MotifStack not plotting?
0
0
Entering edit mode
Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 3 days ago
United States
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]]
motifStack motifStack • 1.5k views
ADD COMMENT
0
Entering edit mode

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    

 

ADD REPLY

Login before adding your answer.

Traffic: 698 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6