[R] RE: new packages: geepack and KMsurv

[Duncan Temple Lang]

The key to the error message 

> Error in dyn.load(x, as.logical(local), as.logical(now)) : 
> 	unable to load shared library "/usr/lib/R/library/acepack/libs/acepack.so":
>   libR.so: cannot open shared object file: No such file or directory
> Error in library(acepack) : .First.lib failed

is the libR.so.  That means that at some stage you compiled R with the
--enable-R-shlib flag and built libR.so.  Then, when you installed a
new version of R, you did not use the --enable-R-shlib flag. So
libR.so was not built. But when a package is installed and libR.so
exists, that package is linked against the libR.so. So when that
previously compiled package is loaded into the new R that has no
libR.so, you get the error message you are seeing.

To get around this problem, either re-install the packages from source
as you mention or rebuild R with the --enable-R-shlib flag passed to
configure. I agree this is annoying. It is a natural issue when we
have component based software; both a blessing and a curse.

 D.

Jari Oksanen wrote:
> 
> jsendak at omniwhittington.co.uk said:
> > I downloaded geepack from your site and installed it from the zip
> > file. However, although it appears under my library directory, I could
> > not load into R.
> 
> I found out that all old packages with compiled code in shared libraries fail to
> load in R-1.6.0. My platform is RH7.3 with the notorious C/G77 compiler, but the
> reason seem not to be changes in compiler, but changes in R. Packages that I had
> compiled and installed day before upgrading to R-1.6.0 failed after upgrading.
> The problem vanishes when the package is re-installed from the source. This is a
> mild nuisance and for several packages I wait that they are ugpraded in CRAN so
> that re-building happens automatically. I am not sure if this is the reason with
> your trouble with binary packages, since your platform is very different. This
> is the output I get with one example package:
> 
> > library(acepack)
> Error in dyn.load(x, as.logical(local), as.logical(now)) : 
> 	unable to load shared library "/usr/lib/R/library/acepack/libs/acepack.so":
>   libR.so: cannot open shared object file: No such file or directory
> Error in library(acepack) : .First.lib failed
> # But it is there:
> 
> > system("ls /usr/lib/R/library/acepack/libs/acepack.so -l")
> -rwxr-xr-x    1 root     root        68548 May 29 11:00 /usr/lib/R/library/acepack/libs/acepack.so
> 
> > dyn.load("/usr/lib/R/library/acepack/libs/acepack.so")
> Error in dyn.load(x, as.logical(local), as.logical(now)) : 
> 	unable to load shared library "/usr/lib/R/library/acepack/libs/acepack.so":
>   libR.so: cannot open shared object file: No such file or directory
> 
> I have tried to find if this new behaviour is documented, but I haven't yet
> found anything, so this may be an "undocumented feature". Who knows?
> 
> cheers, jari oksanen
> -- 
> Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland
> Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061
> email jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/
> 
> 
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-- 
_______________________________________________________________

Duncan Temple Lang                duncan at research.bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-3217
700 Mountain Avenue, Room 2C-259  fax:    (908)582-3340
Murray Hill, NJ  07974-2070       
         http://cm.bell-labs.com/stat/duncan
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