macOS 10.13.6 installation: cannot run C++ compiled programs

[mdozmorov]

Hello,

Running ./configure fails with "configure: error: cannot run C++ compiled programs." A bigger picture - I'm trying to compile ea-utils, which fails with the same error.

The detailed output of ./configure is:

checking whether make sets $(MAKE)... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/Users/mdozmorov/Documents/nobackup/ea-utils/clipper/sparsehash':
configure: error: cannot run C++ compiled programs.

And the full config.log is attached.

Thanks for your help,
Mikhail
config.log

[PhilipDeegan]

ExpressionAnalysis/ea-utils#75

you could try this to see if it works for you

[mdozmorov]

The sparsehash-c11 version doesn't have the configure file. When I just try running make, it still errors:

<... lots of outputs skipped ...>
      testing::internal::UniversalTersePrinter<wchar_t const*>::Print(wchar_t const*, std::__1::basic_ostream<char, std::__1::char_traits<char> >*) in gmock-gtest-all.o
  "_write", referenced from:
      testing::internal::DeathTestImpl::Abort(testing::internal::DeathTest::AbortReason) in gmock-gtest-all.o
ld: symbol(s) not found for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Makefile:46: sparsehash_unittests] Error 1

I'm not very familiar with C code structure and compiling, so not sure where to go from here...

[PhilipDeegan]

https://github.com/sparsehash/sparsehash-c11 is header only - there is no configure required.

make is just compiling the tests, which it looks like you're having trouble with a system call with

[PhilipDeegan]

are you positive your compiler is not misconfigured in some way?

[mdozmorov]

Not sure what may be misconfigured. The system is rather fresh. I've been googling, finding some suggestions about "LD_LIBRARY_PATH" variable (empty in my case), but not sure where to go from there. My configuration files are rather simple: dotfiles.

And, some info about gcc and g++:

/usr/bin/gcc
(base) MacBook-Pro-4:dotfiles mdozmorov$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
(base) MacBook-Pro-4:dotfiles mdozmorov$ which g++
/usr/bin/g++
(base) MacBook-Pro-4:dotfiles mdozmorov$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
(base) MacBook-Pro-4:dotfiles mdozmorov$

Anything obviously misconfigured?

[PhilipDeegan]

clang++ and g++ have different targets
I've found g++ on macos to be quite troublesome

did you install the latest xcode? that has a version of clang > 4 I think and I would suggest using that if possible

[mdozmorov]

Xcode seem up-to-date, Version 10.1 (10B61), no updates. clang version is

clang --version
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Users/mdozmorov/miniconda2/bin
(base) MacBook-Pro-4:Cancer_notes mdozmorov$ which clang
/Users/mdozmorov/miniconda2/bin/clang

Re: "clang++ and g++ have different targets" - anything one can do about it?

[PhilipDeegan]

https://travis-ci.org/mkn/google.sparsehash/jobs/517842961 looks all ok here with OSX 10.2 and CLANG 7

[mdozmorov]

I was following https://embeddedartistry.com/blog/2017/2/20/installing-clangllvm-on-osx. After setting the path and the flags in a terminal session as recommended, I can run make on https://github.com/sparsehash/sparsehash-c11 without errors.

Not sure what to do next to compile sparsehash itself.

[PhilipDeegan]

did you try "./configure" after setting the flags/etc?

[mdozmorov]

Compiling after setting the environment as described https://embeddedartistry.com/blog/2017/2/20/installing-clangllvm-on-osx worked! So, after running make for https://github.com/sparsehash/sparsehash-c11, I could ./configure, make and make install for https://github.com/sparsehash/sparsehash.

As of the bigger picture, ea-utils partially compiled with these setting. Most of the tools can now be run as binaries. One error ('samtools/sam.h' file not found with include; use "quotes" instead), but that is a different story and issue.

Thank you, @dekken, for quick help with this.