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<pre wrap="">Dear all,
I am working with the MEDIPS package and get the following error when
calling the function MEDIPS.CpGenrich:
</pre>
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<pre wrap=""><span class="moz-txt-citetags">> </span>cpgEnrichment_barr<-MEDIPS.CpGenrich(data=barr,extend=fraglen)
</pre>
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<pre wrap="">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:
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<pre wrap=""><span class="moz-txt-citetags">> </span>png("CalibrationPlot.png")
<span class="moz-txt-citetags">> </span> for(bar in calib_list){ #for each barcode:
</pre>
</blockquote>
<pre wrap="">+ 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
</pre>
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