[Bioc-devel] Package download when using functions from affy and oligo

Joris Meys Joris.Meys at ugent.be
Wed May 2 20:35:40 CEST 2018


I've noticed that using certain functions in affy and oligo (eg
oligo::read.celfiles and affy::bg.correct) start with downloading another
package and end with either R crashing or a warning that -after
installation succeeded- the package is not available. After which using
some functions of both packages still crash R.

The warning I get when trying oligo::read.celfiles() on a single CEL file
right after installing it about the pd.hugene.1.0.st.v1 package. The even
more annoying thing is that on my machine it insists on building from
source, whereas on another Windows machine without Rtools, it downloads a

Reason it frustrates the heck out of me, is that both affy and oligo
crashed the R session in different ways. During installation of a package,
during use of a function, and at different points when comparing my machine
with the one of our students. The culprit seems to be in one of the
underlying packages, but I wasn't even able to detect which package is the
culprit, let alone which function crashes everything.

Is there a way around this so I can ensure that at least I have the same
setup as they have and I can try to come up with a reproducible example to
report this critical bug?

Thank you in advance

Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)

tel: +32 (0)9 264 61 79
Biowiskundedagen 2017-2018

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