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

Mon May 14 15:15:19 CEST 2018

Dear all,

sorry for the delayed response, due to some unfortunate events I had to
prioritize my family the past week.

You find an RStudio project in a zipped folder on this link :
https://jorismeys.stackstorage.com/s/3ik0vMwsvueuT5a

It contains a script called testOligo.R that can be sourced and nukes my R
session in the second step of the rma() function. It also contains the
faulty .gz files. If you need more information, don't hesitate to contact
me.

Regarding improving general maintainability, I'm willing to help out on
that. Problem is that I'm rather behind with my own work, so I'm short on
time for the moment. I'll fork affy tomorrow (need to give class now) and
let's start from there then?

Cheers
Joris

On Sat, May 5, 2018 at 5:17 PM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> 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
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> This email message may contain legally privileged and/or confidential
>> >> information.  If you are not the intended recipient(s), or the
>> employee or
>> >> agent responsible for the delivery of this message to the intended
>> >> recipient(s), you are hereby notified that any disclosure, copying,
>> >> distribution, or use of this email message is prohibited.  If you have
>> >> received this message in error, please notify the sender immediately by
>> >> e-mail and delete this email message from your computer. Thank you.
>> >>         [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
>> >> Bioc-devel at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >
>> >
>> >
>> > --
>> > James W. MacDonald, M.S.
>> > Biostatistician
>> > University of Washington
>> > Environmental and Occupational Health Sciences
>> > 4225 Roosevelt Way NE, # 100
>> <https://maps.google.com/?q=4225+Roosevelt+Way+NE,+%23+100+%0D%0A+Seattle+WA+98105&entry=gmail&source=g>
>> > Seattle WA 98105
>> <https://maps.google.com/?q=4225+Roosevelt+Way+NE,+%23+100+%0D%0A+Seattle+WA+98105&entry=gmail&source=g>
>> -6099
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g>

-----------
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

	[[alternative HTML version deleted]]