segfault after window building

[GoogleCodeExporter]

1) What operating system are you using?
ubuntu, R 2.14.0, zinba 2.01
2) What error message was displayed?
--------BUILD WINDOWS COMPLETE-------

 *** caught segfault ***
address 0x567e49, cause 'invalid permissions'

Traceback:
 1: gc()
 2: buildwindowdata(seq = seq, align = align, input = input, twoBit = twoBit,     winSize = winSize, offset = offset, cnvWinSize = cnvWinSize,     cnvOffset = cnvOffset, filelist = filelist, filetype = filetype,     extension = extension, outdir = outfile_subdir)
 3: run.zinba(align = align, numProc = numProc, seq = seq, input = input,     basecountfile = basecountfile, filetype = filetype, offset = 125,     buildwin = 1, outfile = outfile, threshold = threshold, twoBit = twoBit,     cnvOffset = 2500, pquant = 1, winGap = winGap, cnvWinSize = 1e+05,     initmethod = "count", printFullOut = 1, winSize = 250, diff = 0,     pWinSize = 200, extension = extension, method = "mixture",     refinepeaks = refinepeaks, selectmodel = TRUE, selectchr = "chr22",     selecttype = selecttype, selectcovs = selectcovs, FDR = FDR,     interaction = interaction, peakconfidence = peakconfidence)
 4: zinba(refinepeaks = 1, seq = "low.bed", input = "none.bed", filetype = "bed",     align = "./result_zinba/ath1_ext200/", numProc = 4, twoBit = "../zinba/hg19.2bit",     outfile = "./result_zinba/low_none/", extension = 200, basecountfile = "result_zinba/high.basecount",     broad = F, printFullOut = 1)

3) What was the exact command you used that resulted in the error?
see above

4) Please copy and paste any additional screen output that resulted from
running the command
see above

Original issue reported on code.google.com by daiyi...@gmail.com on 6 Mar 2012 at 4:57

[GoogleCodeExporter]

just noticed i didnt copy and paste everything, the commands are the same for 
issue 14 and 15, i wish there was an edit button:
library(zinba)
generateAlignability(
   mapdir='../zinba/map36_hg19/',
   outdir='./result_zinba/ath1_ext200/', 
   athresh=1,  
   extension=200,  
   twoBitFile='../zinba/hg19.2bit'
)

basealigncount(
   inputfile='high.bed', 
   outputfile='result_zinba/high.basecount', 
   extension=200, 
   filetype='bed',
   twoBitFile='../zinba/hg19.2bit' 
)
basealigncount(
   inputfile='mid.bed', 
   outputfile='result_zinba/mid.basecount', 
   extension=200, 
   filetype='bed',
   twoBitFile='../zinba/hg19.2bit' 
)
basealigncount(
   inputfile='none.bed', 
   outputfile='result_zinba/none.basecount', 
   extension=200, 
   filetype='bed',
   twoBitFile='../zinba/hg19.2bit' 
)
zinba(
  refinepeaks=1, 
  seq='high.bed',
  input='none.bed',
  filetype="bed",

  align='./result_zinba/ath1_ext200/',
  numProc=4,                    
  twoBit='../zinba/hg19.2bit',
  outfile="./result_zinba/high_none/",
  extension=200,

  basecountfile='result_zinba/high.basecount',
  broad=F,
  printFullOut=1
)

zinba(
  refinepeaks=1, 
  seq='mid.bed',
  input='none.bed',
  filetype="bed",

  align='./result_zinba/ath1_ext200/',
  numProc=4,                    
  twoBit='../zinba/hg19.2bit',
  outfile="./result_zinba/mid_none/",
  extension=200,

  basecountfile='result_zinba/high.basecount',
  broad=F,
  printFullOut=1
)

Original comment by daiyi...@gmail.com on 6 Mar 2012 at 7:18

[GoogleCodeExporter]

fixed with update

Original comment by homer...@gmail.com on 9 Mar 2012 at 4:08

• Changed state: Fixed