New Rtools sent to CRAN

----- 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