Vicuna Build errors

[Kimberly Davis]

Hello,

I am trying to compile vicuna on my mac (OSX 10.9). I have installed NCBI toolkit V12 with some changes to get it to run on my operating system. 

When I run the make command I am getting a few different errors. I don't know if this is due to the changes I had to make to install the NCBi toolkit or if this is due to some error in compiling Vicuna.

Here is the terminal output:

Kimberlys-MacBook-Pro:VICUNA_v1.3 kimberlydavis$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Users/kimberlydavis/lib

Kimberlys-MacBook-Pro:VICUNA_v1.3 kimberlydavis$ cd src 

Kimberlys-MacBook-Pro:src kimberlydavis$ make 

/usr/bin/g++ -fopenmp -O3 -I/Users/kimberlydavis/include/ncbi-tools++ -L/Users/kimberlydavis/lib *.cpp -o ../bin/vicuna-omp-v1.0 -lpthread -lxalgoalignnw -ltables -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi 

In file included from Contig.cpp:11: 

In file included from ./Contig.h:14: 

./xutil.h:26:10: fatal error: 'omp.h' file not found 

#include <omp.h> 

^ 

1 error generated. 

In file included from Contiger.cpp:11: 

In file included from ./Contiger.h:14: 

In file included from ./Parameter.h:19: 

./xutil.h:26:10: fatal error: 'omp.h' file not found 

#include <omp.h> 

^ 

1 error generated. 

In file included from Delegate.cpp:12: 

In file included from ./Delegate.h:15: 

./xutil.h:26:10: fatal error: 'omp.h' file not found 

#include <omp.h> 

^ 

1 error generated. 

In file included from Diversifier.cpp:12: 

In file included from ./Parameter.h:19: 

./xutil.h:26:10: fatal error: 'omp.h' file not found 

#include <omp.h> 

^ 

1 error generated. 

In file included from Profiler.cpp:11: 

In file included from ./Profiler.h:15: 

In file included from ./Parameter.h:19: 

./xutil.h:26:10: fatal error: 'omp.h' file not found 

#include <omp.h> 

^ 

1 error generated. 

In file included from Reducer.cpp:11: 

In file included from ./Reducer.h:18: 

In file included from ./ReadIndexer.h:14: 

In file included from ./Parameter.h:19: 

./xutil.h:26:10: fatal error: 'omp.h' file not found 

#include <omp.h> 

^ 

1 error generated. 

In file included from Trimmer.cpp:11: 

In file included from ./Trimmer.h:15: 

In file included from ./xny/seq_pair_manip.hpp:21: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:39: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/corelib/ncbistd.hpp:37: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/corelib/ncbistr.hpp:38: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/corelib/tempstr.hpp:39: 

/Users/kimberlydavis/include/ncbi-tools++/corelib/ncbimisc.hpp:51:11: warning: 

'nullptr' macro redefined 

# define nullptr NULL 

^ 

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cstddef:88:9: note: 

previous definition is here 

#define nullptr _VSTD::__get_nullptr_t() 

^ 

In file included from Trimmer.cpp:11: 

In file included from ./Trimmer.h:15: 

In file included from ./xny/seq_pair_manip.hpp:21: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:40: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/corelib/ncbiobj.hpp:39: 

In file included from /Users/kimberlydavis/include/ncbi-tools++/corelib/ncbicntr.hpp:42: 

/Users/kimberlydavis/include/ncbi-tools++/corelib/impl/ncbi_atomic_defs.h:96:12: fatal error: 

'bits/c++config.h' file not found 

# include <bits/c++config.h> 

^ 

1 warning and 1 error generated. 

make: *** [all] Error 1

Any ideas on how I can fix these errors?

Thanks, Kimberly

[Xiao Yang]

Hi Kimberly,

This has little to do with the program or ncbi configuration themselves but

because several standard libraries could not be found (perhaps not

installed) in your OSX 10.9 system such as <omp.h> and <bits/c++config.h>. 

I'm not sure what components you might need to install (perhaps x-code, 

g++ compiler ? ), try search online would be the best bet to resolve the issue.

best

Xiao

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