Entering edit mode
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
What is the error you got in response to
?
Please paste it. Also, what is the value of
report.dir?You can check whether it exists with:
file.exists(report.dir)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