[Bioc-devel] Building embedded library on windows [was: header file hierarchy break some BioC packages]

Patrick Aboyoun paboyoun at fhcrc.org
Thu Sep 11 20:37:46 CEST 2008

There are currently four Bioconductor packages (EBImage, fdrame, Rdisop, 
and Rredland) that include dlls in its source package form. When these 
packages are checked using R CMD check, they all produce warnings 
indicating that they include executable file(s). These warnings make 
sense because they let the user know that this package contains foreign 
executable file(s) that can not be verified to be secure.

When determining the manifest for the BioC 2.3 release, all warnings are 
not viewed equally and no package is not going to make the BioC 2.3 
release solely because it contains dlls. Since the BioC 2.3 release is 
rapidly approaching


leaving Rdisop in its current stable state is the prudent choice. We 
could work together after the BioC 2.3 release, if you want to have the 
dll generated during the build process. For now, if it ain't broke, 
don't fix it for dll construction.


Steffen Neumann wrote:
> On Thu, 2008-08-21 at 09:07 +0200, Steffen Neumann wrote:
>> On Wed, 2008-08-13 at 22:32 +0200, Steffen Neumann wrote:
>>>> On Wed, 2008-08-13 at 09:48 -0700, Herve Pages wrote:
>> ...
>>>> For these packages, the problem seems to be that a number of include
>>>> directives are missing: #include <stdlib.h>, #include <string.h>,
>>>> etc...
>> Being worked on.
> Fixed. 
> There was a thread last year [Bioc-devel CXX on liverpool/lemming]
> which at least helped me get this far with precompiled .dlls, 
> but now Rdisop finishes with a single warning, 
> namely that for executables in Rdisop/src/win/.
> There has recently been a post on bioc-devel on a related issue,
> ([Bioc-devel] EBImage: Devel version on Windows not building)
> where the suggestion was to compile the required .dll 
> for windows as well, instead of providing precompiled libraries,
> but I am unable to get this work in Rdisop, as I have only 
> limited knowledge in building for Windows.
> So I'd love to leave it as is and be able to ignore 
> the warnings in check (just renamed Rdisop/src/win to Rdisop/src/winlibs
> so in 2 days I'll see whether that helps), but if neccessary 
> (and with some help) I can also try to fix the windows build. 
> The embedded library imslib is autoconf/automake/libtoolized after all,
> but these tools are already quite complex on multiple Unix dialects, 
> and w/o any windows experience (and local 64bit development environment)
> I won't manage before BioC-2.3 release in October/November.
> Is there somebody I can talk to regularly on this, 
> if neccessary off-list ?
> Yours,
> Steffen

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