reinit the tree, so we can have metadata

4 files changed, 178 insertions, 0 deletions

diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch
new file mode 100644
index 000000000000..c20ce31ee30e
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch
@@ -0,0 +1,65 @@
+Author: Ole Streicher <debian@liska.ath.cx>
+Description: Fix format security errors
+--- a/src/catout.c
++++ b/src/catout.c
+@@ -999,7 +999,7 @@
+       break;
+ 
+     case ASCII_SKYCAT:
+-      fprintf(ascfile, skycattail);
++	fprintf(ascfile, "%s", skycattail);
+       if (!prefs.pipe_flag)
+         fclose(ascfile);
+       break;
+--- a/src/xml.c
++++ b/src/xml.c
+@@ -696,7 +696,7 @@
+ 		name, ucd);
+       break;
+     case P_STRING:
+-      sprintf(value, (char *)key[i].ptr);
++	sprintf(value, "%s", (char *)key[i].ptr);
+       fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\" arraysize=\"*\""
+ 	" ucd=\"%s\" value=\"%s\"/>\n",
+ 	name, ucd, *value? value: " ");
+@@ -705,13 +705,13 @@
+       n = *(key[i].nlistptr);
+       if (n)
+         {
+-        sprintf(value, ((char **)key[i].ptr)[0]);
++        sprintf(value, "%s", ((char **)key[i].ptr)[0]);
+         fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\""
+ 		" arraysize=\"*\" ucd=\"%s\" value=\"%s",
+ 		name, ucd, *value? value: " ");
+         for (j=1; j<n; j++)
+           {
+-          sprintf(value, ((char **)key[i].ptr)[j]);
++          sprintf(value, "%s", ((char **)key[i].ptr)[j]);
+           fprintf(file, ",%s", *value? value: " ");
+           }
+         fprintf(file, "\"/>\n");
+@@ -722,7 +722,7 @@
+ 		name, ucd);
+       break;
+     case P_KEY:
+-      sprintf(value, key[i].keylist[*((int *)key[i].ptr)]);
++      sprintf(value, "%s", key[i].keylist[*((int *)key[i].ptr)]);
+       fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\" arraysize=\"*\""
+ 	" ucd=\"%s\" value=\"%s\"/>\n",
+ 	name, ucd, value);
+@@ -731,13 +731,13 @@
+       n = *(key[i].nlistptr);
+       if (n)
+         {
+-        sprintf(value, key[i].keylist[((int *)key[i].ptr)[0]]);
++        sprintf(value, "%s", key[i].keylist[((int *)key[i].ptr)[0]]);
+         fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\""
+ 		" arraysize=\"*\" ucd=\"%s\" value=\"%s",
+ 		name, ucd, value);
+         for (j=1; j<n; j++)
+           {
+-          sprintf(value, key[i].keylist[((int *)key[i].ptr)[j]]);
++          sprintf(value, "%s", key[i].keylist[((int *)key[i].ptr)[j]]);
+           fprintf(file, ",%s", value);
+           }
+         fprintf(file, "\"/>\n");
diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch
new file mode 100644
index 000000000000..dd10d4a2c3cd
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch
@@ -0,0 +1,32 @@
+Author: Justin Pryzby <justinpryzby@users.sf.net>
+Description: (guess) Define rpl_malloc if not there.
+--- a/src/misc.c
++++ b/src/misc.c
+@@ -34,6 +34,8 @@
+ #include	<time.h>
+ #include	<sys/time.h>
+ 
++#include <sys/types.h>
++
+ #include	"define.h"
+ #include	"globals.h"
+ 
+@@ -153,3 +155,18 @@
+   }
+ 
+ 
++#if !HAVE_MALLOC
++#undef malloc
++
++// Allocate an N-byte block of memory from the heap.  If N is zero,
++// allocate a 1-byte block.
++void *rpl_malloc(size_t n)
++{
++	void *malloc();
++	if (0==n) {
++		n = 1;
++	}
++
++	return malloc(n);
++}
++#endif
diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch
new file mode 100644
index 000000000000..1b6565089849
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch
@@ -0,0 +1,55 @@
+Author: Justin Pryzby <justinpryzby@users.sf.net>
+Description: (guess) Use mmap only if it exists.
+--- a/src/fits/fitsbody.c
++++ b/src/fits/fitsbody.c
+@@ -64,9 +64,12 @@
+  ***/
+ PIXTYPE	*alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
+   {
++#ifdef	HAVE_MMAP
+    FILE		*file;
+    PIXTYPE	*buffer;
+-   size_t	npix, size, sizeleft, spoonful;
++   size_t	sizeleft, spoonful;
++#endif
++   size_t	npix, size;
+ 
+   if (!body_ramflag)
+     {
+@@ -87,7 +90,9 @@
+ /* Decide if the data will go in physical memory or on swap-space */
+   npix = tab->tabsize/tab->bytepix;
+   size = npix*sizeof(PIXTYPE);
++#if !HAVE_MMAP
+   if (size < body_ramleft)
++#endif
+     {
+ /*-- There should be enough RAM left: try to do a malloc() */
+     if ((tab->bodybuf = malloc(size)))
+@@ -105,6 +110,7 @@
+       tab->bodybuf = NULL;
+     }
+ 
++#if HAVE_MMAP
+   if (size < body_vramleft)
+     {
+ /*-- Convert and copy the data to a swap file, and mmap() it */
+@@ -144,6 +150,7 @@
+       return NULL;
+     return (PIXTYPE *)tab->bodybuf;
+     }
++#endif
+ 
+ /* If no memory left at all: forget it! */
+   return NULL;
+@@ -270,8 +277,10 @@
+     size = (tab->tabsize/tab->bytepix)*sizeof(PIXTYPE);
+     if (tab->swapflag)
+       {
++#if HAVE_MMAP
+       if (munmap(tab->bodybuf, size))
+         warning("Can't unmap ", tab->cat->filename);
++#endif
+       tab->swapflag = 0;
+       tab->bodybuf = NULL;
+       body_vramleft += size;
diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch
new file mode 100644
index 000000000000..2796f63884e3
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch
@@ -0,0 +1,26 @@
+Author: Justin Pryzby <justinpryzby@users.sf.net>
+Description: (guess) Handle the "sigbus" case only if it exists
+--- a/src/fits/fitscleanup.c
++++ b/src/fits/fitscleanup.c
+@@ -164,7 +164,9 @@
+ /* Catch CTRL-Cs */
+   signal(SIGINT, signal_function);
+ /* Catch bus errors */
++#ifdef	SIGBUS // TODO: what if it is an enum?
+   signal(SIGBUS, signal_function);
++#endif
+ /* Catch segmentation faults */
+   signal(SIGSEGV, signal_function);
+ /* Catch floating exceptions */
+@@ -195,9 +197,11 @@
+     case SIGINT:
+       fprintf(stderr, "^C\n");
+       exit(-1);
++#ifdef	SIGBUS
+     case SIGBUS:
+       fprintf(stderr, "bus error\n");
+       exit(-1);
++#endif
+     case SIGSEGV:
+       fprintf(stderr, "segmentation fault\n");
+       exit(-1);