Bioc-devel December 2015

[Bioc-devel] bplapply Processes Sometimes Stall

4 msgs Dec 29

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Dario Strbenac bplapply Processes Sometimes Stall Dec 27, 2015

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Martin Morgan bplapply Processes Sometimes Stall Dec 28, 2015

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Dario Strbenac bplapply Processes Sometimes Stall Dec 28, 2015

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Dario Strbenac bplapply Processes Sometimes Stall Dec 29, 2015

[Bioc-devel] Progress Message Order in bplapply

4 msgs Dec 28

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Dario Strbenac Progress Message Order in bplapply Dec 27, 2015

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Dan Tenenbaum Progress Message Order in bplapply Dec 28, 2015

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Martin Morgan Progress Message Order in bplapply Dec 28, 2015

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Dario Strbenac Progress Message Order in bplapply Dec 28, 2015

[Bioc-devel] bioconductor.org scheduled downtime, Thursday, December 31st, 12:01PM PST

1 msg Dec 28

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Dan Tenenbaum bioconductor.org scheduled downtime, Thursday, December 31st, 12:01PM PST Dec 28, 2015

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

1 msg Dec 28

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Dan Tenenbaum Git-Svn bridge will be removed permanently on January 29, 2016 Dec 28, 2015

[Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

8 msgs Dec 26

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Martin Maechler For integer vectors, `as(x, "numeric")` has no effect. Dec 11, 2015

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John Chambers For integer vectors, `as(x, "numeric")` has no effect. Dec 11, 2015

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Martin Morgan For integer vectors, `as(x, "numeric")` has no effect. Dec 11, 2015

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Martin Maechler For integer vectors, `as(x, "numeric")` has no effect. Dec 12, 2015

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Martin Maechler For integer vectors, `as(x, "numeric")` has no effect. Dec 19, 2015

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John Chambers For integer vectors, `as(x, "numeric")` has no effect. Dec 19, 2015

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Hervé Pagès For integer vectors, `as(x, "numeric")` has no effect. Dec 25, 2015

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John Chambers For integer vectors, `as(x, "numeric")` has no effect. Dec 26, 2015

[Bioc-devel] summarizeOverlaps provide a non existing algorithm argument to findOverlaps

2 msgs Dec 26

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Hervé Pagès summarizeOverlaps provide a non existing algorithm argument to findOverlaps Dec 25, 2015

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Nicolas Delhomme summarizeOverlaps provide a non existing algorithm argument to findOverlaps Dec 26, 2015

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

6 msgs Dec 22

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Arora, Sonali Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Martin Morgan Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Arora, Sonali Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Martin Morgan Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Venkat Malladi Warning: no visible global function definition for ‘seqlevels<-’ Dec 22, 2015

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Martin Morgan Warning: no visible global function definition for ‘seqlevels<-’ Dec 22, 2015

[Bioc-devel] seqlevelsStyle on alternate chromosomes

5 msgs Dec 21

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Michael Lawrence seqlevelsStyle on alternate chromosomes Dec 17, 2015

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Hervé Pagès seqlevelsStyle on alternate chromosomes Dec 17, 2015

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Leonardo Collado Torres seqlevelsStyle on alternate chromosomes Dec 17, 2015

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Michael Lawrence seqlevelsStyle on alternate chromosomes Dec 18, 2015

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Arora, Sonali seqlevelsStyle on alternate chromosomes Dec 21, 2015

[Bioc-devel] summarizeOverlaps provide a non existing algorithm argument to findOverlaps

1 msg Dec 21

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Nicolas Delhomme summarizeOverlaps provide a non existing algorithm argument to findOverlaps Dec 21, 2015

[Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

4 msgs Dec 21

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Ludwig Geistlinger mapIds methods for ExpressionSet and SummarizedExperiment Dec 17, 2015

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Martin Morgan mapIds methods for ExpressionSet and SummarizedExperiment Dec 18, 2015

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Martin Morgan mapIds methods for ExpressionSet and SummarizedExperiment Dec 18, 2015

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Ludwig Geistlinger mapIds methods for ExpressionSet and SummarizedExperiment Dec 21, 2015

[Bioc-devel] as.table not available for HitsList anymore?

3 msgs Dec 20

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Nicolas Delhomme as.table not available for HitsList anymore? Dec 20, 2015

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Martin Morgan as.table not available for HitsList anymore? Dec 20, 2015

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Nicolas Delhomme as.table not available for HitsList anymore? Dec 20, 2015

[Bioc-devel] ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?

