[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: Sunday, September 27, 2015 12:34:08 PM
> Subject: Re: [R-SIG-Win] New Rtools sent to CRAN
> 
> Thanks Dan, this is helpful. Just to confirm: these are packages that
> did not have issues with the regular r-devel (3.3) on windows? For
> example the 'xps' only has some warnings which seem unrelated to the
> toolchain.


Sorry, please drop xps from the list.

Other than that yes, these should be packages that do not have issues with regular r-devel.
Dan


> 
> 
> 
> 
> 
> 
> On Sun, Sep 27, 2015 at 8:59 PM, Dan Tenenbaum
> <dtenenba at fredhutch.org> wrote:
> >
> >
> > ----- 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
> >>
> >> _______________________________________________
> >> R-SIG-windows mailing list
> >> R-SIG-windows at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-windows
> >>
>