----- Original Message ----- > From: "Martyn Plummer" <plumm...@iarc.fr> > To: dtene...@fredhutch.org > Cc: rcpp-devel@lists.r-forge.r-project.org > Sent: Tuesday, March 17, 2015 7:37:14 AM > Subject: Re: [Rcpp-devel] Report on building Bioconductor with the new > toolchain > > 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.
Jeroen replied to me off-list and said this was being worked on and was likely the result of using different flags from the previous version of rtools. However, I note that the third party libraries I'm dealing with were not necessarily built with the old Rtools compilers; in some cases I downloaded pre-built binaries. They were built with mingw though. > But two things are not clear to me > 1) Is it just libraries using C++ that are affected or also libraries > using only C? So far it seems like just C++ (protocol buffers, openbabel, proteome wizard, ROOT, etc..) > 2) What happens if you don't rebuild the library? Usually something like this: ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'ChemmineOB', details: call: inDL(x, as.logical(local), as.logical(now), ...) error: unable to load shared object 'E:/biocbld/bbs-3.1-bioc/R/library/ChemmineOB/libs/i386/ChemmineOB.dll': LoadLibrary failure: Invalid access to memory location. > > > - 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. Good to know, thanks. Dan > > Martyn > > > 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 > > > > _______________________________________________ > > Rcpp-devel mailing list > > Rcpp-devel@lists.r-forge.r-project.org > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > ----------------------------------------------------------------------- > This message and its attachments are strictly confidential. If you > are > not the intended recipient of this message, please immediately notify > the sender and delete it. Since its integrity cannot be guaranteed, > its content cannot involve the sender's responsibility. Any misuse, > any disclosure or publication of its content, either whole or > partial, > is prohibited, exception made of formally approved use > ----------------------------------------------------------------------- > _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel