[Rd] steps for problems compiling a package

Prof Brian Ripley ripley at stats.ox.ac.uk
Fri Jan 7 16:18:56 CET 2011

On Thu, 6 Jan 2011, egc wrote:

> Recently installed 2.12.1 on my CentOS 5.5 box. Install of R went without 
> incident, and packages downloaded and compiled fine. With one exception -- my 
> interest is somewhat in the problems with this particular package, but more 
> in terms of 'what to do if/when a package' doesn't compile properly.

1) For a source package, download it and unpack the tarball.

2) Read the instructions: you missed the README file, which starts

   The rjags package is an interface to the JAGS library.  In order to
   build a binary package, or install from source, you must have a
   matching installation of the JAGS library.

You might also be unaware of 

3) If you run


then config.log will be in the rjags directory.  Which is one reason 
to download and unpack the tarball: it will be in a temporary 
directory if run from install.packages() or INSTALL on the tarball.

4) As for where to ask: see the posting guide!

> The offending package (in this instance) is rjags. When I try to install it 
> using
> install.packages("rjags",lib="/usr/local/lib64/R/library")
> I get the following comiplation messages:
> * installing *source* package "rjags™ ...
> checking for prefix by checking for jags... /usr/bin/jags
> checking whether the C++ compiler works... yes
> checking for C++ compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking Console.h usability... no
> checking Console.h presence... no
> checking for Console.h... no
> configure: error: in `/tmp/Rtmpb64Khr/R.INSTALL6524e7b4/rjags':
> configure: error: "Problem with header file /usr/include/JAGS/Console.h "
> See `config.log' for more details.
> ERROR: configuration failed for package "rjags™
> * removing ‘/usr/local/lib64/R/library/rjags™
> The downloaded packages are in
> ˜/tmp/RtmpwAo4Qp/downloaded_packages™
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages("rjags", lib = "/usr/local/lib64/R/library") :
> installation of package 'rjags' had non-zero exit status
> So, my questions:
> 1. the error messages suggest looking at config.log for details. Will do -- 
> if someone will tell me where to find config.log?
> 2. in cases (such as this) where an individual package throws errors on 
> compilation, what is the recommended ("officially sanctified") approach to 
> dealing with -- post question to r-devel, or to the package maintainer?
> 3. in this particular instance, the problem seems to be related to a header 
> in /usr/include/JAGS No doubt this is because (in fact) /usr/includes/JAGS 
> doesn't exist. Which I suppose brings me back to question (2).
> Thanks in advance...
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> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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