Hello all,

I'd like to use the Bioconductor motifStack function to align multiple DNA sequence motifs as PWMs (Position Weight Matrices).

1.Requires both ghostscript, and the R function grImport for converting. postscript files.  - Have 64 bit GS 9.10 and R 3.01 is installed in 64 bit Windows 7.

2.Environment set as Sys.setenv(R_GSCMD="\"C:\\Program Files\\gs\\gs9.10\\bin\\gswin64c.exe\"")-can open gswin64c directly with this path in the Windows run command.

3. motifStack opens the R plotting window, followed by error messages in the R command line:
Error in grImport::PostScriptTrace(paste(psfilename, ".ps", sep = ""),  :
  status 1 in running command '"C:\Program Files\gs\gs9.10\bin\gswin64c.exe" -q -dBATCH -dNOPAUSE -sDEVICE=pswrite -sOutputFile=C:\Users\millsf\AppData\Local\Temp\RtmpWsUOwL\file1344455f4de4 -sstdout=C:/Users/millsf/AppData/Local/Temp/RtmpWsUOwL/file134475b7b9d.xml capturefile134475b7b9d.ps'
In addition: Warning message:
running command '"C:\Program Files\gs\gs9.10\bin\gswin64c.exe" -q -dBATCH -dNOPAUSE -sDEVICE=pswrite -sOutputFile=C:\Users\millsf\AppData\Local\Temp\RtmpWsUOwL\file1344455f4de4 -sstdout=C:/Users/millsf/AppData/Local/Temp/RtmpWsUOwL/file134475b7b9d.xml capturefile134475b7b9d.ps' had status 1

4. Entered the following directly in the gswin64 command line:
q -dBATCH -dNOPAUSE -sDEVICE=pswrite -sOutputFile=C:\Users\millsf\AppData\Local\Temp\RtmpWsUOwL\file1344455f4de4 -sstdout=C:/Users/millsf/AppData/Local/Temp/RtmpWsUOwL/file134475b7b9d.xml capturefile134475b7b9d.ps

5. And got following response in GS

GS>-q -dBATCH -dNOPAUSE -sDEVICE=pswrite -sOutputFile=C:\Users\millsf\AppData\Lo

cal\Temp\RtmpWsUOwL\file1344455f4de4 -sstdout=C:/Users/millsf/AppData/Local/Temp

/RtmpWsUOwL/file134475b7b9d.xml capturefile134475b7b9d.ps

Error: /undefined in -q

Operand stack:



Execution stack:

   %interp_exit   .runexec2   --nostringval--   --nostringval--   --nostringval-

-   2   %stopped_push   --nostringval--   --nostringval--   %loop_continue   --n

ostringval--   --nostringval--   false   1   %stopped_push   .runexec2   --nostr

ingval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval

--

Dictionary stack:

   --dict:1177/1684(ro)(G)--   --dict:0/20(G)--   --dict:77/200(L)--

Current allocation mode is local

Last OS error: No such file or directory

Current file position is 3

GS>

6. Found the postscript file 134475b7b9d.ps, and clicked on it.  Adobe distiller launches, but doesn't convert the file, giving the following error message:

<?xml version='1.0' encoding='ISO-8859-1' ?>
<picture version='3' xmlns:rgml='http://r-project.org/RGML' source='C:/Users/millsf/AppData/Local/Temp/RtmpWsUOwL/file134475b7b9d.ps' date='2013-09-06 15:37:10' creator='R (3.0.1)' >%%[ Error: undefinedfilename; OffendingCommand: run ]%%Stack:

(C:/Users/millsf/AppData/Local/Temp/RtmpWsUOwL/file134475b7b9d.ps)
%%[ Flushing: rest of job (to end-of-file) will be ignored ]%%

%%[ Warning: PostScript error. No PDF file produced. ] %%


7. According to the following thread (http://r.789695.n4.nabble.com/Re-grImport-ghostscript-problems-td4673693.html), it looks like the Unix/Linux  version of grImport works.  Couldn't find a clear resolution of this problem for Windows.


Many thanks,

Fred Mills, Ph.D.

Staff Scientist

FDA, CDER Division of Therapeutic Proteins

NIH Campus

Bethesda, MD







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