Question

我試圖用命令

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/') 

我的筆記本電腦（Ubuntu的12.04）安裝RNetCDF包，但包不會安裝。請參閱下面的消息：

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 

當我試着使用

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 

錯誤信息被替換

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絕對是/home/my_computer/local/lib/這也是我LD_LIBRARY_PATH 。無可否認，libexpat.so.0是第一個錯誤信息（與install.packages）中的文件之一，位於intel相關文件夾中，看起來與netcdf庫無關。

任何人都可以啓發我嗎？

謝謝。

編輯：好吧，我永遠不會知道發生了什麼事，因爲當我在3天后再次嘗試使用完全相同的install.packages命令行時，安裝的軟件包沒有任何問題......因此，對於可能擁有同樣的問題是註銷R並重新開始，以防萬一在會話中以前的錯誤留在日誌中。

Answer 1

嘗試將--no-test-load添加到R CMD INSTALL，這樣可以避免安裝過程中的錯誤。

然後檢查是否可以在正常的R會話中加載軟件包（使用library(RNetCDF)）。 如果失敗是由於「無法加載共享對象」錯誤：如果R使用您的$ LD_LIBRARY_PATH與Sys.getenv("LD_LIBRARY_PATH")

看的ldd /usr/local/lib/R/site-library/RNetCDF/libs/RNetCDF.so輸出，看看libnetcdf.so.7是否解決

1. 檢查到R中所含的LD_LIBRARY_PATH

BTW路徑，我沒有問題，使用附帶的Ubuntu的安裝libnetcdf RNetCDF（易於得到安裝libnetcdf-dev的[4.1.1]）;除非你確實需要libnetcdf的4.2版本，否則你可能想試試這個。