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