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 [[alternative HTML version deleted]]