Bioc-devel - January 2016 - Thread View

[Bioc-devel] package citation and version is not updated

1 msg Jan 29

Dan Tenenbaum package citation and version is not updated Jan 29, 2016

[Bioc-devel] question about citation file

3 msgs Jan 29

Samuel E Zimmerman question about citation file Jan 29, 2016

Dan Tenenbaum question about citation file Jan 29, 2016

[Bioc-devel] package citation and version is not updated

1 msg Jan 29

Dan Tenenbaum package citation and version is not updated Jan 29, 2016

[Bioc-devel] Vignette building fails

6 msgs Jan 29

Fan, Jean Vignette building fails Jan 28, 2016

Martin Morgan Vignette building fails Jan 28, 2016

Fan, Jean Vignette building fails Jan 28, 2016

Paul Grosu Vignette building fails Jan 28, 2016

Dan Tenenbaum Vignette building fails Jan 28, 2016

Ludwig Geistlinger package citation and version is not updated Jan 29, 2016

[Bioc-devel] fail to build a package after updating Bioconductor packages

4 msgs Jan 28

Yu Sun fail to build a package after updating Bioconductor packages Jan 27, 2016

Ge Tan fail to build a package after updating Bioconductor packages Jan 27, 2016

Fan, Jean fail to build a package after updating Bioconductor packages Jan 27, 2016

Yu Sun fail to build a package after updating Bioconductor packages Jan 28, 2016

[Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008

4 msgs Jan 27

Samuel E Zimmerman package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 Jan 27, 2016

Dan Tenenbaum package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 Jan 27, 2016

Samuel E Zimmerman package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 Jan 27, 2016

Dan Tenenbaum package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 Jan 27, 2016

[Bioc-devel] possible BioGrid/psiquic bug [was Problem with constrained PSICQUIC queries]

1 msg Jan 27

Paul Shannon possible BioGrid/psiquic bug [was Problem with constrained PSICQUIC queries] Jan 27, 2016

[Bioc-devel] Problem with constrained PSICQUIC queries

1 msg Jan 27

Laurent Gatto Problem with constrained PSICQUIC queries Jan 27, 2016

[Bioc-devel] Install devel version, dependancies missing

2 msgs Jan 27

Samuel Wieczorek Install devel version, dependancies missing Jan 27, 2016

Laurent Gatto Install devel version, dependancies missing Jan 27, 2016

[Bioc-devel] C library or C package API for regular expressions

3 msgs Jan 26

Dan Tenenbaum C library or C package API for regular expressions Jan 25, 2016

Jiří Hon C library or C package API for regular expressions Jan 26, 2016

Gabriel Becker C library or C package API for regular expressions Jan 26, 2016

[Bioc-devel] Use of Matrix inside SummarizedExperiment

2 msgs Jan 26

Hervé Pagès Use of Matrix inside SummarizedExperiment Jan 25, 2016

Peter Hickey Use of Matrix inside SummarizedExperiment Jan 26, 2016

[Bioc-devel] Warnings on moscato2 SinglePackage Builder

2 msgs Jan 26

Thomas Lin Pedersen Warnings on moscato2 SinglePackage Builder Jan 20, 2016

Karen Oróstica Warnings on moscato2 SinglePackage Builder Jan 26, 2016

[Bioc-devel] C library or C package API for regular expressions

8 msgs Jan 26

Jiří Hon C library or C package API for regular expressions Jan 23, 2016

Charles Determan C library or C package API for regular expressions Jan 23, 2016

Jiří Hon C library or C package API for regular expressions Jan 25, 2016

Martin Morgan C library or C package API for regular expressions Jan 25, 2016

Jiří Hon C library or C package API for regular expressions Jan 25, 2016

Mike C library or C package API for regular expressions Jan 25, 2016

Hervé Pagès C library or C package API for regular expressions Jan 25, 2016

Jiří Hon C library or C package API for regular expressions Jan 26, 2016

[Bioc-devel] seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles

3 msgs Jan 26

Hervé Pagès seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles Jan 25, 2016

Robert Castelo seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles Jan 26, 2016

Ludwig Geistlinger Announcing the EnrichmentBrowser 2.0 Jan 26, 2016

[Bioc-devel] Use of Matrix inside SummarizedExperiment

1 msg Jan 25

Peter Hickey Use of Matrix inside SummarizedExperiment Jan 25, 2016

[Bioc-devel] Fwd: Git-Svn bridge will be removed permanently on January 29, 2016

1 msg Jan 25

Dan Tenenbaum Git-Svn bridge will be removed permanently on January 29, 2016 Jan 25, 2016

[Bioc-devel] seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles

1 msg Jan 25

Robert Castelo seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles Jan 25, 2016

