conflicting declaration of 'char

Masha Vecherkovskaya mashavecher at gmail.com
Fri Nov 19 06:01:05 UTC 2021


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
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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


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