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Bioc-devel October 2015

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(persistent) issue with rgl dependency on Windows server

3 msgs
Federico Marini (persistent) issue with rgl dependency on Windows server Oct 9, 2015 Dan Tenenbaum (persistent) issue with rgl dependency on Windows server Oct 9, 2015 Federico Marini (persistent) issue with rgl dependency on Windows server Oct 9, 2015

A method for combining SummarizedExperiment objects

4 msgs
Peter Hickey A method for combining SummarizedExperiment objects Oct 14, 2015 Peter Hickey A method for combining SummarizedExperiment objects Oct 14, 2015 Martin Morgan A method for combining SummarizedExperiment objects Oct 15, 2015 Peter Hickey A method for combining SummarizedExperiment objects Oct 20, 2015

Accepting an answer on the support website

5 msgs
Kevin Rue-Albrecht Accepting an answer on the support website Oct 20, 2015 James W. MacDonald Accepting an answer on the support website Oct 20, 2015 Kevin Rue-Albrecht Accepting an answer on the support website Oct 20, 2015 James W. MacDonald Accepting an answer on the support website Oct 20, 2015 Dan Tenenbaum Accepting an answer on the support website Oct 20, 2015

Adding a lengths() method to List class

5 msgs
Michael Lawrence Adding a lengths() method to List class Oct 1, 2015 Peter Hickey Adding a lengths() method to List class Oct 2, 2015 Michael Lawrence Adding a lengths() method to List class Oct 14, 2015 Michael Lawrence Adding a lengths() method to List class Oct 15, 2015 Hervé Pagès Adding a lengths() method to List class Oct 15, 2015

AnnotationHub Update.

1 msg
Jim Java AnnotationHub Update. Oct 20, 2015

BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

1 msg
Cook, Malcolm BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround Oct 1, 2015

BioC 3.2 branch created

8 msgs
Dan Tenenbaum BioC 3.2 branch created Oct 13, 2015 Levi Waldron BioC 3.2 branch created Oct 16, 2015 Dan Tenenbaum BioC 3.2 branch created Oct 16, 2015 Hervé Pagès BioC 3.2 branch created Oct 16, 2015 Dan Tenenbaum BioC 3.2 branch created Oct 16, 2015 Hervé Pagès BioC 3.2 branch created Oct 16, 2015 Diego Diez BioC 3.2 branch created Oct 16, 2015 Dan Tenenbaum BioC 3.2 branch created Oct 16, 2015

Bioc 3.2 devel or release

2 msgs
Laurent Gatto Bioc 3.2 devel or release Oct 19, 2015 Dan Tenenbaum Bioc 3.2 devel or release Oct 19, 2015

BiocGenerics attach when GenomicFeatures imported

4 msgs
Marcin Cieślik BiocGenerics attach when GenomicFeatures imported Oct 19, 2015 Hervé Pagès BiocGenerics attach when GenomicFeatures imported Oct 19, 2015 Marcin Cieślik BiocGenerics attach when GenomicFeatures imported Oct 19, 2015 Hervé Pagès BiocGenerics attach when GenomicFeatures imported Oct 19, 2015

BiocParallel::bpvec() and DNAStringSet objects, problem

2 msgs
Robert Castelo BiocParallel::bpvec() and DNAStringSet objects, problem Oct 1, 2015 Obenchain, Valerie BiocParallel::bpvec() and DNAStringSet objects, problem Oct 7, 2015

Bioconductor 3.2 is released!

1 msg
Dan Tenenbaum Bioconductor 3.2 is released! Oct 14, 2015

Bioconductor Newsletter - October 2015

1 msg
Obenchain, Valerie Bioconductor Newsletter - October 2015 Oct 1, 2015

Bioconductor Workflows: TOC and displaying document details

1 msg
Dan Tenenbaum Bioconductor Workflows: TOC and displaying document details Oct 19, 2015

Bioconductor Workflows: TOC and displaying document details

4 msgs
Andrzej Oleś Bioconductor Workflows: TOC and displaying document details Oct 13, 2015 Aaron Lun Bioconductor Workflows: TOC and displaying document details Oct 22, 2015 Dan Tenenbaum Bioconductor Workflows: TOC and displaying document details Oct 22, 2015 Andrzej Oleś Bioconductor Workflows: TOC and displaying document details Oct 22, 2015

Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ?

