Hi. Could someone please have a look, I can’t figure out this one myself. I’m trying to build a program and make fails with
*error: *conflicting declaration of '*char* ctermid(char*)*' with '*C*' linkage 222 | char **ctermid*(char *); I’ve attacheched all steps I’ve taken. I have also tried to use apple clang, but configure fails Masha
MacBook-Pro:build mashavecher$ export CXX=/opt/local/bin/g++-mp-11 MacBook-Pro:build mashavecher$ export CC=/opt/local/bin/gcc-mp-11 MacBook-Pro:build mashavecher$ /Applications/strelka/configure --jobs=4 --prefix=/Applications/strelka cmake version 3.21.4 (>= 2.8.12) is already installed Using existing cmake: cmake -- ==== Initializing project cmake configuration ==== -- BUILD_TYPE: Release -- CMAKE_PARALLEL: 4 -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/local/bin/gcc-mp-11 - skipped -- Detecting C compile features -- Detecting C compile features - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /opt/local/bin/g++-mp-11 - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- TARGET_ARCHITECTURE: x86_64 -- install prefix: /Applications/strelka -- Found Boost: /opt/local/include (found suitable version "1.76.0", minimum required is "1.58.0") -- Boost component: date_time status: STATIC LIBRARY NOT FOUND -- Boost component: filesystem status: STATIC LIBRARY NOT FOUND -- Boost component: program_options status: STATIC LIBRARY NOT FOUND -- Boost component: serialization status: STATIC LIBRARY NOT FOUND -- Boost component: system status: STATIC LIBRARY NOT FOUND -- Boost component: timer status: STATIC LIBRARY NOT FOUND -- Boost component: chrono status: STATIC LIBRARY NOT FOUND -- Boost component: unit_test_framework status: STATIC LIBRARY NOT FOUND -- Boost version 1.58.0+ not found or found without all required components. Boost will be built from source distribution... -- Unpacking boost library source -- Configuring boost library -- Building boost library -- Successfuly built boost 1.58.0 -- Found Boost: /Applications/strelka/build/bootstrap/boost/include (found suitable version "1.58.0", minimum required is "1.58.0") found components: date_time filesystem program_options serialization system timer chrono unit_test_framework -- Building external tools -- Found ZLIB: /opt/local/lib/libz.dylib (found version "1.2.11") -- zlib found -- Verifying target directories access -- Looking for floorf -- Looking for floorf - found -- Looking for round -- Looking for round - found -- Looking for roundf -- Looking for roundf - found -- Looking for powf -- Looking for powf - found -- Looking for pthread.h CMake Warning (dev) at /opt/local/share/cmake-3.21/Modules/CheckIncludeFile.cmake:82 (message): Policy CMP0075 is not set: Include file check macros honor CMAKE_REQUIRED_LIBRARIES. Run "cmake --help-policy CMP0075" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMAKE_REQUIRED_LIBRARIES is set to: m For compatibility with CMake 3.11 and below this check is ignoring it. Call Stack (most recent call first): /opt/local/share/cmake-3.21/Modules/FindThreads.cmake:146 (CHECK_INCLUDE_FILE) src/cmake/cxxConfigure.cmake:79 (find_package) src/c++/CMakeLists.txt:38 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- No ccache found -- Using compiler: g++ version 11.2.0 -- Building in developer mode: treating compiler warnings as errors -- Adding c++ library subdirectory: test -- Adding c++ library subdirectory: strelka_common -- Adding c++ library subdirectory: starling_common -- Adding c++ test subdirectory: starling_common/test -- Adding c++ library subdirectory: alignment -- Adding c++ test subdirectory: alignment/test -- Adding c++ library subdirectory: assembly -- Adding c++ test subdirectory: assembly/test -- Adding c++ library subdirectory: blt_common -- Adding c++ test subdirectory: blt_common/test -- Adding c++ library subdirectory: calibration -- Adding c++ library subdirectory: errorAnalysis -- Adding c++ library subdirectory: options -- Adding c++ library subdirectory: appstats -- Adding c++ library subdirectory: htsapi -- Adding c++ test subdirectory: htsapi/test -- Adding c++ library subdirectory: common -- Adding c++ library subdirectory: blt_util -- Adding c++ test subdirectory: blt_util/test -- Adding c++ library subdirectory: DumpSequenceAlleleCounts -- Adding c++ library subdirectory: EstimateParametersFromAlleleCounts -- Adding c++ library subdirectory: EstimateVariantErrorRates -- Adding c++ library subdirectory: GetChromDepth -- Adding c++ library subdirectory: GetRegionDepth -- Adding c++ library subdirectory: GetSequenceAlleleCounts -- Adding c++ library subdirectory: MergeRunStats -- Adding c++ library subdirectory: MergeSequenceAlleleCounts -- Adding c++ library subdirectory: starling -- Adding c++ test subdirectory: starling/test -- Adding c++ library subdirectory: strelka -- Adding c++ test subdirectory: strelka/test -- Adding c++ library subdirectory: strelkaNoiseExtractor -- Adding c++ program subdirectory: bin -- Found Doxygen: /opt/local/bin/doxygen (found version "1.9.2") found components: doxygen dot -- Doxygen: /opt/local/bin/doxygen. Dot: /opt/local/bin/dot. -- Creating Doxygen config file: /Applications/strelka/build/src/c++/Doxyfile -- Configuring done -- Generating done -- Build files have been written to: /Applications/strelka/build The build directory /Applications/strelka/build was configured successfully Type "make -C /Applications/strelka/build" to build MacBook-Pro:build mashavecher$ make -C /Applications/strelka/build [ 0%] Built target strelka_source_check [ 0%] Updating buildtime config info -- Detected workflow version: UNKNOWN [ 0%] Built target strelka_buildtime_config [ 0%] Built target strelka_cxx_buildtime_config [ 1%] Building bgzf_extras [ 1%] Built target strelka_bgzfx [ 1%] Unpacking pyflow [ 1%] Building pyflow [ 1%] Built target strelka_pyflow [ 1%] Unpacking CodeMin [ 1%] Built target strelka_codemin [ 1%] Unpacking rapidjson package [ 1%] Built target strelka_rapidjson [ 1%] Unpacking htslib library [ 2%] Building htslib library [ 2%] Unpacking samtools package [ 2%] Building samtools package [ 2%] Built target strelka_samtools [ 2%] Running c++ static analyzer [ 2%] Built target strelka_cppcheck [ 2%] Built target strelka_opt [ 3%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/SiteNoise.cpp.o [ 3%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/SomaticIndelVcfWriter.cpp.o In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/wchar.h:90, from /opt/local/include/gcc11/c++/cwchar:44, from /opt/local/include/gcc11/c++/bits/postypes.h:40, from /opt/local/include/gcc11/c++/iosfwd:40, from /opt/local/include/gcc11/c++/iterator:64, from /Applications/strelka/build/bootstrap/boost/include/boost/next_prior.hpp:15, from /Applications/strelka/build/bootstrap/boost/include/boost/utility.hpp:18, from /Applications/strelka/src/c++/lib/applications/strelka/somatic_result_set.hh:27, from /Applications/strelka/src/c++/lib/applications/strelka/SomaticIndelVcfWriter.hh:26, from /Applications/strelka/src/c++/lib/applications/strelka/SomaticIndelVcfWriter.cpp:23: /opt/local/lib/gcc11/gcc/x86_64-apple-darwin18/11.2.0/include-fixed/stdio.h:222:10: error: conflicting declaration of 'char* ctermid(char*)' with 'C' linkage 222 | char *ctermid(char *); | ^~~~~~~ In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/unistd.h:525, from /Applications/strelka/build/bootstrap/boost/include/boost/config/stdlib/libstdcpp3.hpp:78, from /Applications/strelka/build/bootstrap/boost/include/boost/config.hpp:48, from /Applications/strelka/build/bootstrap/boost/include/boost/core/addressof.hpp:15, from /Applications/strelka/build/bootstrap/boost/include/boost/utility/addressof.hpp:15, from /Applications/strelka/build/bootstrap/boost/include/boost/utility.hpp:12, from /Applications/strelka/src/c++/lib/applications/strelka/somatic_result_set.hh:27, from /Applications/strelka/src/c++/lib/applications/strelka/SomaticIndelVcfWriter.hh:26, from /Applications/strelka/src/c++/lib/applications/strelka/SomaticIndelVcfWriter.cpp:23: /opt/local/lib/gcc11/gcc/x86_64-apple-darwin18/11.2.0/include-fixed/_ctermid.h:26:10: note: previous declaration with 'C++' linkage 26 | char *ctermid(char *); | ^~~~~~~ make[2]: *** [src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/SomaticIndelVcfWriter.cpp.o] Error 1 make[1]: *** [src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/all] Error 2 make: *** [all] Error 2