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Build error Breakdancer 1.3.6

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. 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
breakdancer software-error
• 3,065 views • link
updated by Ram Ram • written by balli.dave • balli.dave

1 answer

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
• 0 views • link
updated by Ram Ram • written by tgi.tabbott tgi.tabbott

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