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

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Jeroen Ooms" <jeroenooms at gmail.com>
> Cc: r-sig-windows at r-project.org
> Sent: Sunday, September 27, 2015 11:57:13 AM
> Subject: Re: [R-SIG-Win] New Rtools sent to CRAN
> 
> 
> 
> ----- 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.

Just FYI, I have reverted to using the 'regular' version of R-devel. So starting tomorrow the build reports generated by building against the experimental version will no longer be available. If you want me to run tests on anything specific, let me know.

Thanks,
Dan



> 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
> 
>