[Bioc-devel] very slow to use intronsByTranscript in GenomicFeatures

hi,

i can reproduce what Jianhong says, i noticed it earlier this week but 
didn't mention because we all know devel is a moving target and so on, 
but since this has been raised now i'll report what i'm getting.

so, this is for Jianhong, if you downgrade the following packages to 
these particular versions:

Biostrings_2.31.3.tar.gz
GenomicRanges_1.15.15.tar.gz
IRanges_1.21.13.tar.gz
XVector_0.3.2.tar.gz

you'll be all fine, unless you need some functionality of later versions 
of them, here is the test with the session information:

suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene))
Warning messages:
1: multiple methods tables found for ?rname?
2: multiple methods tables found for ?rname<-?
3: multiple methods tables found for ?cigar?
4: multiple methods tables found for ?qwidth?
5: multiple methods tables found for ?introns?
system.time(txbygene <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, 
"gene"))
    user  system elapsed
   2.524   0.046   2.575

sessionInfo()
R Under development (unstable) (2013-10-20 r64082)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
  [2] GenomicFeatures_1.15.4
  [3] AnnotationDbi_1.25.9
  [4] Biobase_2.23.3
  [5] GenomicRanges_1.15.11
  [6] XVector_0.3.2
  [7] IRanges_1.21.13
  [8] BiocGenerics_0.9.2
  [9] vimcom_0.9-92
[10] setwidth_1.0-3
[11] colorout_1.0-1

loaded via a namespace (and not attached):
  [1] biomaRt_2.19.1           Biostrings_2.31.3        bitops_1.0-6 

  [4] BSgenome_1.31.7          DBI_0.2-7 
GenomicAlignments_0.99.9
  [7] RCurl_1.95-4.1           Rsamtools_1.15.15        RSQLite_0.11.4 

[10] rtracklayer_1.23.6       stats4_3.1.0             tools_3.1.0 

[13] XML_3.98-1.1             zlibbioc_1.9.0

however, if you go to the bleeding edge of devel BioC:

suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene))
system.time(txbygene <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, 
"gene"))

the previous call never ends until you press CTRL+C:

^C
Error in unlist(lapply(c("seqnames", "ranges", "strand", "mcols"), 
checkCoreGetterReturnedLength)) :
   error in evaluating the argument 'x' in selecting a method for 
function 'unlist': Error in NROW(get(getter)(x)) :
   error in evaluating the argument 'x' in selecting a method for 
function 'NROW': Error in get(getter)(x) :
   error in evaluating the argument 'x' in selecting a method for 
function 'ranges':
Timing stopped at: 24.5 0.072 24.619

sessionInfo()
R Under development (unstable) (2013-10-20 r64082)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C 
LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8 
LC_PAPER=en_US.UTF8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C 
LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.15.4 

  [3] AnnotationDbi_1.25.9                     Biobase_2.23.3 

  [5] GenomicRanges_1.15.15                    XVector_0.3.5 

  [7] IRanges_1.21.17                          BiocGenerics_0.9.2 

  [9] vimcom_0.9-92                            setwidth_1.0-3 

[11] colorout_1.0-1

loaded via a namespace (and not attached):
  [1] biomaRt_2.19.1           Biostrings_2.31.5        bitops_1.0-6 
          BSgenome_1.31.7
  [5] DBI_0.2-7                GenomicAlignments_0.99.9 RCurl_1.95-4.1 
          Rsamtools_1.15.15
  [9] RSQLite_0.11.4           rtracklayer_1.23.6       stats4_3.1.0 
          tools_3.1.0
[13] XML_3.98-1.1             zlibbioc_1.9.0

cheers,
robert.

[Bioc-devel] very slow to use intronsByTranscript in GenomicFeatures

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