[R-sig-Geo] RGDAL installation fail after yum upgrade
D@vid@GIOVANNINI m@ili@g off ext@ec@europ@@eu
D@vid@GIOVANNINI m@ili@g off ext@ec@europ@@eu
Fri Sep 21 11:52:19 CEST 2018
Dear list members,
I'm tring to install RGDAL on a cluster, but after the update of R packages seems not possible to install it.
Below the error message:
> install.packages("rgdal")
Installing package into '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5'
(as 'lib' is unspecified)
trying URL 'https://cran.stat.unipd.it/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/octet-stream' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package 'rgdal' ...
** package 'rgdal' successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib64/R
configure: CC: gcc -m64 -std=gnu99
configure: CXX: g++ -m64
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.11.4
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
checking proj_api.h presence and usability... yes
./configure: line 2126: test: =: unary operator expected
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
/tmp/ccnBOZCl.o: In function `main':
/tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test2.c:20: undefined reference to `pj_ctx_fclose'
collect2: error: ld returned 1 exit status
./configure: line 2242: ./proj_conf_test2: No such file or directory
checking PROJ.4: epsg found and readable... yes
/tmp/ccu3xNdp.o: In function `main':
/tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test3.c:20: undefined reference to `pj_ctx_fclose'
collect2: error: ld returned 1 exit status
./configure: line 2301: ./proj_conf_test3: No such file or directory
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags: -I/usr/include/gdal
configure: Package LIBS: -L/usr/lib64 -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c inverser.c -o inverser.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c local_stubs.c -o local_stubs.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ogr_geom.cpp -o ogr_geom.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ogr_polygons.c -o ogr_polygons.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ogr_proj.cpp -o ogr_proj.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ogrdrivers.cpp -o ogrdrivers.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ogrsource.cpp -o ogrsource.o
ogrsource.cpp: In function 'SEXPREC* ogrReadListColumn(OGRLayer*, SEXP, int, int, int)':
ogrsource.cpp:651:12: warning: unused variable 'DINT_MAX' [-Wunused-variable]
double DINT_MAX = 2251799813685248.0;
^
ogrsource.cpp:652:12: warning: unused variable 'DINT_MIN' [-Wunused-variable]
double DINT_MIN = -2251799813685248.0;
^
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c projectit.cpp -o projectit.o
g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib64 -lgdal -lproj -L/usr/lib64/R/lib -lR
installing to /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rgdal'
finding HTML links ... done
CRS-class html
GDALDataset-class html
GDALDriver-class html
GDALMajorObject-class html
GDALRasterBand-class html
GDALReadOnlyDataset-class html
GDALReadOnlyDataset-methods html
GDALTransientDataset-class html
GridsDatums html
RGB2PCT html
SGDF2PCT html
SpatialGDAL-class html
closeDataset-methods html
displayDataset html
llgrid html
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:11: file link 'Spatial' in package 'sp' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:16: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:17: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
make_EPSG html
nor2k html
projInfo html
project html
readGDAL html
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/readGDAL.Rd:136: file link 'flipVertical' in package 'sp' does not exist and so has been treated as a topic
readOGR html
showWKT html
spTransform-methods html
wrappers html
writeOGR html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so':
/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal'
The downloaded source packages are in
'/tmp/RtmpXrQsj2/downloaded_packages'
Warning message:
In install.packages("rgdal") :
installation of package 'rgdal' had non-zero exit status
I have tried several solutions but without any success.
Have you any idea about the problem?
Thanks in advance
David
[[alternative HTML version deleted]]
More information about the R-sig-Geo
mailing list