[Bioc-devel] GEOquery for Bioc devel

[Dan Tenenbaum]

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" <dtenenba at fredhutch.org>
> To: "Vincent Carey" <stvjc at channing.harvard.edu>
> Cc: "bioc-devel" <bioc-devel at 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" <stvjc at channing.harvard.edu>
>> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> Cc: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, "bioc-devel"
>> <bioc-devel at 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 <dtenenba at 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" <kasperdanielhansen at gmail.com>
>>> > To: "bioc-devel" <bioc-devel at 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]]
>>> >
>>> > _______________________________________________
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>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
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