src/hg/protein/pfamXref/pfamXref.c 1.9
1.9 2009/09/23 18:42:25 angie
Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
Index: src/hg/protein/pfamXref/pfamXref.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/pfamXref/pfamXref.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/hg/protein/pfamXref/pfamXref.c 3 Sep 2008 19:21:01 -0000 1.8
+++ src/hg/protein/pfamXref/pfamXref.c 23 Sep 2009 18:42:25 -0000 1.9
@@ -58,9 +58,9 @@
while (!done)
{
/* get to the beginning of a Pfam record */
idFound = 0;
- while (fgets(line, 1000, inf) != NULL)
+ while (fgets(line, sizeof(line), inf) != NULL)
{
chp = strstr(line, "GF ID");
if (chp != NULL)
{
@@ -75,18 +75,18 @@
pfamID = strdup(chp);
/* Get Pfam AC */
- fgets(line, 1000, inf);
+ mustGetLine(inf, line, sizeof(line));
chp = strstr(line, "GF AC ");
chp = chp + 8;
*(chp + strlen(chp) - 1) = '\0'; // remove LF
chp1 = strstr(chp, ".");
if (chp1 != NULL) *chp1 = '\0';
pfamAC = strdup(chp);
/* Get Pfam description. Please note, Pfam-B does not have this field.*/
- fgets(line, 1000, inf);
+ mustGetLine(inf, line, sizeof(line));
chp = strstr(line, "GF DE ");
chp = chp + 8;
*(chp + strlen(chp) - 1) = '\0'; // remove LF
desc = chp;
@@ -98,9 +98,9 @@
gsDone = 0;
gsFound = 0;
while (!gsDone)
{
- fgets(line, 1000, inf);
+ mustGetLine(inf, line, sizeof(line));
chp = strstr(line, "#=GS ");
if (chp != NULL)
{
chp = strstr(chp, " AC ");
@@ -150,10 +150,10 @@
carefulClose(&o1);
carefulClose(&o2);
sprintf(cond_str, "cat jj.dat | sort | uniq >%s",outputFileName2);
-system(cond_str);
-system("rm jj.dat");
+mustSystem(cond_str);
+mustSystem("rm jj.dat");
return(0);
}