[R-SIG-Mac] Experience with upgrade to 3.3.0 beta

[Prof Brian Ripley]

On 14/04/2016 03:31, David Winsemius wrote:
> I upgraded to 3.3.0 beta from: R-3.3-branch-mavericks-signed.pkg (70Mb, installer incl. GUI)  at the suggestion of Gabor Grothendieck who wanted to know whether Ryacas would install from github in R 3.3.0. So I installed the binary that includes GUI: R.app (which now displays the modern R logo).  It installed without difficulty on El Cap running on an ancient machine (early 2008 MacPro). I then decided to move all my package folders over to the new ../library/ and used a Terminal command to do it:
>
>   cp -r -n /Library/Frameworks/R.framework/Versions/3.2/Resources/library/  /Library/Frameworks/R.framework/Versions/3.3/Resources/library/
>
> I then ran:
>
> update.packages(check.built=TRUE, ask=FALSE)
>
> I replied "y" to questions about building from source and got mostly success on a reasonably large number of packages with just a few problems:
>
>
> The downloaded source packages are in
> 	‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s80000gn/T/RtmpHlANa6/downloaded_packages’
> Warning messages:
> 1: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
>    installation of package ‘rgdal’ had non-zero exit status
> 2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
>    installation of package ‘rgeos’ had non-zero exit status
> 3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
>    installation of package ‘Rglpk’ had non-zero exit status
> 4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
>    installation of package ‘RODBC’ had non-zero exit status
> 5: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
>    installation of package ‘RPostgreSQL’ had non-zero exit status
>
> I tried updating GDAL from
>
> GDAL 1.11 Complete: http://www.kyngchaos.com/files/software/frameworks/GDAL_Complete-1.11.dmg
>
> and then reinstalling rgdal without success
>
> Efforts to install the other failures were ... also failures.
>
>
> None of these packages are essential to my typical use of R, but I'm thinking others may encounter similar problems, so if there are is a better installation process, perhaps you could let the list know.
>

Well, to build rgdal and rgeos from source you need to install the 
corresponding libs from https://r.research.att.com/libs/: I think that 
applies to Rglpk as well.

For RPostgreSQL I need Sys.setenv(PG_INCDIR = "libpq") to workaround a 
bug in the package I reported a couple of years ago.

For RODBC see its manual.  There is a slightly simpler way which will be 
in the next release:

<<
At least for OS X 10.9--11, all that is required for
\code{iODBC} is to unpack the sources and use their headers by
something like

\begin{example}
ODBC_INCLUDE=/path/to/libiodbc-srcs/include' R CMD INSTALL RODBC
\end{example}
 >>

CRAN is only showing OS X build logs for R-release, and the rgdal 
version available is rather old as the log has
configure: error: gdal-config not found or not executable.
so something is wrong with the GDAL installation on the build machine.

Hopefully Simon will see this and get the binary packages built.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford