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