[Bioc-devel] bplapply Processes Sometimes Stall

6 msgs Jan 22

Dario Strbenac bplapply Processes Sometimes Stall Jan 1, 2016

Martin Morgan bplapply Processes Sometimes Stall Jan 3, 2016

Dario Strbenac bplapply Processes Sometimes Stall Jan 17, 2016

Martin Morgan bplapply Processes Sometimes Stall Jan 19, 2016

Dario Strbenac bplapply Processes Sometimes Stall Jan 22, 2016

Martin Morgan bplapply Processes Sometimes Stall Jan 22, 2016

[Bioc-devel] Rsamtools: How to import only the first 1000 or so reads

2 msgs Jan 21

Christian Arnold Rsamtools: How to import only the first 1000 or so reads Jan 21, 2016

Michael Lawrence Rsamtools: How to import only the first 1000 or so reads Jan 21, 2016

[Bioc-devel] Deprecation of cellHTS

1 msg Jan 20

Andrzej Oleś Deprecation of cellHTS Jan 20, 2016

[Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2 msgs Jan 19

Hervé Pagès GenomicFeatures::extractTranscriptSeqs setMethod suggestion Jan 19, 2016

Rainer Johannes GenomicFeatures::extractTranscriptSeqs setMethod suggestion Jan 19, 2016

[Bioc-devel] Versioned (Biobase) "initialize" method

2 msgs Jan 19

Stravs, Michael Versioned (Biobase) "initialize" method Jan 7, 2016

Martin Morgan Versioned (Biobase) "initialize" method Jan 19, 2016

[Bioc-devel] Conference: BioC 2016: Where Software and Biology Connect, Stanford, 24-26 June

1 msg Jan 19

Martin Morgan Conference: BioC 2016: Where Software and Biology Connect, Stanford, 24-26 June Jan 19, 2016

[Bioc-devel] Doubts about version numbers and git-snv bridge

1 msg Jan 18

Dan Tenenbaum Doubts about version numbers and git-snv bridge Jan 18, 2016

[Bioc-devel] topGO - BPontology Building most specific GOs ..... ontology: BP colnames Entry GO CC BP MF PE ( 2631 GO terms found. ) Build GO DAG topology .......... There are no adj nodes for node: GO:1904722

1 msg Jan 18

Witold E Wolski topGO - BPontology Building most specific GOs ..... ontology: BP colnames Entry GO CC BP MF PE ( 2631 GO terms found. ) Build GO DAG topology .......... There are no adj nodes for node: GO:1904722 Jan 18, 2016

[Bioc-devel] Doubts about version numbers and git-snv bridge

1 msg Jan 18

Alessandro Mammana Doubts about version numbers and git-snv bridge Jan 18, 2016

[Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

1 msg Jan 18

Rainer Johannes GenomicFeatures::extractTranscriptSeqs setMethod suggestion Jan 18, 2016

[Bioc-devel] IRanges - PartitioningByEnd not found when package method runs.

7 msgs Jan 14

Ben Ward (TGAC) IRanges - PartitioningByEnd not found when package method runs. Jan 13, 2016

Martin Morgan IRanges - PartitioningByEnd not found when package method runs. Jan 13, 2016

Hervé Pagès IRanges - PartitioningByEnd not found when package method runs. Jan 13, 2016

Ben Ward (TGAC) IRanges - PartitioningByEnd not found when package method runs. Jan 14, 2016

Martin Morgan IRanges - PartitioningByEnd not found when package method runs. Jan 14, 2016

Hervé Pagès IRanges - PartitioningByEnd not found when package method runs. Jan 14, 2016

Michael Lawrence IRanges - PartitioningByEnd not found when package method runs. Jan 14, 2016

[Bioc-devel] ncdf4 not installed on build machines

2 msgs Jan 13

Stephanie M. Gogarten ncdf4 not installed on build machines Jan 13, 2016

Dan Tenenbaum ncdf4 not installed on build machines Jan 13, 2016

[Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

8 msgs Jan 11

Robert Castelo Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Vincent Carey Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Robert Castelo Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Vincent Carey Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Tim Triche, Jr. Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Paul Grosu Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Hervé Pagès Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Rainer Johannes Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

[Bioc-devel] bioconductor.org scheduled downtime, Tuesday, January 19th, 3:00PM PST

1 msg Jan 11

Dan Tenenbaum bioconductor.org scheduled downtime, Tuesday, January 19th, 3:00PM PST Jan 11, 2016

[Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

3 msgs Jan 11

Hervé Pagès Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

Robert Castelo Known Genes replaced by GENCODE genes at UCSC Jan 11, 2016

[Bioc-devel] R / Bioconductor job opportunity: Senior Programmer / Analyst

1 msg Jan 11

Martin Morgan R / Bioconductor job opportunity: Senior Programmer / Analyst Jan 11, 2016

[Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

11 msgs Jan 10

Rainer Johannes Problem with seqnames of TwoBitFile from AnnotationHub Jan 8, 2016

Hervé Pagès Problem with seqnames of TwoBitFile from AnnotationHub Jan 8, 2016

Michael Lawrence Problem with seqnames of TwoBitFile from AnnotationHub Jan 8, 2016

