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vcflib / vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
https://github.com/vcflib/vcflib#vcflib
MIT License
622 stars 221 forks source link

Build from source not working with zig 0.11.0 #399

Open Stikus opened 11 months ago

Stikus commented 11 months ago

Describe the bug

We tried to upgrade zig after 0.11.0 release, but build failed.

To Reproduce Install zig v0.11.0 and try to build from source.

Expected behavior

All building well with zig v0.10.1.

Build log with zig v0.10.1 (cut due to isue size limit) ``` #12 [ 8/12] RUN cd "/soft" && wget -q "https://github.com/vcflib/vcflib/archive/refs/tags/v1.0.9.tar.gz" -O "/soft/vcflib-1.0.9.tar.gz" && tar -xzf "/soft/vcflib-1.0.9.tar.gz" && mv "/soft/vcflib-1.0.9" "/soft/vcflib-1.0.9-src" && git clone --recursive --depth=1 -j8 https://github.com/vcflib/vcflib.git "/soft/vcflib-master" && cp -r "/soft/vcflib-master/contrib"/* "/soft/vcflib-1.0.9-src/contrib" && cd "/soft/vcflib-1.0.9-src" && mkdir -p build && cd build && sed -i -e "s|^\(include_directories(contrib/c-progress-bar).*\)$|\1\ninclude_directories(/soft/htslib-1.19/include)|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e "s|^\(endif(HTSLIB_LOCAL).*\)$|\1\nlink_directories(/soft/htslib-1.19/lib)|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e "s|^\( set(WFA_INCLUDE_DIRS \)${CMAKE_INSTALL_PREFIX}\(/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib).*\)$|\1/soft/WFA2-lib-2.3.4\2|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e "s|^\( find_library(WFALIB \)\(wfa2 wfa\)\().*\)$|\1NAMES \2 PATHS /soft/WFA2-lib-2.3.4/lib\3|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e 's|^\( message(STATUS "ERROR: Can not find libfwa.*\)$|\1\n else(NOT WFALIB)\n message(STATUS "OK: found libfwa: ${WFALIB}")|' "/soft/vcflib-1.0.9-src/CMakeLists.txt" && cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 -DCMAKE_INSTALL_PREFIX="/soft/vcflib-1.0.9" -DWFA_GITMODULE=OFF .. && make && make install && cd "/soft" && rm -r "/soft/vcflib-1.0.9-src" "/soft/vcflib-master" && rm "/soft/vcflib-1.0.9.tar.gz" #12 4.725 Cloning into '/soft/vcflib-master'... #12 9.172 Submodule 'contrib/WFA2-lib' (https://github.com/smarco/WFA2-lib) registered for path 'contrib/WFA2-lib' #12 9.172 Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'contrib/fastahack' #12 9.172 Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'contrib/filevercmp' #12 9.172 Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'contrib/fsom' #12 9.173 Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'contrib/intervaltree' #12 9.173 Submodule 'libVCFH' (https://github.com/edawson/libVCFH.git) registered for path 'contrib/libVCFH' #12 9.173 Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'contrib/multichoose' #12 9.173 Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'contrib/smithwaterman' #12 9.173 Submodule 'contrib/tabixpp' (https://github.com/vcflib/tabixpp.git) registered for path 'contrib/tabixpp' #12 9.173 Submodule 'src/simde' (https://github.com/simd-everywhere/simde-no-tests.git) registered for path 'src/simde' #12 9.178 Cloning into '/soft/vcflib-master/contrib/WFA2-lib'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/filevercmp'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/fsom'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/multichoose'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/intervaltree'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/smithwaterman'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/fastahack'... #12 10.70 Cloning