[R-sig-Debian] problems building and installing some packages in 'unstable'

[Sebastian P. Luque]

On Sun, 27 Jan 2008 11:44:47 -0600,
"Douglas Bates" <bates at stat.wisc.edu> wrote:

> Check if the file $R_HOME/lib/libRblas.so exists. If so, use

> ldd $R_HOME/lib/libRblas.so

libRblas.so doesn't exist at all in my system, and cross-checking with
Dirk, that seems to be ok in AMD64:

http://buildd.debian.org/fetch.cgi?&pkg=r-base&ver=2.6.1-2&arch=amd64&stamp=1200915120&file=log


> to see what further shared objects it needs.

> Then check

> ldd $R_HOME/library/KernSmooth/libs/KernSmooth.so

> It probably has a reference to libRblas.so that is unresolved when you
> check outside of R.

Yes, that's definitely a problem:

,-----[ ldd /usr/lib/R/library/KernSmooth/libs/KernSmooth.so ]
| 	linux-vdso.so.1 =>  (0x00007fff461fd000)
| 	libRblas.so => not found
| 	libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00002b4e64b01000)
| 	libm.so.6 => /lib/libm.so.6 (0x00002b4e64dbd000)
| 	libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002b4e6503e000)
| 	libR.so => /usr/lib/R/lib/libR.so (0x00002b4e65255000)
| 	libc.so.6 => /lib/libc.so.6 (0x00002b4e6575c000)
| 	libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00002b4e65aba000)
| 	libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00002b4e65d49000)
| 	libreadline.so.5 => /lib/libreadline.so.5 (0x00002b4e6601a000)
| 	libpcre.so.3 => /usr/lib/libpcre.so.3 (0x00002b4e66259000)
| 	libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00002b4e6647f000)
| 	libz.so.1 => /usr/lib/libz.so.1 (0x00002b4e66690000)
| 	libdl.so.2 => /lib/libdl.so.2 (0x00002b4e668a7000)
| 	/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
| 	libncurses.so.5 => /lib/libncurses.so.5 (0x00002b4e66aab000)
`-----



> Part of the R startup adds $R_HOME/lib to the LD_LIBRARY_PATH (see the
> shell script $R_HOME/etc/ldpaths or $R_HOME/etc${ARCH}/ldpaths)


Checking on that:

,-----[ ldpaths ]
| : ${JAVA_HOME=}
| : ${R_JAVA_LD_LIBRARY_PATH=}
| : ${R_LD_LIBRARY_PATH=${R_HOME}/lib:/usr/lib/gcc/x86_64-linux-gnu/4.3}
| if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
|   R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
| fi
| if test -z "${LD_LIBRARY_PATH}"; then
|   LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
| else
|   LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
| fi
| export LD_LIBRARY_PATH
`-----

Dirk just hinted to me that my installing mingw32 may have ruined my
building environment variables and other evils.  Can you guys suggest
what to check for?  Thanks for the input!


-- 
Seb