[Bioc-devel] Bioconductor 2.7 Release Schedule

Hervé Pagès hpages at fhcrc.org
Mon Oct 11 23:45:38 CEST 2010

Hi Steffen and developers,

On 10/11/2010 01:57 AM, Steffen Neumann wrote:
> Hi,
> On Fri, 2010-09-17 at 12:32 -0700, Hervé Pagès wrote:
>> your packages pass 'R CMD build' and 'R CMD check' with no
>> warnings: http://bioconductor.org/checkResults/2.7/bioc-LATEST/index.html
>> You might have noticed that there have been a lot of turbulences
>> recently on the Windows builds. We are working on it and hopefully
>> those problems will soon disappear.
> Could you provide an "official" waiver for those pesky
> object file warnings, which 1) don't occur on the last 2.6 builds,
> and 2) only occur on windows ? There seem to be two different checks,
> one just saying "contains object files", the other
> naming them "Subdirectory 'src' contains:"

Yes please ignore those warnings about object files not being
removed from the src/ folder on Windows. This seems to affect
all packages with native code that don't use a Makefile (i.e.,
a *lot* of BioC packages). I reported that problem yesterday on


but got no answer so far (and I don't see any fix coming yet in
svn for R). This problem is new in R 2.12 (hence you don't see it
with the 2.6 builds): it is (again) a regression introduced in
'R CMD build' and 'R CMD check' when those scripts were migrated
from Perl to R. Note that most of those regressions (some of them
more serious than this one) seem to have been fixed in R 2.12 RC
already but there are still a couple of them pending.

Thanks for your comprehension,

> Yours,
> Steffen
> * checking if this is a source package ... WARNING
> Subdirectory 'src' contains:
>    xcms.dll
> * checking if this is a source package ... WARNING
> Subdirectory 'Rdisop/src' contains object files.
> * checking if this is a source package ... WARNING
> Subdirectory 'CAMERA/src' contains object files.
> Subdirectory 'src' contains:
>    CAMERA.dll fastMatch.o

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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