keep getting segmentation fault! arrrggghhhh!!!!!!!!!!

This is a discussion on keep getting segmentation fault! arrrggghhhh!!!!!!!!!! within the C Programming forums, part of the General Programming Boards category; i have run the program multiple times, and have redone it four times. my buddy who's in the same class ...

  1. #1
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    Angry 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

  2. #2
    Registered User linuxdude's Avatar
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    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

  3. #3
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    where whould i insert/replace that peice of code?

  4. #4
    Yes, my avatar is stolen anonytmouse's Avatar
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    >> 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.

  5. #5
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    Quote 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.

  6. #6
    ~viaxd() viaxd's Avatar
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    in your code :
    Code:
    int i;
    ...
    genedata[i].id = atoi(line);
    just do:
    Code:
    int i = 0;

  7. #7
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    Your code has lots of problems. Besides not initializing i, you didn't rewind your file before writing to it, you are writing 500 records when you only need to write the number of records which were read, and your fwrite() is writing too much data.

  8. #8
    ~viaxd() viaxd's Avatar
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    and another thing i noticed, you opened your file for reading with "r" mode, so you cannot write to it.

  9. #9
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    Quote 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

  10. #10
    /*enjoy*/
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    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 ...

  11. #11
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    >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?
    Last edited by swoopy; 04-26-2004 at 03:00 PM.

  12. #12
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    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;
    }

  13. #13
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    Quote 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...

  14. #14
    ATH0 quzah's Avatar
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    To be frank, and I'd rather not, because Frank isn't my name, your code is horribly flawed:
    Code:
    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)){
    1) If your file fails to open, you still end up reading from it anyway.
    2) Don't use feof, because it's not entirely accurate, and has its own problems. It's in the FAQ (link) that no one reads.
    3) I'll stop there, because until that's fixed, there's no point in continuing.

    Quzah.
    Hope is the first step on the road to disappointment.

  15. #15
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    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

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