Hey, I'm having some trouble when using the default clang compiler on the Mac. I get errors like this
$ ./countKmer.out -l -k 1 -i test/toyexample/virus/AJ609634.fasta -o OUTPUT/tmp/KC/AJ609634.fasta -s AJ609634.fasta
option -l: the input file is longseq (need to concatenate lines).
option -k, the value of k, with value `1'
option -i, the input filename, with value `test/toyexample/virus/AJ609634.fasta'
option -o, the output directory, with value `OUTPUT/tmp/KC/AJ609634.fasta'
option -s, the short name, with value `AJ609634.fasta'
outputFileDir: OUTPUT/tmp/KC/AJ609634.fasta/
combinefileName: OUTPUT/tmp/KC/AJ609634.fasta/AJ609634.fasta_combine
dyld: lazy symbol binding failed: Symbol not found: __ZNKSt9basic_iosIcSt11char_traitsIcEEcvbEv
Referenced from: VirHostMatcher/./countKmer.out
Expected in: /usr/lib/libstdc++.6.dylib
dyld: Symbol not found: __ZNKSt9basic_iosIcSt11char_traitsIcEEcvbEv
Referenced from: VirHostMatcher/./countKmer.out
Expected in: /usr/lib/libstdc++.6.dylib
Abort trap: 6
Default version of g++ is
$ /usr/bin/g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 9.0.0 (clang-900.0.37)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
When I compile the c++ code using the gnu gcc compiler from Homebrew (in this case g++-7 (Homebrew GCC 7.2.0) 7.2.0) like this
$ CC="$(brew --prefix)/bin/g++-7" make
and then re-run everything, it works fine.
So (at least on my Mac -- OSX 10.12.6), it looks like the default clang gcc doesn't work but the gnu gcc does work.
Hey, I'm having some trouble when using the default clang compiler on the Mac. I get errors like this
Default version of
g++
isWhen I compile the c++ code using the gnu gcc compiler from Homebrew (in this case
g++-7 (Homebrew GCC 7.2.0) 7.2.0
) like thisand then re-run everything, it works fine.
So (at least on my Mac -- OSX 10.12.6), it looks like the default clang gcc doesn't work but the gnu gcc does work.