Vicuna build errors

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Richard Leggett

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Jan 28, 2014, 7:19:27 AM1/28/14
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I'm trying to compile Vicuna on Centos.

I've build NCBI 7.0.0, set the LD_LIBRARY_PATH and modified the Makefile. However, I'm still getting a stream of errors:

In file included from /usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:43,
                 from xny/seq_pair_manip.hpp:21,
                 from Trimmer.h:15,
                 from ReadIndexer.h:16,
                 from Contig.h:15,
                 from Contig.cpp:11:
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:51: error: expected constructor, destructor, or type conversion before ‘enum’
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:68: error: ‘ncbi::IsForward’ declared as an ‘inline’ variable
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:68: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:69: error: expected ‘,’ or ‘;’ before ‘{’ token
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:75: error: ‘ncbi::IsReverse’ declared as an ‘inline’ variable
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:75: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:76: error: expected ‘,’ or ‘;’ before ‘{’ token
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: ‘ncbi::SameOrientation’ declared as an ‘inline’ variable
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: initializer expression list treated as compound expression
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:84: error: expected ‘,’ or ‘;’ before ‘{’ token
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:90: error: ‘ENa_strand’ does not name a type
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:110: error: expected constructor, destructor, or type conversion before ‘}’ token
In file included from xny/seq_pair_manip.hpp:21,
                 from Trimmer.h:15,
                 from ReadIndexer.h:16,
                 from Contig.h:15,
                 from Contig.cpp:11:
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:213: error: ‘ncbi::objects::ENa_strand’ has not been declared
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:215: error: ‘ncbi::objects::ENa_strand’ has not been declared
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:220: error: ‘ncbi::objects::ENa_strand’ has not been declared
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:223: error: ‘ncbi::objects::ENa_strand’ has not been declared
In file included from /usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/algo/align/nw/nw_aligner.hpp:43,
                 from xny/seq_pair_manip.hpp:21,
                 from Trimmer.h:15,
                 from Contiger.h:16,
                 from Contiger.cpp:11:
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:51: error: expected constructor, destructor, or type conversion before ‘enum’
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:68: error: ‘ncbi::IsForward’ declared as an ‘inline’ variable
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:68: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:69: error: expected ‘,’ or ‘;’ before ‘{’ token
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:75: error: ‘ncbi::IsReverse’ declared as an ‘inline’ variable
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:75: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:76: error: expected ‘,’ or ‘;’ before ‘{’ token
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: ‘ncbi::SameOrientation’ declared as an ‘inline’ variable
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: ‘ENa_strand’ was not declared in this scope
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:83: error: initializer expression list treated as compound expression
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:84: error: expected ‘,’ or ‘;’ before ‘{’ token
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:90: error: ‘ENa_strand’ does not name a type
/usr/users/ga002/leggettr/software/ncbi_7_0_0/include/ncbi-tools++/objects/seqloc/Na_strand.hpp:110: error: expected constructor, destructor, or type conversion before ‘}’ token

It goes on beyond this, but its basically the same errors.

Any tips? I can't run the executable on my system.

Thanks,
Richard

Xiao Yang

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Jan 28, 2014, 8:09:47 AM1/28/14
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Hi Richard,

This looks like the typical error resulted from the failure to export the NCBI library path.
I have two suggestions for this: check the value of LD_LIBRARY_PATH to see if it has
intended value. As a possible alternative, try setting DYLD_LIBRARY_PATH instead,
and see if it resolves the issue.

Best,
Xiao


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- Xiao

Richard Leggett

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Jan 28, 2014, 12:48:49 PM1/28/14
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Hi Xiao,

Many thanks for your quick reply. You're right, I appear to have some libs missing from my NCBI installation. I don't seem to be able to get v7 to finish building, but v12 seems to work fine. I now have Vicuna compiled against NCBI v12 and it appears to run. Is there any issue running with this version of NCBI?

Thanks,
Richard

Xiao Yang

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Jan 28, 2014, 1:12:56 PM1/28/14
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Hi Richard,

As long as it runs, there should not be any issue. Good to know part of v12 
is compatible with v7.

Thanks,
Xiao
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