Segmentation fault using input file stream

Question

I'm receiving this error from my compiler "segmentation fault: core dump". I assume it's from the function I had written but not exactly sure what about the function is wrong.

The program reads from the input file and it outputs results on the screen (cout).

string rna_complement(string line)
{

for(int i = 0; i < line.length(); i++)
{
        switch (line[i])
        {
            case 'A': line[i] = 'U'; break;
            case 'C': line[i] = 'G'; break;
            case 'G': line[i] = 'C'; break;
            case 'U': line[i] = 'A'; break;
            }
}


cout <<"Complement: " <<line <<endl;
}



int main()
{
string line1, line2, line3, line4, line5, line6;
ifstream genesacid;

genesacid.open("genes.txt");
    if(!genesacid.is_open())
    {
        cerr <<"Error: File cannot be opened"<<endl;
        return 0;
    }

            else
            {
                getline(genesacid, line1);
                getline(genesacid, line2);
                getline(genesacid, line3);
                getline(genesacid, line4);
                getline(genesacid, line5);
                getline(genesacid, line6);
            }



cout << "Fragment 1: " <<line1 <<endl;
rna_complement(line1);


cout << "Fragment 2: " <<line2 <<endl;

genesacid.close();


return 0;
}

I'm not very adept in C++ so if any errors you see is obvious, please be mindful of this. I'm slowly learning!

You might start by fixing the inconsistent indentation so we can understand the code better — Sam Miller
– Sam Miller, Commented Mar 19, 2013 at 22:16
The report of the segmentation fault comes not from the compiler, but from the runtime/OS. You can and should run it using a debugger and this will often automatically indicate the spot in the source that triggered the fault. — Brian Cain
– Brian Cain, Commented Mar 19, 2013 at 22:17
it doesnt say which line it happens but when i run the program, it outputs the "fragment 1" then runs the function (which outputs a line) then it displays the error. — user2188311
– user2188311, Commented Mar 19, 2013 at 22:18

Jesse Good · Accepted Answer · 2013-03-19 22:17:32Z

3

I'm guessing it is because you forgot to return something in your function. A seg fault can happen because of this. Also, make sure you have your warning level on high, a good compiler will usually let you know about this.

Here is the C++ standard 6.6.3:

Flowing off the end of a function is equivalent to a return with no value; this results in undefined behavior in a value-returning function.

answered Mar 19, 2013 at 22:17

Jesse Good

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4 Comments

Qaz Over a year ago

For clarity, forgetting to do so is undefined behaviour, and equivalent to return;.

Jesse Good Over a year ago

@chris: Thanks, I added the quote from the standard.

Nik Bougalis Over a year ago

Frankly, the standard is deficient in this case. Ideally, it should be modified to clarify that flowing off the end of such a function should result in a malformed C++ program and a hard error. But that won't happen, so I'd settle for mandating at least a warning.

Qaz Over a year ago

@NikBougalis, Yes, I do forget to do this from time to time. Thankfully, all major compilers I know of do have something to say about this. MSVC gives an error (which is non-standard as far as I'm aware, but the program is simply broken anyway) and GCC and Clang at least warn with the right warning level. I'm very grateful that it's this easy to catch errors.

Thibaut · Accepted Answer · 2013-03-19 22:25:41Z

0

If you don't return anything in the function rna_complement, it should be void. The segmentation fault comes from the call of the destructor of std::string. Alternatively, you can return line since it is a copy. If you want in-place modification of the string, you can pass a reference to it (string &line), and it will modify the string passed in argument.

edited Mar 19, 2013 at 22:25

answered Mar 19, 2013 at 22:20

Thibaut

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2 Comments

Matt Phillips Over a year ago

Odd, I've never used a compiler that didn't give a 'Warning: control reached end of non-void function' or similar in this situation.

Thibaut Over a year ago

clang would complain by default without any flag. gcc without any flag won't complain. gcc -Wall would. Oddly gcc -pedantic doesn't seem to care either.

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