bedtools2
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arq5x
Error: Type checker found wrong number of fields while tokenizing data line.
Dear developers,
I have been using bedtools for very long time on my Mac. Recently I changed the Mac OS to the last Big Sur version. Since that time I started to get the error "Error: Type checker found wrong number of fields while tokenizing data line." during the bedtools intersect command. This problem disappears if I remove headers from bed files or VCF files but this is very inconvenient.
Best regards, Andrey
Could you try cloning from master and testing with that version, as there are some unreleased improvements to the type checking?
Can not build unfortunately:
Building BEDTools:
CXXFLAGS is [-g -Wall -O2 -std=c++11 ] DETECTED_VERSION = v2.29.2-64-gcc714eb0 CURRENT_VERSION = Updating version file.
- compiling src/bedtools.cpp In file included from src/bedtools.cpp:17: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iostream:37: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ios:215: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:14: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/string:504: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/string_view:175: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__string:57: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/algorithm:642: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/utility:204: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:157:8: error: no member named 'uint8_t' in the global namespace using::uint8_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:158:8: error: no member named 'uint16_t' in the global namespace using::uint16_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:159:8: error: no member named 'uint32_t' in the global namespace using::uint32_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:160:8: error: no member named 'uint64_t' in the global namespace using::uint64_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:162:8: error: no member named 'int_least8_t' in the global namespace using::int_least8_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:163:8: error: no member named 'int_least16_t' in the global namespace using::int_least16_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:164:8: error: no member named 'int_least32_t' in the global namespace using::int_least32_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:165:8: error: no member named 'int_least64_t' in the global namespace using::int_least64_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:167:8: error: no member named 'uint_least8_t' in the global namespace using::uint_least8_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:168:8: error: no member named 'uint_least16_t' in the global namespace using::uint_least16_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:169:8: error: no member named 'uint_least32_t' in the global namespace using::uint_least32_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:170:8: error: no member named 'uint_least64_t' in the global namespace using::uint_least64_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:172:8: error: no member named 'int_fast8_t' in the global namespace using::int_fast8_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:173:8: error: no member named 'int_fast16_t' in the global namespace using::int_fast16_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:174:8: error: no member named 'int_fast32_t' in the global namespace using::int_fast32_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:175:8: error: no member named 'int_fast64_t' in the global namespace using::int_fast64_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:177:8: error: no member named 'uint_fast8_t' in the global namespace using::uint_fast8_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:178:8: error: no member named 'uint_fast16_t' in the global namespace using::uint_fast16_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cstdint:179:8: error: no member named 'uint_fast32_t' in the global namespace using::uint_fast32_t; ~~^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make: *** [obj/bedtools.o] Error 1
These errors suggest to me that you need to install the XCode Command Line tools, etc., as it seems your upgrade is missing standard C and C++ libraries.