3 msgs
Arora, Sonali Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ? Oct 9, 2015 Nadia Davidson Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ? Oct 10, 2015 Arora, Sonali Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ? Oct 12, 2015

Builds all pointing to devel

2 msgs
Thomas Lin Pedersen Builds all pointing to devel Oct 29, 2015 Dan Tenenbaum Builds all pointing to devel Oct 29, 2015

Circular dependencies and vignette building

4 msgs
Jonathan Cairns Circular dependencies and vignette building Oct 6, 2015 Hervé Pagès Circular dependencies and vignette building Oct 6, 2015 Dan Tenenbaum Circular dependencies and vignette building Oct 6, 2015 Jonathan Cairns Circular dependencies and vignette building Oct 7, 2015

DLL maps not found while compiling package in Windows machine

1 msg
Miguel Juliá DLL maps not found while compiling package in Windows machine Oct 2, 2015

Documentation Section of Package Landing Page messed up

3 msgs
Arora, Sonali Documentation Section of Package Landing Page messed up Oct 19, 2015 Dan Tenenbaum Documentation Section of Package Landing Page messed up Oct 19, 2015 Arora, Sonali Documentation Section of Package Landing Page messed up Oct 19, 2015

Error in GenomicFeatures::makeTxDbFromUCSC()

5 msgs
Arora, Sonali Error in GenomicFeatures::makeTxDbFromUCSC() Oct 16, 2015 Arora, Sonali Error in GenomicFeatures::makeTxDbFromUCSC() Oct 16, 2015 Michael Lawrence Error in GenomicFeatures::makeTxDbFromUCSC() Oct 16, 2015 Hervé Pagès Error in GenomicFeatures::makeTxDbFromUCSC() Oct 16, 2015 Arora, Sonali Error in GenomicFeatures::makeTxDbFromUCSC() Oct 16, 2015

EuroBioc 2015, Cambridge UK, 7-8 December

1 msg
Laurent Gatto EuroBioc 2015, Cambridge UK, 7-8 December Oct 24, 2015

Git-svn: getting it to work while keeping your git history

4 msgs
Leonardo Collado Torres Git-svn: getting it to work while keeping your git history Oct 15, 2015 Jim Hester Git-svn: getting it to work while keeping your git history Oct 15, 2015 Leonardo Collado Torres Git-svn: getting it to work while keeping your git history Oct 15, 2015 Jim Hester Git-svn: getting it to work while keeping your git history Oct 15, 2015

Github Bioconductor-mirror not updating for repo's that still had bridges?

1 msg
Dan Tenenbaum Github Bioconductor-mirror not updating for repo's that still had bridges? Oct 15, 2015

Github Bioconductor-mirror not updating for repo's that still had bridges?

4 msgs
Leonardo Collado Torres Github Bioconductor-mirror not updating for repo's that still had bridges? Oct 15, 2015 Leonardo Collado Torres Github Bioconductor-mirror not updating for repo's that still had bridges? Oct 15, 2015 Jim Hester Github Bioconductor-mirror not updating for repo's that still had bridges? Oct 15, 2015 Leonardo Collado Torres Github Bioconductor-mirror not updating for repo's that still had bridges? Oct 15, 2015

Help using Git with Bioconductor SVN repositories

3 msgs
Peter Hickey Help using Git with Bioconductor SVN repositories Oct 18, 2015 Elena Grassi Help using Git with Bioconductor SVN repositories Oct 19, 2015 Leonardo Collado Torres Help using Git with Bioconductor SVN repositories Oct 19, 2015

IPI numbers in annotation packages

5 msgs
James W. MacDonald IPI numbers in annotation packages Oct 4, 2015 Marc Carlson IPI numbers in annotation packages Oct 4, 2015 James W. MacDonald IPI numbers in annotation packages Oct 5, 2015 Marc Carlson IPI numbers in annotation packages Oct 5, 2015 James W. MacDonald IPI numbers in annotation packages Oct 5, 2015

IRanges broken in devel?

3 msgs
Bernd Klaus IRanges broken in devel? Oct 20, 2015 Dan Tenenbaum IRanges broken in devel? Oct 20, 2015 Bernd Klaus IRanges broken in devel? Oct 21, 2015

Idea for improved visibility of Bioconductor packages

7 msgs
Thomas Lin Pedersen Idea for improved visibility of Bioconductor packages Oct 29, 2015 Andrzej Oleś Idea for improved visibility of Bioconductor packages Oct 29, 2015 Kasper Daniel Hansen Idea for improved visibility of Bioconductor packages Oct 29, 2015 Thomas Lin Pedersen Idea for improved visibility of Bioconductor packages Oct 29, 2015 Jim Hester Idea for improved visibility of Bioconductor packages Oct 29, 2015 Thomas Lin Pedersen Idea for improved visibility of Bioconductor packages Oct 29, 2015 Jiří Hon Idea for improved visibility of Bioconductor packages Oct 29, 2015

Important: Bioconductor 3.2 branch to be created today - do not commit during this time

1 msg
Dan Tenenbaum Important: Bioconductor 3.2 branch to be created today - do not commit during this time Oct 13, 2015

