尝试在 Linux 上的 R 中安装 rgdal 包的问题

Question

I am trying to install the R (R version 3.2.4 Revised) package 'rgdal' onto my Linux, Ubuntu 14.04, but the package is having difficulties when it tries to load dependencies, specifically sqlite.

The error is as follows:

checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
/usr/lib/libgdal.so: undefined reference to `sqlite3_column_table_name'
collect2: error: ld returned 1 exit status

I updated GDAL/OGR per the instructions here , because I thought that may be the issue. Now when I type gdalinfo or ogrinfo into the terminal a similar error appears:

gdalinfo: symbol lookup error: /usr/lib/libgdal.so.1: undefined 
symbol: sqlite3_column_table_name

When I look in my usr/local/lib the following sqlite libraries are present:

libsqlite3.a libsqlite3.la libsqlite3.so libsqlite3.so.0   
libsqlite3.so.0.8.6

The funny thing is that this package was working fine in R last week and now is broken...

Any help appreciated! Thanks.

-Caitlin

Answer 1

Stumbled across this error when I was trying to upgrade GDAL. The fix was to ENABLE_COLUMN_METADATA when I was configuring sqlite for install with

sudo CFLAGS="-DSQLITE_ENABLE_COLUMN_METADATA=1" ./configure

See the sqlite Compile-time options for more details

Answer 2

Sounds like a problem with that shared library, have install/update anything in your system without using your Package Manager? (I believe its apt?)

The libgdal.so.1 in your system was compiled against some version of the libsqlite libraries, which now after you updated something else, have changed but libgdal is still the same file.

I have never used Ubuntu, but in the Linux i use (arch) this is the reason partial updates are discouraged (like updating only one program, for example)

So I would recommend to try a full system update, or at least update the sqllite libraries.