Thread: keep getting segmentation fault! arrrggghhhh!!!!!!!!!!

i have run the program multiple times, and have redone it four times. my buddy who's in the same class looked at it and said its similar to his, yet his works. this program is supposed to read file data and output it to a random access file.

Code:

#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define SIZE 500

struct data{
        int id;
        char title [SIZE];
        char gene [SIZE];
        char express [SIZE];
        char chrom [SIZE];
        int scount;
};

int main (){

        int i;
        int j;
        struct data genedata[SIZE];
        FILE *dataPtr;
        char temp [SIZE];
        char line [SIZE];



        if(( dataPtr = fopen("Hs.data.filtered", "r")) == NULL)
        {
                printf("File could not be opened.\n");
        }

        else{

        fscanf(dataPtr, "%s", temp);
        if(strcmp(temp, "//") != 0){
        fgets(line, SIZE, dataPtr);
        }

        while( !feof(dataPtr)){

        if (strcmp(temp, "ID") == 0){
        genedata[i].id = atoi(line);
        }

        if (strcmp(temp, "TITLE") == 0){
        strcpy(genedata[i].title, line);
        }

        if (strcmp(temp, "GENE") == 0){
        strcpy(genedata[i].gene, line);
        }

        if (strcmp(temp, "EXPRESS") == 0){
        strcpy(genedata[i].express, line);
        }
        
        if (strcmp(temp, "CHROMOSOME") == 0){
        strcpy(genedata[i].chrom, line);
        }
        
        if (strcmp(temp, "SCOUNT") == 0){
        genedata[i].scount = atoi(line);
        }
        
        i++;
        fscanf (dataPtr, "%s", temp);
        if (strcmp(temp, "//") != 0){
        fgets (line, SIZE, dataPtr);
        }
        
        }           /*close while*/
        
        for (j=1; j<=SIZE; j++){
        fwrite(&genedata, sizeof(struct data), j, dataPtr);
        }
         
        fclose (dataPtr);
        }           /*close else*/
        
        return 0;
}

an example of the input data can be found here: http://texas.eng.uiowa.edu:8088/bme/59_006/Hs.small
i greatly appreciate any help. thanks!
steve

You have an if for if it doesn't open but your once your else ends you still try to write to the file descriptor thus a seg fault try

Code:

if(!dataPtr){
   perror("couln't open file\n");
   exit(1); /*stdlib is needed (which you have*/
}

also dont' use feof in a control loop see faq

where whould i insert/replace that peice of code?

>> You have an if for if it doesn't open but your once your else ends you still try to write to the file descriptor <<

No, that is just the poor formatting of the code.

The seg fault is caused by the fact that the variable i is not initialised before use. Does no ones compiler warn about this?

Code:

        for (j=1; j<=SIZE; j++){
        fwrite(&genedata, sizeof(struct data), j, dataPtr);
        }

The results of this code are likely to be non-optimal.

Originally Posted by anonytmouse

>> You have an if for if it doesn't open but your once your else ends you still try to write to the file descriptor <<

No, that is just the poor formatting of the code.

The seg fault is caused by the fact that the variable i is not initialised before use. Does no ones compiler warn about this?

Code:

        for (j=1; j<=SIZE; j++){
        fwrite(&genedata, sizeof(struct data), j, dataPtr);
        }

The results of this code are likely to be non-optimal.

but i did intialize i and j (since you posted that code). im still cloudy on what you guys are saying.

in your code :

Code:

int i;
...
genedata[i].id = atoi(line);

just do:

Code:

int i = 0;

and another thing i noticed, you opened your file for reading with "r" mode, so you cannot write to it.

Originally Posted by viaxd

and another thing i noticed, you opened your file for reading with "r" mode, so you cannot write to it.

im not supposed to write to it, im supposed to create a random access file called records.dat

if you use c++ you can use "fstream.h"
in these library you can open read and write in the same time in the file ...

here's an updated version of my program:

Code:

              #include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define SIZE 50
                
struct data{
        int id;
        char title [SIZE];
        char gene [SIZE];
        char express [SIZE];
        char chrom [SIZE];
        int scount;
};
        
int main (){
        
        int i=0;
        int j=0;
        struct data genedata[SIZE];
        FILE *dataPtr;
        char temp [SIZE];
        char line [SIZE];
        
         if(( dataPtr = fopen("Hs.data.filtered", "r")) == NULL)
        {
                printf("File could not be opened.\n");
        }
                

        else{  
        
        fscanf(dataPtr, "%s", temp);
        if(strcmp(temp, "//") != 0){
        fgets(line, SIZE, dataPtr);
        }
  
        while( !feof(dataPtr)){

        if (strcmp(temp, "ID") == 0){
        genedata[i].id = atoi(line);
        }
        
        if (strcmp(temp, "TITLE") == 0){
        strcpy(genedata[i].title, line);
        }

        if (strcmp(temp, "GENE") == 0){
        strcpy(genedata[i].gene, line);
        }
         
        if (strcmp(temp, "EXPRESS") == 0){
        strcpy(genedata[i].express, line);
        }
        
        if (strcmp(temp, "CHROMOSOME") == 0){
        strcpy(genedata[i].chrom, line);
        }
         
        if (strcmp(temp, "SCOUNT") == 0){
        genedata[i].scount = atoi(line);
        }
        
        i++;
         
        fscanf (dataPtr, "%s", temp);
        
        if (strcmp(temp, "//") != 0){
        fgets (line, SIZE, dataPtr);
        }
        
        }           /*close while*/
         
        
        if(( dataPtr = fopen( "records.dat", "w")) == NULL){
                printf("error");}
        else{
        for (j=1; j<=i; j++){
        fwrite(&genedata, sizeof(struct data), j, dataPtr);
        }
        }
        
        fclose (dataPtr);
        }           /*close else*/
        
        return 0;
}

Originally Posted by swoopy

>im not supposed to write to it, im supposed to create a random access file called records.dat

Is it possible to drop this class?

i wish, i wish...

ok, so how about this, Frank :P

Code:

if(( dataPtr = fopen("Hs.data.filtered", "r")) == NULL)
        {
                printf("File could not be opened.\n");
                return 0;
        }


        else{

        fscanf(dataPtr, "%s", temp);
        if(strcmp(temp, "//") != 0){
        fgets(line, SIZE, dataPtr);
        }

        /* while( !feof(dataPtr)){ */
        while (fgets(line, sizeof(line), dataPtr) != NULL){

note: i still get the dreaded seg fault