Re: [R] Trouble installing gsl wrapper
On Sat, 30 Oct 2010, Gang Chen wrote: Hi, I'm trying to install the gsl wrapper source code (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux system (OpenSuse 11.1), but encountering the following problem. I've already installed 'gsl' version 1.14 (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's missing? Thanks a lot... Installing the gsl library correctly? I need to guess quite a bit here (and a clean install attempt would have given a few more clues). I suspect you installed into /usr/local/lib whereas your OS probably uses /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be using lib64 for R). In that case ld.so most likely will not find the dynamic library in /usr/local/lib. You can avoid such problems by installing auxiliary software such as gsl from RPMs -- I would be very surprised if OpenSuse did not have gsl and gsl-devel RPMs. Otherwise you need to install from the sources by something like make install libdir=/usr/local/lib64 R CMD INSTALL gsl * installing to library ‘/usr/lib64/R/library’ * installing *source* package ‘gsl’ ... checking for gsl-config... /usr/local/bin/gsl-config checking if GSL version = 1.12... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed yes configure: creating ./config.status config.status: creating src/Makevars ** libs make: Nothing to be done for `all'. This was not a clean install installing to /usr/lib64/R/library/gsl/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so': libgsl.so.0: cannot open shared object file: No such file or directory ERROR: loading failed * removing ‘/usr/lib64/R/library/gsl’ sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trouble installing gsl wrapper
You nailed it, Prof. Ripley! Thanks a lot... Gang On Sat, Oct 30, 2010 at 2:58 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Sat, 30 Oct 2010, Gang Chen wrote: Hi, I'm trying to install the gsl wrapper source code (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux system (OpenSuse 11.1), but encountering the following problem. I've already installed 'gsl' version 1.14 (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's missing? Thanks a lot... Installing the gsl library correctly? I need to guess quite a bit here (and a clean install attempt would have given a few more clues). I suspect you installed into /usr/local/lib whereas your OS probably uses /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be using lib64 for R). In that case ld.so most likely will not find the dynamic library in /usr/local/lib. You can avoid such problems by installing auxiliary software such as gsl from RPMs -- I would be very surprised if OpenSuse did not have gsl and gsl-devel RPMs. Otherwise you need to install from the sources by something like make install libdir=/usr/local/lib64 R CMD INSTALL gsl * installing to library ‘/usr/lib64/R/library’ * installing *source* package ‘gsl’ ... checking for gsl-config... /usr/local/bin/gsl-config checking if GSL version = 1.12... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed yes configure: creating ./config.status config.status: creating src/Makevars ** libs make: Nothing to be done for `all'. This was not a clean install installing to /usr/lib64/R/library/gsl/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so': libgsl.so.0: cannot open shared object file: No such file or directory ERROR: loading failed * removing ‘/usr/lib64/R/library/gsl’ sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trouble installing gsl wrapper
An interesting exchange. The package has some installation tips in Misc.Rd, but perhaps these are not sufficiently prominent. I think it'd be a good idea to include a READ.ME file in inst/doc with installation information, and include a pointer to this in the DESCRIPTION file; I'll adapt parts of this thread for the next release. Robin On Sat, Oct 30, 2010 at 8:14 AM, Gang Chen gangch...@gmail.com wrote: You nailed it, Prof. Ripley! Thanks a lot... Gang On Sat, Oct 30, 2010 at 2:58 PM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Sat, 30 Oct 2010, Gang Chen wrote: Hi, I'm trying to install the gsl wrapper source code (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux system (OpenSuse 11.1), but encountering the following problem. I've already installed 'gsl' version 1.14 (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's missing? Thanks a lot... Installing the gsl library correctly? I need to guess quite a bit here (and a clean install attempt would have given a few more clues). I suspect you installed into /usr/local/lib whereas your OS probably uses /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be using lib64 for R). In that case ld.so most likely will not find the dynamic library in /usr/local/lib. You can avoid such problems by installing auxiliary software such as gsl from RPMs -- I would be very surprised if OpenSuse did not have gsl and gsl-devel RPMs. Otherwise you need to install from the sources by something like make install libdir=/usr/local/lib64 R CMD INSTALL gsl * installing to library ‘/usr/lib64/R/library’ * installing *source* package ‘gsl’ ... checking for gsl-config... /usr/local/bin/gsl-config checking if GSL version = 1.12... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed yes configure: creating ./config.status config.status: creating src/Makevars ** libs make: Nothing to be done for `all'. This was not a clean install installing to /usr/lib64/R/library/gsl/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so': libgsl.so.0: cannot open shared object file: No such file or directory ERROR: loading failed * removing ‘/usr/lib64/R/library/gsl’ sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 -- Robin Hankin Uncertainty Analyst hankin.ro...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Trouble installing gsl wrapper
Hi, I'm trying to install the gsl wrapper source code (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux system (OpenSuse 11.1), but encountering the following problem. I've already installed 'gsl' version 1.14 (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's missing? Thanks a lot... R CMD INSTALL gsl * installing to library ‘/usr/lib64/R/library’ * installing *source* package ‘gsl’ ... checking for gsl-config... /usr/local/bin/gsl-config checking if GSL version = 1.12... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed yes configure: creating ./config.status config.status: creating src/Makevars ** libs make: Nothing to be done for `all'. installing to /usr/lib64/R/library/gsl/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so': libgsl.so.0: cannot open shared object file: No such file or directory ERROR: loading failed * removing ‘/usr/lib64/R/library/gsl’ sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
