search

rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
535 stars 132 forks source link

Installation Error (Error: compilation of Unicycler's C++ component failed) #311

Open ahadlaique opened 1 year ago

ahadlaique commented 1 year ago

:~/Unicycler$ python3 setup.py install running install /home/aaaha/miniconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Cleaning previous compilation: make distclean Platform: Linux Compiler: g++ 9.4.0 rm -f unicycler/src/scoredalignment.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asm.o unicycler/src/global_align.o unicycler/src/overlap_align.o unicycler/src/path_align.o unicycler/src/consensus_align.o unicycler/src/start_end_align.o unicycler/src/miniasm_assembly.o unicycler/src/kmers.o unicycler/src/semi_global_align.o unicycler/src/ref_seqs.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/bseq.o unicycler/src/minimap/sdust.o unicycler/src/minimap/sketch.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/random_alignments.o unicycler/src/string_functions.o unicycler/src/minimap_align.o rm -f unicycler/cpp_functions.so Compiling Unicycler: make -j 8 Platform: Linux Compiler: g++ 9.4.0 g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asm.cpp unicycler/src/miniasm/paf.cpp:1:10: fatal error: zlib.h: No such file or directory 1 | #include | ^~~~ compilation terminated. make: [Makefile:120: unicycler/src/miniasm/paf.o] Error 1 make: Waiting for unfinished jobs.... unicycler/src/miniasm/asm.cpp:6:10: fatal error: zlib.h: No such file or directory 6 | #include | ^~~~ compilation terminated. make: *** [Makefile:120: unicycler/src/miniasm/asm.o] Error 1 Error: compilation of Unicycler's C++ component failed

ahadlaique commented 1 year ago

(base) aaaha@AbdulAhad:~/Unicycler$ pip3 install path/to/Unicycler ERROR: Invalid requirement: 'path/to/Unicycler' Hint: It looks like a path. File 'path/to/Unicycler' does not exist. (base) aaaha@AbdulAhad:~/Unicycler$ cd (base) aaaha@AbdulAhad:~$ pip3 install path/to/Unicycler ERROR: Invalid requirement: 'path/to/Unicycler' Hint: It looks like a path. File 'path/to/Unicycler' does not exist. (base) aaaha@AbdulAhad:~$ cd Unicycler/ (base) aaaha@AbdulAhad:~/Unicycler$ pip3 install ERROR: You must give at least one requirement to install (see "pip help install") (base) aaaha@AbdulAhad:~/Unicycler$ pip3 install ERROR: You must give at least one requirement to install (see "pip help install") (base) aaaha@AbdulAhad:~/Unicycler$ pip3 install git+https://github.com/rrwick/Unicycler.git Collecting git+https://github.com/rrwick/Unicycler.git Cloning https://github.com/rrwick/Unicycler.git to /tmp/pip-req-build-wrfpoyfw Running command git clone --filter=blob:none --quiet https://github.com/rrwick/Unicycler.git /tmp/pip-req-build-wrfpoyfw Resolved https://github.com/rrwick/Unicycler.git to commit 69e712eb95c4b9f8a46aade467260260a9ce7a91 Preparing metadata (setup.py) ... done Building wheels for collected packages: unicycler Building wheel for unicycler (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [57 lines of output] running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/unicycler copying unicycler/string_graph.py -> build/lib/unicycler copying unicycler/bridge_long_read.py -> build/lib/unicycler copying unicycler/unicycler_align.py -> build/lib/unicycler copying unicycler/log.py -> build/lib/unicycler copying unicycler/alignment.py -> build/lib/unicycler copying unicycler/misc.py -> build/lib/unicycler copying unicycler/unicycler.py -> build/lib/unicycler copying unicycler/path_finding.py -> build/lib/unicycler copying unicycler/version.py -> build/lib/unicycler copying unicycler/minimap_alignment.py -> build/lib/unicycler copying unicycler/blast_func.py -> build/lib/unicycler copying unicycler/cpp_wrappers.py -> build/lib/unicycler copying unicycler/assembly_graph_segment.py -> build/lib/unicycler copying unicycler/settings.py -> build/lib/unicycler copying unicycler/read_ref.py -> build/lib/unicycler copying unicycler/bridge_spades_contig.py -> build/lib/unicycler copying unicycler/miniasm_assembly.py -> build/lib/unicycler copying unicycler/assembly_graph_copy_depth.py -> build/lib/unicycler copying unicycler/bridge_long_read_simple.py -> build/lib/unicycler copying unicycler/spades_func.py -> build/lib/unicycler copying unicycler/init.py -> build/lib/unicycler copying unicycler/bridge_miniasm.py -> build/lib/unicycler copying unicycler/bridge_common.py -> build/lib/unicycler copying unicycler/assembly_graph.py -> build/lib/unicycler copying unicycler/bridge_loop_unroll.py -> build/lib/unicycler /home/aaaha/miniconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( installing to build/bdist.linux-x86_64/wheel running install Cleaning previous compilation: make distclean Platform: Linux Compiler: g++ 9.4.0 rm -f unicycler/src/scoredalignment.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asm.o unicycler/src/global_align.o unicycler/src/overlap_align.o unicycler/src/path_align.o unicycler/src/consensus_align.o unicycler/src/start_end_align.o unicycler/src/miniasm_assembly.o unicycler/src/kmers.o unicycler/src/semi_global_align.o unicycler/src/ref_seqs.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/bseq.o unicycler/src/minimap/sdust.o unicycler/src/minimap/sketch.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/random_alignments.o unicycler/src/string_functions.o unicycler/src/minimap_align.o rm -f unicycler/cpp_functions.so Compiling Unicycler: make -j 8 Platform: Linux Compiler: g++ 9.4.0 g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp unicycler/src/miniasm/paf.cpp:1:10: fatal error: zlib.h: No such file or directory 1 | #include | ^~~~ compilation terminated. make: [Makefile:120: unicycler/src/miniasm/paf.o] Error 1 make: Waiting for unfinished jobs.... Error: compilation of Unicycler's C++ component failed [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for unicycler Running setup.py clean for unicycler error: subprocess-exited-with-error

