[Bioc-sig-seq] error with MEDIPS.CpGenrich -> resize + segfault in MEDIPS.plotCalibrationPlot

[Nora Rieber]

Dear all,

I am working with the MEDIPS package and get the following error when
calling the function MEDIPS.CpGenrich:


> > cpgEnrichment_barr<-MEDIPS.CpGenrich(data=barr,extend=fraglen)
>   
Preprocessing...
Error in .local(x, width, fix, use.names, ...) :
  unused argument(s) (start = FALSE)
Calls: MEDIPS.CpGenrich -> resize -> resize -> .local

I checked the resize function which indeed does not require a "start"
argument, the function call in MEDIPS.CpGenrich however looks like this:

ranges(pos2) <- resize(ranges(pos2), extend + 1, start = FALSE)

This sounds like a version problem.
This is my sessionInfo:

R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.16 MEDIPS_1.2
[3] gtools_2.6.2                       BSgenome_1.16.3
[5] Biostrings_2.16.5                  GenomicRanges_1.0.3
[7] IRanges_1.6.6

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 tools_2.11.


Also, later on, when I call MEDIPS.plotCalibrationPlot, I get the
following:


> > png("CalibrationPlot.png")
> >     for(bar in calib_list){    #for each barcode:
>   
+         counter=counter+1
+         MEDIPS.plotCalibrationPlot(data=bar, linearFit=T,
plot_chr="all", rpm=T, xrange=10, main=paste("Calibration plot (bar ",
counter, ")", sep=""))
+     }
Plotting calibration plot for all chromosomes. It is recommended to call
a png() function before!

 *** caught segfault ***
address 0x135d8f794d18, cause 'memory not mapped'

Traceback:
 1: axis(side = side, at = at, labels = labels, ...)
 2: Axis.default(...)
 3: Axis(...)
 4: localAxis(if (is.null(y)) xy$x else x, side = 1, ...)
 5: plot.default(signal, coupling, pch = ".", main = "Calibration
plot",     xlab = paste(descSignal, "", sep = ""), ylab =
paste(seq_pattern,         " coupling factor", sep = ""), col = "lightblue")
 6: plot(signal, coupling, pch = ".", main = "Calibration plot",    
xlab = paste(descSignal, "", sep = ""), ylab =
paste(seq_pattern,         " coupling factor", sep = ""), col = "lightblue")
 7: MEDIPS.plotCalibrationPlot(data = bar, linearFit = T, plot_chr =
"all",     rpm = T, xrange = 10, main = paste("Calibration plot (bar
",         counter, ")", sep = ""))
aborting ...

Is this a problem on my side or is it in the code?

Thank you in advance for your help!

Best,
Nora



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