into '/soft/vcflib-master/contrib/libVCFH'... #12 10.79 Cloning into '/soft/vcflib-master/contrib/tabixpp'... #12 10.89 Cloning into '/soft/vcflib-master/src/simde'... #12 12.81 Submodule path 'contrib/WFA2-lib': checked out 'ab690aa9b3015dc2551387080cbc067d6ab4e490' #12 12.82 Submodule path 'contrib/fastahack': checked out 'bb332654766c2177d6ec07941fe43facf8483b1d' #12 12.84 Submodule path 'contrib/filevercmp': checked out 'df20dcc4a2a772de56e804e8fbbcdef1ac068bbe' #12 12.86 Submodule path 'contrib/fsom': checked out '56695e1611d824cda97f08e932d25d08419170cd' #12 12.88 Submodule path 'contrib/intervaltree': checked out 'aa5937755000f1cd007402d03b6f7ce4427c5d21' #12 12.89 Submodule path 'contrib/libVCFH': checked out '44b6580639a216a484fd96de75a839091f25768a' #12 12.91 Submodule path 'contrib/multichoose': checked out 'e1f94aeb5d52542b000287fd8e0204c78906897e' #12 12.93 Submodule path 'contrib/smithwaterman': checked out '2610e259611ae4cde8f03c72499d28f03f6d38a7' #12 12.94 Submodule path 'contrib/tabixpp': checked out 'ae5cdf846af85bd1d0e310c05e5c67b037f51a25' #12 12.95 Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'contrib/tabixpp/htslib' #12 12.95 Cloning into '/soft/vcflib-master/contrib/tabixpp/htslib'... #12 15.02 Submodule path 'contrib/tabixpp/htslib': checked out '53f980829d3c906ff1d0506212a3e2c8c83b2cb3' #12 15.03 Submodule 'htscodecs' (https://github.com/samtools/htscodecs.git) registered for path 'contrib/tabixpp/htslib/htscodecs' #12 15.03 Cloning into '/soft/vcflib-master/contrib/tabixpp/htslib/htscodecs'... #12 17.50 Submodule path 'contrib/tabixpp/htslib/htscodecs': checked out '3ef17f6fb5b8b6b0ad2d4c1c562165664f0703f8' #12 17.57 Submodule path 'src/simde': checked out 'cbef1c152ad2e73bc8971c306208f55f44b16088' #12 17.69 -- The C compiler identification is GNU 11.4.0 #12 17.75 -- The CXX compiler identification is GNU 11.4.0 #12 17.76 -- Detecting C compiler ABI info #12 17.82 -- Detecting C compiler ABI info - done #12 17.83 -- Check for working C compiler: /usr/bin/cc - skipped #12 17.83 -- Detecting C compile features #12 17.83 -- Detecting C compile features - done #12 17.84 -- Detecting CXX compiler ABI info #12 17.91 -- Detecting CXX compiler ABI info - done #12 17.92 -- Check for working CXX compiler: /usr/bin/c++ - skipped #12 17.92 -- Detecting CXX compile features #12 17.92 -- Detecting CXX compile features - done #12 17.93 -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") #12 17.94 CMake Warning (dev) at /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): #12 17.94 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules #12 17.94 are removed. Run "cmake --help-policy CMP0148" for policy details. Use #12 17.94 the cmake_policy command to set the policy and suppress this warning. #12 17.94 #12 17.94 Call Stack (most recent call first): #12 17.94 /usr/local/share/cmake/pybind11/pybind11Tools.cmake:50 (find_package) #12 17.94 /usr/local/share/cmake/pybind11/pybind11Common.cmake:188 (include) #12 17.94 /usr/local/share/cmake/pybind11/pybind11Config.cmake:250 (include) #12 17.94 CMakeLists.txt:19 (find_package) #12 17.94 This warning is for project developers. Use -Wno-dev to suppress it. #12 17.94 #12 17.95 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.10.12", minimum required is "3.6") #12 17.97 -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so #12 17.97 -- Performing Test HAS_FLTO #12 18.07 -- Performing Test HAS_FLTO - Success #12 18.07 -- Found pybind11: /usr/local/include (found version "2.11.1") #12 18.08 -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") #12 18.08 -- Looking for BZ2_bzCompressInit #12 18.14 -- Looking for BZ2_bzCompressInit - found #12 18.14 -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so #12 18.19 -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found #12 18.19 -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so #12 18.25 -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found #12 18.25 -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so #12 18.30 -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - found #12 18.30 -- Found LibLZMA: /usr/lib/x86_64-linux-gnu/liblzma.so (found version "5.2.5") #12 18.31 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") #12 18.36 -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.81.0") #12 18.36 -- #12 18.36 #12 18.85 -- Found OpenMP_C: -fopenmp (found version "4.5") #12 18.93 -- Found OpenMP_CXX: -fopenmp (found version "4.5") #12 18.93 -- Found OpenMP: TRUE (found version "4.5") #12 18.93 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD #12 18.99 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success #12 18.99 -- Found Threads: TRUE #12 18.99 -- Checking for module 'htslib' #12 19.00 -- Found htslib, version 1.19 #12 19.03 -- Checking for module 'tabixpp' #12 19.03 -- No package 'tabixpp' found #12 19.03 -- OK: found libfwa: /soft/WFA2-lib-2.3.4/lib/libwfa2.so #12 19.03 -- WFA using include /soft/WFA2-lib-2.3.4/include/wfa2lib #12 19.05 -- Configuring done (1.4s) #12 19.24 -- Generating done (0.2s) #12 19.25 -- Build files have been written to: /soft/vcflib-1.0.9-src/build #12 19.28 [ 0%] Creating directories for 'ZIG-EXT' #12 19.29 [ 0%] No download step for 'ZIG-EXT' #12 19.29 [ 0%] No update step for 'ZIG-EXT' #12 19.30 [ 1%] No patch step for 'ZIG-EXT' #12 19.30 [ 2%] No configure step for 'ZIG-EXT' #12 19.31 [ 2%] Performing build step for 'ZIG-EXT' #12 28.43 [ 3%] No install step for 'ZIG-EXT' #12 28.43 [ 3%] Completed 'ZIG-EXT' #12 28.44 [ 3%] Built target ZIG-EXT #12 28.45 [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o #12 29.32 [ 4%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o #12 30.96 [ 4%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o #12 31.87 [ 5%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o #12 34.12 [ 5%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o #12 34.44 [ 6%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o #12 35.04 [ 6%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o #12 35.49 [ 7%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o #12 36.09 [ 7%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o #12 36.40 [ 8%] Building CXX object CMakeFiles/vcflib.dir/src/rkmh.cpp.o #12 36.92 [ 8%] Building CXX object CMakeFiles/vcflib.dir/src/murmur3.cpp.o #12 36.95 [ 9%] Building CXX object CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o #12 37.60 [ 9%] Building CXX object CMakeFiles/vcflib.dir/src/cigar.cpp.o #12 38.10 [ 10%] Building CXX object CMakeFiles/vcflib.dir/src/allele.cpp.o #12 38.41 [ 10%] Building CXX object CMakeFiles/vcflib.dir/contrib/fastahack/Fasta.cpp.o #12 39.11 [ 11%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/SmithWatermanGotoh.cpp.o #12 39.74 [ 11%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/Repeats.cpp.o #12 40.10 [ 12%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/IndelAllele.cpp.o #12 40.39 [ 12%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/disorder.cpp.o #12 40.54 [ 13%] Building CXX object CMakeFiles/vcflib.dir/contrib/smithwaterman/LeftAlign.cpp.o #12 41.19 [ 13%] Building C object CMakeFiles/vcflib.dir/contrib/fsom/fsom.c.o ... #12 DONE 246.6s ```

