Hi all, I have successfully made and installed both gdal, and proj.4, but still cannot get rgdal to be installed in R. I think i'm very close. I do not have root access, if that matters, i've installed everything locally. I'm using debian on a beowulf cluster. I call: install.packages("rgdal", .libPaths()[1], configure.args "--with-gdal-config=/usr/local/pkg/gdal/bin/gdal-config --with-proj-include=/nfs/user08/bw4sz/include --with-proj-lib=/nfs/user08/bw4sz/lib") i've defeated the gdal-config and the api_proj.h file errors that have plagued others. Now i believe i've run into a smaller problem. The package downloads and installs but it fails the lazy loading test ** 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 '/nfs/user08/bw4sz/library/rgdal/libs/rgdal.so': libgdal.so.1: cannot open shared object file: No such file or directory Error: loading failed with the R.Version()> R.Version()$platform [1] "x86_64-unknown-linux-gnu" $arch [1] "x86_64" $os [1] "linux-gnu" $system [1] "x86_64, linux-gnu" $status [1] "" $major [1] "2" $minor [1] "14.2" $year [1] "2012" $month [1] "02" $day [1] "29" $`svn rev` [1] "58522" $language [1] "R" $version.string [1] "R version 2.14.2 (2012-02-29)" Any thoughts are appreciated, Best, ben please forgive cross-posting on R-sig geo for those who subscribe to both. Ben Weinstein Graduate Student Ecology and Evolution Stony Brook University http://life.bio.sunysb.edu/~bweinste/index.html [[alternative HTML version deleted]]
On 17 October 2012 at 14:19, Ben Weinstein wrote: | Hi all, | | I have successfully made and installed both gdal, and proj.4, but still | cannot get rgdal to be installed in R. I think i'm very close. I do not | have root access, if that matters, i've installed everything locally. I'm | using debian on a beowulf cluster. | | I call: | | install.packages("rgdal", .libPaths()[1], configure.args | "--with-gdal-config=/usr/local/pkg/gdal/bin/gdal-config | --with-proj-include=/nfs/user08/bw4sz/include | --with-proj-lib=/nfs/user08/bw4sz/lib") | | i've defeated the gdal-config and the api_proj.h file errors that have | plagued others. Now i believe i've run into a smaller problem. | | The package downloads and installs but it fails the lazy loading test | | | ** 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 | '/nfs/user08/bw4sz/library/rgdal/libs/rgdal.so': | libgdal.so.1: cannot open shared object file: No such file or directory The dynamic linker thinks there should be a file (or a softlink) resolve libgdal.so.1, yet there is none. You need to address that issue. Dirk | Error: loading failed | | with the R.Version() | | > R.Version() | $platform | [1] "x86_64-unknown-linux-gnu" | | $arch | [1] "x86_64" | | $os | [1] "linux-gnu" | | $system | [1] "x86_64, linux-gnu" | | $status | [1] "" | | $major | [1] "2" | | $minor | [1] "14.2" | | $year | [1] "2012" | | $month | [1] "02" | | $day | [1] "29" | | $`svn rev` | [1] "58522" | | $language | [1] "R" | | $version.string | [1] "R version 2.14.2 (2012-02-29)" | | Any thoughts are appreciated, | | Best, | | ben | | please forgive cross-posting on R-sig geo for those who subscribe to both. | | Ben Weinstein | Graduate Student | Ecology and Evolution | Stony Brook University | | http://life.bio.sunysb.edu/~bweinste/index.html | | [[alternative HTML version deleted]] | | _______________________________________________ | R-SIG-Debian mailing list | R-SIG-Debian at r-project.org | https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
OB On 17 October 2012 at 15:29, Ben Weinstein wrote: | Hi dirk, | | Thanks for your response! I appreciate all help. I can see that the file does | not exist. I'm wondering on what level this error is?occurring? with the | rgdal package, with the gdal source or with the proj source. I believe it is | the rgdal package. Are you familiar with this package, perhaps there is a | stable version that i should find. I was able to overcome the other errors, but | as you note the error simply notifies me that a file does not exist. I am not really familiar with gdal and the spatial stack, but as this has come before, I did in fact verify at some point or other that the packages "just build" in my (fairly standard Ubuntu / Debian) environment. Which they do -- as CRAN tests (among other systems) on a stock Debian testing too. Now, on my box, I have edd at max:~$ ls -l /usr/lib/libgdal* -rw-r--r-- 1 root root 17832142 Nov 24 2011 /usr/lib/libgdal1.7.0.a lrwxrwxrwx 1 root root 22 Nov 24 2011 /usr/lib/libgdal1.7.0.so -> libgdal1.7.0.so.1.14.3 lrwxrwxrwx 1 root root 22 Nov 24 2011 /usr/lib/libgdal1.7.0.so.1 -> libgdal1.7.0.so.1.14.3 -rw-r--r-- 1 root root 8148488 Nov 24 2011 /usr/lib/libgdal1.7.0.so.1.14.3 edd at max:~$ And the soft link with the trailing .1 and .1.14.3 are typically added by the package management system when the -dev package is installed. Your situation is a little different as you have local libraries. To that extent, the list is not really a good source of help for your non-standard problem. Dirk | Thanks again for your help, | | Ben | | | On Wed, Oct 17, 2012 at 3:14 PM, Dirk Eddelbuettel <edd at debian.org> wrote: | | | On 17 October 2012 at 14:19, Ben Weinstein wrote: | | Hi all, | | | | I have successfully made and installed both gdal, and proj.4, but still | | cannot get rgdal to be installed in R. I think i'm very close. I do not | | have root access, if that matters, i've installed everything locally. I'm | | using debian on a beowulf cluster. | | | | I call: | | | | install.packages("rgdal", .libPaths()[1], configure.args | | "--with-gdal-config=/usr/local/pkg/gdal/bin/gdal-config | | --with-proj-include=/nfs/user08/bw4sz/include | | --with-proj-lib=/nfs/user08/bw4sz/lib") | | | | i've defeated the gdal-config and the api_proj.h file errors that have | | plagued others. Now i believe i've run into a smaller problem. | | | | The package downloads and installs but it fails the lazy loading test | | | | | | ** 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 | | '/nfs/user08/bw4sz/library/rgdal/libs/rgdal.so': | | ? libgdal.so.1: cannot open shared object file: No such file or | directory | | The dynamic linker thinks there should be a file (or a softlink) resolve | libgdal.so.1, yet there is none. | | You need to address that issue. | | Dirk | | | Error: loading failed | | | | with the R.Version() | | | | > R.Version() | | $platform | | [1] "x86_64-unknown-linux-gnu" | | | | $arch | | [1] "x86_64" | | | | $os | | [1] "linux-gnu" | | | | $system | | [1] "x86_64, linux-gnu" | | | | $status | | [1] "" | | | | $major | | [1] "2" | | | | $minor | | [1] "14.2" | | | | $year | | [1] "2012" | | | | $month | | [1] "02" | | | | $day | | [1] "29" | | | | $`svn rev` | | [1] "58522" | | | | $language | | [1] "R" | | | | $version.string | | [1] "R version 2.14.2 (2012-02-29)" | | | | Any thoughts are appreciated, | | | | Best, | | | | ben | | | | please forgive cross-posting on R-sig geo for those who subscribe to | both. | | | | Ben Weinstein | | Graduate Student | | Ecology and Evolution | | Stony Brook University | | | | http://life.bio.sunysb.edu/~bweinste/index.html | | | | ? ? ? [[alternative HTML version deleted]] | | | | _______________________________________________ | | R-SIG-Debian mailing list | | R-SIG-Debian at r-project.org | | https://stat.ethz.ch/mailman/listinfo/r-sig-debian | | -- | Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com | | | | | -- | Ben Weinstein | Graduate Student | Ecology and Evolution | Stony Brook University | | http://life.bio.sunysb.edu/~bweinste/index.html | -- Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
Greetings On Wed, Oct 17, 2012 at 1:19 PM, Ben Weinstein <benweinstein2010 at gmail.com> wrote:> Hi all, > > I have successfully made and installed both gdal, and proj.4, but still > cannot get rgdal to be installed in R. I think i'm very close. I do not > have root access, if that matters, i've installed everything locally. I'm > using debian on a beowulf cluster. > > I call: > > install.packages("rgdal", .libPaths()[1], configure.args > "--with-gdal-config=/usr/local/pkg/gdal/bin/gdal-config > --with-proj-include=/nfs/user08/bw4sz/include > --with-proj-lib=/nfs/user08/bw4sz/lib") > > i've defeated the gdal-config and the api_proj.h file errors that have > plagued others. Now i believe i've run into a smaller problem. > > The package downloads and installs but it fails the lazy loading test >Suppose before you try the build, you add that "libs" directory to the dynamic linker path, such as export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/nfs/user08/bw4sz/library/rgdal/libs/rgdal.so Then try the build. If that works, then you have a sortof classic "user in a Unix environment" problem. Either you need a system administrator to install that library and the devel stuff for it in the usual places, or you need to do some work to add the libs folder to your LD_LIBRARY_PATH. What do you think? pj> > ** 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 > '/nfs/user08/bw4sz/library/rgdal/libs/rgdal.so': > libgdal.so.1: cannot open shared object file: No such file or directory > Error: loading failed > > with the R.Version() > >> R.Version() > $platform > [1] "x86_64-unknown-linux-gnu" > > $arch > [1] "x86_64" > > $os > [1] "linux-gnu" > > $system > [1] "x86_64, linux-gnu" > > $status > [1] "" > > $major > [1] "2" > > $minor > [1] "14.2" > > $year > [1] "2012" > > $month > [1] "02" > > $day > [1] "29" > > $`svn rev` > [1] "58522" > > $language > [1] "R" > > $version.string > [1] "R version 2.14.2 (2012-02-29)" > > Any thoughts are appreciated, > > Best, > > ben > > please forgive cross-posting on R-sig geo for those who subscribe to both. > > Ben Weinstein > Graduate Student > Ecology and Evolution > Stony Brook University > > http://life.bio.sunysb.edu/~bweinste/index.html > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian-- Paul E. Johnson Professor, Political Science Assoc. Director 1541 Lilac Lane, Room 504 Center for Research Methods University of Kansas University of Kansas http://pj.freefaculty.org http://quant.ku.edu