[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453
Bug 1457453 depends on bug 1457451, which changed state.

Bug 1457451 Summary: Review Request: R-SummarizedExperiment - 
SummarizedExperiment container
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA
Last Closed||2017-06-21 08:19:57



--- Comment #8 from Fedora Update System  ---
R-3.4.0-2.fc25, R-BH-1.62.0.1-2.fc25, R-Biobase-2.36.2-1.fc25,
R-BiocGenerics-0.22.0-1.fc25, R-BiocParallel-1.10.1-1.fc25,
R-Biostrings-2.44.0-1.fc25, R-BufferedMatrix-1.40.0-1.fc25,
R-BufferedMatrixMethods-1.40.0-1.fc25, R-DBI-0.6.1-1.fc25,
R-DelayedArray-0.2.7-1.fc25, R-GenomeInfoDb-1.12.1-1.fc25,
R-GenomeInfoDbData-0.99.0-1.fc25, R-GenomicAlignments-1.12.1-1.fc25,
R-GenomicRanges-1.28.3-1.fc25, R-IRanges-2.10.1-1.fc25, R-R6-2.2.1-1.fc25,
R-RCurl-1.95.4.8-1.fc25, R-RInside-0.2.14-2.fc25, R-RODBC-1.3.15-1.fc25,
R-RSQLite-1.1.2-2.fc25, R-Rcompression-0.93.2-15.fc25,
R-Rsamtools-1.28.0-1.fc25, R-Rsolid-0.9.31-20.fc25, R-S4Vectors-0.14.3-1.fc25,
R-SummarizedExperiment-1.6.3-1.fc25, R-XML-3.98.1.7-1.fc25,
R-XVector-0.16.0-1.fc25, R-acepack-1.4.1-2.fc25, R-affy-1.54.0-1.fc25,
R-affyio-1.46.0-1.fc25, R-biglm-0.9.1-8.fc25, R-bitops-1.0.6-5.fc25,
R-caTools-1.17.1-4.fc25, R-digest-0.6.12-1.fc25, R-expm-0.999.2-1.fc25,
R-futile.logger-1.4.3-1.fc25, R-futile.options-1.0.0-1.fc25,
R-highlight-0.4.7.1-2.fc25, R-lambda.r-1.1.9-1.fc25, R-littler-0.3.2-2.fc25,
R-lmtest-0.9.35-1.fc25, R-maanova-1.46.1-1.fc25, R-magrittr-1.5-1.fc25,
R-matrixStats-0.52.2-1.fc25, R-msm-1.6.4-1.fc25, R-multtest-2.32.0-1.fc25,
R-mvtnorm-1.0.6-1.fc25, R-plogr-0.1.1-1.fc25, R-preprocessCore-1.38.1-1.fc25,
R-qtl-1.40.8-3.fc25, R-rlecuyer-0.3.4-1.fc25, R-rtracklayer-1.36.3-1.fc25,
R-snow-0.4.2-1.fc25, R-testthat-1.0.2-1.fc25, R-waveslim-1.7.5-4.fc25,
R-wavethresh-4.6.8-1.fc25, rkward-0.6.5-6.fc25, rpy-2.8.5-4.fc25 has been
pushed to the Fedora 25 stable repository. If problems still persist, please
make note of it in this bug report.

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453
Bug 1457453 depends on bug 1457390, which changed state.

Bug 1457390 Summary: Review Request: R-snow - Simple Network of Workstations
https://bugzilla.redhat.com/show_bug.cgi?id=1457390

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453
Bug 1457453 depends on bug 1457391, which changed state.

Bug 1457391 Summary: Review Request: R-futile.options - Futile options 
management
https://bugzilla.redhat.com/show_bug.cgi?id=1457391

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453
Bug 1457453 depends on bug 1456973, which changed state.

Bug 1456973 Summary: Review Request: R-GenomeInfoDbData - Species and taxonomy 
ID look up tables used by GenomeInfoDb
https://bugzilla.redhat.com/show_bug.cgi?id=1456973

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA



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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Fedora Update System  changed:

