I tried installing rgdal with configure.args but no luck.
Installed gdal version:
gdal-config
gdal binary tools found:
ls /usr/bin | grep gdal gdal2tiles.py gdal2xyz.py gdaladdo gdal_auth.py gdalbuildvrt gdal_calc.py gdalchksum.py gdalcompare.py gdal-config gdal_contour gdaldem gdal_edit.py gdalenhance gdal_fillnodata.py gdal_grid gdalident.py gdalimport.py gdalinfo gdallocationinfo gdalmanage gdal_merge.py gdalmove.py gdal_polygonize.py gdal_proximity.py gdal_rasterize gdal_retile.py gdalserver gdal_sieve.py gdalsrsinfo gdaltindex gdaltransform gdal_translate gdalwarp
found proj header files:
ls /usr/include | grep proj libprojectM libprojectM-qt org_proj4_Projections.h proj_api.h projects.h
found proj lib files:
ls /usr/lib | grep proj libproj.a libprojectM-qt.so libprojectM-qt.so.1 libprojectM-qt.so.1.10 libprojectM.so libprojectM.so.2 libprojectM.so.2.1.0 libproj.la libproj.so libproj.so.0 libproj.so.0.7.0
Installed packages about gdal:
dpkg -l | grep gdal ii gdal-bin 1.11.2+dfsg-1~exp2~trusty amd64 Geospatial Data Abstraction Library - Utility programs ii libgdal-dev 1.11.2+dfsg-1~exp2~trusty amd64 Geospatial Data Abstraction Library - Development files ii libgdal1-dev 1.11.2+dfsg-1~exp2~trusty all Geospatial Data Abstraction Library - Transitional package ii libgdal1h 1.11.2+dfsg-1~exp2~trusty amd64 Geospatial Data Abstraction Library ii python-gdal 1.11.2+dfsg-1~exp2~trusty amd64 Python bindings to the Geospatial Data Abstraction Library dpkg -l | grep proj ii libgeo-proj4-perl 1.05-1 amd64 PROJ.4 library for cartographic projections ii libproj-dev 4.8.0-2ubuntu2 amd64 Cartographic projection library (development files) ii libproj0 4.8.0-2ubuntu2 amd64 Cartographic projection library ii libprojectm-dev 2.1.0+dfsg-1build2 amd64 Advanced Milkdrop-compatible music visualization library - dev ii libprojectm-qt-dev 2.1.0+dfsg-1build2 amd64 projectM Qt4 (development files) ii libprojectm-qt1 2.1.0+dfsg-1build2 amd64 projectM Qt4 bindings ii libprojectm2 2.1.0+dfsg-1build2 amd64 Advanced Milkdrop-compatible music visualization library ii proj-bin 4.8.0-2ubuntu2 amd64 Cartographic projection library (tools) ii proj-data 4.8.0-2ubuntu2 amd64 Cartographic projection filter and library (datum package) ii projectm-data 2.1.0+dfsg-1build2 all Advanced Milkdrop-compatible music visualization library - data ii xfwm4 4.11.1-2ubuntu2 amd64 window manager of the Xfce project install.packages('rgdal',type='source', configure.args = paste('--with-gdal-config=/usr/bin/gdal-config', '--with-proj-lib=/usr/lib', '--with-proj-include=/usr/include') ) Installing package into '/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2' (as 'lib' is unspecified) trying URL 'http://mirrors.ustc.edu.cn/CRAN/src/contrib/rgdal_0.9-2.tar.gz' Content type 'application/gzip' length 1627386 bytes (1.6 MB) ================================================== downloaded 1.6 MB * installing *source* package 'rgdal' ... ** package 'rgdal' successfully unpacked and MD5 sums checked configure: CC: gcc -std=gnu99 configure: CXX: g++ configure: rgdal: 0.9-2 checking for /usr/bin/svnversion... no configure: svn revision: 526 configure: gdal-config set to /usr/bin/gdal-config checking gdal-config exists... yes checking gdal-config executable... yes checking gdal-config usability... yes configure: GDAL: 1.11.2 checking GDAL version >= 1.6.3... yes checking GDAL version < 2... yes checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 grep that handles long lines and -e... /bin/grep checking for egrep... /bin/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 gdal.h usability... yes checking gdal.h presence... yes checking for gdal.h... yes checking gdal: linking with --libs only... yes checking GDAL: /usr/share/gdal/1.11/pcs.csv readable... 