xdrfile-1.1.4-src.patch

diff xdrfile-1.1.4/src/xdrfile.c src/xdrfile.c
1,4d0
< /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 
<  *
<  * $Id$
<  *
635c631
< 			fprintf(stderr,"major breakdown in encodeints - num %u doesn't "
---
> 			fprintf(stderr,"(xdrfile error) major breakdown in encodeints - num %u doesn't "
795a792
> 	const float* ptrstart = ptr;
801c798,799
< 	if(xfp==NULL || ptr==NULL)
---
> 	if(xfp==NULL || ptr==NULL) {
>         fprintf(stderr, "(xdrfile error) Null pointer issue\n");
802a801
> 	}
804c803,804
< 	if(tmp==0)
---
> 	if(tmp==0) {
>         fprintf(stderr, "(xdrfile error) Size could not be read\n");
805a806
> 	}
808c809
< 		fprintf(stderr, "Requested to decompress %d coords, file contains %d\n",
---
> 		fprintf(stderr, "(xdrfile error) Requested to decompress %d coords, file contains %d\n",
818c819
< 			fprintf(stderr,"Cannot allocate memory for decompressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for decompressing coordinates.\n");
825c826
< 			fprintf(stderr,"Cannot allocate memory for decompressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for decompressing coordinates.\n");
863c864,865
< 	if (xdrfile_read_int(&smallidx,1,xfp) == 0)	
---
> 	if (xdrfile_read_int(&smallidx,1,xfp) == 0)	{
> 	    fprintf(stderr,"(xdrfile error) Undocumented error 1");
864a867
> 	}
877,879c880,881
< 	if (xdrfile_read_int(buf2,1,xfp) == 0)
< 		return 0;
< 	if (xdrfile_read_opaque((char *)&(buf2[3]),(unsigned int)buf2[0],xfp) == 0)
---
> 	if (xdrfile_read_int(buf2,1,xfp) == 0) {
> 	    fprintf(stderr, "(xdrfile error) Undocumented error 2");
880a883,887
> 	}
> 	if (xdrfile_read_opaque((char *)&(buf2[3]),(unsigned int)buf2[0],xfp) == 0) {
> 	    fprintf(stderr, "(xdrfile error) Undocumented error 3");
>         return 0;
> 	}
920a928,932
> 		if ((lfp-ptrstart)+run > size3)
> 		{
> 			fprintf(stderr, "(xdrfile error) Buffer overrun during decompression.\n");
> 			return 0;
> 		}
979c991,996
< 		sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;
---
> 		sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];
> 		if (sizesmall[0]==0 || sizesmall[1]==0 || sizesmall[2]==0)
> 		{
> 			fprintf(stderr, "(xdrfile error) Undefined error.\n");
> 			return 0;
> 		}
1014c1031
< 			fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for compressing coordinates.\n");
1021c1038
< 			fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for compressing coordinates.\n");
1059c1076
< 			fprintf(stderr,"Internal overflow compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Internal overflow compressing coordinates.\n");
1074c1091
< 			fprintf(stderr,"Internal overflow compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Internal overflow compressing coordinates.\n");
1111c1128
< 		fprintf(stderr,"Internal overflow compressing coordinates.\n");
---
> 		fprintf(stderr, "(xdrfile error) Internal overflow compressing coordinates.\n");
1305c1322
< 		fprintf(stderr, "Requested to decompress %d coords, file contains %d\n",
---
> 		fprintf(stderr, "(xdrfile error) Requested to decompress %d coords, file contains %d\n",
1315c1332
< 			fprintf(stderr,"Cannot allocate memory for decompression coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for decompression coordinates.\n");
1322c1339
< 			fprintf(stderr,"Cannot allocate memory for decompressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for decompressing coordinates.\n");
1504c1521
< 			fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for compressing coordinates.\n");
1510c1527
< 			fprintf(stderr,"Cannot allocate memory for compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Cannot allocate memory for compressing coordinates.\n");
1548c1565
< 			fprintf(stderr,"Internal overflow compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Internal overflow compressing coordinates.\n");
1562c1579
< 			fprintf(stderr,"Internal overflow compressing coordinates.\n");
---
> 			fprintf(stderr, "(xdrfile error) Internal overflow compressing coordinates.\n");
1598c1615
< 		fprintf(stderr,"Internal overflow compressing coordinates.\n");
---
> 		fprintf(stderr, "(xdrfile error) Internal overflow compressing coordinates.\n");
diff xdrfile-1.1.4/src/xdrfile_trr.c src/xdrfile_trr.c
1,4d0
< /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 
<  *
<  * $Id$
<  *
101,103c97,106
< 	if (xdrfile_read_int(&magic,1,xd) != 1)
< 		return exdrINT;
<   
---
> 	if (xdrfile_read_int(&magic,1,xd) != 1) {
> 	    /* modification by RTM to return the right EOF code
> 	    this is what's happening in the XTC code */
> 	    if (bRead)
> 			return exdrENDOFFILE;
>         else
> 		    return exdrINT;
>     }
> 	if (magic != GROMACS_MAGIC)
> 		return exdrMAGIC;
449a453
> 
486a491,519
> int read_trr_nframes(char *fn, unsigned long *nframes) {
>     XDRFILE *xd;
>     int result, step;
>     float time, lambda;
> 	int natoms;
> 	matrix box;
> 	rvec *x;
> 	*nframes = 0;
> 
> 	read_trr_natoms(fn, &natoms);
> 	x = malloc(natoms * sizeof(*x));
> 
>     xd = xdrfile_open(fn, "r");
>     if (NULL == xd)
>         return exdrFILENOTFOUND;
> 
> 	do {
> 		result = read_trr(xd, natoms, &step, &time, &lambda,
> 						  box, x, NULL, NULL);
> 		if (exdrENDOFFILE != result) {
> 			(*nframes)++;
> 		}
> 	} while (result == exdrOK);
> 
> 	xdrfile_close(xd);
> 	free(x);
>     return exdrOK;
> }
> 
diff xdrfile-1.1.4/src/xdrfile_xtc.c src/xdrfile_xtc.c
104a105,133
> int read_xtc_nframes(char* fn, unsigned long *nframes) {
>     XDRFILE *xd;
>     int result, step;
>     float time;
> 	int natoms;
> 	matrix box;
> 	rvec *x;
> 	float prec;
> 	*nframes = 0;
> 
> 	read_xtc_natoms(fn, &natoms);
> 	x = malloc(natoms * sizeof(*x));
> 
>     xd = xdrfile_open(fn, "r");
>     if (NULL == xd)
>         return exdrFILENOTFOUND;
> 
> 	do {
> 		result = read_xtc(xd, natoms, &step, &time, box, x, &prec);
> 		if (exdrENDOFFILE != result) {
> 			(*nframes)++;
> 		}
> 	} while (result == exdrOK);
> 
> 	xdrfile_close(xd);
> 	free(x);
>     return exdrOK;
> }
> 
117c146
<   
---
>