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Dear Laurent,
as already mentioned in one of my last emails I always get the following error using my branch https://github.com/sgibb/MSnbase/tree/addIdentificationData :
It is very crazy because the error is thrown but R doesn't stop. The
MSnExp
object is created correctly, e.g.:
The
master
branch (MSnbase == 1.11.10
) does not show this error.Just for documentation: a similar error was described for Reference Classes by Martin Morgan in 2011
https://stat.ethz.ch/pipermail/r-devel/2011-December/062773.html
Via
git bisect
I tried to find the commit which introduced the error. I rungit bisect
twice and get the following commit both times: sgibb@22358bdI am total confused because this commit has nothing to do with
readMSData
and in fact I did not changed/touchedreadMSData.R
at all.Using R's debug function I could identify the following line throwing the error (
MSnbase/R/readMSData.R
Line 247 in dea3344
fl <- sapply(assaydata, fromFile)
I do not understand why this error occurs. According to https://stat.ethz.ch/pipermail/r-devel/2011-December/062773.html it has something to do with the
methods
package (and ReferenceClasses which are not involved in this line). That's why I decided to access the slotfromFile
directly and avoid the use of thefromFile,Spectrum-method
. And that fixes the error for me.As I already mentioned I do not understand why the error occurs and I am not sure that my workaround is reasonable.
Could you reproduce the error using my
addIdentificationData
branch? What is your opinion about this workaround?Best wishes,
Sebastian