On 01/11/16 21:08, Kirill M?ller wrote:> Did you reinstall the gsl package [1]?Apparently not. I did a complete update.packages() which reinstalled a great number of packages (I have a great number in my personal library). There were complaints about 4 packages, one of which was "copula", but "gsl" was not one of them. I would have *thought* that if "gsl" needed to be reinstalled, then update.packages() would have done this. It also makes no sense to me --- the install of "copula" complained about not being able to find a shared object library (presumably of fortran or C or some such code), not about being unable to load "gsl". Be that as it were, I did an install (a reinstall) of "gsl" successfully and then the install of copula was also smooth and successful. Thanks. cheers, Rolf Turner> -Kirill > > > [1] https://cran.r-project.org/web/packages/gsl/index.html > > > On 01.11.2016 04:17, Rolf Turner wrote: >> >> I have just upgraded to the latest R (3.3.2) and thought I should >> update my library of contributed packages. >> >> Ran into problems with "copula". Got the error: >> >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> unable to load shared object '/home/rolf/Rlib/gsl/libs/gsl.so': >>> libgsl.so.0: cannot open shared object file: No such file or directory >> >> So after a bit of googling around I did: >> >> sudo apt-get install libgsl2 >> sudo apt-get install libgsl-dev >> >> both of which ran successfully. >> >> Still no joy, but. What *else* do I need to do? >> >> I am running Ubuntu 16.04.1.
The error message mentions (perhaps not very clearly) that the shared library installed with the gsl R package could not be loaded. Chances are that the gsl package (and as a consequence the copula package, too) didn't work before you upgraded. This can happen e.g. if the dependent system library (libgsl-dev?) is upgraded. update.packages() doesn't try to load any packages, which would be necessary to detect this scenario. -Kirill On 01.11.2016 09:45, Rolf Turner wrote:> On 01/11/16 21:08, Kirill M?ller wrote: >> Did you reinstall the gsl package [1]? > > Apparently not. I did a complete update.packages() which reinstalled a > great number of packages (I have a great number in my personal library). > There were complaints about 4 packages, one of which was "copula", but > "gsl" was not one of them. > > I would have *thought* that if "gsl" needed to be reinstalled, then > update.packages() would have done this. > > It also makes no sense to me --- the install of "copula" complained > about not being able to find a shared object library (presumably of > fortran or C or some such code), not about being unable to load "gsl". > > Be that as it were, I did an install (a reinstall) of "gsl" > successfully and then the install of copula was also smooth and > successful. > > Thanks. > > cheers, > > Rolf Turner > >> -Kirill >> >> >> [1] https://cran.r-project.org/web/packages/gsl/index.html >> >> >> On 01.11.2016 04:17, Rolf Turner wrote: >>> >>> I have just upgraded to the latest R (3.3.2) and thought I should >>> update my library of contributed packages. >>> >>> Ran into problems with "copula". Got the error: >>> >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> unable to load shared object '/home/rolf/Rlib/gsl/libs/gsl.so': >>>> libgsl.so.0: cannot open shared object file: No such file or >>>> directory >>> >>> So after a bit of googling around I did: >>> >>> sudo apt-get install libgsl2 >>> sudo apt-get install libgsl-dev >>> >>> both of which ran successfully. >>> >>> Still no joy, but. What *else* do I need to do? >>> >>> I am running Ubuntu 16.04.1.
On 1 November 2016 at 09:52, Kirill M?ller wrote: | The error message mentions (perhaps not very clearly) that the shared | library installed with the gsl R package could not be loaded. Chances | are that the gsl package (and as a consequence the copula package, too) | didn't work before you upgraded. This can happen e.g. if the dependent | system library (libgsl-dev?) is upgraded. | | update.packages() doesn't try to load any packages, which would be | necessary to detect this scenario. Spot on. What happens is that a) the Debian package system updated GSL via libgsl* to the gsl-2.* b) the R package manager knows nothing about it which why the latter couldn't tell Rolf; R's gsl package just fails to load. In a fully integrated system a) can trigger b) and smoothly update the _R_ package gsl as a consequense of the _Debian_ library gsl changing. (That's how Debian works internally.) Here our coupling is looser. The only remedy, sadly, is a bit of "been there, done there" which is how Kirill spotted what to do. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org