I am running R version 3.1.2 and launched champ.process() using the default command in the documentation as a first attempt. All the proper .cvs and iDat files are presumably in the home folder.
The command is accepted, the output folder is created, and the two .cvs files are read in when all of a sudden the program returns "Killed" and R quits; I find myself at the unix prompt.
Am I doing something fundamentally wrong or am I just too noob to get this?
bash$
> library(ChAMP)
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: âBiocGenericsâ
The following objects are masked from âpackage:parallelâ:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from âpackage:statsâ:
xtabs
The following objects are masked from âpackage:baseâ:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: ChAMPdata
Loading required package: Illumina450ProbeVariants.db
Warning message:
replacing previous import by âRPMM::ebayesâ when loading âChAMPâ
> champ.process(fromIDAT = TRUE, fromFile = FALSE, directory = getwd(), resultsDir =
+ paste(getwd(), "resultsChamp20141210_01", sep = "/"), methValue = "B", filterDetP = TRUE,
+ detPcut = 0.01, filterXY = TRUE, removeDetP = 0, filterBeads = TRUE, beadCutoff =
+ 0.05, filterNoCG = FALSE, QCimages = TRUE, batchCorrect = TRUE, runSVD =
+ TRUE, studyInfo = FALSE, infoFactor = c(), norm = "BMIQ", adjust.method = "BH",
+ adjPVal = 0.05, runDMR = TRUE, runCNA = TRUE, plotBMIQ = TRUE, DMRpval = 0.05,
+ sampleCNA=TRUE,plotSample = TRUE,groupFreqPlots=TRUE,freqThreshold=0.3, bedFile
+ = FALSE, methProfile = FALSE, controlProfile = FALSE)
Loading data from /projects/sequence_analysis/vol1/schasse/workspace/IlluminaMethylUCSF/NIDA01_NIDA02
[read.450k.sheet] Found the following CSV files:
[1] "/projects/sequence_analysis/vol1/schasse/workspace/IlluminaMethylUCSF/NIDA01_NIDA02/NIDA01_02samplesheet.csv"
[2] "/projects/sequence_analysis/vol1/schasse/workspace/IlluminaMethylUCSF/NIDA01_NIDA02/playdata.csv"
Killed
bash$
sessionInfo() output
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ChAMP_1.4.0 Illumina450ProbeVariants.db_1.1.1
[3] ChAMPdata_1.1.2 minfi_1.12.0
[5] bumphunter_1.6.0 locfit_1.5-9.1
[7] iterators_1.0.7 foreach_1.4.2
[9] Biostrings_2.34.0 XVector_0.6.0
[11] GenomicRanges_1.18.3 GenomeInfoDb_1.2.3
[13] IRanges_2.0.0 S4Vectors_0.4.0
[15] lattice_0.20-29 Biobase_2.26.0
[17] BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] annotate_1.44.0
[2] AnnotationDbi_1.28.1
[3] base64_1.1
[4] beanplot_1.2
[5] cluster_1.15.3
[6] codetools_0.2-9
[7] DBI_0.3.1
[8] digest_0.6.6
[9] DNAcopy_1.40.0
[10] doRNG_1.6
[11] genefilter_1.48.1
[12] grid_3.1.2
[13] IlluminaHumanMethylation450kmanifest_0.4.0
[14] illuminaio_0.8.0
[15] impute_1.40.0
[16] limma_3.22.1
[17] marray_1.44.0
[18] MASS_7.3-35
[19] Matrix_1.1-4
[20] matrixStats_0.12.2
[21] mclust_4.4
[22] mgcv_1.8-3
[23] multtest_2.22.0
[24] nlme_3.1-118
[25] nor1mix_1.2-0
[26] pkgmaker_0.22
[27] plyr_1.8.1
[28] preprocessCore_1.28.0
[29] quadprog_1.5-5
[30] R.methodsS3_1.6.1
[31] RColorBrewer_1.1-2
[32] Rcpp_0.11.3
[33] registry_0.2
[34] reshape_0.8.5
[35] rngtools_1.2.4
[36] RPMM_1.20
[37] RSQLite_1.0.0
[38] siggenes_1.40.0
[39] splines_3.1.2
[40] stringr_0.6.2
[41] survival_2.37-7
[42] sva_3.12.0
[43] tools_3.1.2
[44] wateRmelon_1.6.0
[45] XML_3.98-1.1
[46] xtable_1.7-4
[47] zlibbioc_1.12.0
