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 finishes without 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
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 finishes without 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
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
freesurfer@nmr.mgh.harvard.edu
-
Arman Eshaghi -
Z K