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OndrejSladky / kmercamel

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
MIT License
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error: use of undeclared identifier 'get_current_dir_name' #26

Closed karel-brinda closed 1 year ago

karel-brinda commented 1 year ago

Version: `* d1b1c19 - (HEAD -> maketest, origin/maketest) Updated README.md (18 hours ago) 

$ make test
g++ -g -Wall -Wno-unused-function -std=c++17 -O2 -isystem googletest/googletest/include -I googletest/googletest/include unittest.cpp gtest-all.o -pthread -o kmerstest
In file included from unittest.cpp:1:
./parser_unittest.h:12:42: error: use of undeclared identifier 'get_current_dir_name'
        std::string path = (std::string) get_current_dir_name();
                                         ^
In file included from unittest.cpp:2:
./kmers_unittest.h:85:28: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                {0b1001LL, "GC"},
                           ^~~~
                           {   }
./kmers_unittest.h:86:28: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                {0b1011LL, "AGT"},
                           ^~~~~
                           {    }
./kmers_unittest.h:87:26: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                {0b11LL, "T"},
                         ^~~
                         {  }
./kmers_unittest.h:88:93: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                {0b111111'01111111'11111111'11111111'11111111'11111111'11111111'11111110LL, "TTTCTTTTTTTTTTTTTTTTTTTTTTTTTTG"},
                                                                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                            {                                }
In file included from unittest.cpp:4:
./greedy_unittest_ac.h:69:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, 1, 0, 0, 0, 0, 0, 0},
                                                 ^~~~~~~~~~
                                                 {         }
./greedy_unittest_ac.h:70:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, -1, 2, -1, -1, 0, 1, 1},
                                                 ^~~~~~~~~~~~~
                                                 {            }
./greedy_unittest_ac.h:71:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, -1, -1, 4, 3, 0, 2, 2},
                                                 ^~~~~~~~~~~~
                                                 {           }
./greedy_unittest_ac.h:72:47: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0}, -1, -1, -1, -1, 0, 3, 3},
                                              ^~~~~~~~~~~~~~
                                              {             }
./greedy_unittest_ac.h:73:47: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{1}, -1, -1, -1, -1, 0, 3, 4},
                                              ^~~~~~~~~~~~~~
                                              {             }
./greedy_unittest_ac.h:97:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, 1, 0, 0, 0, 0, 0, 0},
                                                 ^~~~~~~~~~
                                                 {         }
./greedy_unittest_ac.h:98:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, -1, 2, -1, -1, 0, 1, 1},
                                                 ^~~~~~~~~~~~~
                                                 {            }
./greedy_unittest_ac.h:99:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, 4, -1, -1, 3, 0, 2, 2},
                                                 ^~~~~~~~~~~~
                                                 {           }
./greedy_unittest_ac.h:100:47: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0}, -1, -1, -1, -1, 0, 3, 3},
                                              ^~~~~~~~~~~~~~
                                              {             }
./greedy_unittest_ac.h:101:47: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{1}, -1, -1, -1, -1, 0, 3, 4},
                                              ^~~~~~~~~~~~~~
                                              {             }
./greedy_unittest_ac.h:104:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, 1, 0, 0, 0, 0, 0, 0},
                                                 ^~~~~~~~~~
                                                 {         }
./greedy_unittest_ac.h:105:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, -1, 2, -1, -1, 0, 1, 1},
                                                 ^~~~~~~~~~~~~
                                                 {            }
./greedy_unittest_ac.h:106:50: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0, 1}, 4, -1, -1, 3, 0, 2, 2},
                                                 ^~~~~~~~~~~~
                                                 {           }
./greedy_unittest_ac.h:107:47: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{0}, -1, -1, -1, -1, 0, 3, 3},
                                              ^~~~~~~~~~~~~~
                                              {             }
./greedy_unittest_ac.h:108:47: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ACState{std::list<size_t>{1}, -1, -1, -1, -1, 1, 3, 4},
                                              ^~~~~~~~~~~~~~
                                              {             }
19 warnings and 1 error generated.
make: *** [kmerstest] Error 1
GordonHoklinder commented 1 year ago

Ooof, it seems that this function is linux-only. I changed it to something which seems to be "the standard since c++ 17" so hope it works on MacOS as well.