Minor (impossible to trigger?) bug in assay, SummarizedExperiment0, character-method

2 msgs
Peter Hickey Minor (impossible to trigger?) bug in assay, SummarizedExperiment0, character-method Oct 9, 2015 Martin Morgan Minor (impossible to trigger?) bug in assay, SummarizedExperiment0, character-method Oct 10, 2015

Missing "release-3.2" branch of my package

3 msgs
Rainer Johannes Missing "release-3.2" branch of my package Oct 19, 2015 Jim Hester Missing "release-3.2" branch of my package Oct 19, 2015 Rainer Johannes Missing "release-3.2" branch of my package Oct 19, 2015

Moderating "answers" into comments on other answers/comments on the support site?

4 msgs
Ryan Moderating "answers" into comments on other answers/comments on the support site? Oct 8, 2015 Dan Tenenbaum Moderating "answers" into comments on other answers/comments on the support site? Oct 8, 2015 Michael Lawrence Moderating "answers" into comments on other answers/comments on the support site? Oct 8, 2015 Dan Tenenbaum Moderating "answers" into comments on other answers/comments on the support site? Oct 8, 2015

New biocView - RiboSeq

2 msgs
Arora, Sonali New biocView - RiboSeq Oct 20, 2015 Arora, Sonali New biocView - RiboSeq Oct 22, 2015

New package: FindMyFriends - Comparative microbial genomics

1 msg
Thomas Lin Pedersen New package: FindMyFriends - Comparative microbial genomics Oct 15, 2015

New package: LOLA - Locus overlap analysis for enrichment of genomic ranges

1 msg
Nathan Sheffield New package: LOLA - Locus overlap analysis for enrichment of genomic ranges Oct 20, 2015

New package: MEAL - Methylation and Expression AnaLyzer

1 msg
Ruiz Arenas, Carlos New package: MEAL - Methylation and Expression AnaLyzer Oct 15, 2015

New packages: DAPAR and Prostar

1 msg
Samuel Wieczorek New packages: DAPAR and Prostar Oct 16, 2015

PLEASE READ: devel packages in release channel

1 msg
Dan Tenenbaum PLEASE READ: devel packages in release channel Oct 28, 2015

Package Submission

4 msgs
ZHANG Yu Package Submission Oct 12, 2015 Dan Tenenbaum Package Submission Oct 12, 2015 ZHANG Yu Package Submission Oct 12, 2015 ZHANG Yu Package Submission Oct 12, 2015

RiboProfiling: a new Bioconductor package for ribo-seq data analysis

1 msg
Alexandra Popa RiboProfiling: a new Bioconductor package for ribo-seq data analysis Oct 9, 2015

S4 Method of ExpressionSet Signature Not Found

6 msgs
Dario Strbenac S4 Method of ExpressionSet Signature Not Found Oct 22, 2015 Michael Lawrence S4 Method of ExpressionSet Signature Not Found Oct 22, 2015 Dario Strbenac S4 Method of ExpressionSet Signature Not Found Oct 22, 2015 Michael Lawrence S4 Method of ExpressionSet Signature Not Found Oct 22, 2015 Bernd Klaus S4 Method of ExpressionSet Signature Not Found Oct 23, 2015 Michael Lawrence S4 Method of ExpressionSet Signature Not Found Oct 23, 2015

SICtools: a new Bioconductor package to discover SNV/Indel differences between two paired-bam files

1 msg
Gmail2 SICtools: a new Bioconductor package to discover SNV/Indel differences between two paired-bam files Oct 12, 2015

SV4Vectors installation problem

6 msgs
Marcin Cieślik SV4Vectors installation problem Oct 15, 2015 Martin Morgan SV4Vectors installation problem Oct 15, 2015 Michael Lawrence SV4Vectors installation problem Oct 15, 2015 Hervé Pagès SV4Vectors installation problem Oct 15, 2015 Michael Lawrence SV4Vectors installation problem Oct 16, 2015 Marcin Cieślik SV4Vectors installation problem Oct 16, 2015

Updating package NEWS files for Bioconductor 3.2 release announcement (and biocViews)

1 msg
Dan Tenenbaum Updating package NEWS files for Bioconductor 3.2 release announcement (and biocViews) Oct 7, 2015

VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

8 msgs
Robert Castelo VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 21, 2015 Michael Lawrence VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 21, 2015 Hervé Pagès VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 21, 2015 Michael Lawrence VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 21, 2015 Hervé Pagès VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 21, 2015 Michael Lawrence VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 21, 2015 Robert Castelo VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 22, 2015 Michael Lawrence VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges Oct 22, 2015

Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary?

