I'm having problems getting lumiR.batch to import files since I upgraded to R v3.2.0 and lumi v2.20.0 this morning. These are files that imported just fine last week. When I now try to make a lumiBatch object, I get this error:
> DCdata <- 'FinalReport_nonorm_nobkgd.txt' > DClumi <- lumiR.batch(DCdata, sampleInfoFile='DC-SIS.txt') Inputting the data ... Inputting the data ... Error in match.call(lumiR) : ... used in a situation where it does not exist > traceback() 9: match.call(lumiR) 8: print(match.call(lumiR)) 7: eval(expr, envir, enclos) 6: eval(expr, pf) 5: withVisible(eval(expr, pf)) 4: evalVis(expr) 3: capture.output(print(match.call(lumiR))) 2: lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, verbose = FALSE, ...) 1: lumiR.batch(DCdata, sampleInfoFile = "DC-SIS.txt") > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  lumi_2.20.0 Biobase_2.28.0 BiocGenerics_0.14.0 BiocInstaller_1.18.1 loaded via a namespace (and not attached):  mclust_5.0.0 base64_1.1 Rcpp_0.11.5 locfit_1.5-9.1  lattice_0.20-31 nleqslv_2.7 Rsamtools_1.20.0 Biostrings_2.36.0  digest_0.6.8 foreach_1.4.2 GenomeInfoDb_1.4.0 plyr_1.8.1  futile.options_1.0.0 stats4_3.2.0 RSQLite_1.0.0 bumphunter_1.8.0  zlibbioc_1.14.0 GenomicFeatures_1.20.0 annotate_1.46.0 S4Vectors_0.6.0  Matrix_1.2-0 preprocessCore_1.30.0 splines_3.2.0 BiocParallel_1.2.0  stringr_0.6.2 RCurl_1.95-4.5 biomaRt_2.24.0 rtracklayer_1.28.0  multtest_2.24.0 pkgmaker_0.22 mgcv_1.8-6 GEOquery_2.34.0  quadprog_1.5-5 IRanges_2.2.0 codetools_0.2-11 matrixStats_0.14.0  XML_3.98-1.1 reshape_0.8.5 GenomicAlignments_1.4.0 MASS_7.3-40  bitops_1.0-6 grid_3.2.0 nlme_3.1-120 xtable_1.7-4  registry_0.2 affy_1.46.0 DBI_0.3.1 KernSmooth_2.23-14  XVector_0.8.0 genefilter_1.50.0 affyio_1.36.0 doRNG_1.6  limma_3.24.0 minfi_1.14.0 futile.logger_1.4 nor1mix_1.2-0  lambda.r_1.1.7 RColorBrewer_1.1-2 iterators_1.0.7 siggenes_1.42.0  tools_3.2.0 illuminaio_0.10.0 rngtools_1.2.4 survival_2.38-1  methylumi_2.14.0 AnnotationDbi_1.30.0 colorspace_1.2-6 GenomicRanges_1.20.1  beanplot_1.2 >
Has anyone else had a similar problem recently, or have any suggestions how I might fix it or work around it? I have tried removing and reinstalling R and Bioconductor, but I get the same problem. I also see if if I do a fresh install on a machine that has not had R installed on it previously.