[R-SIG-Win] New Rtools sent to CRAN

[Dan Tenenbaum]

----- Original Message -----
> From: "Jeroen Ooms" <jeroenooms at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: r-sig-windows at r-project.org
> Sent: Thursday, September 24, 2015 3:13:03 PM
> Subject: Re: [R-SIG-Win] New Rtools sent to CRAN
> 
> Hi Dan,
> 
> Currently the r-devel builds from CRAN still use the old tool chain.
> A
> copy of r-devel which has been configured with the new tool chain is
> available from
> http://www.stat.ucla.edu/~jeroen/mingw-w64/R-experimental-r69418.exe
> 
> This build has BINPREF (the path to the compiler) hardcoded to the
> default location of the new tool chains. To change it you would need
> to edit this variable in C:\Program
> Files\R\R-experimental\etc\x64\Makeconf and C:\Program
> Files\R\R-experimental\etc\i386\Makeconf.
> 
> We are currently discussing how to design it such that you can set
> the
> path to the compiler using an environment variable.
> 
> 
> > I ran the Bioconductor builds overnight using this toolchain and
> > recent R-devel and did not notice anything odd with packages
> > containing native code, which means either the new toolchain is
> > working perfectly (which is wonderful) or gcc-4.6.3 is still being
> > used and maybe I need to do something to faciliate the use of
> > gcc-4.9.3. Can you advise?
> 
> 
> We're talking to CRAN on how to coordinate the migration to the new
> tool chain. If you have bioc packages that link to external c++
> libraries, those need a rebuild. The most current information is
> available from: https://github.com/rwinlib/r-base#readme
> 

OK, I ran the Bioconductor builds with the new toolchain and the experimental version of R-devel.
A number of packages fail to install/compile which worked before with regular R-devel. Some of these are fairly important packages which have a lot of reverse dependencies.

The build report is here:

http://bioconductor.org/checkResults/3.3/bioc-LATEST/windows2.bioconductor.org-index.html#show=timeout,error

The list of packages with compilation errors not appearing in the normal build are:

affxparser
AffyTiling
arrayQualityMetrics
bamsignals
ChemmineOB
deepSNV
flowMatch
flowWorkspace
GeneNetworkBuilder
HilbertVisGUI
mzR
Rdisop
xps

You can view the build report for one of these packages by replacing PACKAGENAME with one of the packages above in this link:

http://bioconductor.org/checkResults/3.3/bioc-LATEST/PACKAGENAME/windows2.bioconductor.org-install.html

For example, for affxparser:

http://bioconductor.org/checkResults/3.3/bioc-LATEST/affxparser/windows2.bioconductor.org-install.html

FYI
Thanks,
Dan