Re: [Bioc-devel] bamFlagAsBitMatrix error (?bug)

2014-12-14 Thread Hervé Pagès 

Hi,

On 12/14/2014 01:29 PM, Valerie Obenchain wrote:

This should be fixed now (thanks Martin).

We recently deprecated the flag 'isNotPrimaryRead' in favor of
'isNotPrimaryAlignment' (Rsamtools devel).


The new name is actually isSecondaryAlignment.

H.


This affected
GenomicAlignments and others ...

~/b/Rpacks$ grep -lr isNotPrimaryRead *
CoverageView/R/cov.matrix.R
CoverageView/R/cov.interval.R
gage/vignettes/RNA-seqWorkflow.Rnw
hiReadsProcessor/R/hiReadsProcessor.R
QDNAseq/man/binReadCounts.Rd
QDNAseq/R/binReadCounts.R
Rsamtools/NEWS
Rsamtools/man/ScanBamParam-class.Rd
Rsamtools/R/methods-ScanBamParam.R
SplicingGraphs/inst/unitTests/test_countReads-methods.R
SplicingGraphs/inst/scripts/TSPC-utils.R
SplicingGraphs/vignettes/SplicingGraphs.Rnw
SplicingGraphs/man/assignReads.Rd
SplicingGraphs/man/txpath-methods.Rd
systemPipeR/R/utilities.R


These packages should be clear (of this error) on tomorrow's builds.

Thanks.
Val

On 12/14/2014 09:15 AM, Valerie Obenchain wrote:

Hi Sean,

Yes, we are aware of the problem, thanks. Hopefully this will be
resolved for tomorrows builds ... we'll post back when it's fixed.

Val

On 12/14/2014 08:33 AM, Sean Davis wrote:

Hi, Martin, Val, and Herve.

This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments.  Perhaps this is related to some bitnames
being deprecated?

Thanks,
Sean



library(GenomicAlignments)
sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate =
FALSE))
x = readGAlignmentPairs(LOCALBAMS[180],param=sbp)

Error in bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead") :
   invalid bitname(s): isNotPrimaryRead

traceback()

8: stop("invalid bitname(s): ", in1string)
7: bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead")
6: .make_GAlignmentPairs_from_GAlignments(gal, use.mcols = use.mcols)
5: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
4: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
3: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
2: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
1: readGAlignmentPairs(LOCALBAMS[180], param = sbp)

sessionInfo()

R Under development (unstable) (2014-11-18 r66997)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats4parallel  stats graphics  grDevices datasets  utils
methods   base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.7
  AnnotationDbi_1.29.11
  [4] GenomicAlignments_1.3.14stringr_0.6.2
   plotrix_3.5-10
  [7] pd.huex.1.0.st.v2_3.10.0RSQLite_1.0.0
   DBI_0.3.1
[10] limma_3.23.2oligo_1.31.0
  Biobase_2.27.0
[13] oligoClasses_1.29.3 knitr_1.8
   VariantAnnotation_1.13.19
[16] Rsamtools_1.19.15   Biostrings_2.35.7
   XVector_0.7.3
[19] GenomicRanges_1.19.21   GenomeInfoDb_1.3.7
  IRanges_2.1.33
[22] S4Vectors_0.5.14BiocGenerics_0.13.3
   BiocInstaller_1.17.1

loaded via a namespace (and not attached):
  [1] BBmisc_1.8BSgenome_1.35.8   BatchJobs_1.5
BiocParallel_1.1.9RCurl_1.95-4.5XML_3.98-1.1
  [7] affxparser_1.39.3-1   affyio_1.35.0 base64enc_0.1-2
biomaRt_2.23.5bit_1.1-12bitops_1.0-6
[13] brew_1.0-6checkmate_1.5.1   codetools_0.2-9
digest_0.6.6  evaluate_0.5.5fail_1.2
[19] ff_2.2-13 foreach_1.4.2 formatR_1.0
htmltools_0.2.6   iterators_1.0.7   knitrBootstrap_1.0.0
[25] markdown_0.7.4preprocessCore_1.29.0 rmarkdown_0.3.3
rtracklayer_1.27.6sendmailR_1.2-1   splines_3.2.0
[31] tools_3.2.0   yaml_2.1.13   zlibbioc_1.13.0

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] bamFlagAsBitMatrix error (?bug)

2014-12-14 Thread Valerie Obenchain 

This should be fixed now (thanks Martin).

We recently deprecated the flag 'isNotPrimaryRead' in favor of 
'isNotPrimaryAlignment' (Rsamtools devel). This affected 
GenomicAlignments and others ...


~/b/Rpacks$ grep -lr isNotPrimaryRead *
CoverageView/R/cov.matrix.R
CoverageView/R/cov.interval.R
gage/vignettes/RNA-seqWorkflow.Rnw
hiReadsProcessor/R/hiReadsProcessor.R
QDNAseq/man/binReadCounts.Rd
QDNAseq/R/binReadCounts.R
Rsamtools/NEWS
Rsamtools/man/ScanBamParam-class.Rd
Rsamtools/R/methods-ScanBamParam.R
SplicingGraphs/inst/unitTests/test_countReads-methods.R
SplicingGraphs/inst/scripts/TSPC-utils.R
SplicingGraphs/vignettes/SplicingGraphs.Rnw
SplicingGraphs/man/assignReads.Rd
SplicingGraphs/man/txpath-methods.Rd
systemPipeR/R/utilities.R


These packages should be clear (of this error) on tomorrow's builds.

Thanks.
Val

On 12/14/2014 09:15 AM, Valerie Obenchain wrote:

Hi Sean,

Yes, we are aware of the problem, thanks. Hopefully this will be
resolved for tomorrows builds ... we'll post back when it's fixed.

Val

On 12/14/2014 08:33 AM, Sean Davis wrote:

Hi, Martin, Val, and Herve.

This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments.  Perhaps this is related to some bitnames
being deprecated?

Thanks,
Sean



library(GenomicAlignments)
sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate =
FALSE))
x = readGAlignmentPairs(LOCALBAMS[180],param=sbp)

Error in bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead") :
   invalid bitname(s): isNotPrimaryRead

traceback()

8: stop("invalid bitname(s): ", in1string)
7: bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead")
6: .make_GAlignmentPairs_from_GAlignments(gal, use.mcols = use.mcols)
5: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
4: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
3: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
2: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
1: readGAlignmentPairs(LOCALBAMS[180], param = sbp)

sessionInfo()

R Under development (unstable) (2014-11-18 r66997)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats4parallel  stats graphics  grDevices datasets  utils
methods   base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.7
  AnnotationDbi_1.29.11
  [4] GenomicAlignments_1.3.14stringr_0.6.2
   plotrix_3.5-10
  [7] pd.huex.1.0.st.v2_3.10.0RSQLite_1.0.0
   DBI_0.3.1
[10] limma_3.23.2oligo_1.31.0
  Biobase_2.27.0
[13] oligoClasses_1.29.3 knitr_1.8
   VariantAnnotation_1.13.19
[16] Rsamtools_1.19.15   Biostrings_2.35.7
   XVector_0.7.3
[19] GenomicRanges_1.19.21   GenomeInfoDb_1.3.7
  IRanges_2.1.33
[22] S4Vectors_0.5.14BiocGenerics_0.13.3
   BiocInstaller_1.17.1

loaded via a namespace (and not attached):
  [1] BBmisc_1.8BSgenome_1.35.8   BatchJobs_1.5
BiocParallel_1.1.9RCurl_1.95-4.5XML_3.98-1.1
  [7] affxparser_1.39.3-1   affyio_1.35.0 base64enc_0.1-2
biomaRt_2.23.5bit_1.1-12bitops_1.0-6
[13] brew_1.0-6checkmate_1.5.1   codetools_0.2-9
digest_0.6.6  evaluate_0.5.5fail_1.2
[19] ff_2.2-13 foreach_1.4.2 formatR_1.0
htmltools_0.2.6   iterators_1.0.7   knitrBootstrap_1.0.0
[25] markdown_0.7.4preprocessCore_1.29.0 rmarkdown_0.3.3
rtracklayer_1.27.6sendmailR_1.2-1   splines_3.2.0
[31] tools_3.2.0   yaml_2.1.13   zlibbioc_1.13.0

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] bamFlagAsBitMatrix error (?bug)

2014-12-14 Thread Valerie Obenchain 

Hi Sean,

Yes, we are aware of the problem, thanks. Hopefully this will be 
resolved for tomorrows builds ... we'll post back when it's fixed.


Val

On 12/14/2014 08:33 AM, Sean Davis wrote:

Hi, Martin, Val, and Herve.

This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments.  Perhaps this is related to some bitnames
being deprecated?

