Fix format-security and SLOT operators

(Portage version: 2.2.17/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 218 insertions, 6 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index df43290cf514..d25cf848f78c 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/ncbi-tools
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.96 2013/06/12 11:31:50 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.97 2015/03/02 14:09:51 jlec Exp $
+
+  02 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch,
+  +files/ncbi-tools-2.2.26-format-security.patch, ncbi-tools-2.2.26-r2.ebuild:
+  Fix format-security and SLOT operators
 
   12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-2.2.26-r2.ebuild,
   files/ncbirc:
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
new file mode 100644
index 000000000000..bbc4623609c8
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch
@@ -0,0 +1,81 @@
+ corelib/ncbilcl.beos | 2 +-
+ corelib/ncbilcl.hlx  | 2 +-
+ corelib/ncbilcl.lnx  | 4 ++--
+ corelib/ncbilcl.plx  | 2 +-
+ corelib/ncbilcl.qnx  | 2 +-
+ 5 files changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos
+index f720567..fe6346f 100644
+--- a/corelib/ncbilcl.beos
++++ b/corelib/ncbilcl.beos
+@@ -77,7 +77,7 @@
+ #endif
+ 
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-#define _SVID_SOURCE 1
++#define _DEFAULT_SOURCE 1
+ 
+ 
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx
+index 1492f93..0e98fb6 100644
+--- a/corelib/ncbilcl.hlx
++++ b/corelib/ncbilcl.hlx
+@@ -67,7 +67,7 @@
+ #endif
+ 
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-/*#define _SVID_SOURCE 1 */
++/*#define _DEFAULT_SOURCE 1 */
+ 
+ 
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx
+index 46e2978..b3256b3 100644
+--- a/corelib/ncbilcl.lnx
++++ b/corelib/ncbilcl.lnx
+@@ -65,7 +65,7 @@
+ * fixes for new RedHat6.2
+ *
+ * Revision 6.3  2000/02/10 16:36:32  vakatov
+-* Added _SVID_SOURCE
++* Added _DEFAULT_SOURCE
+ *
+ * Revision 6.2  1999/07/12 05:50:49  vakatov
+ * Avoid redefinition of #_REENTRANT
+@@ -141,7 +141,7 @@
+ #endif
+ 
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-#define _SVID_SOURCE 1
++#define _DEFAULT_SOURCE 1
+ #define _GNU_SOURCE 1
+ 
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx
+index bf5824c..f2b53e1 100644
+--- a/corelib/ncbilcl.plx
++++ b/corelib/ncbilcl.plx
+@@ -68,7 +68,7 @@
+ #endif
+ 
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-/*#define _SVID_SOURCE 1 */
++/*#define _DEFAULT_SOURCE 1 */
+ 
+ 
+ /*----------------------------------------------------------------------*/
+diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx
+index c3d1f0a..4b27bd1 100644
+--- a/corelib/ncbilcl.qnx
++++ b/corelib/ncbilcl.qnx
+@@ -72,7 +72,7 @@
+ #endif
+ 
+ /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */
+-#define _SVID_SOURCE 1
++#define _DEFAULT_SOURCE 1
+ 
+ 
+ 
diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
new file mode 100644
index 000000000000..c12feff51af1
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch
@@ -0,0 +1,124 @@
+ api/alignmgr2.c    |  2 +-
+ api/pgppop.c       |  2 +-
+ api/txalign.c      | 10 +++++-----
+ desktop/seqpanel.c |  4 ++--
+ tools/spidey.c     |  4 ++--
+ 5 files changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/api/alignmgr2.c b/api/alignmgr2.c
+index 5b43ef3..4b9007e 100644
+--- a/api/alignmgr2.c
++++ b/api/alignmgr2.c
+@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn
+                spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode);
+                ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1);
+                buf[ctr] = '\0';
+-               fprintf(ofp, buf);
++               fprintf(ofp, "%s", buf);
+                SeqPortFree(spp);
+             }
+          }
+diff --git a/api/pgppop.c b/api/pgppop.c
+index d16d79d..b359378 100644
+--- a/api/pgppop.c
++++ b/api/pgppop.c
+@@ -2994,7 +2994,7 @@ Char DefLine[255];
+ 			if (szSeq){
+ 				if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL,
+ 					NULL,NULL)) continue;
+-				fprintf(fp,szSeq);
++				fprintf(fp, "%s", szSeq);
+ 				fprintf(fp,"\n");
+ 				MemFree(szSeq);
+ 			}
+diff --git a/api/txalign.c b/api/txalign.c
+index 5877f9c..cb35fbc 100644
+--- a/api/txalign.c
++++ b/api/txalign.c
+@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+ 					if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
+ 					  Char checkboxBuf[200];
+ 					  sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb);
+-					  sprintf(docbuf+pos,checkboxBuf);
++					  sprintf(docbuf+pos,"%s", checkboxBuf);
+ 					  
+ 					  pos += StringLen(checkboxBuf);
+ 					}
+ 				
+ 					html_len = StringLen(HTML_buffer);
+-					sprintf(docbuf+pos, HTML_buffer);
