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 <jorism...@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, <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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel