[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.
> 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
> 

Actually, the error will not always be in the INSTALL phase so instead use a url like this:

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

And click on the red ERROR icon(s).

Dan


> FYI
> Thanks,
> Dan
> 
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