Experience with upgrade to 3.3.0 beta
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