Thanks Sean! It looks like it does build and check. But the last commit was made after the daily deadline (4:20PM Seattle time) so this won't be available via biocLite() till Tuesday sometime. It can be installed via git or svn in the meantime.
Dan ----- Original Message ----- > From: "Sean Davis" <seand...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Vincent Carey" <st...@channing.harvard.edu>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Sunday, May 8, 2016 5:00:41 PM > Subject: Re: [Bioc-devel] GEOquery for Bioc devel > Hi, all. > > Sorry for the hiccup. The problem appears to have stemmed from NCBI GEO > switching to using https for GEO data tables. This is not a highly-used > feature, but it was enough to break the build. It should be fixed (cross > fingers) in Devel. If fixed in devel, I will backport to release. > > Sean > >> On May 8, 2016, at 11:52 AM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: >> >> GEOquery is available in release (3.3), though not the most recent version. >> Hopefully release and not devel is being used in the edX class; the devel >> builds are not yet stable, but should be later today. In any case, it's >> early-cycle devel. >> >> Dan >> >> >> ----- Original Message ----- >>> From: "Dan Tenenbaum" <dtene...@fredhutch.org> >>> To: "Vincent Carey" <st...@channing.harvard.edu> >>> Cc: "bioc-devel" <bioc-devel@r-project.org> >>> Sent: Sunday, May 8, 2016 8:49:09 AM >>> Subject: Re: [Bioc-devel] GEOquery for Bioc devel >> >>> Maybe. If the package does not build for many days on end, it's more than >>> flakiness and one wonders if the service is usable at all. >>> Tests that indicate this seem appropriate to me, though I agree false >>> positives >>> can be annoying. >>> Dan >>> >>> >>> ----- Original Message ----- >>>> From: "Vincent Carey" <st...@channing.harvard.edu> >>>> To: "Dan Tenenbaum" <dtene...@fredhutch.org> >>>> Cc: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel" >>>> <bioc-devel@r-project.org> >>>> Sent: Sunday, May 8, 2016 8:46:57 AM >>>> Subject: Re: [Bioc-devel] GEOquery for Bioc devel >>> >>>> Hmm. Very important piece of software so we should try to remedy this. I >>>> had assigned some GEOquery problems in the edX class and there were some >>>> people who could not get getGEO to work, but the problem seemed >>>> intermittent. There was a workaround posted on the support site which >>>> involved separate steps for assay and platform data acquisition; ultimately >>>> the solution data object was just made available directly. >>>> >>>> Can/should we make the build/distribution process robust to data server >>>> flakiness? The user may encounter intermittent problems, but the software >>>> should still be available IMHO. >>>> Reduce server-dependent tests and examples? >>>> >>>> On Sun, May 8, 2016 at 11:08 AM, Dan Tenenbaum <dtene...@fredhutch.org> >>>> wrote: >>>> >>>>> It has not built since the devel (3.4) builds started. Apparently GEO has >>>>> been pretty flaky. >>>>> Dan >>>>> >>>>> >>>>> ----- Original Message ----- >>>>>> From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> >>>>>> To: "bioc-devel" <bioc-devel@r-project.org> >>>>>> Sent: Sunday, May 8, 2016 5:54:59 AM >>>>>> Subject: [Bioc-devel] GEOquery for Bioc devel >>>>> >>>>>> I don't see GEOquery for Bioc devel. Is that a mistake somehow? >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
