Comments (5)
I think this is fixed in the newest version of ASTRID. You might still have errors depending on how your java environment is set up. I can try and help figure them out if you do.
from astrid.
I'm having a similar problem using bazel build //src:ASTRID-phydstar -c opt
with the most recent version of ASTRID. It's failing giving the following error:
ERROR: /home/jamessw3/software/ASTRID/src/BUILD:3:10: Linking of rule '//src:ASTRID-phydstar' failed (Exit 1): gcc failed: error executing command /usr/bin/gcc @bazel-out/k8-opt/bin/src/ASTRID-phydstar-2.params
Use --sandbox_debug to see verbose messages from the sandbox gcc failed: error executing command /usr/bin/gcc @bazel-out/k8-opt/bin/src/ASTRID-phydstar-2.params
Use --sandbox_debug to see verbose messages from the sandbox
bazel-out/k8-opt/bin/_solib_k8/_U_S_Ssrc_CASTRID-phydstar___Ulocal_Ujdk_Sjre_Slib_Samd64/libdeploy.so: error: undefined reference to 'jws_g_list_length'
bazel-out/k8-opt/bin/_solib_k8/_U_S_Ssrc_CASTRID-phydstar___Ulocal_Ujdk_Sjre_Slib_Samd64/libdeploy.so: error: undefined reference to 'jws_g_list_nth_data'
bazel-out/k8-opt/bin/_solib_k8/_U_S_Ssrc_CASTRID-phydstar___Ulocal_Ujdk_Sjre_Slib_Samd64/libdeploy.so: error: undefined reference to 'native_trace'
bazel-out/k8-opt/bin/_solib_k8/_U_S_Ssrc_CASTRID-phydstar___Ulocal_Ujdk_Sjre_Slib_Samd64/libnpjp2.so: error: undefined reference to 'std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char)'
bazel-out/k8-opt/bin/src/DistanceMethods/_objs/PhyDStar/phydstar.o:phydstar.cpp:function BioNJStar(TaxonSet&, DistanceMatrix&, std::vector<std::string, std::allocator<std::string> >&): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
Target //src:ASTRID-phydstar failed to build
Use --verbose_failures to see the command lines of failed build steps.
INFO: Elapsed time: 18.142s, Critical Path: 10.18s
INFO: 16 processes: 3 internal, 13 processwrapper-sandbox.
FAILED: Build did NOT complete successfully
Let me know if there's any other information that would be helpful. Thanks!
from astrid.
This is the java compilation error I referred to in my last comment. You might try ensuring you have the java developer kit installed. However, are you sure you want to use phydstar? The procedure that ASTRID will suggest if you give it a dataset with missing elements is far superior.
from astrid.
The command for that would be like
ASTRID -i -o -u -n -s
You could also use the new --cache option which writes the distance matrix to a file in Phylip format, and run phyd* manually on that.
from astrid.
I'll look into both of those options. Thanks!
from astrid.
Related Issues (9)
- fatal build error: missing DistanceMatrix.hpp HOT 5
- Switching the default method for missing data to `-u -s` or `-u -n -s` HOT 3
- Expose UPGMA* as a standalone method
- `-u -n -s`, difference from `-u -s` HOT 1
- Remove experimental OCTAL support
- Crash with free() invalid: size() HOT 4
- Error message in latest Mac OS X release HOT 3
- Potential memory leak during iterations
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from astrid.