[Rd] More strange R CMD build/check errors on Windows

Hervé Pagès hpages at fhcrc.org
Tue Sep 14 20:23:44 CEST 2010

Hi Uwe,

On 09/14/2010 04:49 AM, Uwe Ligges wrote:
> On 12.09.2010 12:10, Hervé Pagès wrote:
>> Hi Peter,
>> On 09/12/2010 01:51 AM, Peter Dalgaard wrote:
>>> On 09/12/2010 08:10 AM, Hervé Pagès wrote:
>>> ...
>>>> AFAICT those problems were never seen before (i.e. with R< 2.12).
>>>> They show up randomly everyday for a small number of packages
>>>> (between 10 and 20 out of 400). The set of victims changes everyday
>>>> and any package seems to be a potential victim (I've not been able
>>>> to observe any obvious pattern so far).
>>>> Does anyone have any idea what could make 'R CMD build' and
>>>> 'R CMD check' so confused/unreliable on Windows?
> Brian had some ideas that the problems are related to the shell that is
> used. Is the problem still apparent in a very recent R-devel from few
> days ago? I am just back from vacations and have not updated yet.
> I experienced the same problems and I am just iterating automatically if
> typical problems are apparent from the log files. I hope some if not all
> parts are solved now and will do some new test runs shortly.

Sounds good. I just upgraded to R-2.12 (2010-09-13 r52905) on our 32-bit
Windows machine and I'll report here tomorrow after the next build run
has completed. I can already see that this new R solves the issue I
reported here:



> Best,
> Uwe
>>>> Thanks,
>>>> H.
>>> Antivirus software? I suspect you already ruled that out, but it has
>>> been the culprit for problems with mysteriously disappearing
>>> intermediate files in several cases, so I thought I'd mention it.
>> Actually I didn't try that yet because we still build BioC release
>> (using R-2.11.1) on these 2 Windows boxes and we don't see any of
>> those problems for the release builds. But I will. Could it be that
>> the fact that 'R CMD build' and 'R CMD check' are R-based in R-2.12
>> (and not Perl-based anymore) make them more fragile when something
>> like an antivirus is messing around with the filesystem?
>> Thanks for the suggestion,
>> H.

Hervé Pagès

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