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 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