× python setup.py clean did not run successfully. │ exit code: 1 ╰─> [6 lines of output] usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

  error: option --all not recognized
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed cleaning build dir for unicycler Failed to build unicycler Installing collected packages: unicycler Running setup.py install for unicycler ... error error: subprocess-exited-with-error

× Running setup.py install for unicycler did not run successfully. │ exit code: 1 ╰─> [23 lines of output] running install /home/aaaha/miniconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Cleaning previous compilation: make distclean Platform: Linux Compiler: g++ 9.4.0 rm -f unicycler/src/scoredalignment.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asm.o unicycler/src/global_align.o unicycler/src/overlap_align.o unicycler/src/path_align.o unicycler/src/consensus_align.o unicycler/src/start_end_align.o unicycler/src/miniasm_assembly.o unicycler/src/kmers.o unicycler/src/semi_global_align.o unicycler/src/ref_seqs.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/bseq.o unicycler/src/minimap/sdust.o unicycler/src/minimap/sketch.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/random_alignments.o unicycler/src/string_functions.o unicycler/src/minimap_align.o rm -f unicycler/cpp_functions.so Compiling Unicycler: make -j 8 Platform: Linux Compiler: g++ 9.4.0 g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp unicycler/src/miniasm/paf.cpp:1:10: fatal error: zlib.h: No such file or directory 1 | #include | ^~~~ compilation terminated. g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp make: [Makefile:120: unicycler/src/miniasm/paf.o] Error 1 make: Waiting for unfinished jobs.... Error: compilation of Unicycler's C++ component failed [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> unicycler

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure. (base) aaaha@AbdulAhad:~/Unicycler$ python3 setup.py install --makeargs "CXX=icpc" running install /home/aaaha/miniconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( Cleaning previous compilation: make distclean Platform: Linux Compiler: g++ 9.4.0 rm -f unicycler/src/scoredalignment.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asm.o unicycler/src/global_align.o unicycler/src/overlap_align.o unicycler/src/path_align.o unicycler/src/consensus_align.o unicycler/src/start_end_align.o unicycler/src/miniasm_assembly.o unicycler/src/kmers.o unicycler/src/semi_global_align.o unicycler/src/ref_seqs.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/bseq.o unicycler/src/minimap/sdust.o unicycler/src/minimap/sketch.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/random_alignments.o unicycler/src/string_functions.o unicycler/src/minimap_align.o rm -f unicycler/cpp_functions.so Compiling Unicycler: make -j 8 CXX=icpc Platform: Linux /bin/sh: 1: icpc: not found Falling back to -dumpversion as compiler did not support -dumpfullversion make: icpc: No such file or directory Compiler: unknown icpc -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -Wall -Wextra -pedantic -mtune=native -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp make: icpc: No such file or directory make: *** [Makefile:120: unicycler/src/scoredalignment.o] Error 127 Error: compilation of Unicycler's C++ component failed

lrvdijk commented 1 year ago

I have the same issue, while zlib is both installed system-wide and in my conda environment...