   What|Removed |Added

 Status|MODIFIED|ON_QA



--- Comment #7 from Fedora Update System  ---
R-3.4.0-2.fc25, R-BH-1.62.0.1-2.fc25, R-Biobase-2.36.2-1.fc25,
R-BiocGenerics-0.22.0-1.fc25, R-BiocParallel-1.10.1-1.fc25,
R-Biostrings-2.44.0-1.fc25, R-BufferedMatrix-1.40.0-1.fc25,
R-BufferedMatrixMethods-1.40.0-1.fc25, R-DBI-0.6.1-1.fc25,
R-DelayedArray-0.2.7-1.fc25, R-GenomeInfoDb-1.12.1-1.fc25,
R-GenomeInfoDbData-0.99.0-1.fc25, R-GenomicAlignments-1.12.1-1.fc25,
R-GenomicRanges-1.28.3-1.fc25, R-IRanges-2.10.1-1.fc25, R-R6-2.2.1-1.fc25,
R-RCurl-1.95.4.8-1.fc25, R-RInside-0.2.14-2.fc25, R-RODBC-1.3.15-1.fc25,
R-RSQLite-1.1.2-2.fc25, R-Rcompression-0.93.2-15.fc25,
R-Rsamtools-1.28.0-1.fc25, R-Rsolid-0.9.31-20.fc25, R-S4Vectors-0.14.3-1.fc25,
R-SummarizedExperiment-1.6.3-1.fc25, R-XML-3.98.1.7-1.fc25,
R-XVector-0.16.0-1.fc25, R-acepack-1.4.1-2.fc25, R-affy-1.54.0-1.fc25,
R-affyio-1.46.0-1.fc25, R-biglm-0.9.1-8.fc25, R-bitops-1.0.6-5.fc25,
R-caTools-1.17.1-4.fc25, R-digest-0.6.12-1.fc25, R-expm-0.999.2-1.fc25,
R-futile.logger-1.4.3-1.fc25, R-futile.options-1.0.0-1.fc25,
R-highlight-0.4.7.1-2.fc25, R-lambda.r-1.1.9-1.fc25, R-littler-0.3.2-2.fc25,
R-lmtest-0.9.35-1.fc25, R-maanova-1.46.1-1.fc25, R-magrittr-1.5-1.fc25,
R-matrixStats-0.52.2-1.fc25, R-msm-1.6.4-1.fc25, R-multtest-2.32.0-1.fc25,
R-mvtnorm-1.0.6-1.fc25, R-plogr-0.1.1-1.fc25, R-preprocessCore-1.38.1-1.fc25,
R-qtl-1.40.8-3.fc25, R-rlecuyer-0.3.4-1.fc25, R-rtracklayer-1.36.3-1.fc25,
R-snow-0.4.2-1.fc25, R-testthat-1.0.2-1.fc25, R-waveslim-1.7.5-4.fc25,
R-wavethresh-4.6.8-1.fc25, rkward-0.6.5-6.fc25, rpy-2.8.5-4.fc25 has been
pushed to the Fedora 25 testing repository. If problems still persist, please
make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here:
https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453



--- Comment #6 from Fedora Update System  ---
R-3.4.0-2.fc25 R-BH-1.62.0.1-2.fc25 R-Biobase-2.36.2-1.fc25
R-BiocGenerics-0.22.0-1.fc25 R-BiocParallel-1.10.1-1.fc25
R-Biostrings-2.44.0-1.fc25 R-BufferedMatrix-1.40.0-1.fc25
R-BufferedMatrixMethods-1.40.0-1.fc25 R-DBI-0.6.1-1.fc25
R-DelayedArray-0.2.7-1.fc25 R-GenomeInfoDb-1.12.1-1.fc25
R-GenomeInfoDbData-0.99.0-1.fc25 R-GenomicAlignments-1.12.1-1.fc25
R-GenomicRanges-1.28.3-1.fc25 R-IRanges-2.10.1-1.fc25 R-R6-2.2.1-1.fc25
R-RCurl-1.95.4.8-1.fc25 R-RInside-0.2.14-2.fc25 R-RODBC-1.3.15-1.fc25
R-RSQLite-1.1.2-2.fc25 R-Rcompression-0.93.2-15.fc25 R-Rsamtools-1.28.0-1.fc25
R-Rsolid-0.9.31-20.fc25 R-S4Vectors-0.14.3-1.fc25
R-SummarizedExperiment-1.6.3-1.fc25 R-XML-3.98.1.7-1.fc25
R-XVector-0.16.0-1.fc25 R-acepack-1.4.1-2.fc25 R-affy-1.54.0-1.fc25
R-affyio-1.46.0-1.fc25 R-biglm-0.9.1-8.fc25 R-bitops-1.0.6-5.fc25
R-caTools-1.17.1-4.fc25 R-digest-0.6.12-1.fc25 R-expm-0.999.2-1.fc25
R-futile.logger-1.4.3-1.fc25 R-futile.options-1.0.0-1.fc25
R-highlight-0.4.7.1-2.fc25 R-lambda.r-1.1.9-1.fc25 R-littler-0.3.2-2.fc25
R-lmtest-0.9.35-1.fc25 R-maanova-1.46.1-1.fc25 R-magrittr-1.5-1.fc25
R-matrixStats-0.52.2-1.fc25 R-msm-1.6.4-1.fc25 R-multtest-2.32.0-1.fc25
R-mvtnorm-1.0.6-1.fc25 R-plogr-0.1.1-1.fc25 R-preprocessCore-1.38.1-1.fc25
R-qtl-1.40.8-3.fc25 R-rlecuyer-0.3.4-1.fc25 R-rtracklayer-1.36.3-1.fc25
R-snow-0.4.2-1.fc25 R-testthat-1.0.2-1.fc25 R-waveslim-1.7.5-4.fc25
R-wavethresh-4.6.8-1.fc25 rkward-0.6.5-6.fc25 rpy-2.8.5-4.fc25 has been
submitted as an update to Fedora 25.
https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |MODIFIED