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 configure: PROJ.4 version: > 4.8.0 /tmp/ccsGVxP9.o: In function `main': /tmp/RtmpOqwz92/R.INSTALL23317ae38fc4/rgdal/proj_conf_test.c:20: undefined reference to `pj_ctx_fclose' collect2: error: ld returned 1 exit status ./configure: line 3735: ./proj_conf_test: No such file or directory checking PROJ.4: epsg found and readable... yes /tmp/ccaNfCUo.o: In function `main': /tmp/RtmpOqwz92/R.INSTALL23317ae38fc4/rgdal/proj_conf_test.c:20: undefined reference to `pj_ctx_fclose' collect2: error: ld returned 1 exit status ./configure: line 3810: ./proj_conf_test: No such file or directory checking PROJ.4: conus found and readable... yes configure: Package CPP flags: -I/usr/include/gdal -I/usr/include configure: Package LIBS: -L/usr/lib -lgdal -L/usr/lib -lproj configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c OGR_write.cpp -o OGR_write.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c gdal-bindings.cpp -o gdal-bindings.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c local_stubs.c -o local_stubs.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogr_geom.cpp -o ogr_geom.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogr_polygons.c -o ogr_polygons.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogr_proj.cpp -o ogr_proj.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogrdrivers.cpp -o ogrdrivers.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogrsource.cpp -o ogrsource.o g++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/sp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c projectit.cpp -o projectit.o g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib -lgdal -L/usr/lib -lproj -L/usr/lib/R/lib -lR installing to /home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs/rgdal.so': /home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets Error: loading failed Execution halted ERROR: loading failed * removing '/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal' Warning in install.packages : installation of package 'rgdal' had non-zero exit status
EDIT: I tried install.packages ('rgdal') without any configure.args. I have the same error. Now I am trying to install rgdal with compiled proj4 4.9.1 and export LD_LIBRARY_PATH to proj4 4.9.1. Unfortunately, he again failed. Here is my new script.sh:
export LD_LIBRARY_PATH=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/lib:/usr/lib:$LD_LIBRARY_PATH sudo R CMD REMOVE rgdal R CMD INSTALL rgdal_0.9-2.tar.gz --byte-compile --configure-args='--with-gdal-config=/usr/bin/gdal-config --with-proj-lib=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/lib --with-proj-include=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/include --with-proj-share=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/share/proj'
All is well, but failed during testing:
installing to /home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs/rgdal.so': /home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets Error: loading failed Execution halted ERROR: loading failed * removing '/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal'
Update : Finally, I reviewed this question. Firstly, uninstalling proj4-4.8 using apt-get.
sudo apt-get remove libproj-dev
Secondly, adding my compiled path proj4-4.9 lib to a new conf file (e.g. rgdal.conf) along the path '/etc/ld.so.conf.d/'.
cd /etc/ld.so.conf.d sudo touch rgdal.conf echo 'the lib path of proj4-4.9' | sudo tee -a rgdal.conf
And then by installing rgdal with configure.args, referring to the compiled lib proj4-4.9 path.
export LD_LIBRARY_PATH=the lib path of proj4-4.9:$LD_LIBRARY_PATH sudo R CMD REMOVE rgdal R CMD INSTALL rgdal_0.9-2.tar.gz --byte-compile --configure-args='--with-gdal-config=/usr/bin/gdal-config --with-proj-lib=compiled path of proj4-4.9/lib --with-proj-include=compiled path of proj4-4.9/include --with-proj-share=compiled path of proj4-4.9/share/proj'
Now everything is all right. But I was not able to install any version of rgdal with proj4-4.8 and default configure.args. I already cleared the proj4 files as suggested by @Pascal. Therefore, I do not quite know this problem.