Screenshots

image

Build log with zig v0.11.0 ``` #12 [ 8/12] RUN cd "/soft" && wget -q "https://github.com/vcflib/vcflib/archive/refs/tags/v1.0.9.tar.gz" -O "/soft/vcflib-1.0.9.tar.gz" && tar -xzf "/soft/vcflib-1.0.9.tar.gz" && mv "/soft/vcflib-1.0.9" "/soft/vcflib-1.0.9-src" && git clone --recursive --depth=1 -j8 https://github.com/vcflib/vcflib.git "/soft/vcflib-master" && cp -r "/soft/vcflib-master/contrib"/* "/soft/vcflib-1.0.9-src/contrib" && cd "/soft/vcflib-1.0.9-src" && mkdir -p build && cd build && sed -i -e "s|^\(include_directories(contrib/c-progress-bar).*\)$|\1\ninclude_directories(/soft/htslib-1.19/include)|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e "s|^\(endif(HTSLIB_LOCAL).*\)$|\1\nlink_directories(/soft/htslib-1.19/lib)|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e "s|^\( set(WFA_INCLUDE_DIRS \)${CMAKE_INSTALL_PREFIX}\(/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib).*\)$|\1/soft/WFA2-lib-2.3.4\2|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e "s|^\( find_library(WFALIB \)\(wfa2 wfa\)\().*\)$|\1NAMES \2 PATHS /soft/WFA2-lib-2.3.4/lib\3|" "/soft/vcflib-1.0.9-src/CMakeLists.txt" && sed -i -e 's|^\( message(STATUS "ERROR: Can not find libfwa.*\)$|\1\n else(NOT WFALIB)\n message(STATUS "OK: found libfwa: ${WFALIB}")|' "/soft/vcflib-1.0.9-src/CMakeLists.txt" && cmake -DPYTHON_EXECUTABLE=/usr/bin/python3.10 -DCMAKE_INSTALL_PREFIX="/soft/vcflib-1.0.9" -DWFA_GITMODULE=OFF .. && make && make install && cd "/soft" && rm -r "/soft/vcflib-1.0.9-src" "/soft/vcflib-master" && rm "/soft/vcflib-1.0.9.tar.gz" #12 4.718 Cloning into '/soft/vcflib-master'... #12 10.71 Submodule 'contrib/WFA2-lib' (https://github.com/smarco/WFA2-lib) registered for path 'contrib/WFA2-lib' #12 10.71 Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'contrib/fastahack' #12 10.71 Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'contrib/filevercmp' #12 10.71 Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'contrib/fsom' #12 10.71 Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'contrib/intervaltree' #12 10.71 Submodule 'libVCFH' (https://github.com/edawson/libVCFH.git) registered for path 'contrib/libVCFH' #12 10.71 Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'contrib/multichoose' #12 10.71 Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'contrib/smithwaterman' #12 10.71 Submodule 'contrib/tabixpp' (https://github.com/vcflib/tabixpp.git) registered for path 'contrib/tabixpp' #12 10.71 Submodule 'src/simde' (https://github.com/simd-everywhere/simde-no-tests.git) registered for path 'src/simde' #12 10.71 Cloning into '/soft/vcflib-master/contrib/WFA2-lib'... #12 12.25 Cloning into '/soft/vcflib-master/contrib/fsom'... #12 12.25 Cloning into '/soft/vcflib-master/contrib/filevercmp'... #12 12.25 Cloning into '/soft/vcflib-master/contrib/intervaltree'... #12 12.25 Cloning into '/soft/vcflib-master/contrib/multichoose'... #12 12.25 Cloning into '/soft/vcflib-master/contrib/smithwaterman'... #12 12.25 Cloning into '/soft/vcflib-master/contrib/fastahack'... #12 12.35 Cloning into '/soft/vcflib-master/src/simde'... #12 14.02 Cloning into '/soft/vcflib-master/contrib/tabixpp'... #12 14.02 Cloning into '/soft/vcflib-master/contrib/libVCFH'... #12 14.07 Submodule path 'contrib/WFA2-lib': checked out 'ab690aa9b3015dc2551387080cbc067d6ab4e490' #12 14.09 Submodule path 'contrib/fastahack': checked out 'bb332654766c2177d6ec07941fe43facf8483b1d' #12 14.10 Submodule path 'contrib/filevercmp': checked out 'df20dcc4a2a772de56e804e8fbbcdef1ac068bbe' #12 14.12 Submodule path 'contrib/fsom': checked out '56695e1611d824cda97f08e932d25d08419170cd' #12 14.14 Submodule path 'contrib/intervaltree': checked out 'aa5937755000f1cd007402d03b6f7ce4427c5d21' #12 14.16 Submodule path 'contrib/libVCFH': checked out '44b6580639a216a484fd96de75a839091f25768a' #12 14.17 Submodule path 'contrib/multichoose': checked out 'e1f94aeb5d52542b000287fd8e0204c78906897e' #12 