Open iPsychonaut opened 7 months ago
Hi,
The make step that produces the error should have some error message that shows at which step it has an error. You can try piping the error to a file i.e.
./build_all.sh 2>&1 > build.log
And see in build.log if there are any error message produced, or send the file here for me to check.
Thank you.
Different from OP, but attaching my build.log file.
build_all.sh fails to build any of the tools, seems to choke on dealing with ./suk
I can get run_all.sh to work up until line 158 and then get the error:
./run_all.sh: line 158: ./suk: is a directory
presumably because build_all.sh should have used to ./suk directory to create executable ./suk
I have attempted to build the repo but have been met with other errors mentioned above, and am currently facing this error:
make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: *** [Makefile:156: all] Error 2
Here are the steps I took to build: mamba install -y -c conda-forge -c bioconda -c r zlib openmp minimap2 samtools pysam biopython
I experienced the same error during building. I built the overlap, scaffold and suk individually according to the build_all.sh, and the polisher module would not build correctly. I got the same error: make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: [Makefile:156: all] Error 2
To fix, I edited the Monitor.hpp files and CMakeList.txt in the polisher folder: CMakeLists.txt Monitor.hpp
cd polisher
cd external/install/htslib
autoreconf --install
autoreconf
./configure --prefix=$(pwd) --disable-bz2 --disable-lzma
make -j 10
make install
cd ../../..
mkdir -p build
cd build
#edit monitor.hpp and cmakelists.txt
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j 10
Hope this helps :)
I have attempted to build the repo but have been met with other errors mentioned above, and am currently facing this error: make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: *** [Makefile:156: all] Error 2 Here are the steps I took to build: mamba install -y -c conda-forge -c bioconda -c r zlib openmp minimap2 samtools pysam biopython
I experienced the same error during building. I built the overlap, scaffold and suk individually according to the build_all.sh, and the polisher module would not build correctly. I got the same error: make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: [Makefile:156: all] Error 2
To fix, I edited the Monitor.hpp files and CMakeList.txt in the polisher folder: CMakeLists.txt Monitor.hpp
cd polisher cd external/install/htslib autoreconf --install autoreconf ./configure --prefix=$(pwd) --disable-bz2 --disable-lzma make -j 10 make install cd ../../.. mkdir -p build cd build #edit monitor.hpp and cmakelists.txt cmake -DCMAKE_BUILD_TYPE=Release .. make -j 10
Hope this helps :)
That really works. Thanks a lot!
I have attempted to build the repo but have been met with other errors mentioned above, and am currently facing this error:
make[2]: [CMakeFiles/hypo.dir/build.make:104: CMakeFiles/hypo.dir/src/Hypo.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:561: CMakeFiles/hypo.dir/all] Error 2 make: *** [Makefile:156: all] Error 2
Here are the steps I took to build: mamba install -y -c conda-forge -c bioconda -c r zlib openmp minimap2 samtools pysam biopython