Standalone package error


#1

Hi All,

I’m getting the following error when running the “./package_mrtrix -standalone”. I’m compiling on Centos 7 and moving to Centos 6. The software builds with no errors on Centos7.

mrtrix3]# ./package_mrtrix -standalone
This script collates all the executables and runtime dependencies needed for
MRtrix3, and creates a GZ compressed archive suitable for deployment on other
systems. It takes all executables found in the bin/ folder and the MRtrix3
library from the lib/ folder. It is up to the user to ./configure and ./build
the software first.

       Stand-alone installation on systems without necessary dependencies
================================================================================

If the -standalone option is also supplied, this script will also attempt to
collate system libraries from the current system, allowing you to install onto
a target system without the necessary dependencies. This is particularly useful
for  installation on HPC systems and other centrally managed systems that often
run older distributions, and where users have little or no control over the
installation of required packages.

$ ./configure
$ ./build
$ ./package_mrtrix [-standalone]

Press enter to proceed (or Ctrl-C to abort)...
- collating MRtrix3 executables and library...
- collating dependent system libraries...
bin/5tt2gmwmi: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/mrtrix3/bin/../lib/libmrtrix.so)
bin/5tt2vis: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/mrtrix3/bin/../lib/libmrtrix.so)
bin/5ttcheck: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by bin/5ttcheck)
bin/5ttcheck: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/mrtrix3/bin/../lib/libmrtrix.so)
bin/5ttedit: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/mrtrix3/bin/../lib/libmrtrix.so)
bin/afdconnectivity: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by bin/afdconnectivity)
bin/afdconnectivity: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/local/mrtrix3/bin/../lib/libmrtrix.so)

#2

Ok, my guess is you have the correct libraries installed in a location listed in the LD_LIBRARY_PATH environment variable, but maybe this variable wasn’t set when you invoked the package_mrtrix command, or that variable doesn’t get propagated all the way through to the sub-shells where the ldd command is invoked.

Can you make sure that you can actually invoke a command like mrinfo properly, then in the same shell, type:

ldd bin/mrinfo
echo $LD_LIBRARY_PATH

And post the full output of those two commands. That might give us a better idea of what’s going on…