Hervé Pagès Problem with seqnames of TwoBitFile from AnnotationHub Jan 8, 2016

Rainer Johannes Problem with seqnames of TwoBitFile from AnnotationHub Jan 9, 2016

Martin Morgan Problem with seqnames of TwoBitFile from AnnotationHub Jan 9, 2016

Michael Lawrence Problem with seqnames of TwoBitFile from AnnotationHub Jan 9, 2016

Tim Triche, Jr. Problem with seqnames of TwoBitFile from AnnotationHub Jan 9, 2016

Hervé Pagès Problem with seqnames of TwoBitFile from AnnotationHub Jan 9, 2016

Rainer Johannes Problem with seqnames of TwoBitFile from AnnotationHub Jan 10, 2016

Michael Lawrence Problem with seqnames of TwoBitFile from AnnotationHub Jan 10, 2016

[Bioc-devel] Use of EnsDb in the AnnotationDbi framework

2 msgs Jan 10

Rainer Johannes Use of EnsDb in the AnnotationDbi framework Jan 7, 2016

Martin Morgan Use of EnsDb in the AnnotationDbi framework Jan 10, 2016

[Bioc-devel] Bioconductor GSOC sponsorship?

1 msg Jan 9

Martin Morgan Bioconductor GSOC sponsorship? Jan 9, 2016

[Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

2 msgs Jan 8

Rainer Johannes Problem with seqnames of TwoBitFile from AnnotationHub Jan 8, 2016

Michael Lawrence Problem with seqnames of TwoBitFile from AnnotationHub Jan 8, 2016

[Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

3 msgs Jan 7

Michael Love Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Jan 7, 2016

Kasper Daniel Hansen Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Jan 7, 2016

Martin Morgan Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Jan 7, 2016

[Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

2 msgs Jan 6

Ludwig Geistlinger mapIds methods for ExpressionSet and SummarizedExperiment Jan 6, 2016

Martin Morgan mapIds methods for ExpressionSet and SummarizedExperiment Jan 6, 2016

[Bioc-devel] Build checks not representing updates to packages

1 msg Jan 6

Dan Tenenbaum Build checks not representing updates to packages Jan 6, 2016

[Bioc-devel] Build checks not representing updates to packages

1 msg Jan 6

Venkat Malladi Build checks not representing updates to packages Jan 6, 2016

[Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

2 msgs Jan 6

Tim Triche, Jr. Common workflow to build an microarray annatation package, like hgu133a.db Jan 5, 2016

Zhilong Jia Common workflow to build an microarray annatation package, like hgu133a.db Jan 6, 2016

[Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

3 msgs Jan 5

Zhilong Jia Common workflow to build an microarray annatation package, like hgu133a.db Jan 5, 2016

Tim Triche, Jr. Common workflow to build an microarray annatation package, like hgu133a.db Jan 5, 2016

James W. MacDonald Common workflow to build an microarray annatation package, like hgu133a.db Jan 5, 2016

[Bioc-devel] Creating Biostrings DNAStringSet from Rcpp/C++

3 msgs Jan 5

Sean Davis Creating Biostrings DNAStringSet from Rcpp/C++ Jan 5, 2016

Michael Lawrence Creating Biostrings DNAStringSet from Rcpp/C++ Jan 5, 2016

Hervé Pagès Creating Biostrings DNAStringSet from Rcpp/C++ Jan 5, 2016

[Bioc-devel] Bioconductor Newsletter: January 2016

1 msg Jan 5

Obenchain, Valerie Bioconductor Newsletter: January 2016 Jan 5, 2016

[Bioc-devel] Updating CausalR package after igraph fix

2 msgs Jan 5

Glyn Bradley Updating CausalR package after igraph fix Jan 5, 2016

Obenchain, Valerie Updating CausalR package after igraph fix Jan 5, 2016

[Bioc-devel] mcols<-() behaviour inheriting from Vector vs GRanges

3 msgs Jan 5

Hervé Pagès mcols<-() behaviour inheriting from Vector vs GRanges Jan 4, 2016

Malcolm Perry mcols<-() behaviour inheriting from Vector vs GRanges Jan 5, 2016

[Bioc-devel] Update released version of Package

6 msgs Jan 4

Dan Tenenbaum Update released version of Package Jan 4, 2016

Wolfgang Huber Update released version of Package Jan 4, 2016

Dan Tenenbaum Update released version of Package Jan 4, 2016

Venkat Malladi Update released version of Package Jan 4, 2016

Dan Tenenbaum Update released version of Package Jan 4, 2016

[Bioc-devel] Updated package submission policies

1 msg Jan 4

Martin Morgan Updated package submission policies Jan 4, 2016

[Bioc-devel] mcols<-() behaviour inheriting from Vector vs GRanges

1 msg Jan 4

Malcolm Perry mcols<-() behaviour inheriting from Vector vs GRanges Jan 4, 2016

[Bioc-devel] Update released version of Package

1 msg Jan 4

Venkat Malladi Update released version of Package Jan 4, 2016

Bioc-devel January 2016