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Installation on computer cluster possibly interfering with building metabat2.cpp.o?

Issue #76 resolved
Former user created an issue

Hi,

I'm installing Metabat2 on a computer cluster, and I'm wondering if this is the reason my Metabat2 installation isn't working. Relevant output from 'make' step of installation is reproduced below.

Best,

Katharine Dickson

[ 68%] Checking the git repository for changes...
make[2]: warning:  Clock skew detected.  Your build may be incomplete.
[ 68%] Built target check_git_repository
make[2]: Warning: File `src/CMakeFiles/metabat2.dir/progress.make' has modification time 1e+02 s in the future
make[2]: warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Warning: File `src/CMakeFiles/metabat2.dir/progress.make' has modification time 1e+02 s in the future
[ 72%] Building CXX object src/CMakeFiles/metabat2.dir/metabat2.cpp.o
In file included from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.h:35,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.cpp:1:
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:8:18: error: atomic: No such file or directory
In file included from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:24,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.h:35,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.cpp:1:
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_config.hh:10: error: ‘constexpr’ does not name a type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_config.hh:13: error: ‘constexpr’ does not name a type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_config.hh:20: error: ‘constexpr’ does not name a type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_config.hh:26: error: expected constructor, destructor, or type conversion before ‘double’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_config.hh:31: error: ‘constexpr’ does not name a type
In file included from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:25,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.h:35,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.cpp:1:
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_util.hh:93: error: expected ‘;’ before ‘noexcept’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_util.hh:101: error: expected ‘;’ before ‘double’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_util.hh:124: error: expected ‘;’ before ‘noexcept’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_util.hh:131: error: expected ‘;’ before ‘size_t’
In file included from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:26,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.h:35,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.cpp:1:
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:30: error: expected nested-name-specifier before ‘key_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:30: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:30: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:30: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:31: error: expected nested-name-specifier before ‘mapped_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:31: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:31: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:31: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:32: error: expected nested-name-specifier before ‘value_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:32: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:32: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:32: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:33: error: expected nested-name-specifier before ‘allocator_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:33: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:33: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:33: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:34: error: expected nested-name-specifier before ‘partial_t’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:34: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:34: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:34: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:35: error: expected nested-name-specifier before ‘size_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:35: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:35: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:35: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:36: error: expected nested-name-specifier before ‘reference’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:36: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:36: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:36: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:37: error: expected nested-name-specifier before ‘const_reference’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:37: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:37: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:37: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:38: error: expected nested-name-specifier before ‘pointer’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:38: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:38: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:38: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:39: error: expected nested-name-specifier before ‘const_pointer’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:39: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:39: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:39: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:51: error: expected ‘;’ before ‘noexcept’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:51: error: expected ‘;’ before ‘{’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:51: error: expected unqualified-id before ‘{’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:53: error: ISO C++ forbids declaration of ‘value_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:53: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:57: error: expected ‘;’ before ‘value_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:57: error: ISO C++ forbids declaration of ‘value_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:57: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:61: error: expected ‘;’ before ‘const’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:61: error: ISO C++ forbids declaration of ‘key_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:61: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:64: error: expected ‘;’ before ‘key_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:64: error: ISO C++ forbids declaration of ‘key_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:64: error: expected ‘;’ before ‘&&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:68: error: expected ‘;’ before ‘const’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:68: error: ISO C++ forbids declaration of ‘mapped_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:68: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:71: error: expected ‘;’ before ‘mapped_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:71: error: ISO C++ forbids declaration of ‘mapped_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:71: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:73: error: expected ‘;’ before ‘partial_t’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:73: error: ‘partial_t’ does not name a type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:74: error: ISO C++ forbids declaration of ‘partial_t’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:74: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:76: error: expected ‘;’ before ‘bool’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:76: error: ‘size_type’ has not been declared
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:77: error: expected ‘;’ before ‘(’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:79: error: expected ‘;’ before ‘private’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:82: error: expected nested-name-specifier before ‘storage_value_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:82: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:82: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:82: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:84: error: ISO C++ forbids declaration of ‘storage_value_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:84: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:88: error: expected ‘;’ before ‘storage_value_type’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:88: error: ISO C++ forbids declaration of ‘storage_value_type’ with no type
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:88: error: expected ‘;’ before ‘&’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:93: error: expected ‘;’ before ‘std’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:93: error: ‘storage_value_type’ was not declared in this scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:94: error: ‘storage_value_type’ was not declared in this scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:94: error: a function call cannot appear in a constant-expression
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:94: error: template argument 1 is invalid
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:94: error: template argument 2 is invalid
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:95: error: template argument 1 is invalid
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:96: error: expected ‘::’ before ‘values_’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:97: error: ‘partial_t’ was not declared in this scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:97: error: template argument 1 is invalid
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:102: error: expected nested-name-specifier before ‘alloc_traits_’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:102: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:102: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:102: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:103: error: expected nested-name-specifier before ‘storage_value_traits_’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:103: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:103: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:103: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:105: error: expected nested-name-specifier before ‘bucket_traits_’
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:105: error: using-declaration for non-member at class scope
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:105: error: expected ‘;’ before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:105: error: expected unqualified-id before ‘=’ token
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/libcuckoo_bucket_container.hh:108: error: expected ‘)’ before ‘hp’
In file included from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.h:35,
                 from /home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/metabat2.cpp:1:
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:1211: error: expected ‘}’ before end of line
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:1211: error: expected unqualified-id before end of line
/home/kdickson/Mining/berkeleylab-metabat-236d20e76303/src/cuckoohash_map.hh:1211: error: expected declaration before end of line
make[2]: *** [src/CMakeFiles/metabat2.dir/metabat2.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/metabat2.dir/all] Error 2
make: *** [all] Error 2

Comments (2)

  1. Rob Egan

    It looks like you are using an ancient compiler that does not support atomics. What is your compiler and version?

    The requirements to build are:

    • gcc/g++ >= 4.9 or intel >= 18.0.1.163 or llvm >= 8.0

    ‌

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