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Bioc-devel March 2014

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Monday, March 31, 2014 3 emails
Hervé Pagès svn repository for data experiment packages now having branches too Andrzej Oleś svn repository for data experiment packages now having branches too Julian Gehring rtracklayer: Export to bigwig with unused seqlevels
Sunday, March 30, 2014 1 email
Mariano Alvarez Viper package is now publicly available
Saturday, March 29, 2014 5 emails
Michael Lawrence Overflow in as(rlelist, "IntegerList" Hervé Pagès Overflow in as(rlelist, "IntegerList" Gabriel Becker Overflow in as(rlelist, "IntegerList" Michael Lawrence Overflow in as(rlelist, "IntegerList" Gabriel Becker Overflow in as(rlelist, "IntegerList"
Friday, March 28, 2014 5 emails
Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Michael Lawrence flank function with start argument a named vector Michael Lawrence rtracklayer: Export to bigwig with unused seqlevels Leonard Goldstein flank function with start argument a named vector Julian Gehring rtracklayer: Export to bigwig with unused seqlevels
Thursday, March 27, 2014 9 emails
Diana LOW (IMCB) Git-svn bridge Hervé Pagès GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Hervé Pagès Conflicting definitions for function redefined as S4 generics Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files James W. MacDonald Apparent error in illuminaHumanv4.db Taku Tokuyasu Apparent error in illuminaHumanv4.db Elena Grassi Roar - detecting 3'UTR shortening with standard RNAseq data Ulrich Bodenhofer Conflicting definitions for function redefined as S4 generics
Wednesday, March 26, 2014 8 emails
rcaloger To Bioc Team: OneChannelGUI error Dan Tenenbaum To Bioc Team: OneChannelGUI error rcaloger To Bioc Team: OneChannelGUI error Hervé Pagès Conflicting definitions for function redefined as S4 generics Michael Lawrence Conflicting definitions for function redefined as S4 generics Gabriel Becker Conflicting definitions for function redefined as S4 generics Michael Lawrence Conflicting definitions for function redefined as S4 generics Ulrich Bodenhofer Conflicting definitions for function redefined as S4 generics
Tuesday, March 25, 2014 8 emails
Ryan Bug in les:::cdfDuplicates Michael Lawrence SummarizedExperiment Valerie Obenchain file registry - feedback Valerie Obenchain Cytogenetic bands Peter Haverty SummarizedExperiment Tim Triche, Jr. SummarizedExperiment Peter Haverty SummarizedExperiment Julian Gehring Bug in les:::cdfDuplicates
Monday, March 24, 2014 6 emails
Kasper Daniel Hansen SummarizedExperiment Ryan Bug in les:::cdfDuplicates Hervé Pagès parsing embedded FASTA data Vincent Carey SummarizedExperiment Martin Morgan SummarizedExperiment Laurent Gatto Bioconductor git-svn bridge is available
Sunday, March 23, 2014 1 email
rcaloger Warning: loading Rplot failed
Saturday, March 22, 2014 3 emails
Dan Tenenbaum Warning: loading Rplot failed rcaloger Warning: loading Rplot failed Ilari Scheinin Cytogenetic bands
Friday, March 21, 2014 9 emails
Hervé Pagès report a minor bug in GenomicRanges Michael Lawrence restrictToSNV for VCF Hervé Pagès restrictToSNV for VCF Michael Lawrence restrictToSNV for VCF Michael Love GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Martin Morgan restrictToSNV for VCF Ou, Jianhong report a minor bug in GenomicRanges Hervé Pagès report a minor bug in GenomicRanges Ou, Jianhong report a minor bug in GenomicRanges
Thursday, March 20, 2014 3 emails
Kasper Daniel Hansen SummarizedExperiment Hervé Pagès restrictToSNV for VCF Hervé Pagès restrictToSNV for VCF
Wednesday, March 19, 2014 13 emails
Michael Lawrence restrictToSNV for VCF Sean Davis restrictToSNV for VCF Valerie Obenchain restrictToSNV for VCF Michael Lawrence restrictToSNV for VCF Vincent Carey restrictToSNV for VCF Michael Lawrence restrictToSNV for VCF Michael Lawrence restrictToSNV for VCF Stephanie M. Gogarten restrictToSNV for VCF Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Michael Love GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Valerie Obenchain GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files Michael Love GenomicAlignments: using asMates=TRUE and yieldSize with paired-end BAM files