14.19 Submodule path 'contrib/smithwaterman': checked out '2610e259611ae4cde8f03c72499d28f03f6d38a7' #12 14.21 Submodule path 'contrib/tabixpp': checked out 'ae5cdf846af85bd1d0e310c05e5c67b037f51a25' #12 14.21 Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'contrib/tabixpp/htslib' #12 14.21 Cloning into '/soft/vcflib-master/contrib/tabixpp/htslib'... #12 16.16 Submodule path 'contrib/tabixpp/htslib': checked out '53f980829d3c906ff1d0506212a3e2c8c83b2cb3' #12 16.17 Submodule 'htscodecs' (https://github.com/samtools/htscodecs.git) registered for path 'contrib/tabixpp/htslib/htscodecs' #12 16.17 Cloning into '/soft/vcflib-master/contrib/tabixpp/htslib/htscodecs'... #12 21.09 Submodule path 'contrib/tabixpp/htslib/htscodecs': checked out '3ef17f6fb5b8b6b0ad2d4c1c562165664f0703f8' #12 21.16 Submodule path 'src/simde': checked out 'cbef1c152ad2e73bc8971c306208f55f44b16088' #12 21.29 -- The C compiler identification is GNU 11.4.0 #12 21.35 -- The CXX compiler identification is GNU 11.4.0 #12 21.36 -- Detecting C compiler ABI info #12 21.41 -- Detecting C compiler ABI info - done #12 21.42 -- Check for working C compiler: /usr/bin/cc - skipped #12 21.42 -- Detecting C compile features #12 21.43 -- Detecting C compile features - done #12 21.43 -- Detecting CXX compiler ABI info #12 21.50 -- Detecting CXX compiler ABI info - done #12 21.51 -- Check for working CXX compiler: /usr/bin/c++ - skipped #12 21.51 -- Detecting CXX compile features #12 21.51 -- Detecting CXX compile features - done #12 21.52 -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") #12 21.52 CMake Warning (dev) at /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): #12 21.52 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules #12 21.52 are removed. Run "cmake --help-policy CMP0148" for policy details. Use #12 21.52 the cmake_policy command to set the policy and suppress this warning. #12 21.52 #12 21.52 Call Stack (most recent call first): #12 21.52 /usr/local/share/cmake/pybind11/pybind11Tools.cmake:50 (find_package) #12 21.52 /usr/local/share/cmake/pybind11/pybind11Common.cmake:188 (include) #12 21.52 /usr/local/share/cmake/pybind11/pybind11Config.cmake:250 (include) #12 21.52 CMakeLists.txt:19 (find_package) #12 21.52 This warning is for project developers. Use -Wno-dev to suppress it. #12 21.52 #12 21.54 -- Found PythonInterp: /usr/bin/python3.10 (found suitable version "3.10.12", minimum required is "3.6") #12 21.55 -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so #12 21.55 -- Performing Test HAS_FLTO #12 21.65 -- Performing Test HAS_FLTO - Success #12 21.65 -- Found pybind11: /usr/local/include (found version "2.11.1") #12 21.66 -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") #12 21.66 -- Looking for BZ2_bzCompressInit #12 21.71 -- Looking for BZ2_bzCompressInit - found #12 21.71 -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so #12 21.76 -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found #12 21.76 -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so #12 21.81 -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found #12 21.81 -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so #12 21.86 -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - found #12 21.86 -- Found LibLZMA: /usr/lib/x86_64-linux-gnu/liblzma.so (found version "5.2.5") #12 21.87 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") #12 21.92 -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.81.0") #12 21.92 -- #12 21.92 #12 22.40 -- Found OpenMP_C: -fopenmp (found version "4.5") #12 22.48 -- Found OpenMP_CXX: -fopenmp (found version "4.5") #12 22.48 -- Found OpenMP: TRUE (found version "4.5") #12 22.48 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD #12 22.54 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success #12 22.54 -- Found Threads: TRUE #12 22.54 -- Checking for module 'htslib' #12 22.55 -- Found htslib, version 1.19 #12 