Bug 490722
| Summary: | Review Request: R-BSgenome - Infrastructure for Biostrings-based genome data packages | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Pierre-YvesChibon <pingou> |
| Component: | Package Review | Assignee: | Mattias Ellert <mattias.ellert> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | medium | Docs Contact: | |
| Priority: | medium | ||
| Version: | rawhide | CC: | fedora-package-review, notting |
| Target Milestone: | --- | Flags: | mattias.ellert:
fedora-review+
kevin: fedora-cvs+ |
| Target Release: | --- | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Fixed In Version: | 2.4.1-1.fc11 | Doc Type: | Bug Fix |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2009-07-02 05:49:26 UTC | Type: | --- |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | 490721 | ||
| Bug Blocks: | |||
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Description
Pierre-YvesChibon
2009-03-17 18:16:37 UTC
Package does not build due to missing BuildRequires: Error: package 'Biostrings' required by 'BSgenome' could not be found Execution halted ERROR: lazy loading failed for package 'BSgenome' arf there is a missing BR on R-Biostrings Updated: Spec URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome-1.10.5-2.fc10.src.rpm Fedora review R-BSgenome-1.10.5-1.fc10.src.rpm (2009-05-11) * OK ! Needs attention * rpmlint output R-BSgenome.noarch: W: one-line-command-in-%post /usr/lib/rpm/R-make-search-index.sh R-BSgenome.noarch: W: one-line-command-in-%postun /usr/lib/rpm/R-make-search-index.sh 2 packages and 1 specfiles checked; 0 errors, 2 warnings. The one-line-command warnings are standard for R packages * Package is named according to R packaging guidelines * Package follows R packaging guidelines * The package is licensed under a Fedora approved license (Artistic 2.0) * The license matches what is written in the DESCRIPTION file No license/copyright statements that contradict this was found * License text not included in the package (OK since the stated licence does not require it). * Specfile is written in legible English and uses macros consitently * Source matches upstream 9e9f8793065e5c49c07240c6cdcade9c BSgenome_1.10.5.tar.gz 9e9f8793065e5c49c07240c6cdcade9c SRPM/BSgenome_1.10.5.tar.gz ! However it is not the latest version (1.12.0 is available for BioC 2.4) * Package compiles in mock (Fedora 10) ! BuildRequires and Requires look sane, but Is the "Requires: R-biobase" appropriate? It is not listed as a Depends or Imports on the package web site. (It will be dragged in as a dependency of the R-Biostrings package which is a direct dependency) * %check is present, but disabled with the comment - which makes sense. * The package owns the directories it creates * No duplicate files * %files has %defattrs, and permissions are sane. * %clean clears %buildroot * Package contains permissable content * Package doesn't own other's directories * %install clears %buildroot * Installed filenames are valid UTF8 (even valid ASCII) * Scriptlets are sane (In reply to comment #5) > Fedora review R-BSgenome-1.10.5-1.fc10.src.rpm (2009-05-11) > ! However it is not the latest version (1.12.0 is available for BioC 2.4) > ! BuildRequires and Requires look sane, but > > Is the "Requires: R-biobase" appropriate? It is not listed as a > Depends or Imports on the package web site. (It will be dragged in > as a dependency of the R-Biostrings package which is a direct > dependency) > Corrected in : Spec URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome.spec SRPM URL: http://pingou.fedorapeople.org/RPMs/R-BSgenome-1.12.0-1.fc10.src.rpm There is one tiny issue left - which I should have noted earlier: According to https://fedoraproject.org/wiki/Packaging/R#Documentation_files the NAMESPACE file should not be marked %doc. I trust you can fix that before importing the package to cvs. Package approved. Thanks for the review (once again :-) ), I will fix the %doc before importing New Package CVS Request ======================= Package Name: R-BSgenome Short Description: Infrastructure shared by all the Biostrings-based genome data packages Owners: pingou Branches: F-10 F-11 InitialCC: cvs done. R-BSgenome-1.12.0-2.fc10 has been submitted as an update for Fedora 10. http://admin.fedoraproject.org/updates/R-BSgenome-1.12.0-2.fc10 R-BSgenome-1.12.0-2.fc11 has been submitted as an update for Fedora 11. http://admin.fedoraproject.org/updates/R-BSgenome-1.12.0-2.fc11 R-BSgenome-1.12.0-2.fc10 has been pushed to the Fedora 10 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 R-BSgenome'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-5661 R-BSgenome-1.12.0-2.fc11 has been pushed to the Fedora 11 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 R-BSgenome'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F11/FEDORA-2009-5694 R-Biobase-2.4.1-1.fc10,R-RUnit-0.4.22-1.fc10,R-IRanges-1.2.3-1.fc10,R-BSgenome-1.12.2-1.fc10,R-BufferedMatrixMethods-1.8.0-3.fc10,R-Biostrings-2.12.6-1.fc10 has been submitted as an update for Fedora 10. http://admin.fedoraproject.org/updates/R-Biobase-2.4.1-1.fc10,R-RUnit-0.4.22-1.fc10,R-IRanges-1.2.3-1.fc10,R-BSgenome-1.12.2-1.fc10,R-BufferedMatrixMethods-1.8.0-3.fc10,R-Biostrings-2.12.6-1.fc10 R-Biobase-2.4.1-1.fc11,R-RUnit-0.4.22-1.fc11,R-IRanges-1.2.3-1.fc11,R-BSgenome-1.12.2-1.fc11,R-BufferedMatrixMethods-1.8.0-3.fc11,R-Biostrings-2.12.6-1.fc11 has been submitted as an update for Fedora 11. http://admin.fedoraproject.org/updates/R-Biobase-2.4.1-1.fc11,R-RUnit-0.4.22-1.fc11,R-IRanges-1.2.3-1.fc11,R-BSgenome-1.12.2-1.fc11,R-BufferedMatrixMethods-1.8.0-3.fc11,R-Biostrings-2.12.6-1.fc11 R-Biobase-2.4.1-1.fc10, R-RUnit-0.4.22-1.fc10, R-IRanges-1.2.3-1.fc10, R-BSgenome-1.12.2-1.fc10, R-BufferedMatrixMethods-1.8.0-3.fc10, R-Biostrings-2.12.6-1.fc10 has been pushed to the Fedora 10 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 R-Biobase R-RUnit R-IRanges R-BSgenome R-BufferedMatrixMethods R-Biostrings'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-6530 R-Biobase-2.4.1-1.fc11, R-RUnit-0.4.22-1.fc11, R-IRanges-1.2.3-1.fc11, R-BSgenome-1.12.2-1.fc11, R-BufferedMatrixMethods-1.8.0-3.fc11, R-Biostrings-2.12.6-1.fc11 has been pushed to the Fedora 11 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 R-Biobase R-RUnit R-IRanges R-BSgenome R-BufferedMatrixMethods R-Biostrings'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F11/FEDORA-2009-6673 R-Biobase-2.4.1-1.fc10, R-RUnit-0.4.22-1.fc10, R-IRanges-1.2.3-1.fc10, R-BSgenome-1.12.2-1.fc10, R-BufferedMatrixMethods-1.8.0-3.fc10, R-Biostrings-2.12.6-1.fc10 has been pushed to the Fedora 10 stable repository. If problems still persist, please make note of it in this bug report. R-Biobase-2.4.1-1.fc11, R-RUnit-0.4.22-1.fc11, R-IRanges-1.2.3-1.fc11, R-BSgenome-1.12.2-1.fc11, R-BufferedMatrixMethods-1.8.0-3.fc11, R-Biostrings-2.12.6-1.fc11 has been pushed to the Fedora 11 stable repository. If problems still persist, please make note of it in this bug report. |