Entering edit mode
Dear Dr. Fred,
Thank you for your choice to try motifStack. When you using MacBook,
just try motifStack without setting R_GSCMD.
For linux system or mac, a GhostScript executable will be searched by
name on your path when R_GSCMD is unset. You can also try to use
command:
which gs
in you terminal.
In my case, my GhostScript is installed at "/usr/local/bin/gs"
And you can try Sys.setenv(R_GSCMD="/usr/local/bin/gs") before draw
motifs or just do not set this for a mac.
For window 7, I will copy my code to you later.
Good luck.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
From: <mills>, Frederick
<frederick.mills@fda.hhs.gov<mailto:frederick.mills@fda.hhs.gov>>
Date: Friday, December 13, 2013 2:51 PM
To: Jianhong Ou
<jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>>
Subject: MotifStack not plotting?
Dear Dr. Ou,
Not sure if I should address this to you or bioc-
devel@r-project.org<mailto:bioc-devel@r-project.org>. I having an
issue on one Ubuntu/R-Bioconductor installation with motitStack.
I installed Biolinux on a partition on my iMac, giving me Ubuntu
12.04. Upgraded to R 3.01, Bioconductor Workflow install, BiocLite,
and installed the following
source("http://bioconductor.org/biocLite.R"<http: bioconductor.org="" bi="" oclite.r%22="">) biocLite(c("MotifDb", "GenomicFeatures",
"TxDb.Scerevisiae.UCSC.sacCer3.sgdGene","org.Sc.sgd.db",
"BSgenome.Scerevisiae.UCSC.sacCer3", "motifStack", "seqLogo")-as per
the Bioconductor examples for TF binding sites. Also grImport and
MotIV. I set the R working directory as setwd( /usr/local/lib/R
/site-library and the Ghostscript executable is at
/usr/bin/ghostscript. motifStack works fine with this installation.
However, I have a MacBook Pro at home on which I've installed Ubuntu
13.10, and then installed R 3.01, and then the same packages as above.
I also set the R working directory as above and Ghostacript is at the
same location. Everything works except motifStack, which opens a
blank plot window and gives the following errors.
Error in grImport::PostScriptTrace(paste(psfilename, ".ps", sep = ""),
: status 1 in running command '/usr/bin/ghostscript -q -dBATCH
-dNOPAUSE -sDEVICE=pswrite -sOutputFile=/dev/null
-sstdout=/tmp/Rtmp8UuHLT/filea5a4df42eac.xml capturefilea5a4df42eac.ps
If I run the above command in terminal, still no luck. I've tried
setting the environment with Sys.setenv(R_GSCMD="/usr/bin/gs")-same
result. Running Ghostscript from the terminal opens a blank plot
window, as does running grid within R.
I've had a very similar experience trying to use motifStack in a
Windows 7 environment.
Anyway, not an absolute necessity, but it would be great if I could
get this second installation working.
Thanks very much,
Fred Mills, Ph.D. Staff Scientist
FDA, CDER
NIH Campus, Bethesda, MD
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This is not working for me in mac. Not sure where the GhostScript is
---
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] motifStack_1.26.0 Biostrings_2.50.1 XVector_0.22.0 IRanges_2.16.0 S4Vectors_0.20.1
[6] ade4_1.7-13 MotIV_1.38.0 BiocGenerics_0.28.0 grImport_0.9-1 XML_3.98-1.16