Bioc-devel - November 2016 - Subject View

A handful of check to follow up on R CMD BiocCheck

11 msgs · Nov 2 – Nov 10

AnnotationHub needed in the description of the ExperimentHubData

1 msg · Nov 30

Obenchain, Valerie AnnotationHub needed in the description of the ExperimentHubData Nov 30, 2016

AnnotationHub needed in the description of the ExperimentHubData

1 msg · Nov 30

Marcin Kosiński AnnotationHub needed in the description of the ExperimentHubData Nov 30, 2016

Availability shield URLs

3 msgs · Nov 2 – Nov 8

Leonardo Collado Torres Availability shield URLs Nov 2, 2016 Martin Morgan Availability shield URLs Nov 8, 2016 Leonardo Collado Torres Availability shield URLs Nov 8, 2016

Bioc-devel Digest, Vol 152, Issue 10

2 msgs · Nov 6 – Nov 6

rcaloger Bioc-devel Digest, Vol 152, Issue 10 Nov 6, 2016 Dario Strbenac Bioc-devel Digest, Vol 152, Issue 10 Nov 6, 2016

Bioc-devel, Travis & OS X build failure

1 msg · Nov 20

Alexey Sergushichev Bioc-devel, Travis & OS X build failure Nov 20, 2016

BiocStyle issue

5 msgs · Nov 22 – Nov 24

Yu, Guangchuang BiocStyle issue Nov 22, 2016 Leonardo Collado Torres BiocStyle issue Nov 22, 2016 Yu, Guangchuang BiocStyle issue Nov 22, 2016 Andrzej Oleś BiocStyle issue Nov 23, 2016 Andrzej Oleś BiocStyle issue Nov 24, 2016

Bioconductor devel BUILD/CHECK not running

2 msgs · Nov 16 – Nov 16

Hoffman, Gabriel Bioconductor devel BUILD/CHECK not running Nov 16, 2016 Martin Morgan Bioconductor devel BUILD/CHECK not running Nov 16, 2016

Bug in setdiff() for signature 'IRangesList, IRangesList'?

3 msgs · Nov 7 – Nov 7

Leonard Goldstein Bug in setdiff() for signature 'IRangesList, IRangesList'? Nov 7, 2016 Michael Lawrence Bug in setdiff() for signature 'IRangesList, IRangesList'? Nov 7, 2016 Leonard Goldstein Bug in setdiff() for signature 'IRangesList, IRangesList'? Nov 7, 2016

Coverage test badge not updating

5 msgs · Nov 1 – Nov 22

Leonardo Collado Torres Coverage test badge not updating Nov 1, 2016 Hervé Pagès Coverage test badge not updating Nov 1, 2016 Obenchain, Valerie Coverage test badge not updating Nov 18, 2016 Leonardo Collado Torres Coverage test badge not updating Nov 18, 2016 Obenchain, Valerie Coverage test badge not updating Nov 22, 2016

Error processing scater vignette Mac OS X Sierra

2 msgs · Nov 30 – Nov 30

Davis McCarthy Error processing scater vignette Mac OS X Sierra Nov 30, 2016 Leonardo Collado Torres Error processing scater vignette Mac OS X Sierra Nov 30, 2016

Error with InteractionSet package

2 msgs · Nov 8 – Nov 8

Ioannis Vardaxis Error with InteractionSet package Nov 8, 2016 Aaron Lun Error with InteractionSet package Nov 8, 2016

Feasibility of Parallel Extraction of Matches with extractAllMatches

2 msgs · Nov 16 – Nov 16

Dario Strbenac Feasibility of Parallel Extraction of Matches with extractAllMatches Nov 16, 2016 Hervé Pagès Feasibility of Parallel Extraction of Matches with extractAllMatches Nov 16, 2016

