[BioC] Problem running HumMeth27QCReport after upgrading R to 2.15
Niles Oien [guest]
guest at bioconductor.org
Wed May 23 18:46:50 CEST 2012
Hi,
I just upgraded R from 2.14 to 2.15 and I am finding that the HumMeth27QCReport package no longer runs, even on the demo data that come with the package.
What I do is :
library(HumMeth27QCReport)
Dir <- "/my/dir/Methylation/demo27"
Plat <- "Hum27"
ImportDataR <- ImportData(Dir)
ControlResults <- getAssayControls(ImportDataR,
platform=Plat)
QCResults <- QCCheck(ImportDataR, pval=0.05)
normMvalues <- HumMeth27QCReport(ImportDataR,
platform=Plat, pval=0.05, ChrX=FALSE, "euclidian")
but for the calls to QCCheck() and HumMeth27QCReport() I get the message :
Error in gregexpr(sep.i, dataLine1)[[1]] : subscript out of bounds
Any suggestions would be appreciated, I am appending my sessionInfo() from R.
Thanks,
Niles Oien, University of Colorado, Boulder, USA.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] tcltk grid splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.4.4 HumMeth27QCReport_1.2.14 tcltk2_1.2-3
[4] WriteXLS_2.1.0 plotrix_3.4-1 gplots_2.10.1
[7] KernSmooth_2.23-7 caTools_1.12 bitops_1.0-4.1
[10] gdata_2.8.2 gtools_2.6.2 Hmisc_3.9-3
[13] survival_2.36-14 amap_0.8-7 IlluminaHumanMethylation450k.db_1.4.6
[16] IlluminaHumanMethylation27k.db_1.4.6 org.Hs.eg.db_2.7.1 RSQLite_0.11.1
[19] DBI_0.2-5 AnnotationDbi_1.18.0 lumi_2.8.0
[22] nleqslv_1.9.3 methylumi_2.2.0 ggplot2_0.9.1
[25] reshape2_1.2.1 scales_0.2.1 Biobase_2.16.0
[28] BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] affy_1.34.0 affyio_1.24.0 annotate_1.34.0 bigmemory_4.2.11 Biostrings_2.24.1 BSgenome_1.24.0
[7] cluster_1.14.2 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 DNAcopy_1.30.0 GenomicRanges_1.8.6
[13] genoset_1.6.0 hdrcde_2.16 IRanges_1.14.3 labeling_0.1 lattice_0.20-6 MASS_7.3-18
[19] Matrix_1.0-6 memoise_0.1 mgcv_1.7-16 munsell_0.3 nlme_3.1-103 plyr_1.7.1
[25] preprocessCore_1.18.0 proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1 Rsamtools_1.8.4 rtracklayer_1.16.1
[31] stats4_2.15.0 stringr_0.6 tools_2.15.0 XML_3.9-4 xtable_1.7-0 zlibbioc_1.2.0
-- output of sessionInfo():
Error in gregexpr(sep.i, dataLine1)[[1]] : subscript out of bounds
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