[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-21 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |CLOSED
 Resolution|--- |ERRATA
Last Closed||2017-06-21 08:19:52



--- 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 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-21 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451
Bug 1457451 depends on bug 1457449, which changed state.

Bug 1457449 Summary: Review Request: R-DelayedArray - Delayed operations on 
array-like objects
https://bugzilla.redhat.com/show_bug.cgi?id=1457449

   What|Removed |Added

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



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[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-10 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

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 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-09 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

Fedora Update System  changed:

   What|Removed |Added

 Status|ON_QA   |MODIFIED



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[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-09 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451



--- 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 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-09 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

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 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-08 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451



--- 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 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-08 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451



--- 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 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-08 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

Fedora Update System  changed:

   What|Removed |Added

 Status|ASSIGNED|MODIFIED



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[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-07 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451



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

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[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-06-06 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

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 package build log has some warnings related to documentation
generation durung the build:

Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/Assays-class.Rd:117:
missing file link 'SimpleList'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:116:
missing file link 'DataFrame'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:119:
missing file link 'DataFrame'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:122:
missing file link 'GRanges'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123:
missing file link 'GRangesList'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126:
missing file link 'GRanges'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126:
missing file link 'GRangesList'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:151:
missing file link 'GRanges'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:152:
missing file link 'GRangesList'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216:
missing file link 'shift'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:217:
missing file link 'isDisjoint'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:218:
missing file link 'coverage'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:219:
missing file link 'findOverlaps'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220:
missing file link 'nearest'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:264:
missing file link 'shift'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:265:
missing file link 'isDisjoint'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:266:
missing file link 'coverage'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:267:
missing file link 'findOverlaps'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268:
missing file link 'nearest'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271:
missing file link 'GRanges'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:133:
missing file link 'mcols'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:206:
missing file link 'mcols'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:393:
missing file link 'DataFrame'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:393:
missing file link 'SimpleList'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:394:
missing file link 'Annotated'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:396:
missing file link 'metadata'
Rd warning:
/builddir/build/BUILD/SummarizedExperiment/SummarizedExperiment/man/SummarizedExperiment-class.Rd:397:
missing file link 'mcols'
Rd warning:

[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-05-31 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

Tom "spot" Callaway  changed:

   What|Removed |Added

 Blocks||1457453




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1457453
[Bug 1457453] Review Request: R-GenomicAlignments - Representation and
manipulation of short genomic alignments
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[Bug 1457451] Review Request: R-SummarizedExperiment - SummarizedExperiment container

2017-05-31 Thread bugzilla 
https://bugzilla.redhat.com/show_bug.cgi?id=1457451

Tom "spot" Callaway  changed:

   What|Removed |Added

 Depends On||1457449




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1457449
[Bug 1457449] Review Request: R-DelayedArray - Delayed operations on
array-like objects
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