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Kathrin.Klee
•
0
@kathrinklee-22265
Last seen 5.2 years ago
I'm trying to run the quality control function of RnBeads:
rnb.run.qc(rnbs, reportDir)
but it results in the following error:
Error in logger.error(em) : Could not create file. GhostScript was not found
I'm using RStudio under Windows. So I installed GhostScript and set the environment variable for R:
Sys.setenv(GS_CMD="C:/Program Files/gs/gs9.50/bin/gswin64c.exe")
But it seems it doesn't work. I still get the same error that GhostScript was not found.
If I use Sys.getenv()
GhostScript is there on the list of environment variables, but tools::find_gs_cmd("gswin64c.exe")
results in:
gswin64c.exe
""
Any suggestions what is going wrong here?
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
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.hg19_1.16.0 RnBeads_2.2.0 plyr_1.8.4
[4] methylumi_2.30.0 minfi_1.30.0 bumphunter_1.26.0
[7] locfit_1.5-9.1 iterators_1.0.12 foreach_1.4.7
[10] Biostrings_2.52.0 XVector_0.24.0 SummarizedExperiment_1.14.1
[13] DelayedArray_0.10.0 BiocParallel_1.18.1 FDb.InfiniumMethylation.hg19_2.2.0
[16] org.Hs.eg.db_3.8.2 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.36.4
[19] AnnotationDbi_1.46.1 reshape2_1.4.3 scales_1.0.0
[22] Biobase_2.44.0 illuminaio_0.26.0 matrixStats_0.54.0
[25] limma_3.40.6 gridExtra_2.3 gplots_3.0.1.1
[28] ggplot2_3.2.1 fields_9.9 maps_3.3.0
[31] spam_2.3-0 dotCall64_1.0-0 ff_2.2-14
[34] bit_1.1-14 cluster_2.0.8 MASS_7.3-51.4
[37] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 IRanges_2.18.2
[40] S4Vectors_0.22.0 BiocGenerics_0.30.0 knitr_1.24
[43] getopt_1.20.3
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 siggenes_1.58.0 mclust_5.4.5 base64_2.0 rstudioapi_0.10
[6] remotes_2.1.0 bit64_0.9-7 xml2_1.2.2 codetools_0.2-16 splines_3.6.0
[11] scrime_1.3.5 zeallot_0.1.0 Rsamtools_2.0.0 annotate_1.62.0 HDF5Array_1.12.2
[16] readr_1.3.1 compiler_3.6.0 httr_1.4.1 backports_1.1.4 assertthat_0.2.1
[21] Matrix_1.2-17 lazyeval_0.2.2 prettyunits_1.0.2 tools_3.6.0 gtable_0.3.0
[26] glue_1.3.1 GenomeInfoDbData_1.2.1 dplyr_0.8.3 doRNG_1.7.1 Rcpp_1.0.2
[31] vctrs_0.2.0 multtest_2.40.0 nlme_3.1-139 preprocessCore_1.46.0 gdata_2.18.0
[36] rtracklayer_1.44.3 DelayedMatrixStats_1.6.0 xfun_0.9 stringr_1.4.0 rngtools_1.4
[41] gtools_3.8.1 XML_3.98-1.20 beanplot_1.2 zlibbioc_1.30.0 hms_0.5.1
[46] GEOquery_2.52.0 rhdf5_2.28.0 RColorBrewer_1.1-2 memoise_1.1.0 pkgmaker_0.27
[51] biomaRt_2.40.4 reshape_0.8.8 stringi_1.4.3 RSQLite_2.1.2 genefilter_1.66.0
[56] caTools_1.17.1.2 bibtex_0.4.2 rlang_0.4.0 pkgconfig_2.0.2 bitops_1.0-6
[61] nor1mix_1.3-0 lattice_0.20-38 purrr_0.3.2 Rhdf5lib_1.6.0 labeling_0.3
[66] GenomicAlignments_1.20.1 tidyselect_0.2.5 magrittr_1.5 R6_2.4.0 DBI_1.0.0
[71] pillar_1.4.2 withr_2.1.2 survival_2.44-1.1 RCurl_1.95-4.12 tibble_2.1.3
[76] crayon_1.3.4 KernSmooth_2.23-15 progress_1.2.2 data.table_1.12.2 blob_1.2.0
[81] digest_0.6.20 xtable_1.8-4 tidyr_0.8.3 openssl_1.4.1 munsell_0.5.0
[86] registry_0.5-1 quadprog_1.5-7 askpass_1.1
Dear Kathrin,
You'll also have to add the path to the Ghostscript executable to your
PATH
environment variable as described in the RnBeads FAQ under rnbeads.org/faq.html. Under Windows 7, for instance, you can specify that in the Control Panel in the Systems properties.I hope that helps,
Michael
Dear Michael,
thanks a lot for your answer and help! That was it.
Best & thanks Kathrin