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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Fedora Update System  changed:

   What|Removed |Added

 Status|MODIFIED|ON_QA



--- Comment #5 from Fedora Update System  ---
R-3.4.0-2.fc25, R-RCurl-1.95.4.8-1.fc25, R-Rcompression-0.93.2-15.fc25,
R-XML-3.98.1.7-1.fc25, R-bitops-1.0.6-5.fc25, rkward-0.6.5-6.fc25,
rpy-2.8.5-4.fc25 has been pushed to the Fedora 25 testing repository. If
problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here:
https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453



--- Comment #4 from Fedora Update System  ---
R-3.4.0-2.fc25 R-RCurl-1.95.4.8-1.fc25 R-Rcompression-0.93.2-15.fc25
R-XML-3.98.1.7-1.fc25 R-bitops-1.0.6-5.fc25 rkward-0.6.5-6.fc25
rpy-2.8.5-4.fc25 has been submitted as an update to Fedora 25.
https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Fedora Update System  changed:

   What|Removed |Added

 Status|ASSIGNED|MODIFIED



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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453



--- Comment #3 from Fedora Update System  ---
R-3.4.0-2.fc25 R-RCurl-1.95.4.8-1.fc25 R-Rcompression-0.93.2-15.fc25
R-XML-3.98.1.7-1.fc25 R-bitops-1.0.6-5.fc25 rkward-0.6.5-6.fc25
rpy-2.8.5-4.fc25 has been submitted as an update to Fedora 25.
https://bodhi.fedoraproject.org/updates/FEDORA-2017-17bcc534b7

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453



--- Comment #2 from Gwyn Ciesla  ---
Package request has been approved:
https://admin.fedoraproject.org/pkgdb/package/rpms/R-GenomicAlignments

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[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Mattias Ellert  changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 CC||mattias.ell...@physics.uu.s
   ||e
   Assignee|nob...@fedoraproject.org|mattias.ell...@physics.uu.s
   ||e
  Flags||fedora-review+



--- Comment #1 from Mattias Ellert  ---
Package Review
==

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated


Issues:
===

The build log shows several warninings about variables that may be
used without having been initialized:

cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:880:6: warning: 'Roffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:878:6: warning: 'Loffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:1064:6: warning: 'Roffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]
cigar_utils.c:1062:6: warning: 'Loffset' may be used uninitialized in this
function [-Wmaybe-uninitialized]

Uninitialized variables can lead to random behaviour of the program,
so addressing these or reporting it upstream might be a good idea.

The log also shows several warnings about missing file links from the
documentaion generation. This is quite a long list, so I will not copy
it here. It is not critical, but if it can be fixed ...

APPROVED.

= MUST items =

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[-]: Development (unversioned) .so files in -devel subpackage, if present.
 Note: Unversioned so-files in private %_libdir subdirectory (see
 attachment). Verify they are not in ld path.
 This is not a developmen symlink.
 This file is not in the default library path.
[-]: Header files in -devel subpackage, if present.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.

Generic:
[x]: Package is licensed with an open-source compatible license and meets
 other legal requirements as defined in the legal section of Packaging
 Guidelines.
 DESCRIPTION file states "License: Artistic-2.0".
 No other license statements found in sources.
[-]: 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 %license.
 No license file in the sources.
[x]: License field in the package spec file matches the actual license.
 Spec file states "License: Artistic 2.0".
[-]: License file installed when any subpackage combination is installed.
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[-]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
 names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
 Provides are present.
[x]: Requires correct, justified where necessary.
 The Requires matches the Depends/Imports in the DESCRIPTION files
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
 one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
 Note: There are rpmlint 

[Bug 1457453] Review Request: R-GenomicAlignments - Representation and manipulation of short genomic alignments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1457453

Tom "spot" Callaway  changed:

   What|Removed |Added

 Depends On||1457451, 1457390, 1457391,
   ||1456973




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1456973
[Bug 1456973] Review Request: R-GenomeInfoDbData - Species and taxonomy ID
look up tables used by GenomeInfoDb
https://bugzilla.redhat.com/show_bug.cgi?id=1457390
[Bug 1457390] Review Request: R-snow - Simple Network of Workstations
https://bugzilla.redhat.com/show_bug.cgi?id=1457391
[Bug 1457391] Review Request: R-futile.options - Futile options management
https://bugzilla.redhat.com/show_bug.cgi?id=1457451
[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment
container
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