lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0
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@jeremy-martinson-7630
Last seen 7.5 years ago
Pittsburgh PA, USA

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. 

lumi • 1.3k views
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Pan Du ▴ 80
@pan-du-4535
Last seen 7.7 years ago
United States
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 >
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Entering edit mode
Pan Du ▴ 80
@pan-du-4535
Last seen 7.7 years ago
United States
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 >
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@jeremy-martinson-7630
Last seen 7.5 years ago
Pittsburgh PA, USA

Pan

Thanks so much for looking into this so quickly and sending a new version to try with my dataset. This works just fine, and I can import my data now, less than 24 hours after first posting the problem. Awesome! 

cheers

Jeremy 

 

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