Thanks,
Sean



library(GenomicAlignments)
sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE))
x = readGAlignmentPairs(LOCALBAMS[180],param=sbp)

Error in bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead") :
   invalid bitname(s): isNotPrimaryRead

traceback()

8: stop("invalid bitname(s): ", in1string)
7: bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead")
6: .make_GAlignmentPairs_from_GAlignments(gal, use.mcols = use.mcols)
5: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
4: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
param = param, with.which_label = with.which_label)
3: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
2: readGAlignmentPairsFromBam(file = file, use.names = use.names,
...)
1: readGAlignmentPairs(LOCALBAMS[180], param = sbp)

sessionInfo()

R Under development (unstable) (2014-11-18 r66997)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats4parallel  stats graphics  grDevices datasets  utils
methods   base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.7
  AnnotationDbi_1.29.11
  [4] GenomicAlignments_1.3.14stringr_0.6.2
   plotrix_3.5-10
  [7] pd.huex.1.0.st.v2_3.10.0RSQLite_1.0.0
   DBI_0.3.1
[10] limma_3.23.2oligo_1.31.0
  Biobase_2.27.0
[13] oligoClasses_1.29.3 knitr_1.8
   VariantAnnotation_1.13.19
[16] Rsamtools_1.19.15   Biostrings_2.35.7
   XVector_0.7.3
[19] GenomicRanges_1.19.21   GenomeInfoDb_1.3.7
  IRanges_2.1.33
[22] S4Vectors_0.5.14BiocGenerics_0.13.3
   BiocInstaller_1.17.1

loaded via a namespace (and not attached):
  [1] BBmisc_1.8BSgenome_1.35.8   BatchJobs_1.5
BiocParallel_1.1.9RCurl_1.95-4.5XML_3.98-1.1
  [7] affxparser_1.39.3-1   affyio_1.35.0 base64enc_0.1-2
biomaRt_2.23.5bit_1.1-12bitops_1.0-6
[13] brew_1.0-6checkmate_1.5.1   codetools_0.2-9
digest_0.6.6  evaluate_0.5.5fail_1.2
[19] ff_2.2-13 foreach_1.4.2 formatR_1.0
htmltools_0.2.6   iterators_1.0.7   knitrBootstrap_1.0.0
[25] markdown_0.7.4preprocessCore_1.29.0 rmarkdown_0.3.3
rtracklayer_1.27.6sendmailR_1.2-1   splines_3.2.0
[31] tools_3.2.0   yaml_2.1.13   zlibbioc_1.13.0

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] bamFlagAsBitMatrix error (?bug)

2014-12-14 Thread Sean Davis 
Hi, Martin, Val, and Herve.

This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments.  Perhaps this is related to some bitnames
being deprecated?

Thanks,
Sean


> library(GenomicAlignments)
> sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE))
> x = readGAlignmentPairs(LOCALBAMS[180],param=sbp)
Error in bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead") :
  invalid bitname(s): isNotPrimaryRead
> traceback()
8: stop("invalid bitname(s): ", in1string)
7: bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead")
6: .make_GAlignmentPairs_from_GAlignments(gal, use.mcols = use.mcols)
5: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
   param = param, with.which_label = with.which_label)
4: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
   param = param, with.which_label = with.which_label)
3: readGAlignmentPairsFromBam(file = file, use.names = use.names,
   ...)
2: readGAlignmentPairsFromBam(file = file, use.names = use.names,
   ...)
1: readGAlignmentPairs(LOCALBAMS[180], param = sbp)
> sessionInfo()
R Under development (unstable) (2014-11-18 r66997)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats4parallel  stats graphics  grDevices datasets  utils
methods   base

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.7
 AnnotationDbi_1.29.11
 [4] GenomicAlignments_1.3.14stringr_0.6.2
  plotrix_3.5-10
 [7] pd.huex.1.0.st.v2_3.10.0RSQLite_1.0.0
  DBI_0.3.1
[10] limma_3.23.2oligo_1.31.0
 Biobase_2.27.0
[13] oligoClasses_1.29.3 knitr_1.8
  VariantAnnotation_1.13.19
[16] Rsamtools_1.19.15   Biostrings_2.35.7
  XVector_0.7.3
[19] GenomicRanges_1.19.21   GenomeInfoDb_1.3.7
 IRanges_2.1.33
[22] S4Vectors_0.5.14BiocGenerics_0.13.3
  BiocInstaller_1.17.1

loaded via a namespace (and not attached):
 [1] BBmisc_1.8BSgenome_1.35.8   BatchJobs_1.5
BiocParallel_1.1.9RCurl_1.95-4.5XML_3.98-1.1
 [7] affxparser_1.39.3-1   affyio_1.35.0 base64enc_0.1-2
biomaRt_2.23.5bit_1.1-12bitops_1.0-6
[13] brew_1.0-6checkmate_1.5.1   codetools_0.2-9
digest_0.6.6  evaluate_0.5.5fail_1.2
[19] ff_2.2-13 foreach_1.4.2 formatR_1.0
htmltools_0.2.6   iterators_1.0.7   knitrBootstrap_1.0.0
[25] markdown_0.7.4preprocessCore_1.29.0 rmarkdown_0.3.3
rtracklayer_1.27.6sendmailR_1.2-1   splines_3.2.0
[31] tools_3.2.0   yaml_2.1.13   zlibbioc_1.13.0

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel