Question: RnBeads set ghost script environment variable
0
gravatar for Kathrin.Klee
5 weeks ago by
Kathrin.Klee0 wrote:

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
rnbeads ghostscript • 69 views
ADD COMMENTlink written 5 weeks ago by Kathrin.Klee0

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

ADD REPLYlink written 4 weeks ago by mscherer10

Dear Michael,

thanks a lot for your answer and help! That was it.

Best & thanks Kathrin

ADD REPLYlink written 4 weeks ago by Kathrin.Klee0
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