[R-SIG-Mac] problems installing gstat

[Prof Brian Ripley]

On 29/10/2014 08:31, Raphael.Viscarra-Rossel at csiro.au wrote:
> Hello
>
> I am wondering if anyone else is having problems installing gstat in R
> 3.1.1 on yosemite (and also mavericks)?
>
> I looked for similar problems on the web but found very little on this.

You need to do this at the OS command line and look at the log, but 
something is wrong with your compiler installation.

If you upgraded to Yosemite, did you re-install the Xcode command-line 
tools (which the upgrade is prone to partially remove)?  See the manual: 
http://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X .

If that has been done, try in a Terminal

curl -O http://cran.csiro.au/src/contrib/gstat_1.0-19.tar.gz
tar xf gstat_1.0-19.tar.gz
R CMD INSTALL gstat

and look at gstat/config.log .  (This assumes you have the dependencies 
installed, but that seems to be the case.)

Note to the gstat maintainer: you should not be checking for gcc.  From 
'Writing R Extensions'

CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`

should be added early in configure.in .  OS X usually does have a 'gcc' 
command, but it is really clang, and 'gcc' is not correct on other OSes.

>
> sessionInfo and errors below.
>
> HelpŠ. please?
>
> Raphael.
>
>
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_3.1.1
>
>
>
>> install.packages('gstat',type="source", repos='http://cran.csiro.au/')
> Installing package into Œ/Users/vis010/Library/R/3.1/library¹
> (as Œlib¹ is unspecified)
> trying URL 'http://cran.csiro.au/src/contrib/gstat_1.0-19.tar.gz'
> Content type 'application/x-gzip' length 2045717 bytes (2.0 Mb)
> opened URL
> ==================================================
> downloaded 2.0 Mb
>
> * installing *source* package Œgstat¹ ...
> ** package Œgstat¹ successfully unpacked and MD5 sums checked
> creating cache ./config.cache
> checking for gcc... gcc
> checking whether the C compiler (gcc  ) works... no
> configure: error: installation or configuration problem: C compiler cannot
> create executables.
> ERROR: configuration failed for package Œgstat¹
> * removing Œ/Users/vis010/Library/R/3.1/library/gstat¹
> * restoring previous Œ/Users/vis010/Library/R/3.1/library/gstat¹
>
> The downloaded source packages are in
> 	Œ/private/var/folders/zk/jzsww5w169g2zbl5hp260575y_7z7l/T/RtmpwsAqM6/downl
> oaded_packages¹
> Warning message:
> In install.packages("gstat", type = "source", repos =
> "http://cran.csiro.au/") :
>    installation of package Œgstat¹ had non-zero exit status
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK