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

James W. MacDonald jmacdon at UW.EDU
Fri May 4 23:33:49 CEST 2018

I think there are multiple complaints here, so I'll take them one at a time.

On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Joris,
> Sorry I don't have much to offer here. I've cc'd the authors of oligo and
> affy who may have some insight.
> Valerie
> On 05/02/2018 11:35 AM, Joris Meys wrote:
> Dear,
> 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.

This is true for oligo, and perhaps a bit annoying. If you don't have the
package installed already, it gets the package, installs it, and then says
it's not available. This is an easy enough fix.

After which using
> some functions of both packages still crash R.

I don't know what to do with that. What functions?

> 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
> binary.

That is an options setting that gets changed when you install Rtools. The
'pkgType' option gets set to 'both' because you can now install both kinds.
And in install.packages it ends up getting switched from 'both' to
'source'. I haven't dug any further into that because I am not sure I see
why it's a problem. In the end there isn't a difference between installing
a source or a binary pdInfoPackage, and trying to get it to 'do the right
thing' might have some unforeseen consequences that I would rather not have
to worry about. This is really an 'if it ain't broke, don't fix it'
scenario, IMO.

> 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.

I understand your frustration, but that's not enough to go on. I have
never, in like 18 years, had either oligo or affy randomly segfault on me.
I understand that it is happening for you, but unless you can come up with
a reproducible example, it's not possible for anybody to help.

> 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?

Again, I am not sure what to do with that. I am not sure what 'a way around
this' pertains to, and ensuring you have the same setup as 'they have'
seems to be something only you can accomplish. Is there some reason you
cannot ensure that you have the same setup on two different computers?



> Thank you in advance
> Joris
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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