[R-sig-Debian] Install rgdal, lazy loading error

[Dirk Eddelbuettel]

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]]
|     |
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|    
|     --
|     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