++					sprintf(docbuf+pos, "%s", HTML_buffer);
+ 					pos += html_len;
+ 				
+ 					pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, 
+@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+                                             sprintf(HTML_buffer, "<a name = THC%ld></a><a href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\">", (long) oip->id, (long) oip->id);
+                                             
+                                             html_len = StringLen(HTML_buffer);
+-                                            sprintf(docbuf+pos, HTML_buffer);
++                                            sprintf(docbuf+pos, "%s", HTML_buffer);
+                                             pos += html_len;
+                                             pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, 
+ 					    		tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
+@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+                                             sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id);
+                                             
+                                             html_len = StringLen(HTML_buffer);
+-                                            sprintf(docbuf+pos, HTML_buffer);
++                                            sprintf(docbuf+pos, "%s", HTML_buffer);
+                                             pos += html_len;
+                                             pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, 
+ 					    		tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon);
+@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean
+ 		  if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){
+ 		    Char checkboxBuf[200];
+ 		    sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb);
+-		    sprintf(docbuf+pos,checkboxBuf);
++		    sprintf(docbuf+pos,"%s",checkboxBuf);
+ 		  
+ 		    pos += StringLen(checkboxBuf);
+ 		  }
+diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c
+index 2e78e13..c7538aa 100644
+--- a/desktop/seqpanel.c
++++ b/desktop/seqpanel.c
+@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx
+                                          seqbuf, alnbuf, &alnbuf_len,
+                                          show_substitutions);
+               MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len);
+-              fprintf (fp, printed_line);
++              fprintf (fp, "%s", printed_line);
+             }
+             fprintf (fp, "\n");
+             start = stop + 1;
+@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile
+                                        seqbuf, alnbuf, &alnbuf_len,
+                                        show_substitutions);
+             MemCpy (printed_line, alnbuf, alnbuf_len);
+-            fprintf (fp, printed_line);
++            fprintf (fp, "%s", printed_line);
+             start = stop + 1;
+             stop += seq_chars_per_row;
+           }
+diff --git a/tools/spidey.c b/tools/spidey.c
+index d6ce62d..ac9f59a 100644
+--- a/tools/spidey.c
++++ b/tools/spidey.c
+@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose
+                           fprintf(ofp2, " ");
+                           ctr++;
+                       }
+-                      fprintf(ofp2, buf);
++                      fprintf(ofp2, "%s", buf);
+                       if (spp){
+                           SeqPortFree(spp);
+                       }
+@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S
+                         ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10);
+                         if (ctr > 0)
+                            buf[ctr] = '\0';
+-                        fprintf(ofp2, buf);
++                        fprintf(ofp2, "%s", buf);
+                         SeqPortFree(spp);
+                      }
+                      done = TRUE;
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
index 5a170d413b4b..5a3f1ca33f32 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild,v 1.6 2013/06/12 11:31:50 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild,v 1.7 2015/03/02 14:09:51 jlec Exp $
 
 EAPI=5
 
@@ -18,7 +18,7 @@ IUSE="doc static-libs X"
 RDEPEND="
 	app-shells/tcsh
 	dev-lang/perl
-	media-libs/libpng
+	media-libs/libpng:0=
 	X? ( x11-libs/motif:0 )"
 DEPEND="${RDEPEND}"
 
@@ -39,7 +39,9 @@ pkg_setup() {
 src_prepare() {
 	epatch \
 		"${FILESDIR}"/${PN}-extra_vib.patch \
-		"${FILESDIR}"/${P}-bfr-overflow.patch
+		"${FILESDIR}"/${P}-bfr-overflow.patch \
+		"${FILESDIR}"/${P}-format-security.patch \
+		"${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch
 
 	if use ppc || use ppc64; then
 		epatch "${FILESDIR}"/${PN}-lop.patch