[MINC-users] Installing RMINC

[Simon Eskildsen]

Hi Jason,

No worries. I'll revert to the newest 2.x for now.

Thanks,
Simon


On Thu, Aug 15, 2013 at 2:56 PM, Jason Lerch <jason at mouseimaging.ca> wrote:

> 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
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> _______________________________________________
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> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>