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
http://www-fis.iarc.fr/~martyn/software/jags/
3) If you run
R CMD INSTALL rjags
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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--
Brian D. Ripley, rip...@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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