Hi Jeremy Thanks for sending the test data. As you said, it runs well for old versions, but has problem for the new R and Bioc release. After I checked the code, I found the error was caused by capture.output of match.call returns (for the purpose of tracking operation history of the data). I guess the R version update changed the behavior of capture.output function. I have just fixed the problem by changing the code. The new version is: lumi_2.20.1 or lumi_2.21.1. Thanks for reporting the problem! Pan On Mon, Apr 20, 2015 at 11:55 AM, Jeremy Martinson [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Jeremy Martinson <https: support.bioconductor.org="" u="" 7630=""/> wrote Question: > lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0 > <https: support.bioconductor.org="" p="" 66821=""/>: > > 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: > [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] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_2.20.0 Biobase_2.28.0 BiocGenerics_0.14.0 BiocInstaller_1.18.1 > > loaded via a namespace (and not attached): > [1] mclust_5.0.0 base64_1.1 Rcpp_0.11.5 locfit_1.5-9.1 > [5] lattice_0.20-31 nleqslv_2.7 Rsamtools_1.20.0 Biostrings_2.36.0 > [9] digest_0.6.8 foreach_1.4.2 GenomeInfoDb_1.4.0 plyr_1.8.1 > [13] futile.options_1.0.0 stats4_3.2.0 RSQLite_1.0.0 bumphunter_1.8.0 > [17] zlibbioc_1.14.0 GenomicFeatures_1.20.0 annotate_1.46.0 S4Vectors_0.6.0 > [21] Matrix_1.2-0 preprocessCore_1.30.0 splines_3.2.0 BiocParallel_1.2.0 > [25] stringr_0.6.2 RCurl_1.95-4.5 biomaRt_2.24.0 rtracklayer_1.28.0 > [29] multtest_2.24.0 pkgmaker_0.22 mgcv_1.8-6 GEOquery_2.34.0 > [33] quadprog_1.5-5 IRanges_2.2.0 codetools_0.2-11 matrixStats_0.14.0 > [37] XML_3.98-1.1 reshape_0.8.5 GenomicAlignments_1.4.0 MASS_7.3-40 > [41] bitops_1.0-6 grid_3.2.0 nlme_3.1-120 xtable_1.7-4 > [45] registry_0.2 affy_1.46.0 DBI_0.3.1 KernSmooth_2.23-14 > [49] XVector_0.8.0 genefilter_1.50.0 affyio_1.36.0 doRNG_1.6 > [53] limma_3.24.0 minfi_1.14.0 futile.logger_1.4 nor1mix_1.2-0 > [57] lambda.r_1.1.7 RColorBrewer_1.1-2 iterators_1.0.7 siggenes_1.42.0 > [61] tools_3.2.0 illuminaio_0.10.0 rngtools_1.2.4 survival_2.38-1 > [65] methylumi_2.14.0 AnnotationDbi_1.30.0 colorspace_1.2-6 GenomicRanges_1.20.1 > [69] 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. > > ------------------------------ > > You may reply via email or visit lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0 >

Hi Jeremy I didn't remember I changed the lumiR.batch function. Can you send me some example data to repeat your error? You can send it to my personal email: dupan.mail (at) gmail. Thanks! Pan On Mon, Apr 20, 2015 at 11:55 AM, Jeremy Martinson [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Jeremy Martinson <https: support.bioconductor.org="" u="" 7630=""/> wrote Question: > lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0 > <https: support.bioconductor.org="" p="" 66821=""/>: > > 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: > [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] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_2.20.0 Biobase_2.28.0 BiocGenerics_0.14.0 BiocInstaller_1.18.1 > > loaded via a namespace (and not attached): > [1] mclust_5.0.0 base64_1.1 Rcpp_0.11.5 locfit_1.5-9.1 > [5] lattice_0.20-31 nleqslv_2.7 Rsamtools_1.20.0 Biostrings_2.36.0 > [9] digest_0.6.8 foreach_1.4.2 GenomeInfoDb_1.4.0 plyr_1.8.1 > [13] futile.options_1.0.0 stats4_3.2.0 RSQLite_1.0.0 bumphunter_1.8.0 > [17] zlibbioc_1.14.0 GenomicFeatures_1.20.0 annotate_1.46.0 S4Vectors_0.6.0 > [21] Matrix_1.2-0 preprocessCore_1.30.0 splines_3.2.0 BiocParallel_1.2.0 > [25] stringr_0.6.2 RCurl_1.95-4.5 biomaRt_2.24.0 rtracklayer_1.28.0 > [29] multtest_2.24.0 pkgmaker_0.22 mgcv_1.8-6 GEOquery_2.34.0 > [33] quadprog_1.5-5 IRanges_2.2.0 codetools_0.2-11 matrixStats_0.14.0 > [37] XML_3.98-1.1 reshape_0.8.5 GenomicAlignments_1.4.0 MASS_7.3-40 > [41] bitops_1.0-6 grid_3.2.0 nlme_3.1-120 xtable_1.7-4 > [45] registry_0.2 affy_1.46.0 DBI_0.3.1 KernSmooth_2.23-14 > [49] XVector_0.8.0 genefilter_1.50.0 affyio_1.36.0 doRNG_1.6 > [53] limma_3.24.0 minfi_1.14.0 futile.logger_1.4 nor1mix_1.2-0 > [57] lambda.r_1.1.7 RColorBrewer_1.1-2 iterators_1.0.7 siggenes_1.42.0 > [61] tools_3.2.0 illuminaio_0.10.0 rngtools_1.2.4 survival_2.38-1 > [65] methylumi_2.14.0 AnnotationDbi_1.30.0 colorspace_1.2-6 GenomicRanges_1.20.1 > [69] 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. > > ------------------------------ > > You may reply via email or visit lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0 >