On Sun, 16 Jan 2011, alessandro.sarre...@inwind.it wrote:
Dear R experts,
I'm trying to install rgdal in my R 2.11.1 (Ubuntu 10.10).
I have as an ouput the following messages. It seems that there are problems
with libgdal1.7.0 or sqlite3...
Could someboby help me?
You would do better to ask on R-sig-geo for this particular package,
and ask the maintainer or on R-devel more generally about installing
source packages (see the posting guide). But
- Your R is need of updating (see the posting guide)
- GDAL 1.7.0 is really rather old
- The bug seems to be in your libgdal installation: if libgdal was
compiled with sqlite support, libgdal.so should be linked to
libsqlite3. Do you have sqlite3 installed (not the RSQLite package,
but the uduntu package)? If not, please install it. You can check
for missing dependencies by (in the terminal)
ldd /usr/lib/libgdal.so
If 'libsqlite3.so.0' is not there, you need to modify rgdal (I know,
because you need to do similar things with a static libgdal). On my
Mac I need to alter rgdal/src/Makevars.in to be
PKG_LIBS=@PKG_LIBS@ -lproj -lsqlite3 -lexpat -ltiff -ljpeg -lpng -lz -ldl
-lcurl -lssl -lcrypto -lz
and so I guess you need at least
PKG_LIBS=@PKG_LIBS@ -lsqlite3
But because GDAL can be installed with lots of optional facilities
(one of which is sqlite3), you may need to ask Ubuntu support for
exactly what is needed to link against their build. Or compile
current GDAL from the sources for yourself.
Thanks a lot!
Ale
install.packages()
Warning in install.packages() :
argument 'lib' is missing: using '/home/ale/R/i686-pc-linux-gnu-library/2.
11'
trying URL 'http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/RSQLite_0.9-4.
tar.gz'
Content type 'application/x-gzip' length 1298948 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb
* installing *source* package ‘RSQLite’ ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
checking for library containing fdatasync... none required
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -
DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c RS-DBI.c -o RS-DBI.o
gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -
DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c RS-SQLite.c -o RS-SQLite.o
gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -
DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c param_binding.c -o
param_binding.o
gcc -std=gnu99 -I/usr/share/R/include -DRSQLITE_USE_BUNDLED_SQLITE -
DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -
DSQLITE_SOUNDEX -DTHREADSAFE=0 -fpic -g -O2 -c sqlite-all.c -o sqlite-all.
o
sqlite-all.c:1: warning: extra tokens at end of #ifdef directive
mkdir -p ../inst/include
cp sqlite/sqlite3.h ../inst/include
cp sqlite/sqlite3ext.h ../inst/include
gcc -std=gnu99 -shared -o RSQLite.so RS-DBI.o RS-SQLite.o param_binding.o
sqlite-all.o -L/usr/lib/R/lib -lR
installing to /home/ale/R/i686-pc-linux-gnu-library/2.11/RSQLite/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (RSQLite)
The downloaded packages are in
‘/tmp/RtmprTwixW/downloaded_packages’
install.packages()
Warning in install.packages() :
argument 'lib' is missing: using '/home/ale/R/i686-pc-linux-gnu-library/2.
11'
trying URL 'http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/rgdal_0.6-33.tar.
gz'
Content type 'application/x-gzip' length 1422992 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb
* installing *source* package ‘rgdal’ ...
gdal-config: gdal-config
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... yes
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_int'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_double'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_text'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_double'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_blob'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_step'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_get_table'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_open'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free_table'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_bytes'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_blob'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_last_insert_rowid'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_name'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_int'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_finalize'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_text'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_count'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_decltype'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_type'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_errmsg'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free'
collect2: ld returned 1 exit status
./configure: line 3065: ./proj_conf_test: No such file or directory
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_int'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_double'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_exec'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_text'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_double'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_blob'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_step'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_get_table'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_open'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free_table'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_reset'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_bytes'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_blob'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_last_insert_rowid'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_name'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_prepare'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_int'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_finalize'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_bind_text'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_count'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_close'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_decltype'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_column_type'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_errmsg'
/usr/lib/libgdal1.7.0.so: undefined reference to `sqlite3_free'
collect2: ld returned 1 exit status
./configure: line 3099: ./proj_conf_test: No such file or directory
Package CPP flags: -I/usr/include/gdal
Package LIBS: -L/usr/lib -lgdal1.7.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c OGR_write.cpp -o OGR_write.o
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c gdal-bindings.cpp -o gdal-
bindings.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-
pc-linux-gnu-library/2.11/sp/include" -fpic -g -O2 -c local_stubs.c -o
local_stubs.o
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_geom.cpp -o ogr_geom.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-
pc-linux-gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_polygons.c -o
ogr_polygons.o
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c ogr_proj.cpp -o ogr_proj.o
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c ogrsource.cpp -o ogrsource.o
g++ -I/usr/share/R/include -I/usr/include/gdal -I"/home/ale/R/i686-pc-linux-
gnu-library/2.11/sp/include" -fpic -g -O2 -c projectit.cpp -o projectit.o
g++ -shared -o rgdal.so OGR_write.o gdal-bindings.o local_stubs.o ogr_geom.o
ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib -
lgdal1.7.0 -lproj -L/usr/lib/R/lib -lR
installing to /home/ale/R/i686-pc-linux-gnu-library/2.11/rgdal/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 library '/home/ale/R/i686-pc-linux-gnu-library/2.
11/rgdal/libs/rgdal.so':
/usr/lib/libgdal1.7.0.so.1: undefined symbol: sqlite3_bind_int
ERROR: loading failed
* removing ‘/home/ale/R/i686-pc-linux-gnu-library/2.11/rgdal’
The downloaded packages are in
‘/tmp/RtmprTwixW/downloaded_packages’
Warning message:
In install.packages() :
installation of package 'rgdal' had non-zero exit status
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--
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)
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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
