Thanks for the update. We will examine your patch and possibly include it, or some form of it, into the development tree.
-Zeke
On 09/11/2014 07:54 AM, Arman Eshaghi wrote:
I found the problem and would like to report a bug here. The problem is related to the faulty configure.in file produced during setup_configure. The faulty snippet is
202 ac_have_gcc_44="no" 203 if test "${CC}" = "gcc"; then 204 gcc --version | head -n 1 | awk '{print $2 $3}' | grep "GCC(4.4.)" >& /dev/null 205 if test "$?" = "0"; then 206 AC_MSG_NOTICE(Have gcc 4.4) 207 ac_have_gcc_44="yes" 208 fi 209 fi
which does work for gcc 4.4, but not for newer gcc (my case gcc=4.8), there should be another check for gcc 4.8, such as:
ac_have_gcc_48="no" if test "${CC}" = "gcc"; then gcc --version | head -n 1 | awk '{print $2 $3}' | grep "4.8." >& /dev/null if test "$?" = "0"; then AC_MSG_NOTICE(Have gcc 4.8) ac_have_gcc_48="yes" fi fi
if test "$ac_have_gcc_48" = "yes"; then AC_MSG_NOTICE(Copying /usr/bin/libtool overtop the PROG_LIBTOOL) cp /usr/bin/libtool . fi
This is not an elegant solution, but resolves the issue.
All the best, Arman
On Thu, Sep 11, 2014 at 1:50 AM, Arman Eshaghi arman.eshaghi@gmail.com wrote:
Hi,
I'm trying to compile Freesurfer current dev version from read only cvs repo according to developers guide on my machine with Ubuntu 14.04, gcc 4.8.2, I proceed as follows in dev/ directory:
1- ./setup_configure: which finishes without error 2- ./configure with vxl and mni library directory flags, also finisheswithout errors 3- make: it finishes with errors, specifically it seems to be a problem regarding the libtools mismatch of version, here is an example error I get from mri_segment source:
/bin/bash ../libtool --tag=CC --mode=link g++ -I../include -L/usr/lib64 -L/usr/X11R6/lib64 -L/opt/mni_library/lib -L/opt/vxl/build/lib -o mri_segment_ms mri_segment_ms.o ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib ../libtool: line 469: CDPATH: command not found libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.7ubuntu1, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.7ubuntu1 libtool: and run autoconf again. make: *** [mri_segment] Error 63
Error message seems to be pretty obvious and what I have done so far (in vain) are: 1- autoreconf -ivf 2- deleting alocal.m4 from dev, reconfiguring 3- issuing the command `make maintainer-clean` and reconfiguring and recompiling with make 4- libtoolize --force 5- deleting config.status, configure, Makefile.in, autom4te.cache
I would be much grateful if anyone could help me here.
All the best, Arman
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer