[Bioc-devel] GEOquery for Bioc devel

[Sean Davis]

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 <dtenenba at 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" <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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