Dear MRtrix experts,
first of all many congrats for MRtrix3 it is great!
I m trying to install MRtrix3Tissue long side MRtrix3 but I am keeping getting an error during ./configure
(failing of C++ compliance test). However, g++ and clang (I tried with both) are updated and I have just updated MRtrix3 to the latest release on the same machine without any problems.
I am running Ubuntu 19.10
would you have any suggestion?
Thanks!
Nicola
I paste here the configure.log
REPORT:
MRtrix3Tissue build type requested: release version
MRtrix3Tissue is a fork of the MRtrix3 project
REPORT: WARNING: Anaconda removed from PATH to avoid conflicts
REPORT: Detecting OS: linux
REPORT: Looking for compiler [/usr/bin/g++-9]:
EXEC <<
CMD: /usr/bin/g++-9 --version
EXIT: 0
STDOUT:
g++-9 (Ubuntu 9.2.1-9ubuntu2) 9.2.1 20191008
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>>
REPORT: g++-9 (Ubuntu 9.2.1-9ubuntu2) 9.2.1 20191008
REPORT: Checking for C++11 compliance:
COMPILE /tmp/tmp3bg8hr8w.cpp:
---
#include <cstddef>
struct Base {
Base (int);
};
struct Derived : Base {
using Base::Base;
};
int main() {
Derived D (int); // check for contructor inheritance
return 0;
}
---
EXEC <<
CMD: /usr/bin/g++-9 -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/nicola/anaconda3/include /tmp/tmp3bg8hr8w.cpp -o /tmp/tmp3bg8hr8w.o
EXIT: 0
>>
EXEC <<
CMD: /home/nicola/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld /tmp/tmp3bg8hr8w.o -Wl,--sort-common,--as-needed -pthread -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/nicola/anaconda3/lib -Wl,-rpath-link,/home/nicola/anaconda3/lib -L/home/nicola/anaconda3/lib -o a.out
EXIT: 1
STDERR:
/home/nicola/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld: unrecognized option '-Wl,--sort-common,--as-needed'
/home/nicola/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ld: use the --help option for usage information
>>
error deleting temporary file "a.out": No such file or directory
REPORT: test failed (see configure.log for details)
ERROR: no suitable compiler found!
Set the CXX environment variable to inform 'configure' of the path to the
compiler on your system, as follows:
$ export CXX=/usr/bin/g++-5.5
$./configure
(amend with the actual path to the compiler on your system)
If you are using a compiler other than gcc or clang, you can also set the CXX_ARGS
environment variable to specify how your compiler expects different arguments
to be presented on the command line, for instance as follows:
$ export CXX_ARGS="-c CFLAGS SRC -o OBJECT"
$ ./configure
See the file 'configure.log' for details. MRtrix3Tissue is a fork of the
MRtrix3 project. The functionality of the configure script is unmodified,
so when experiencing problems with this script, you might be able to find
assistance in the MRtrix3 community forum at http://community.mrtrix.org/.
Make sure to include the full contents of the 'configure.log' file to
enable community members to help you efficiently. If you believe there are
bugs or other issues with the script, it might be useful to flag these to
MRtrix3 developers as well, as bug fixes are likely to be useful to both
MRtrix3 and MRtrix3Tissue.