4 msgs Dec 19

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Lorena Pantano ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

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Martin Morgan ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

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Martin Morgan ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

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Michael Love ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

[Bioc-devel] git svn trouble on release branch

1 msg Dec 18

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Jim Hester git svn trouble on release branch Dec 18, 2015

[Bioc-devel] git svn trouble on release branch

3 msgs Dec 18

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Kyle Bemis git svn trouble on release branch Dec 18, 2015

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Leonardo Collado Torres git svn trouble on release branch Dec 18, 2015

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Jim Hester git svn trouble on release branch Dec 18, 2015

[Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

2 msgs Dec 17

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Obenchain, Valerie R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 17, 2015

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Brad Friedman R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 17, 2015

[Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

3 msgs Dec 17

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Dan Tenenbaum R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 14, 2015

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Martin Morgan R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 14, 2015

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Obenchain, Valerie R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 17, 2015

[Bioc-devel] Extending biovizBase and ggbio packages

12 msgs Dec 16

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Rainer Johannes Extending biovizBase and ggbio packages Dec 14, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 14, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 14, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 14, 2015

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Martin Morgan Extending biovizBase and ggbio packages Dec 14, 2015

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Jim Hester Extending biovizBase and ggbio packages Dec 14, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 14, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 15, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 15, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 15, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 16, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 16, 2015

[Bioc-devel] what is SummarizedExperiment a Vector of?

7 msgs Dec 15

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Michael Lawrence what is SummarizedExperiment a Vector of? Dec 15, 2015

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Vincent Carey what is SummarizedExperiment a Vector of? Dec 15, 2015

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Michael Lawrence what is SummarizedExperiment a Vector of? Dec 15, 2015

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Vincent Carey what is SummarizedExperiment a Vector of? Dec 15, 2015

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Hervé Pagès what is SummarizedExperiment a Vector of? Dec 15, 2015

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Michael Lawrence what is SummarizedExperiment a Vector of? Dec 15, 2015

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Hervé Pagès what is SummarizedExperiment a Vector of? Dec 15, 2015

[Bioc-devel] R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

1 msg Dec 14

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Brad Friedman R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 14, 2015

[Bioc-devel] strange bug in a BioC workflow that only appears on Jenkis

3 msgs Dec 14

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Dan Tenenbaum strange bug in a BioC workflow that only appears on Jenkis Dec 4, 2015

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Bernd Klaus strange bug in a BioC workflow that only appears on Jenkis Dec 7, 2015

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Bernd Klaus strange bug in a BioC workflow that only appears on Jenkis Dec 14, 2015

[Bioc-devel] Issue with pushing git commits to SVN

3 msgs Dec 13

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Federico Comoglio Issue with pushing git commits to SVN Dec 12, 2015

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Jim Hester Issue with pushing git commits to SVN Dec 13, 2015

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Federico Comoglio Issue with pushing git commits to SVN Dec 13, 2015

[Bioc-devel] do SummarizedExperiments really need colnames?

2 msgs Dec 13

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Peter Hickey do SummarizedExperiments really need colnames? Dec 6, 2015

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Martin Morgan do SummarizedExperiments really need colnames? Dec 13, 2015

[Bioc-devel] Error in NSBS

2 msgs Dec 11

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Hervé Pagès Error in NSBS Dec 11, 2015

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Michael Lawrence Error in NSBS Dec 11, 2015

[Bioc-devel] Error in NSBS

2 msgs Dec 11

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Krithika Bhuvaneshwar [kb472@georgetown.edu] Error in NSBS Dec 10, 2015

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Hervé Pagès Error in NSBS Dec 11, 2015

[Bioc-devel] support for BEDPE import/export in rtracklayer?

2 msgs Dec 8

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Aaron Lun support for BEDPE import/export in rtracklayer? Dec 8, 2015

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Michael Lawrence support for BEDPE import/export in rtracklayer? Dec 8, 2015

[Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

2 msgs Dec 7

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Hervé Pagès Is there a way to change the name of R package that is already published on bioconductor? Dec 2, 2015

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Marcin Kosiński Is there a way to change the name of R package that is already published on bioconductor? Dec 7, 2015

[Bioc-devel] segfault when using RleList in DataFrames

2 msgs Dec 7

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Hervé Pagès segfault when using RleList in DataFrames Dec 7, 2015

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Leonard Goldstein segfault when using RleList in DataFrames Dec 7, 2015

[Bioc-devel] segfault when using RleList in DataFrames

1 msg Dec 6

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Peter Hickey segfault when using RleList in DataFrames Dec 6, 2015

[Bioc-devel] segfault when using RleList in DataFrames

1 msg Dec 5

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Leonard Goldstein segfault when using RleList in DataFrames Dec 5, 2015

[Bioc-devel] do SummarizedExperiments really need colnames?

