[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


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 :

Dir <- "/my/dir/Methylation/demo27"
Plat <- "Hum27"
ImportDataR <- ImportData(Dir)
ControlResults <- getAssayControls(ImportDataR,

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.


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)

[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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