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 >> >> >> >> >> >> 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@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 > Seattle WA 98105-6099 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
