main.cpp

int main(int argc, char **argv) {
  google::protobuf::Arena arena;
  std::ifstream in("<path>");
  m::cheminot::data::Graph* graphBuf = google::protobuf::Arena::CreateMessage<m::cheminot::data::Graph>(&arena);
  graphBuf->ParseFromIstream(&in);
  in.close();
}

message.proto

syntax = "proto3";
option cc_enable_arenas = true;

package m.cheminot.data;

message Graph {
  map<string, Vertice> vertices = 1;
}

message Vertice {
  string id = 1;
  string name = 2;
  repeated string edges = 3;
  repeated StopTime stopTimes = 4;
}

message StopTime {
  string tripId = 1;
  string arrival = 2;
  string departure = 3;
  string stopId = 4;
  int32 pos = 5;
}

message CalendarDates {
  map<string, CalendarExceptions> exceptionsByServiceId = 1;
}

message CalendarExceptions {
  repeated CalendarDate calendarDates = 1;
}

message CalendarDate {
  string serviceId = 1;
  string date = 2;
  int32 exceptionType = 3;
}

message Calendar {
  string serviceId = 1;
  string monday = 2;
  string tuesday = 3;
  string wednesday = 4;
  string thursday = 5;
  string friday = 6;
  string saturday = 7;
  string sunday = 8;
  string startDate = 9;
  string endDate = 10;
}

message TripStopIds {
  repeated string stopIds = 1;
}

output

main(44728,0x7fff77496300) malloc: *** error for object 0x7ffb8ac04ed0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
[1]    44728 abort      ./main

Have you figured out the problem?