3 msgs Dec 5

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Aaron Lun do SummarizedExperiments really need colnames? Dec 5, 2015

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Martin Morgan do SummarizedExperiments really need colnames? Dec 5, 2015

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Aaron Lun do SummarizedExperiments really need colnames? Dec 5, 2015

[Bioc-devel] Tracing a build error on moscato2: could it be that pandoc is not updated?

1 msg Dec 4

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Dan Tenenbaum Tracing a build error on moscato2: could it be that pandoc is not updated? Dec 4, 2015

[Bioc-devel] error when combining objects inheriting from GRangesList

2 msgs Dec 4

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Hervé Pagès error when combining objects inheriting from GRangesList Dec 4, 2015

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Leonard Goldstein error when combining objects inheriting from GRangesList Dec 4, 2015

[Bioc-devel] ncdf deprecation

2 msgs Dec 4

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Hervé Pagès ncdf deprecation Dec 1, 2015

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Dan Tenenbaum ncdf deprecation Dec 4, 2015

[Bioc-devel] error when combining objects inheriting from GRangesList

1 msg Dec 4

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Leonard Goldstein error when combining objects inheriting from GRangesList Dec 4, 2015

[Bioc-devel] New instance types for Bioconductor AMI

1 msg Dec 4

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Dan Tenenbaum New instance types for Bioconductor AMI Dec 4, 2015

[Bioc-devel] New instance types for Bioconductor AMI

1 msg Dec 4

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Thomas Lin Pedersen New instance types for Bioconductor AMI Dec 4, 2015

[Bioc-devel] include .DollarNames.ExpressionSet in Biobase?

3 msgs Dec 4

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Angerer, Philipp include .DollarNames.ExpressionSet in Biobase? Dec 4, 2015

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Martin Morgan include .DollarNames.ExpressionSet in Biobase? Dec 4, 2015

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Martin Morgan include .DollarNames.ExpressionSet in Biobase? Dec 4, 2015

[Bioc-devel] Test coverage for packages not calculated/updated?

1 msg Dec 4

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Rainer Johannes Test coverage for packages not calculated/updated? Dec 4, 2015

[Bioc-devel] Unexpected behaviour with Assays and Vector classes

1 msg Dec 3

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Martin Morgan Unexpected behaviour with Assays and Vector classes Dec 3, 2015

[Bioc-devel] strange bug in a BioC workflow that only appears on Jenkis

1 msg Dec 3

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Bernd Klaus strange bug in a BioC workflow that only appears on Jenkis Dec 3, 2015

[Bioc-devel] winbuilder1 in the workflow CI system offline ...

1 msg Dec 3

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Bernd Klaus winbuilder1 in the workflow CI system offline ... Dec 3, 2015

[Bioc-devel] namespace GenomicRanges

1 msg Dec 2

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Hervé Pagès namespace GenomicRanges Dec 2, 2015

[Bioc-devel] namespace GenomicRanges

1 msg Dec 2

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Karl Stamm namespace GenomicRanges Dec 2, 2015

[Bioc-devel] winbuilder1 in the workflow CI system offline ...

1 msg Dec 2

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Brian Long winbuilder1 in the workflow CI system offline ... Dec 2, 2015

[Bioc-devel] winbuilder1 in the workflow CI system offline ...

2 msgs Dec 2

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Bernd Klaus winbuilder1 in the workflow CI system offline ... Dec 2, 2015

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Brian Long winbuilder1 in the workflow CI system offline ... Dec 2, 2015

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

2 msgs Dec 2

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Thomas Girke systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 1, 2015

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Hervé Pagès systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 2, 2015

[Bioc-devel] Tracing a build error on moscato2: could it be that pandoc is not updated?

1 msg Dec 2

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Leonardo Collado Torres Tracing a build error on moscato2: could it be that pandoc is not updated? Dec 2, 2015

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

2 msgs Dec 1

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Cook, Malcolm systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 1, 2015

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Hervé Pagès systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 1, 2015

[Bioc-devel] New package: FamAgg - familial aggregation analysis in large pedigrees

1 msg Dec 1

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Rainer Johannes New package: FamAgg - familial aggregation analysis in large pedigrees Dec 1, 2015