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Problem building NGS-TOOLS from source #34

Closed jmechua-itsrdc closed 9 months ago

jmechua-itsrdc commented 1 year ago

Hi, I tried cloning and building NGS-TOOLS from github. I encountered an error. Please find the error below.

make

cd /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj; cmake -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY=/home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/lib -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=/home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/ncbi/ngs-tools/bin/.. -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DVDB_INCDIR=/home/joanna/Documents/NCBI/ncbi-vdb/interfaces -DVDB_LIBDIR=/usr/local/ncbi/ncbi-vdb/lib64 -DVDB_ILIBDIR= -DSRATOOLS_SRCDIR= -DSRATOOLS_BINDIR= -DVERSION=3.0.8 -DMAJVERS=3 -DPLATFORM=x86_64 -DOUTDIR=/home/joanna/ncbi-outdir/ngs-tools/.. /home/joanna/Documents/NCBI/ngs-tools CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

CMAKE_VERSION=3.27.7 CMAKE_CXX_STANDARD=11 -- Could NOT find Java (missing: Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE Java_JAVADOC_EXECUTABLE) (found version "11.0.20") CMake Warning at build/env.cmake:213 (message): NGS includes are not found in /ngs/ngs-sdk. Call Stack (most recent call first): CMakeLists.txt:31 (include)

-- Found NCBI-VDB includes in /home/joanna/Documents/NCBI/ncbi-vdb/interfaces. Looking for NCBI-VDB libraries... -- Configuring done (0.1s) -- Generating done (0.1s) -- Build files have been written to: /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj make -C /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ --no-print-directory [ 4%] Building C object libs/tk-version/src/CMakeFiles/tk-version.dir/toolkit.vers.c.o [ 4%] Linking C static library /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/libtk-version.a [ 4%] Built target tk-version [ 4%] Building CXX object tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/DumpReferenceFASTA.cpp.o /home/joanna/Documents/NCBI/ngs-tools/tools/dump_ref_fasta/DumpReferenceFASTA.cpp:27:10: fatal error: ngs/ncbi/NGS.hpp: No such file or directory 27 | #include <ngs/ncbi/NGS.hpp> | ^~~~~~ compilation terminated. make[3]: [tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/build.make:76: tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/DumpReferenceFASTA.cpp.o] Error 1 make[2]: [CMakeFiles/Makefile2:399: tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/all] Error 2 make[1]: [Makefile:166: all] Error 2 make: [/home/joanna/Documents/NCBI/ngs-tools/build/Makefile.env:386: cmake] Error 2

Can you help me identify the problem? Thanks.

klymenko commented 11 months ago

Run the following:

cd /home/joanna/Documents/NCBI/ngs-tools
git checkout master
git pull

Then rerun configure and make.