Feedback wanted on design of fixed-width Ranges class

8 msgs · Nov 23 – Nov 23

Files removed from svn are not disappearing from Git mirror

4 msgs · Nov 14 – Nov 15

James Collins Files removed from svn are not disappearing from Git mirror Nov 14, 2016 Hervé Pagès Files removed from svn are not disappearing from Git mirror Nov 14, 2016 Martin Morgan Files removed from svn are not disappearing from Git mirror Nov 15, 2016 James Collins Files removed from svn are not disappearing from Git mirror Nov 15, 2016

FlipFlop Ignores Read Strand and Requires Antiquated File Formats

2 msgs · Oct 31 – Nov 1

Dario Strbenac FlipFlop Ignores Read Strand and Requires Antiquated File Formats Oct 31, 2016 Wolfgang Huber FlipFlop Ignores Read Strand and Requires Antiquated File Formats Nov 1, 2016

GSL on Windows

3 msgs · Nov 18 – Nov 20

Dong Li GSL on Windows Nov 18, 2016 Dan Tenenbaum GSL on Windows Nov 18, 2016 Dong Li GSL on Windows Nov 20, 2016

GenomeInfoDb::Seqinfo(genome) broken?

7 msgs · Nov 3 – Nov 3

Raymond Cavalcante GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016 Vincent Carey GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016 Raymond Cavalcante GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016 Michael Lawrence GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016 Hervé Pagès GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016 Hervé Pagès GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016 Raymond Cavalcante GenomeInfoDb::Seqinfo(genome) broken? Nov 3, 2016

Help needed to reproduce my crash report

2 msgs · Nov 15 – Nov 16

Ted Wong Help needed to reproduce my crash report Nov 15, 2016 Martin Morgan Help needed to reproduce my crash report Nov 16, 2016

Issue with biovizBase::parseArgsForAes(), likely just a namespace issue

2 msgs · Nov 23 – Nov 24

Leonardo Collado Torres Issue with biovizBase::parseArgsForAes(), likely just a namespace issue Nov 23, 2016 Michael Lawrence Issue with biovizBase::parseArgsForAes(), likely just a namespace issue Nov 24, 2016

OrganismDb package for Drosophila.melanogaster

5 msgs · Nov 14 – Nov 16

Pariksheet Nanda OrganismDb package for Drosophila.melanogaster Nov 14, 2016 Obenchain, Valerie OrganismDb package for Drosophila.melanogaster Nov 15, 2016 Martin Morgan OrganismDb package for Drosophila.melanogaster Nov 15, 2016 Martin Morgan OrganismDb package for Drosophila.melanogaster Nov 15, 2016 Pariksheet Nanda OrganismDb package for Drosophila.melanogaster Nov 16, 2016

Problem with git-mirror

1 msg · Nov 4

Kevin RUE Problem with git-mirror Nov 4, 2016

Question about sumbition process and biocviews

14 msgs · Nov 5 – Nov 12

Reset SVN repo to earlier state

3 msgs · Nov 16 – Nov 16

Lukas Weber Reset SVN repo to earlier state Nov 16, 2016 Martin Morgan Reset SVN repo to earlier state Nov 16, 2016 Lukas Weber Reset SVN repo to earlier state Nov 16, 2016

Rgraphviz on ppc64le needs updated config.{sub, guess}

2 msgs · Nov 22 – Nov 23

Daniel Axtens Rgraphviz on ppc64le needs updated config.{sub, guess} Nov 22, 2016 Kasper Daniel Hansen Rgraphviz on ppc64le needs updated config.{sub, guess} Nov 23, 2016

SRAdb::sraConvert returns results in arbitrary order

2 msgs · Nov 17 – Nov 21

Ryan SRAdb::sraConvert returns results in arbitrary order Nov 17, 2016 Jack Zhu SRAdb::sraConvert returns results in arbitrary order Nov 21, 2016

Subversion Log Stalled

2 msgs · Nov 10 – Nov 10

Dario Strbenac Subversion Log Stalled Nov 10, 2016 Martin Morgan Subversion Log Stalled Nov 10, 2016