22.57 -- Checking for module 'tabixpp' #12 22.58 -- No package 'tabixpp' found #12 22.58 -- OK: found libfwa: /soft/WFA2-lib-2.3.4/lib/libwfa2.so #12 22.58 -- WFA using include /soft/WFA2-lib-2.3.4/include/wfa2lib #12 22.59 -- Configuring done (1.3s) #12 22.80 -- Generating done (0.2s) #12 22.81 -- Build files have been written to: /soft/vcflib-1.0.9-src/build #12 22.83 [ 0%] Creating directories for 'ZIG-EXT' #12 22.84 [ 0%] No download step for 'ZIG-EXT' #12 22.85 [ 0%] No update step for 'ZIG-EXT' #12 22.85 [ 1%] No patch step for 'ZIG-EXT' #12 22.86 [ 2%] No configure step for 'ZIG-EXT' #12 22.87 [ 2%] Performing build step for 'ZIG-EXT' #12 26.71 /soft/vcflib-1.0.9-src/src/zig/build.zig:7:19: error: no field or member function named 'standardReleaseOptions' in 'Build' #12 26.71 /soft/zig-linux-x86_64-0.11.0/lib/std/Build.zig:1:1: note: struct declared here #12 26.73 make[2]: *** [CMakeFiles/ZIG-EXT.dir/build.make:86: ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-build] Error 2 #12 26.73 make[1]: *** [CMakeFiles/Makefile2:284: CMakeFiles/ZIG-EXT.dir/all] Error 2 #12 26.73 make: *** [Makefile:146: all] Error 2 #12 ERROR: process "/bin/sh -c cd \"$SOFT\" && wget -q \"[https://github.com/vcflib/vcflib/archive/refs/tags/v${VCFLIB_VERSION}.tar.gz\](https://github.com/vcflib/vcflib/archive/refs/tags/v$%7BVCFLIB_VERSION%7D.tar.gz/)" -O \"$SOFT/vcflib-${VCFLIB_VERSION}.tar.gz\" && tar -xzf \"$SOFT/vcflib-${VCFLIB_VERSION}.tar.gz\" && mv \"$SOFT/vcflib-${VCFLIB_VERSION}\" \"$SOFT/vcflib-${VCFLIB_VERSION}-src\" && git clone --recursive --depth=1 -j8 https://github.com/vcflib/vcflib.git \"$SOFT/vcflib-master\" && cp -r \"$SOFT/vcflib-master/contrib\"/* \"$SOFT/vcflib-${VCFLIB_VERSION}-src/contrib\" && cd \"$SOFT/vcflib-${VCFLIB_VERSION}-src\" && mkdir -p build && cd build && sed -i -e \"s|^\\(include_directories(contrib/c-progress-bar).*\\)$|\\1\\ninclude_directories(${HTSLIB_DIR}/include)|\" \"$SOFT/vcflib-${VCFLIB_VERSION}-src/CMakeLists.txt\" && sed -i -e \"s|^\\(endif(HTSLIB_LOCAL).*\\)$|\\1\\nlink_directories(${HTSLIB_DIR}/lib)|\" \"$SOFT/vcflib-${VCFLIB_VERSION}-src/CMakeLists.txt\" && sed -i -e \"s|^\\( set(WFA_INCLUDE_DIRS \\)\\${CMAKE_INSTALL_PREFIX}\\(/\\${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib).*\\)$|\\1$SOFT/WFA2-lib-${WFA2_VERSION}\\2|\" \"$SOFT/vcflib-${VCFLIB_VERSION}-src/CMakeLists.txt\" && sed -i -e \"s|^\\( find_library(WFALIB \\)\\(wfa2 wfa\\)\\().*\\)$|\\1NAMES \\2 PATHS $SOFT/WFA2-lib-${WFA2_VERSION}/lib\\3|\" \"$SOFT/vcflib-${VCFLIB_VERSION}-src/CMakeLists.txt\" && sed -i -e 's|^\\( message(STATUS \"ERROR: Can not find libfwa.*\\)$|\\1\\n else(NOT WFALIB)\\n message(STATUS \"OK: found libfwa: ${WFALIB}\")|' \"$SOFT/vcflib-${VCFLIB_VERSION}-src/CMakeLists.txt\" && cmake -DPYTHON_EXECUTABLE=/usr/bin/python3.10 -DCMAKE_INSTALL_PREFIX=\"$SOFT/vcflib-${VCFLIB_VERSION}\" -DWFA_GITMODULE=OFF .. && make && make install && cd \"$SOFT\" && rm -r \"$SOFT/vcflib-${VCFLIB_VERSION}-src\" \"$SOFT/vcflib-master\" && rm \"$SOFT/vcflib-${VCFLIB_VERSION}.tar.gz\"" did not complete successfully: exit code: 2 ```

Additional context

Here is the line causing problem: https://github.com/vcflib/vcflib/blob/master/src/zig/build.zig#L7

Looks like there were some major changes in zig v0.11.0. Some similar links for this problem:

serge2016 commented 11 months ago

Same here. Help, please...

pettyalex commented 7 months ago

The docs specify to use zig 0.10.0, vcflib doesn't support any newer versions at this time.

I've been wanting to poke at Zig, so I'll take a peek at what it would take to update it.

Stikus commented 1 month ago

@pettyalex @pjotrp Hello, any news about latest zig support?

pjotrp commented 1 week ago

vcflib was updated to support zig latest. We are still waiting for upstream distros to incorporate Zig. There are some recent developments that may make that possible because someone is working on the bootstrap from source again.