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Problems installing CDO on RHEL 5.4, even libs4cd0

Added by roberto jarawan over 12 years ago

During the make process after awhile it clunks out with this:

make2: Entering directory `/cdo-1.5.2/cdo-1.5.2/libcdi/app'
/bin/sh ../libtool --tag=CC --mode=link gcc -std=gnu99 -g -O2 -pthread -o cdi cdi.o ../src/libcdi.la -lz -lm -lz -lm
../libtool: eval: line 6446: unexpected EOF while looking for matching `"'
../libtool: eval: line 6447: syntax error: unexpected end of file
libtool: link: gcc -std=gnu99 -g -O2 -pthread -o cdi cdi.o ../src/.libs/libcdi.a -lz -lm -pthread
../src/.libs/libcdi.a(cdi_error.o): In function `__strcspn_c1':
/usr/include/bits/string2.h:974: multiple definition of `__strcspn_c1'
cdi.o:/usr/include/bits/string2.h:974: first defined here
../src/.libs/libcdi.a(cdi_error.o): In function `__strcspn_c2':
/usr/include/bits/string2.h:985: multiple definition of `__strcspn_c2'

(continued in full_make_error.txt)

I'm kind of starting to lose my mind, I already have netcdf4.1.1 on my system but without hdf5, I got to the point of starting from scratch in another dir and trying out libs4cdo but during the make of hdf5 it fails as well..

libs4cdo error:

H5Ztrans.c:(.text+0x6e00): multiple definition of `mknod'
.libs/H5.o:H5.c:(.text+0x10a0): first defined here
.libs/H5Ztrans.o: In function `stat64':
H5Ztrans.c:(.text+0x6e20): multiple definition of `stat64'
.libs/H5.o:H5.c:(.text+0x10c0): first defined here
.libs/H5Ztrans.o: In function `lstat64':
H5Ztrans.c:(.text+0x6e30): multiple definition of `lstat64'
.libs/H5.o:H5.c:(.text+0x10d0): first defined here
.libs/H5Ztrans.o: In function `fstat64':
H5Ztrans.c:(.text+0x6e40): multiple definition of `fstat64'
.libs/H5.o:H5.c:(.text+0x10e0): first defined here
collect2: error: ld returned 1 exit status
make5: * [libhdf5.la] Error 1
make5: Leaving directory `/root/tools/libs4cdo-0.0.9/hdf5-1.8.7/src'
make4: [all] Error 2
make4: Leaving directory `/root/tools/libs4cdo-0.0.9/hdf5-1.8.7/src'
make3: [all-recursive] Error 1
make3: Leaving directory `/root/tools/libs4cdo-0.0.9/hdf5-1.8.7'
make2: [hdf5-1.8.7] Error 2
make2: Leaving directory `/root/tools/libs4cdo-0.0.9'
make1: [all] Error 2
make1: Leaving directory `/root/tools/libs4cdo-0.0.9'
make: * [libs4cdo] Error 2

any help would be appreciated I've spent 2 days on this thus far! thanks

-rob

full_make_error.txt (93.3 KB) full_make_error.txt

Replies (4)

RE: Problems installing CDO on RHEL 5.4, even libs4cd0 - Added by Ralf Mueller over 12 years ago

Looks a bit like using old object files...

Anyhow, please provide the config.log from the CDO configure call. And for not mixing up CDO and libs4cdo, please configure CDO without any external libraries, i.e. just use ./configure

RE: Problems installing CDO on RHEL 5.4, even libs4cd0 - Added by Ralf Mueller over 12 years ago

Do you still get the first error?

It is libtool-related, Try the following steps, each of them followed by make
  • One possible reason is your compiler setup. Could you use a system compiler instead of experimental gcc-4.7.0?
  • You might set you gcc with CC when calling configure
  • Install autoconf+libtool yourself and run autoreconf -v in the CDO source directory
  • Install libtool and run libtoolize and ./configure

BTW: There is a fedora package for CDO: https://admin.fedoraproject.org/pkgdb/acls/name/cdo

HTH
Ralf

RE: Problems installing CDO on RHEL 5.4, even libs4cd0 - Added by roberto jarawan over 12 years ago

I didn't realize i was using gcc-trunk 4.7, after doing all the above and setting CC=/usr/bin/gcc it didnt work the first time but then a reinstall of libtool and using autoconf got me a little farther, then downgrading finally a few versions of libtool and it finally compiled! thank you :)

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