rnBeads error for the report path
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@brennahott-8948
Last seen 6.4 years ago
United States

Hello, 

I am getting this error even though this path does not exist. Is there something I am missing?

rnb.run.analysis(dir.reports=report.dir, sample.sheet=sample.annotation,
+ data.dir=idat.dir, data.type="infinium.idat.dir")
Error in rnb.run.analysis(dir.reports = report.dir, sample.sheet = sample.annotation,  : 
  Could not initialize reports in ~/RnBeads/analysis/reports ; make sure this path does not exist.

sessioninfo gave me an error, traceback gave me no output.

 

Thanks, 

Brenna

software error rnbeads • 1.2k views
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What is the error you got in response to

sessionInfo()

?

Please paste it. Also, what is the value of report.dir?

You can check whether it exists with:

file.exists(report.dir)

 

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R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RnBeads_1.0.0                           plyr_1.8.3                              methylumi_2.14.0                       
 [4] minfi_1.14.0                            bumphunter_1.8.0                        locfit_1.5-9.1                         
 [7] iterators_1.0.8                         foreach_1.4.3                           Biostrings_2.36.4                      
[10] XVector_0.8.0                           lattice_0.20-33                         FDb.InfiniumMethylation.hg19_2.2.0     
[13] org.Hs.eg.db_3.1.2                      RSQLite_1.0.0                           DBI_0.3.1                              
[16] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2 GenomicFeatures_1.20.6                  AnnotationDbi_1.30.1                   
[19] reshape2_1.4.1                          scales_0.3.0                            Biobase_2.28.0                         
[22] illuminaio_0.10.0                       matrixStats_0.14.2                      limma_3.24.15                          
[25] gridExtra_2.0.0                         gplots_2.17.0                           ggplot2_1.0.1                          
[28] fields_8.2-1                            maps_3.0.0-2                            spam_1.2-1                             
[31] ff_2.2-13                               bit_1.1-12                              cluster_2.0.3                          
[34] RColorBrewer_1.1-2                      MASS_7.3-44                             GenomicRanges_1.20.8                   
[37] GenomeInfoDb_1.4.3                      IRanges_2.2.9                           S4Vectors_0.6.6                        
[40] BiocGenerics_0.14.0                    

loaded via a namespace (and not attached):
 [1] nor1mix_1.2-1           splines_3.2.2           gtools_3.5.0            doRNG_1.6               Rsamtools_1.20.5       
 [6] quadprog_1.5-5          digest_0.6.8            colorspace_1.2-6        preprocessCore_1.30.0   GEOquery_2.34.0        
[11] siggenes_1.42.0         XML_3.98-1.3            biomaRt_2.24.1          genefilter_1.50.0       zlibbioc_1.14.0        
[16] xtable_1.7-4            gdata_2.17.0            BiocParallel_1.2.22     annotate_1.46.1         beanplot_1.2           
[21] pkgmaker_0.22           proto_0.3-10            survival_2.38-3         magrittr_1.5            mclust_5.0.2           
[26] nlme_3.1-122            tools_3.2.2             registry_0.3            stringr_1.0.0           munsell_0.4.2          
[31] rngtools_1.2.4          lambda.r_1.1.7          base64_1.1              caTools_1.17.1          futile.logger_1.4.1    
[36] RCurl_1.95-4.7          bitops_1.0-6            gtable_0.1.2            codetools_0.2-14        multtest_2.24.0        
[41] reshape_0.8.5           GenomicAlignments_1.4.2 rtracklayer_1.28.10     futile.options_1.0.0    KernSmooth_2.23-15     
[46] stringi_0.5-5           Rcpp_0.12.1            

file.exists(report.dir came back [1] TRUE

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