[Bioc-devel] openSUSE 11.0/gcc 4.3.1: changes in standard header file hierarchy break some BioC packages

[Herve Pages]

Hi BioC developers,

I've set up a new build machine for the BioC software. The name is wilson1
and it's running 64-bit openSUSE 11.0 (latest openSUSE release):

   http://bioconductor.org/checkResults/2.3/bioc-LATEST/

Please watch carefully the build results for your package(s), it's very
important that they pass the build/check test on openSUSE 11.0 too for the
next BioC release.

The default compiler on openSUSE 11.0 is gcc 4.3.1:

   http://bioconductor.org/checkResults/2.3/bioc-LATEST/wilson1-NodeInfo.html

A few packages with C/C++ code don't compile anymore with gcc 4.3.1. These
include:

   - adSplit
   - affxparser
   - GeneR
   - GeneticsBase
   - plier
   - Rdisop
   - Rtreemix
   - XDE

For these packages, the problem seems to be that a number of include
directives are missing: #include <stdlib.h>, #include <string.h>, etc...
Everything was compiling fine so far (i.e. with gcc < 4.3.1), even without
those includes, but somewhere between gcc 4.2.1 (openSUSE 10.3) and gcc 4.3.1,
it seems that the C/C++ standard header files have been reorganized and some
files that used to be indirectly included are not anymore. Unfortunately this
breaks code that was relying on these indirect inclusions.

Other packages with C/C++ code that breaks on openSUSE 11.0:

   - EBImage: in openSUSE 11.0, the Wand library that the EBImage C++ code needs
         to be linked to has been renamed MagickWand.

   - GeneRfold: the ViennaRNA package was missing on wilson1 but this is fixed now.

   - xcms: an obscure problem that seems to be caused by an internal compiler
         error.

Please don't hesitate to post here if you need help to fix your package. Thanks!

Cheers,
H.