[BioC] dev2bitmap error, 'gs' cannot be found

Boel Brynedal Boel.Brynedal at ki.se
Mon Jul 21 17:19:56 CEST 2008

Dear List,

I am using the Category package to do some gene enrichment analysis, and
usually save my KEGGmnplot's using a dev2bitmap command. This has worked
just fine, until suddenly earlier today I got this error-message:

> dev2bitmap("04610_080721.jpg",type="jpeg", height = 10, width = 10,
res = 200)
Error in dev2bitmap("04610_CSF080721.jpg", type = "jpeg", height = 10,  :
  sorry, 'gs' cannot be found

I don't know what this means, it seems to be something about my
(From dev2bitmap function:)
gsexe <- Sys.getenv("R_GSCMD")
    if (is.null(gsexe) || !nzchar(gsexe)) {
        gsexe <- "gs"
        rc <- system(paste(shQuote(gsexe), "-help > /dev/null"))
        if (rc != 0)
            stop("sorry, 'gs' cannot be found")
I cant figure out how to fix this.
Any help or tips would be greatly appreciated.

Thank you,

SessionInfo etc below:

> sessionInfo()
R version 2.7.1 (2008-06-23)


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] KEGG.db_2.2.0        hgu133plus2.db_2.2.0 Category_2.6.0
 [4] graph_1.18.1         annotate_1.18.0      xtable_1.5-2
 [7] AnnotationDbi_1.2.2  RSQLite_0.6-9        DBI_0.2-4
[10] simpleaffy_2.16.0    genefilter_1.20.0    survival_2.34-1
[13] affyPLM_1.16.0       gcrma_2.12.1         matchprobes_1.12.0
[16] affy_1.18.2          preprocessCore_1.2.0 affyio_1.8.0
[19] Biobase_2.0.1

loaded via a namespace (and not attached):
[1] cluster_1.11.11 RBGL_1.16.0

And this is what I am trying to save, a plot that works just fine:
KEGGmnplot("04610", eS, group=groupMO, data="hgu133plus2",
main=paste(KEGGPATHID2NAME[["04610"]], paste("Overall:",
round(tA["04610"], 3)), sep="\n"))

Boel Brynedal, MSc, PhD student
Karolinska  Institutet
Department of Clinical neuroscience

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