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

[Joris Meys]

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
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