From hpages at fhcrc.org  Tue Sep 14 20:23:44 2010
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Tue, 14 Sep 2010 11:23:44 -0700
Subject: [Rd] More strange R CMD build/check errors on Windows
In-Reply-To: <4C8F613E.8070407@statistik.tu-dortmund.de>
References: <4C8C6ECB.5080705@fhcrc.org> <4C8C94A3.3080600@gmail.com>
	<4C8CA70C.40109@fhcrc.org>
	<4C8F613E.8070407@statistik.tu-dortmund.de>
Message-ID: <4C8FBDB0.4060106@fhcrc.org>

Hi Uwe,

On 09/14/2010 04:49 AM, Uwe Ligges wrote:
>
>
> On 12.09.2010 12:10, Herv? Pag?s wrote:
>> Hi Peter,
>>
>> On 09/12/2010 01:51 AM, Peter Dalgaard wrote:
>>> On 09/12/2010 08:10 AM, Herv? Pag?s 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:

   https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html

Thanks!
H.


>
> 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.
>>


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] More strange R CMD build/check errors on Windows
=?windows-1252?Q?Herv=E9_Pag=E8s?=