Tuesday, March 18, 2014 6 emails
Julian Gehring restrictToSNV for VCF Hervé Pagès parsing embedded FASTA data Valerie Obenchain restrictToSNV for VCF Michael Lawrence parsing embedded FASTA data Gabriel Becker parsing embedded FASTA data Michael Lawrence Problem with rtracklayer package
Monday, March 17, 2014 11 emails
Michael Lawrence parsing embedded FASTA data Hervé Pagès parsing embedded FASTA data Michael Lawrence parsing embedded FASTA data Valerie Obenchain concat problem with CharacterList in mcols of GRanges Hervé Pagès concat problem with CharacterList in mcols of GRanges Dan Tenenbaum The importance of bumping (incrementing) package version numbers Antti Honkela Unreproducible build check warning Hervé Pagès Unreproducible build check warning Valerie Obenchain Unreproducible build check warning Valerie Obenchain concat problem with CharacterList in mcols of GRanges Antti Honkela Unreproducible build check warning
Sunday, March 16, 2014 3 emails
Vincent Carey concat problem with CharacterList in mcols of GRanges Vincent Carey concat problem with CharacterList in mcols of GRanges Cook, Malcolm rJava .jpackage("RDAVIDWebService") segfaults in restored R session
Saturday, March 15, 2014 1 email
Dan Tenenbaum fatal error when installing BioC devel on R devel
Friday, March 14, 2014 3 emails
Dan Tenenbaum package submission deadline is next week - Thursday March 20 Dan Tenenbaum fatal error when installing BioC devel on R devel Martin Rijlaarsdam fatal error when installing BioC devel on R devel
Thursday, March 13, 2014 3 emails
Martin Morgan fatal error when installing BioC devel on R devel Dan Tenenbaum fatal error when installing BioC devel on R devel Martin Rijlaarsdam fatal error when installing BioC devel on R devel
Wednesday, March 12, 2014 20 emails
Michael Love 'droplevels' argument in `[` method for SummarizedExperiment? Steve Lianoglou 'droplevels' argument in `[` method for SummarizedExperiment? Michael Lawrence 'droplevels' argument in `[` method for SummarizedExperiment? Martin Morgan 'droplevels' argument in `[` method for SummarizedExperiment? Ryan 'droplevels' argument in `[` method for SummarizedExperiment? Marc Carlson RE : AnnotationDbi and select function Wolfgang Huber 'droplevels' argument in `[` method for SummarizedExperiment? Marc Carlson RE : AnnotationDbi and select function Servant Nicolas RE : AnnotationDbi and select function Marc Carlson AnnotationDbi and select function James W. MacDonald AnnotationDbi and select function Servant Nicolas AnnotationDbi and select function Andrzej Oleś BiocStyle and fonts Martin Morgan BiocStyle and fonts Laurent Gatto BiocStyle and fonts Andrzej Oleś BiocStyle and fonts Kasper Daniel Hansen BiocStyle and fonts Michael Lawrence file registry - feedback Laurent Gatto BiocStyle and fonts Andrzej Oleś BiocStyle and fonts
Tuesday, March 11, 2014 18 emails
Leonard Goldstein readGAlignmentPairs function broken? Hervé Pagès file registry - feedback Michael Lawrence file registry - feedback Michael Lawrence file registry - feedback Valerie Obenchain file registry - feedback Laurent Gatto BiocStyle and fonts Martin Morgan BiocStyle and fonts Hervé Pagès file registry - feedback Hervé Pagès file registry - feedback Laurent Gatto BiocStyle and fonts Valerie Obenchain file registry - feedback Hector Corrada Bravo file registry - feedback Valerie Obenchain file registry - feedback Michael Lawrence file registry - feedback Michael Lawrence file registry - feedback Vincent Carey file registry - feedback Gabriel Becker file registry - feedback Michael Lawrence file registry - feedback
Monday, March 10, 2014 6 emails
Hervé Pagès file registry - feedback Valerie Obenchain file registry - feedback Arora, Sonali New biocViews for devel branch. Djork-Arné Clevert Conference Announcement - CAMDA 2014 James W. MacDonald deprecated extractTranscriptsFromGenome rcaloger deprecated extractTranscriptsFromGenome
Friday, March 7, 2014 1 email
Hervé Pagès readGAlignmentPairs function broken?