我正在尝试使用以下命令在笔记本电脑(Ubuntu 12.04)上安装RNetCDF软件包
install.packages('RNetCDF',lib='/home/my_computer/RSCRIPTS/R_LIB/',configure.args="--with-netcdf-include='/home/my_computer/bin/libs4cdo-0.0.10/netcdf-4.2/include/' --with-netcdf-lib='/home/my_computer/local/bin' --with-hdf5-lib='/home/my_computer/local/lib/' --with-udunits-include='/usr/local/lib/' --with-udunits-lib='/usr/local/lib/'",repos='http://star-www.st-andrews.ac.uk/cran/')
但该软件包无法安装。请参阅以下消息:
trying URL 'http://star-www.st-andrews.ac.uk/cran/src/contrib/RNetCDF_1.6.1-2.tar.gz'
Content type 'application/x-gzip' length 70301 bytes (68 Kb)
opened URL
==================================================
downloaded 68 Kb
* installing *source* package ‘RNetCDF’ ...
** package ‘RNetCDF’ successfully unpacked and MD5 sums checked
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 for nc_open in -lnetcdf... yes
checking for utInit in -ludunits2... no
checking for utScan in -ludunits2... yes
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 netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking udunits.h usability... yes
checking udunits.h presence... yes
checking for udunits.h... yes
configure: creating ./config.status
config.status: creating R/load.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -I/usr/local/lib/ -I/home/bauduinm/bin/libs4cdo-0.0.10/netcdf-4.2/include/ -fpic -O3 -pipe -g -c RNetCDF.c -o RNetCDF.o
gcc -std=gnu99 -shared -o RNetCDF.so RNetCDF.o -ludunits2 -lnetcdf -L/home/my_computer/local/lib/ -L/usr/local/lib/ -L/home/my_computer/local/bin -lexpat -L/usr/lib/R/lib -lR
installing to /home/my_computer/RSCRIPTS/R_LIB/RNetCDF/libs
** R
** 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 '/home/my_computer/RSCRIPTS/R_LIB/RNetCDF /libs/RNetCDF.so':
libexpat.so.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/my_computer/RSCRIPTS/R_LIB/RNetCDF’
The downloaded packages are in
‘/tmp/Rtmpl5MniY/downloaded_packages’
Warning message:
In install.packages("RNetCDF", lib = "/home/my_computer/RSCRIPTS/R_LIB/", :
installation of package ‘RNetCDF’ had non-zero exit status
当我尝试
sudo R CMD INSTALL --libary='/home/my_computer/RSCRIPTS/R_LIB/' --configure-args="--with-netcdf-include='/home/my_computer/bin/libs4cdo-0.0.10/netcdf-4.2/include/' --with-netcdf-lib='/home/my_computer/local/lib/' --with-hdf5-lib='/home/my_computer/local/lib/' --with-udunits-include=/usr/local/lib/ --with-udunits-lib=/usr/local/lib/" /home/my_computer/Downloads/RNetCDF_1.6.1-2.tar.gz
错误消息被替换为
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/RNetCDF/libs/RNetCDF.so':
libnetcdf.so.7: cannot open shared object file: No such file or directory
libnetcdf.so.7肯定在
/home/my_computer/local/lib/中，这也是我的LD_LIBRARY_PATH。可以肯定的是，libexpat.so.0是第一个错误消息(带有install.packages)中的文件之一，位于与intel相关的文件夹中，这些文件夹看起来与netcdf库没有任何关系。谁能启发我？
谢谢。
编辑:好吧，我永远不会知道发生了什么，因为三天后当我再次尝试使用完全相同的
install.packages命令行安装了该软件包时，没有任何问题...所以我对可能存在相同问题的人的唯一建议是注销R并重新开始，以防万一之前 session 中的某些错误仍保留在日志中。 最佳答案
尝试将--no-test-load添加到R CMD INSTALL，这将避免安装过程中的错误。
然后检查是否可以在正常的R session 中加载软件包(使用library(RNetCDF))。
如果由于“无法加载共享对象”错误而失败:
Sys.getenv("LD_LIBRARY_PATH")一起使用ldd /usr/local/lib/R/site-library/RNetCDF/libs/RNetCDF.so的输出，并查看libnetcdf.so.7是否已解析为R的LD_LIBRARY_PATH 顺便说一句，我使用Ubuntu随附的libnetcdf安装RNetCDF没问题(apt-get install libnetcdf-dev [版本4.1.1])；除非您确实需要libnetcdf 4.2版本，否则您可能要尝试一下。
关于RNetCDF无法打开共享库文件，我们在Stack Overflow上找到一个类似的问题：https://stackoverflow.com/questions/16487113/