我尝试安装rgdal但configure.args没有运气。
安装的gdal版本：
gdal-config --version
1.11.2
ogrinfo --version
GDAL 1.11.2, released 2015/02/10
找到 gdal 二进制工具：
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
找到 proj 头文件：
ls /usr/include | grep proj
libprojectM
libprojectM-qt
org_proj4_Projections.h
proj_api.h
projects.h
找到 proj lib 文件：
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
关于 gdal 的安装包：
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
编辑：我试过 install.packages('rgdal') 没有任何 configure.args。我得到了同样的错误。现在，我正在尝试使用已编译的 proj4 4.9.1 安装 rgdal，并将 LD_LIBRARY_PATH 导出到 proj4 4.9.1。不幸的是，它又失败了。这是我的新 script.sh：
export LD_LIBRARY_PATH=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/lib:/usr/lib:$LD_LIBRARY_PATH
sudo R CMD REMOVE rgdal
R CMD INSTALL rgdal_0.9-2.tar.gz --byte-compile --configure-args='--with-gdal-config=/usr/bin/gdal-config --with-proj-lib=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/lib --with-proj-include=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/include --with-proj-share=/home/wangchl/R-scripting/R-install/proj-4.9.1/ccc/share/proj'
一切都很好，但测试时失败：
installing to /home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs/rgdal.so':
/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/wangchl/R/x86_64-pc-linux-gnu-library/3.2/rgdal’
更新：最后，我解决了这个问题。首先，通过 apt-get 删除 proj4-4.8。
sudo apt-get remove libproj-dev
其次，将我编译好的proj4-4.9 lib路径添加到'/etc/ld.so.conf.d/'路径下的一个新的conf文件（如rgdal.conf）中。
cd /etc/ld.so.conf.d
sudo touch rgdal.conf
echo 'the lib path of proj4-4.9' | sudo tee -a rgdal.conf
然后，使用 configure.args 安装 rgdal，引用 proj4-4.9 的编译 lib 路径。
export LD_LIBRARY_PATH=the lib path of proj4-4.9:$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'
现在，一切都很好。但是我无法使用 proj4-4.8 和默认的 configure.args 安装任何版本的 rgdal。我已经按照@Pascal 的建议清理了 proj4 的文件。所以我不确定这个问题的确切原因。