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

[Vincent Carey]

How about a google drive?  This problem of autodownloading should be
addressed directly.
These facilities are still important but their maintenance is clearly a
lower priority as the
technologies handled have diminished use in the field.  I think we should
be able to team up and remove autoinstallation elements of these packages,
and
perhaps improve general maintainability -- Joris, can you pick
one, make a github repo that we can collaborate on revising, and then
we can start?  It will involve a deprecation process.

On Sat, May 5, 2018 at 10:54 AM, Joris Meys <jorismeys at gmail.com> wrote:

> Thank you for the answer.
>
> I was trying to create a reproducible example before I vented maybe a bit
> too much in my previous mail.
>
> I managed to get closer to the problem and it is related to data that was
> corrupted at download. I can send you a reproducible example that bombs R,
> but I will have to send the specific data files as well. How do I send them
> best?
>
> Cheers
> Joris
>
> On Sat, 5 May 2018, 00:09 James W. MacDonald, <jmacdon at uw.edu> wrote:
>
> > 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?
> >
> > Best,
> >
> > Jim
> >
> >
> >>
> >> Thank you in advance
> >> Joris
> >>
> >>
> >>
> >>
> >>
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> >
> >
> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > University of Washington
> > Environmental and Occupational Health Sciences
> > 4225 Roosevelt Way NE, # 100
> > Seattle WA 98105-6099
> >
>
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