[MINC-users] Installing RMINC

[Jason Lerch]

Hi Simon,

mincLm uses one of the Fortran linear algebra routines that came with R back in the 1.x series - they have removed it from the 3.x series, unfortunately, hence this error. We've been meaning to replace that code with something that works with R 3.x, but have not yet got around to it. Hopefully we'll have an update which compiles with R 3.x in the next few weeks. (R 2.x still works with RMINC).

Sorry about that.

Jason

On 2013-08-15, at 8:44 AM, Simon Eskildsen <eskild at gmail.com> wrote:

> 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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