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

Martyn Plummer plummerm at iarc.fr
Tue Mar 17 15:37:14 CET 2015

On Mon, 2015-03-16 at 12:08 -0700, Dan Tenenbaum wrote:
> 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.

That sounds like a show stopper to me. We certainly don't want to have
to rebuild third party libraries. But two things are not clear to me
1) Is it just libraries using C++ that are affected or also libraries
using only C?
2) What happens if you don't rebuild the library?
> - 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

That one is just a typo. To pass an option (e.g. --enable-auto-import)
to the linker one should use -Wl not -WI. So it is good that the new
tool chain is picking this up.


> 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
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