Fix diamond

[RNAer]

Fix #16 , #41 , and #35 .

[mortonjt]

Hmmm. I'm still getting the following error when I try to test this build on my osx.

dyld: lazy symbol binding failed: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Users/mortonjt/miniconda2/envs/_test/bin/diamond
  Expected in: /usr/lib/libstdc++.6.dylib

dyld: Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
  Referenced from: /Users/mortonjt/miniconda2/envs/_test/bin/diamond
  Expected in: /usr/lib/libstdc++.6.dylib

/Users/mortonjt/miniconda2/conda-bld/test-tmp_dir/run_test.sh: line 3: 14191 Trace/BPT trap: 5       diamond -h
TESTS FAILED: diamond-0.7.10-1

[RNAer]

It is not uploaded to anaconda until merged. You were still installing the old one.

@Jorge-C , would mind taking a look at this PR?

[mortonjt]

I didn't use the upload to anaconda - I used conda build.

That's the correct way to test it right?

On Thu, Dec 17, 2015 at 11:18 PM, Zech Xu notifications@github.com wrote:

It is not uploaded to anaconda until merged. You were still installing the old one.

@Jorge-C https://github.com/Jorge-C , would mind taking a look at this PR?

— Reply to this email directly or view it on GitHub https://github.com/biocore/conda-recipes/pull/55#issuecomment-165699656.

[RNAer]

I tested it again by building locally. don't see problem on my mac...

[mortonjt]

Just found out that there was some left over crap in my virtualenv.

So :+1:

[mortonjt]

Something funky is going on, when I run

conda build Diamond

I get

+ make
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_encoding.o algo/blast/core/blast_encoding.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_stat.o algo/blast/core/blast_stat.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_filter.o algo/blast/core/blast_filter.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_util.o algo/blast/core/blast_util.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_message.o algo/blast/core/blast_message.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_erf.o algo/blast/core/ncbi_erf.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_options.o algo/blast/core/blast_options.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_math.o algo/blast/core/ncbi_math.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_program.o algo/blast/core/blast_program.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_std.o algo/blast/core/ncbi_std.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_psi_priv.o algo/blast/core/blast_psi_priv.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/raw_scoremat.o algo/blast/core/raw_scoremat.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_query_info.o algo/blast/core/blast_query_info.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_seg.o algo/blast/core/blast_seg.c
g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o main.o main.cpp
main.cpp:23:10: fatal error: 'boost/program_options.hpp' file not found
#include <boost/program_options.hpp>
         ^
1 error generated.
make: *** [main.o] Error 1

But when I run conda install --use-local Diamond

Its able to install Diamond just fine.

Not sure if this is a problem. Otherwise, we should try to get this merged.

[RNAer]

I thought you tested it previously?

Firstly, do you have boost (> 1.53)? And, do you have an already built one in local dir?

On Mon, Jan 4, 2016 at 11:06 AM, mortonjt notifications@github.com wrote:

Something funky is going on, when I run

conda build Diamond

I get

• make gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_encoding.o algo/blast/core/blast_encoding.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_stat.o algo/blast/core/blast_stat.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_filter.o algo/blast/core/blast_filter.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_util.o algo/blast/core/blast_util.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_message.o algo/blast/core/blast_message.c gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_erf.o algo/blast/core/ncbi_erf.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_options.o algo/blast/core/blast_options.c gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_math.o algo/blast/core/ncbi_math.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_program.o algo/blast/core/blast_program.c gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_std.o algo/blast/core/ncbi_std.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_psi_priv.o algo/blast/core/blast_psi_priv.c gcc -O3 -DNDEBUG -c -o algo/blast/core/raw_scoremat.o algo/blast/core/raw_scoremat.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_query_info.o algo/blast/core/blast_query_info.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_seg.o algo/blast/core/blast_seg.c g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o main.o main.cpp main.cpp:23:10: fatal error: 'boost/program_options.hpp' file not found#include <boost/program_options.hpp> ^ 1 error generated. make: *\ [main.o] Error 1

But when I run conda install --use-local Diamond

Its able to install Diamond just fine.

Not sure if this is a problem. Otherwise, we should try to get this merged.

— Reply to this email directly or view it on GitHub https://github.com/biocore/conda-recipes/pull/55#issuecomment-168772406.

[mortonjt]

I just ditched homebrew, in favor of macports. Its working on my machine now.

[mortonjt]

@RNAer , @Jorge-C want to merge this?