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Published
20 hours ago •
sanger-pathogens
sanger-pathogens
Installation issue Assembly-Stats on Mac
Hi, I am trying to install assembly stats via manual installation on my machine. I have installed zlib via Homebrew ahead of the installation. I have downloaded the .gz file, positioned it into my Applications folder and then proceeded to the installation as indicated on your page.
I recover multiple errors. First, while running "make test" i have this problem:
Running tests...
Test project /Applications/assembly-stats-master/build
Start 1: runUnitTests
Could not find executable runUnitTests
Looked in the following places:
runUnitTests
runUnitTests
Release/runUnitTests
Release/runUnitTests
Debug/runUnitTests
Debug/runUnitTests
MinSizeRel/runUnitTests
MinSizeRel/runUnitTests
RelWithDebInfo/runUnitTests
RelWithDebInfo/runUnitTests
Deployment/runUnitTests
Deployment/runUnitTests
Development/runUnitTests
Development/runUnitTests
Unable to find executable: runUnitTests
1/1 Test #1: runUnitTests .....................***Not Run 0.00 sec
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 0.00 sec
The following tests FAILED:
1 - runUnitTests (Not Run)
Errors while running CTest
Output from these tests are in: /Applications/assembly-stats-master/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.
make: *** [test] Error 8
Secondly, when i run "make install":
[ 5%] Building CXX object gtest-1.7.0/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 10%] Linking CXX static library libgtest.a
[ 10%] Built target gtest
[ 15%] Building CXX object gtest-1.7.0/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 21%] Linking CXX static library libgtest_main.a
[ 21%] Built target gtest_main
[ 26%] Building CXX object CMakeFiles/filetype.dir/filetype.cpp.o
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:18:
/Applications/assembly-stats-master/build/external/bxzstr/include/stream_wrapper.hpp:17:33: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
virtual ~stream_wrapper() = default;
^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:19:
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:62:18: error: exception specification of overriding function is more lax than base version
const char * what() const noexcept { return _msg.c_str(); }
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/exception:107:25: note: overridden virtual function is here
virtual const char* what() const _NOEXCEPT;
^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:19:
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:62:30: error: expected ';' at end of declaration list
const char * what() const noexcept { return _msg.c_str(); }
^
;
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:61:41: error: member initializer '_msg' does not name a non-static data member or base class
Exception(const std::string& msg) : _msg(msg) {}
^~~~~~~~~
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:152:18: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
ifstream() = default;
^
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:172:18: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
ofstream() = default;
^
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:191:17: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
fstream() = default;
^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:20:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/compression_types.hpp:14:
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:64:18: error: exception specification of overriding function is more lax than base version
const char * what() const noexcept { return _msg.c_str(); }
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/exception:107:25: note: overridden virtual function is here
virtual const char* what() const _NOEXCEPT;
^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:20:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/compression_types.hpp:14:
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:64:30: error: expected ';' at end of declaration list
const char * what() const noexcept { return _msg.c_str(); }
^
;
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:25:34: error: member initializer '_msg' does not name a non-static data member or base class
bzException(const int ret) : _msg("bzlib: ") {
^~~~~~~~~~~~~~~
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:28:17: error: use of undeclared identifier '_msg'
_msg += "BZ_CONFIG_ERROR: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:31:3: error: use of undeclared identifier '_msg'
_msg += "BZ_SEQUENCE_ERROR: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:34:3: error: use of undeclared identifier '_msg'
_msg += "BZ_PARAM_ERROR: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:37:3: error: use of undeclared identifier '_msg'
_msg += "BZ_MEM_ERROR: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:40:3: error: use of undeclared identifier '_msg'
_msg += "BZ_DATA_ERROR: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:43:3: error: use of undeclared identifier '_msg'
_msg += "BZ_DATA_ERROR_MAGIC: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:46:3: error: use of undeclared identifier '_msg'
_msg += "BZ_IO_ERROR: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:49:3: error: use of undeclared identifier '_msg'
_msg += "BZ_UNEXPECTED_EOF: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:52:3: error: use of undeclared identifier '_msg'
_msg += "BZ_OUTBUFF_FULL: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:57:3: error: use of undeclared identifier '_msg'
_msg += "[" + oss.str() + "]: ";
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:60:9: error: use of undeclared identifier '_msg'
_msg += ret;
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:62:42: error: member initializer '_msg' does not name a non-static data member or base class
bzException(const std::string msg) : _msg(msg) {}
^~~~~~~~~
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:87:5: error: exception specification of overriding function is more lax than base version
~bz_stream_wrapper() {
^
/Applications/assembly-stats-master/build/external/bxzstr/include/stream_wrapper.hpp:17:13: note: overridden virtual function is here
virtual ~stream_wrapper() = default;
^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:20:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/compression_types.hpp:14:
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:95:31: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
int decompress(const int) override {
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:100:45: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
int compress(const int _flags = BZ_RUN) override {
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:105:29: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
bool stream_end() const override { return this->ret == BZ_STREAM_END; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:106:23: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
bool done() const override { return this->stream_end(); }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:108:36: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
const uint8_t* next_in() const override { return (uint8_t*)bz_stream::next_in; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:109:27: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
long avail_in() const override { return bz_stream::avail_in; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:110:31: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
uint8_t* next_out() const override { return (uint8_t*)bz_stream::next_out; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:111:28: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
long avail_out() const override { return bz_stream::avail_out; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:113:47: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
void set_next_in(const unsigned char* in) override { bz_stream::next_in = (char*)in; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:114:38: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
void set_avail_in(const long in) override { bz_stream::avail_in = in; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:115:42: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
void set_next_out(const uint8_t* in) override { bz_stream::next_out = (char*)in; }
^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:116:39: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
void set_avail_out(const long in) override { bz_stream::avail_out = in; }
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
16 warnings and 20 errors generated.
make[2]: *** [CMakeFiles/filetype.dir/filetype.cpp.o] Error 1
make[1]: *** [CMakeFiles/filetype.dir/all] Error 2
make: *** [all] Error 2
I have consulted multiple web resources but I could not find a solution. How can I fix this?
