Question: Build error Breakdancer 1.3.6
0
gravatar for balli.dave
4.7 years ago by
balli.dave0
United States
balli.dave0 wrote:

I am trying to install Breakdancer v1.3.6 for analysis of structural variants.  I am receiving an error message when I follow the installation instructions from the github repository (https://github.com/genome/breakdancer/blob/master/INSTALL.md).  What should I do?

 

$ git clone --recursive https://github.com/genome/breakdancer.git
...
Resolving deltas: 100% (38/38), done.
Submodule path 'build-common': checked out '...'

$ cd breakdancer
$ mkdir build
$ cd build

$ cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
...
-- Build files have been written to: .../breakdancer/build

$ make

[ 14%] Built target boost-libs
[ 28%] Built target samtools-lib
[ 28%] Built target deps
[ 29%] Performing build step for 'gtest160'
[ 50%] Building CXX object CMakeFiles/gtest.dir/src/gtest-all.cc.o
In file included from /Users/dballi/NGS_tools/breakdancer/build/vendor/src/gtest160/src/gtest-all.cc:39:
In file included from /Users/dballi/NGS_tools/breakdancer/build/vendor/src/gtest160/include/gtest/gtest.h:57:
In file included from /Users/dballi/NGS_tools/breakdancer/build/vendor/src/gtest160/include/gtest/internal/gtest-internal.h:40:
/Users/dballi/NGS_tools/breakdancer/build/vendor/src/gtest160/include/gtest/internal/gtest-port.h:499:13: fatal error:
      'tr1/tuple' file not found
#   include <tr1/tuple>  // NOLINT
            ^
1 error generated.
make[5]: *** [CMakeFiles/gtest.dir/src/gtest-all.cc.o] Error 1
make[4]: *** [CMakeFiles/gtest.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [vendor/src/gtest160-stamp/gtest160-build] Error 2
make[1]: *** [CMakeFiles/gtest160.dir/all] Error 2
make: *** [all] Error 2
sequencing software error • 1.6k views
ADD COMMENTlink modified 4.7 years ago by tgi.tabbott220 • written 4.7 years ago by balli.dave0
0
gravatar for tgi.tabbott
4.7 years ago by
tgi.tabbott220
United States
tgi.tabbott220 wrote:

This is fixed in the latest development version of breakdancer. If you're actually trying to build v1.3.6 (by doing git checkout v1.3.6), then set the environment variable CXXFLAGS to -DGTEST_USE_OWN_TR1_TUPLE=1. For bash:

git clone ...

...

git checkout v1.3.6

export CXXFLAGS=-DGTEST_USE_OWN_TR1_TUPLE=1

mkdir build

cd build

cmake .. -D...

make

 

export

ADD COMMENTlink written 4.7 years ago by tgi.tabbott220
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