Installation error

[DanielEWeeks]

Trying to install on a Centos 7 machine

$ uname -a
Linux ****.***.pitt.edu 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

running an old version of C++

$ c++ --version
c++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
$ cmake --version
cmake version 3.27.0-rc3

and it fails (output & error messages below). I suspect this is because I need a newer version of gcc - is this correct, or is there another fix that would not require me to update gcc?

cget install zlib,http://zlib.net/fossils/zlib-1.2.11.tar.gz
cget install -f requirements.txt
Downloading https://github.com/statgen/savvy/archive/019a1ddaa9ec588f807f234f68787862f94ea057.tar.gz
  [######################################################################]  100%
Extracting archive /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/019a1ddaa9ec588f807f234f68787862f94ea057.tar.gz ...
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Configuring done (1.3s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CGET_CMAKE_DIR
    CGET_CMAKE_ORIGINAL_SOURCE_FILE


-- Build files have been written to: /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/build
[ 11%] Building CXX object CMakeFiles/savvy.dir/src/savvy/reader.cpp.o
[ 11%] Building CXX object CMakeFiles/savvy.dir/src/savvy/site_info.cpp.o
[ 16%] Building CXX object CMakeFiles/savvy.dir/src/savvy/region.cpp.o
[ 33%] Building CXX object CMakeFiles/savvy.dir/src/savvy/sav_reader.cpp.o
[ 38%] Building CXX object CMakeFiles/savvy.dir/src/savvy/savvy.cpp.o
[ 38%] Building CXX object CMakeFiles/savvy.dir/src/savvy/vcf_reader.cpp.o
[ 38%] Building CXX object CMakeFiles/savvy.dir/src/savvy/utility.cpp.o
[ 44%] Building CXX object CMakeFiles/savvy.dir/src/savvy/varint.cpp.o
In file included from /usr/include/c++/4.8.2/ios:43:0,
                 from /usr/include/c++/4.8.2/ostream:38,
                 from /usr/include/c++/4.8.2/iterator:64,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/varint.hpp:12,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/sav_reader.hpp:11,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/sav_reader.cpp:7:
/usr/include/c++/4.8.2/streambuf: In constructor ‘shrinkwrap::stdio::filebuf::filebuf(shrinkwrap::stdio::filebuf::self_type&&)’:
/usr/include/c++/4.8.2/streambuf:802:7: error: ‘std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private
       basic_streambuf(const basic_streambuf& __sb)
       ^
In file included from /home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/istream.hpp:4:0,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/sav_reader.hpp:20,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/sav_reader.cpp:7:
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp:27:20: error: within this context
         fp_(src.fp_)
                    ^
In file included from /usr/include/c++/4.8.2/ios:43:0,
                 from /usr/include/c++/4.8.2/ostream:38,
                 from /usr/include/c++/4.8.2/iterator:64,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/varint.hpp:12,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/sav_reader.hpp:11,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/sav_reader.cpp:7:
/usr/include/c++/4.8.2/streambuf: In member function ‘shrinkwrap::stdio::filebuf::self_type& shrinkwrap::stdio::filebuf::operator=(shrinkwrap::stdio::filebuf::self_type&&)’:
/usr/include/c++/4.8.2/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private
       operator=(const basic_streambuf& __sb)
       ^
In file included from /home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/istream.hpp:4:0,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/sav_reader.hpp:20,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/sav_reader.cpp:7:
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp:36:51: error: within this context
           std::streambuf::operator=(std::move(src));
                                                   ^
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp: In member function ‘void shrinkwrap::stdio::filebuf::swap(shrinkwrap::stdio::filebuf::self_type&)’:
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp:45:9: error: ‘swap’ is not a member of ‘std::streambuf {aka std::basic_streambuf<char>}’
         std::streambuf::swap(src);
         ^
In file included from /usr/include/c++/4.8.2/ios:43:0,
                 from /usr/include/c++/4.8.2/ostream:38,
                 from /usr/include/c++/4.8.2/iterator:64,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/site_info.hpp:16,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/reader.hpp:10,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/reader.cpp:7:
/usr/include/c++/4.8.2/streambuf: In constructor ‘shrinkwrap::stdio::filebuf::filebuf(shrinkwrap::stdio::filebuf::self_type&&)’:
/usr/include/c++/4.8.2/streambuf:802:7: error: ‘std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private
       basic_streambuf(const basic_streambuf& __sb)
       ^
In file included from /home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/istream.hpp:4:0,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/sav_reader.hpp:20,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/reader.hpp:11,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/reader.cpp:7:
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp:27:20: error: within this context
         fp_(src.fp_)
                    ^
In file included from /usr/include/c++/4.8.2/ios:43:0,
                 from /usr/include/c++/4.8.2/ostream:38,
                 from /usr/include/c++/4.8.2/iterator:64,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/site_info.hpp:16,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/reader.hpp:10,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/reader.cpp:7:
/usr/include/c++/4.8.2/streambuf: In member function ‘shrinkwrap::stdio::filebuf::self_type& shrinkwrap::stdio::filebuf::operator=(shrinkwrap::stdio::filebuf::self_type&&)’:
/usr/include/c++/4.8.2/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private
       operator=(const basic_streambuf& __sb)
       ^
In file included from /home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/istream.hpp:4:0,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/sav_reader.hpp:20,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/include/savvy/reader.hpp:11,
                 from /home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/savvy-019a1ddaa9ec588f807f234f68787862f94ea057/src/savvy/reader.cpp:7:
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp:36:51: error: within this context
           std::streambuf::operator=(std::move(src));
                                                   ^
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp: In member function ‘void shrinkwrap::stdio::filebuf::swap(shrinkwrap::stdio::filebuf::self_type&)’:
/home/shared_data/software/raremetal/raremetal-master/cget/include/shrinkwrap/stdio.hpp:45:9: error: ‘swap’ is not a member of ‘std::streambuf {aka std::basic_streambuf<char>}’
         std::streambuf::swap(src);
         ^
gmake[2]: *** [CMakeFiles/savvy.dir/src/savvy/reader.cpp.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
gmake[2]: *** [CMakeFiles/savvy.dir/src/savvy/sav_reader.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/savvy.dir/all] Error 2
gmake: *** [all] Error 2
Command failed: ['/usr/local/bin/cmake', '--build', '/home/shared_data/software/raremetal/raremetal-master/cget/cget/build/tmp-acf389cfb58247a38e5e5ddf7df45342/build', '--config', 'Release', '--', '-j', '48']
Failed to build package statgen/savvy

[jonathonl]

You are correct. GCC v4.8 does not fully support C++ 11. You can check if there is a newer version already installed by running scl --list | grep devtoolset. You can use anything greater than devtoolset-4.

[DanielEWeeks]

Thank you - a newer version was already available, and, after switching to that, I was able to get it to compile:

$ scl --list | grep devtoolset
devtoolset-8
$ scl enable devtoolset-8 bash
$ gcc --version
gcc (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)

Test 1 failed - should I be concerned about that?

75% tests passed, 1 tests failed out of 4

Total Test time (real) =   6.11 sec

The following tests FAILED:
	  1 - test_tut_rmw_kin (Failed)

[jonathonl]

Running the test with make CTEST_OUTPUT_ON_FAILURE=1 test should print more information about the failure. If diff failed, I would check whether the differences are meaningful (i.e., not small rounding differences in the numbers).

NOTE: I have encountered weirdness with other software compiled with alternate devtoolsets on centos7/rhel7.