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gtDMMB / gtfold

GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.
http://gtfold.sourceforge.net/
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Undefined Reference Error During Make #8

Open OwenTC opened 2 years ago

OwenTC commented 2 years ago

I am installing gtfold using cmake in Ubuntu 18.04. I am getting the following undefined reference error during linking when I run make. I have GMP installed not sure what else would be causing this issue. I've checked that gmp is in $PKG_CONFIG_PATH.

/usr/bin/cmake -Hgtfold -Bgtfold --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start gtfold/CMakeFiles gtfold/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory 'gtfold'
make -f CMakeFiles/gtfold.dir/build.make CMakeFiles/gtfold.dir/depend
make[2]: Entering directory 'gtfold'
cd gtfold && /usr/bin/cmake -E cmake_depends "Unix Makefiles" gtfold gtfold gtfold gtfold gtfold/CMakeFiles/gtfold.dir/DependInfo.cmake --color=
make[2]: Leaving directory 'gtfold'
make -f CMakeFiles/gtfold.dir/build.make CMakeFiles/gtfold.dir/build
make[2]: Entering directory 'gtfold'
[  3%] Linking CXX executable bin/gtfold
/usr/bin/cmake -E cmake_link_script CMakeFiles/gtfold.dir/link.txt --verbose=1
/usr/bin/c++   -g   -DNDEBUG            -rdynamic -fvisibility=default            -I/usr/local/include -I/usr/local/include -Igtfold-mfe/include            -D_GNU_SOURCE -DGNU_SOURCE -D__USE_GNU            -DGTFOLD_PACKAGE_VERSION="1.0.0"   -g   -DNDEBUG            -rdynamic -fvisibility=default            -I/usr/local/include -I/usr/local/include -Igtfold-mfe/include            -D_GNU_SOURCE -DGNU_SOURCE -D__USE_GNU            -DGTFOLD_PACKAGE_VERSION="1.0.0"    -lpthread -flto -fno-fat-lto-objects   -g   -DNDEBUG            -rdynamic -fvisibility=default            -I/usr/local/include -I/usr/local/include -Igtfold-mfe/include            -D_GNU_SOURCE -DGNU_SOURCE -D__USE_GNU            -DGTFOLD_PACKAGE_VERSION="1.0.0"    -lpthread CMakeFiles/gtfold.dir/gtfold-mfe/src/binexe-utils/main.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/AdvancedDouble.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/boltzmann_main.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/constraints.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/global.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/key.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/loader.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/mfe_main.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/options.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/partition-func-d2.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/pf-shel-check.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/random-sample.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/shapereader.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/stochastic-sampling-d2.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/stochastic-sampling.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/subopt_main.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/subopt_traceback.cc.o CMakeFiles/gtfold.dir/gtfold-mfe/src/utils.cc.o  -o bin/gtfold 
/tmp/ccUlVZWy.ltrans0.ltrans.o: In function `rnd_u1(int, int, int*)':
gtfold/gtfold-mfe/src/stochastic-sampling.cc:435: undefined reference to `EC_new'
gtfold/gtfold-mfe/src/stochastic-sampling.cc:435: undefined reference to `EB_new'
...
/tmp/ccUlVZWy.ltrans5.ltrans.o: In function `batch_sample_and_dump':
gtfold/gtfold-mfe/include/stochastic-sampling-d2.h:1576: undefined reference to `RT'
collect2: error: ld returned 1 exit status
CMakeFiles/gtfold.dir/build.make:544: recipe for target 'bin/gtfold' failed
make[2]: *** [bin/gtfold] Error 1
make[2]: Leaving directory 'gtfold'
CMakeFiles/Makefile2:70: recipe for target 'CMakeFiles/gtfold.dir/all' failed
make[1]: *** [CMakeFiles/gtfold.dir/all] Error 2
make[1]: Leaving directory 'gtfold'
Makefile:132: recipe for target 'all' failed
make: *** [all] Error 2