4 msgs
Leonardo Collado Torres Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary? Oct 29, 2015 Dan Tenenbaum Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary? Oct 29, 2015 Andrzej Oleś Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary? Oct 29, 2015 Leonardo Collado Torres Vignette questions: location of html BiocStyle vignette, fake + real vignettes not necessary? Oct 30, 2015

broken awards system on BioC support site

2 msgs
Aaron Lun broken awards system on BioC support site Oct 14, 2015 Dan Tenenbaum broken awards system on BioC support site Oct 14, 2015

error in stable AnnotationHub

2 msgs
Kasper Daniel Hansen error in stable AnnotationHub Oct 10, 2015 Martin Morgan error in stable AnnotationHub Oct 11, 2015

ideas for ScanBamParam filters

3 msgs
Michael Lawrence ideas for ScanBamParam filters Oct 16, 2015 Martin Morgan ideas for ScanBamParam filters Oct 16, 2015 Michael Lawrence ideas for ScanBamParam filters Oct 16, 2015

question regarding change to release version of package

4 msgs
Samuel E Zimmerman question regarding change to release version of package Oct 21, 2015 Jim Hester question regarding change to release version of package Oct 21, 2015 Dan Tenenbaum question regarding change to release version of package Oct 21, 2015 Kasper Daniel Hansen question regarding change to release version of package Oct 21, 2015

readGAlignmentPairs with discordant strand

11 msgs
Michael Lawrence readGAlignmentPairs with discordant strand Oct 16, 2015 Martin Morgan readGAlignmentPairs with discordant strand Oct 16, 2015 Michael Lawrence readGAlignmentPairs with discordant strand Oct 16, 2015 Hervé Pagès readGAlignmentPairs with discordant strand Oct 16, 2015 Michael Lawrence readGAlignmentPairs with discordant strand Oct 16, 2015 Hervé Pagès readGAlignmentPairs with discordant strand Oct 16, 2015 Michael Lawrence readGAlignmentPairs with discordant strand Oct 16, 2015 Michael Lawrence readGAlignmentPairs with discordant strand Oct 17, 2015 Martin Morgan readGAlignmentPairs with discordant strand Oct 17, 2015 Michael Lawrence readGAlignmentPairs with discordant strand Oct 17, 2015 Hervé Pagès readGAlignmentPairs with discordant strand Oct 19, 2015

regioneR failing to build and causing other packages to fail

1 msg
Dan Tenenbaum regioneR failing to build and causing other packages to fail Oct 1, 2015

regioneR failing to build and causing other packages to fail

1 msg
DjekidelMohamed nadhir regioneR failing to build and causing other packages to fail Oct 1, 2015

riboSeqR error - matrix of zeros output from riboSeqR::readingFrame()

3 msgs
Arora, Sonali riboSeqR error - matrix of zeros output from riboSeqR::readingFrame() Oct 26, 2015 Tom Hardcastle riboSeqR error - matrix of zeros output from riboSeqR::readingFrame() Oct 27, 2015 Arora, Sonali riboSeqR error - matrix of zeros output from riboSeqR::readingFrame() Oct 27, 2015

svn woes

3 msgs
Vincent Carey svn woes Oct 28, 2015 Dan Tenenbaum svn woes Oct 28, 2015 Vincent Carey svn woes Oct 28, 2015

systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

6 msgs
Arora, Sonali systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Oct 22, 2015 Thomas Girke systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Oct 22, 2015 Thomas Girke systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Oct 25, 2015 Hervé Pagès systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Oct 26, 2015 Thomas Girke systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Oct 26, 2015 Arora, Sonali systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Oct 26, 2015

test coverage in Release packages

3 msgs
Ramon Diaz-Uriarte test coverage in Release packages Oct 18, 2015 Dan Tenenbaum test coverage in Release packages Oct 20, 2015 Ramon Diaz-Uriarte test coverage in Release packages Oct 21, 2015

upgrading

7 msgs
Kasper Daniel Hansen upgrading Oct 20, 2015 Jim Hester upgrading Oct 20, 2015 Robert Castelo upgrading Oct 20, 2015 Bernd Klaus upgrading Oct 20, 2015 Ramon Diaz-Uriarte upgrading Oct 20, 2015 Martin Morgan upgrading Oct 20, 2015 Kasper Daniel Hansen upgrading Oct 20, 2015

zzz.R in GenoView

5 msgs
Dan Tenenbaum zzz.R in GenoView Oct 5, 2015 Hervé Pagès zzz.R in GenoView Oct 5, 2015 Dan Tenenbaum zzz.R in GenoView Oct 5, 2015 Kasper Daniel Hansen zzz.R in GenoView Oct 5, 2015 Hervé Pagès zzz.R in GenoView Oct 5, 2015