[MINC-users] Installing RMINC

[Simon Eskildsen]

Hi all,

I just upgraded R to the latest version - 3.0.1 (2013-05-16) on a linux
mint distro and wanted to install RMINC. However, I run into trouble:

$ R CMD INSTALL RMINC_0.5.tar.gz
--configure-args='--with-build-path=/home/fristed/pack LIBS=-ldl'
* installing to library ‘/home/fristed/pack/lib64/R/library’
* installing *source* package ‘RMINC’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for library m... yes
checking for library netcdf... yes
checking for library z... yes
checking for library hdf5... yes
checking for library minc2... yes
configure: creating ./config.status
config.status: creating src/Makevars
ERROR: a 'NAMESPACE' file is required
* removing ‘/home/fristed/pack/lib64/R/library/RMINC’

Well, this new version of R does not create the missing namespace file.
Luckily the latest RMINC code on github has the namespace file. So:

$ git clone https://github.com/mcvaneede/RMINC.git RMINC
--snip--
$ R CMD INSTALL RMINC
--configure-args='--with-build-path=/home/fristed/pack LIBS=-ldl'
* installing to library ‘/home/fristed/pack/lib64/R/library’
* installing *source* package ‘RMINC’ ...
checking for gcc... gcc -std=gnu99
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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for library m... yes
checking for library netcdf... yes
checking for library z... yes
checking for library hdf5... yes
checking for library minc2... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make: Nothing to be done for `all'.
installing to /home/fristed/pack/lib64/R/library/RMINC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RMINC-userGuide.Rnw’
   ‘VBMstats.Rnw’
   ‘mincIO-userGuide.Rnw’
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/home/fristed/pack/lib64/R/library/RMINC/libs/RMINC.so':
  /home/fristed/pack/lib64/R/library/RMINC/libs/RMINC.so: undefined symbol:
ch2inv_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/fristed/pack/lib64/R/library/RMINC’

Got further, but now there seems to be a linker problem. Running ldd on
RMINC.so (before it's removed) reveals no library lookup issues.

Any idea why this happens and/or where to find ch2inv_ ?

Simon