What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation

2 msgs · Nov 3 – Nov 3

Marcin Kosiński What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation Nov 3, 2016 Marcin Kosiński What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation Nov 3, 2016

adding new features to current release branch

4 msgs · Nov 17 – Nov 17

Anand MT adding new features to current release branch Nov 17, 2016 Martin Morgan adding new features to current release branch Nov 17, 2016 Kasper Daniel Hansen adding new features to current release branch Nov 17, 2016 Anand MT adding new features to current release branch Nov 17, 2016

build report date - devel

2 msgs · Nov 24 – Nov 24

Aurora Torrente build report date - devel Nov 24, 2016 Obenchain, Valerie build report date - devel Nov 24, 2016

can't fix the bug: Error: 'devel' version requires a more recent R

2 msgs · Nov 10 – Nov 10

Jurat Shayidin can't fix the bug: Error: 'devel' version requires a more recent R Nov 10, 2016 Martin Morgan can't fix the bug: Error: 'devel' version requires a more recent R Nov 10, 2016

can't install CRAN Packages after installed devel version of R and Bioc 3.4

12 msgs · Nov 11 – Nov 11

chimera Attempts to Open Non-existent File

3 msgs · Nov 2 – Nov 6

Dario Strbenac chimera Attempts to Open Non-existent File Nov 2, 2016 James W. MacDonald chimera Attempts to Open Non-existent File Nov 3, 2016 Dario Strbenac chimera Attempts to Open Non-existent File Nov 6, 2016

download stats

6 msgs · Nov 8 – Nov 29

Kasper Daniel Hansen download stats Nov 8, 2016 Kasper Daniel Hansen download stats Nov 8, 2016 Hervé Pagès download stats Nov 8, 2016 Kasper Daniel Hansen download stats Nov 8, 2016 Antonio Colaprico download stats Nov 29, 2016 Hervé Pagès download stats Nov 29, 2016

lumi package is not available

5 msgs · Nov 9 – Nov 10

Martin Morgan lumi package is not available Nov 9, 2016 James W. MacDonald lumi package is not available Nov 9, 2016 Martin Morgan lumi package is not available Nov 9, 2016 James W. MacDonald lumi package is not available Nov 9, 2016 Gang Feng lumi package is not available Nov 10, 2016

makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)

4 msgs · Nov 13 – Nov 13

Jialin Ma makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF) Nov 13, 2016 Vincent Carey makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF) Nov 13, 2016 Jialin Ma makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF) Nov 13, 2016 Martin Morgan makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF) Nov 13, 2016

problems installing cran dependencies with BioC devel in mac

13 msgs · Nov 30 – Nov 30

programming note: return() is a function call

2 msgs · Nov 14 – Nov 14

Martin Morgan programming note: return() is a function call Nov 14, 2016 Rainer Johannes programming note: return() is a function call Nov 14, 2016

recent changes in ggplot2 break some packages

4 msgs · Nov 14 – Nov 14

Ramon Diaz-Uriarte recent changes in ggplot2 break some packages Nov 14, 2016 Diego Diez recent changes in ggplot2 break some packages Nov 14, 2016 Ramon Diaz-Uriarte recent changes in ggplot2 break some packages Nov 14, 2016 Hervé Pagès recent changes in ggplot2 break some packages Nov 14, 2016

single package builder

1 msg · Nov 15

Shepherd, Lori single package builder Nov 15, 2016

spb updates

1 msg · Nov 22

Shepherd, Lori spb updates Nov 22, 2016

still issues with ggplot2/ggproto in Mac OS X, stable

3 msgs · Nov 22 – Nov 23

Ramon Diaz-Uriarte still issues with ggplot2/ggproto in Mac OS X, stable Nov 22, 2016 Hervé Pagès still issues with ggplot2/ggproto in Mac OS X, stable Nov 22, 2016 Ramon Diaz-Uriarte still issues with ggplot2/ggproto in Mac OS X, stable Nov 23, 2016

stuck in setting up Bioconductor GitHub

3 msgs · Nov 15 – Nov 16

Leif Väremo stuck in setting up Bioconductor GitHub Nov 15, 2016 Dan Tenenbaum stuck in setting up Bioconductor GitHub Nov 15, 2016 Leif Väremo stuck in setting up Bioconductor GitHub Nov 16, 2016

svn and git-mirror not synced

5 msgs · Nov 28 – Nov 29

Leif Väremo svn and git-mirror not synced Nov 28, 2016 Martin Morgan svn and git-mirror not synced Nov 29, 2016 Leif Väremo svn and git-mirror not synced Nov 29, 2016 Martin Morgan svn and git-mirror not synced Nov 29, 2016 Leif Väremo svn and git-mirror not synced Nov 29, 2016

svn permissions

3 msgs · Nov 20 – Nov 20

Kasper Daniel Hansen svn permissions Nov 20, 2016 Dan Tenenbaum svn permissions Nov 20, 2016 Kasper Daniel Hansen svn permissions Nov 20, 2016

unexpected error : BiocInstaller - unable to access the index for reporitory

1 msg · Nov 14

Jurat Shayidin unexpected error : BiocInstaller - unable to access the index for reporitory Nov 14, 2016

vmatchPattern Returns Out of Bounds Indices

4 msgs · Nov 16 – Nov 18

Dario Strbenac vmatchPattern Returns Out of Bounds Indices Nov 16, 2016 Hervé Pagès vmatchPattern Returns Out of Bounds Indices Nov 17, 2016 Dario Strbenac vmatchPattern Returns Out of Bounds Indices Nov 18, 2016 Hervé Pagès vmatchPattern Returns Out of Bounds Indices Nov 18, 2016

Bioc-devel November 2016

A handful of check to follow up on R CMD BiocCheck

AnnotationHub needed in the description of the ExperimentHubData

AnnotationHub needed in the description of the ExperimentHubData

Availability shield URLs

Bioc-devel Digest, Vol 152, Issue 10

Bioc-devel, Travis & OS X build failure

BiocStyle issue

Bioconductor devel BUILD/CHECK not running

Bug in setdiff() for signature 'IRangesList, IRangesList'?

Coverage test badge not updating

Error processing scater vignette Mac OS X Sierra

Error with InteractionSet package

Feasibility of Parallel Extraction of Matches with extractAllMatches

Feedback wanted on design of fixed-width Ranges class

Files removed from svn are not disappearing from Git mirror

FlipFlop Ignores Read Strand and Requires Antiquated File Formats

GSL on Windows

GenomeInfoDb::Seqinfo(genome) broken?

Help needed to reproduce my crash report

Issue with biovizBase::parseArgsForAes(), likely just a namespace issue

OrganismDb package for Drosophila.melanogaster

Problem with git-mirror

Question about sumbition process and biocviews

Reset SVN repo to earlier state

Rgraphviz on ppc64le needs updated config.{sub, guess}

SRAdb::sraConvert returns results in arbitrary order

Subversion Log Stalled

What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation

adding new features to current release branch

build report date - devel

can't fix the bug: Error: 'devel' version requires a more recent R

can't install CRAN Packages after installed devel version of R and Bioc 3.4

chimera Attempts to Open Non-existent File

download stats

lumi package is not available

makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)

problems installing cran dependencies with BioC devel in mac

programming note: return() is a function call

recent changes in ggplot2 break some packages

single package builder

spb updates

still issues with ggplot2/ggproto in Mac OS X, stable

stuck in setting up Bioconductor GitHub

svn and git-mirror not synced

svn permissions

unexpected error : BiocInstaller - unable to access the index for reporitory

vmatchPattern Returns Out of Bounds Indices