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, <jmac...@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.obench...@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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