[Rcpp-devel] Report on building Bioconductor with the new toolchain

[Dan Tenenbaum]

Hi,

Pardon me if this is off-topic but it looks from recent discussion like several people here are working on helping Duncan with the new toolchain and I thought some reports about issues with it might be welcome/helpful. If not, please ignore this email or suggest a more appropriate place for it (since Duncan is traveling, I thought R-devel might be a less appropriate place).

Bioconductor has been running with the new toolchain for a few days. The main issues seem to be:

- If a package links against another C/C++ library, that library needs to be rebuilt from source using the compilers in the new Rtools. This can be fairly painful for some windows libraries. In one case (protobuf) the appropriate version of ranlib was not run against the 64-bit static library; I ended up doing this by hand.

- A package (Rgraphviz) failed because of a line in Makevars.win:
gcc.exe: error: unrecognized command line option '-WI,--enable-auto-import'
removing the line:
PKG_LIBS += -WI,--enable-auto-import 
fixed the problem

There are several other packages that have problems related to the new toolchain, but I haven't figured out exactly what they are yet. Our build report (http://bioconductor.org/checkResults/devel/bioc-LATEST/) has more information. Here are the specific packages (the report contains a reference to their source in svn; you can check them out with the username readonly and password readonly):

http://bioconductor.org/checkResults/devel/bioc-LATEST/affxparser/moscato2-install.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/AffyTiling/moscato2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/DNAcopy/moscato2-install.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/GeneSelectMMD/moscato2-buildsrc.html
http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/moscato2-install.html


Let me know if you have any questions about this.

Thanks,
Dan