment #16 from Alex Lancaster alexl@users.sourceforge.net 2008-10-11 00:59:24 EDT --- Package Change Request ====================== Package Name: pypop New Branches: EL-5 Owners: alexlan
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Kevin Fenzi kevin@tummy.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs? |fedora-cvs+
--- Comment #17 from Kevin Fenzi kevin@tummy.com 2008-10-12 22:16:17 EDT --- cvs done.
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