[Bioc-devel] GEOquery for Bioc devel

[Dan Tenenbaum]

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" <seandavi at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Vincent Carey" <stvjc at channing.harvard.edu>, "bioc-devel" <bioc-devel at 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 <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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>>>>> 
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