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

[Jeroen Ooms]

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.






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
>>
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>>