[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
environment.
(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,
Boel
SessionInfo etc below:
> sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-unknown-linux-gnu
locale:
....
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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