Fix format-security and SLOT operators
authorJustin Lecher <jlec@gentoo.org>
Mon, 2 Mar 2015 14:09:52 +0000 (14:09 +0000)
committerJustin Lecher <jlec@gentoo.org>
Mon, 2 Mar 2015 14:09:52 +0000 (14:09 +0000)
Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

sci-biology/ncbi-tools/ChangeLog
sci-biology/ncbi-tools/Manifest
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch [new file with mode: 0644]
sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch [new file with mode: 0644]
sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild

index df43290cf5146b084eb467e7fcac367835590f55..d25cf848f78c48c30e88a873f0c73a7be72b9b00 100644 (file)
@@ -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:
index f9e44aee715730ff1290c84a7360f380ff6837b3..1541881b21581325b82e07e731bc1445080fac88 100644 (file)
@@ -2,19 +2,33 @@
 Hash: SHA512
 
 AUX 21ncbi-r1 232 SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 SHA512 cddde027eb42ce34862c35ad0d809de3738301ea57aec2f84a447efa00eeedbeb528df29390041a1f947dd955d43cabac525316d343aafef001f1de21f5da2d9 WHIRLPOOL d70b9bc3a2b1cdec9c6d2def8b06c70dc0f847992a0720f036a7d2d1e0c90bd8a6a390c7f87c24edd2b0f6326a1d9e0fd0059db20ede0e791cc6ff0c46b8cc70
+AUX ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch 2283 SHA256 fe41b8c4cf389f66471eb5711542b22f3bac2793038fb1d5b427052f30a27de8 SHA512 87cc2442e65d6d3a0fedd2501324834461cfcbbfa9adf83b0f070d5f4d77a1a30c8b9fd22a35263b705c2baefd0dfc11f53d27683b0357d2cd6f74cf379b7979 WHIRLPOOL ef45d0b80d27d1bbd0b76c4b63547a45e72b1bd0fa8cca61c0912f9352edf1a2cc1059395fdb7a9af909723b0209e36028d102ea4115bd1ea294c616e6ce7df8
 AUX ncbi-tools-2.2.26-bfr-overflow.patch 3712 SHA256 65418ea20b92561b1811bec0cd63d79c645afe86ce60f72b852c4860ff4ffe2f SHA512 f88ffb38ca70ffc200943ee9c44d0d3828eec2c681622c8a6eae90f0a59bf6de0e0f609b5a24b42803a39bf0b6d7d203a323a18cead749120e84affbe7405397 WHIRLPOOL a5cc4399a377a0436b30991ae21c9bb385763942ba8df169d70898fdbf206c1cfb910bd63d34f94d55ca2ef607e5abf0b1571a72ef94e44531492ef8cfdc8ea3
+AUX ncbi-tools-2.2.26-format-security.patch 6358 SHA256 7b8f59ffe69f87e07210b745c3438a058b9c6ff924b08418e3b6872fa8f59de3 SHA512 9a33c19913bae7c91bb888177acc89f608c8fd6616c258c73a39ba7c69fa9a3e40d66578a4cf61410300c3d5be851890f2b110c2e6e4580ab71546993b6afcc4 WHIRLPOOL ed07a77bd9ac358330773ef05285bd773e5953e9759bf9ec6d32d558e3d15f04652f7edd9305addcbdf84f1226e69189cf7c34fb82162fc7da19a13f3ea91ec7
 AUX ncbi-tools-asn2all.patch 1190 SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed SHA512 1dab51d76454bbe5b153b0a0c01d7c18557d9cf3849ef7892d10333c4ffab0c8365779266a659d5d18e57247cb793fc236540e539e1ce844e6d8d3d9084c20a0 WHIRLPOOL 37b5b0f30be2ad023daeac2ee828ebe68babca49368d1901d327a1d77cfd0e0e0c03ad6826a5afe501bdb3d1752b567fbb620526acc59071e450309a27727df5
 AUX ncbi-tools-extra_vib.patch 1393 SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1 SHA512 faef4b98f7ec4ab842c8a0b99caaf47855f84c2c5f7b6a967bce05afc7d0cc69925a3867da2834778c980dd5b9f848d3ef969eb3be8ea0bac20e937127dcba00 WHIRLPOOL 190278df576d5169c2dddcd6e37b464165f058bcc715be675897635cc7d90fd65b14f73a6306e027482eb7f524541828e0d305247c357a87592c6a34675e1b1b
 AUX ncbi-tools-lop.patch 701 SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352 WHIRLPOOL 7d0a9ba13c6ede034ac71870f802ee75945e13944742ffd19086ce71127b97807ea1c87f97d6b3d7a96f5e7fb24b6110f03836a3f0967d1f23e68ca1de4e755a
 AUX ncbirc 57 SHA256 6a9c895368ad801c9b04e08486771c7a96f3f26e81748d81d6c088b4aa97208b SHA512 0b9b68116b362ccc625623abf4e959abfb8555c31117216eefe3093fe2dd122c3ce508fe389c07a069d6f4322d889718e455de65dd3ab7d55a16d947ecb07cfd WHIRLPOOL ecd8c2c38b59801273a1392e02df3e6dbd5ed8331847823f69e878cbea74e2b4488ecce7aed4096d095d9912315b66d75d3dfdc1f6276651854dd6b5265ae795
 DIST ncbi-tools-2.2.26.tar.gz 68691452 SHA256 d8fffac25efc8ca894c707c840a4797a8a949ae6fd983d2f91c9972f788efb7d SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 WHIRLPOOL 6f390a4487b7ebf9d5ca31018f3b33602a695e4b0a4b090952fec9c7e8c3956edc197e75ffd32588f9431cc04b4262a2ca2e3b0ba50dd622ed73a4da6655a956
-EBUILD ncbi-tools-2.2.26-r2.ebuild 4565 SHA256 32ce9578dcb0401f90a2aee14e4abbaf19adeb38c25576dc0e3874a923f3e873 SHA512 08b0d5f1c4637c3cf999d63c6fa65cc79a0267360728a081169366f8994e6d027f14fd84d476720980641cc77b2fce79a35d7f100cc373232d06481cfc78b49d WHIRLPOOL 4eadb082f362fdcc3c4ea2f4d620a8c488ded22a3a994fdeaed40ad92bae19bb4255148ac8cc863e6a5e8aacb601701c4939db448dd397de1a43c0d4a73e6391
-MISC ChangeLog 19046 SHA256 eb10385213f1cfaf34ded4fb6dcd466f99c66e0872ae9b0e1261fc4584b729e1 SHA512 15bac7ec4afcd5d9afbfd4fd4a56d92203bc2187258382dfc1c4180fe07607a31d435a904fbb266ff4bce531ef4aefa2a2f17d7a67ef331d9c4d4841ba1ca419 WHIRLPOOL f4325e277e83359914848d42641ff82664db9961013062a1b1ef211356bc6b249a695bd57d2a265a50dba6ec353ffcbe40b2b6aecdfcd6a0eff9365d0b25f05d
+EBUILD ncbi-tools-2.2.26-r2.ebuild 4658 SHA256 7ba3a8eba9ab3b917487170be22f8ca9795b1fb9519b6963bb619ae4be4b4dca SHA512 e6899f524b59b6aee5546e6cbc6920aac1ed20a9a0f90fa611de69437a15f0766203221cebd73d1de182ab6c7eb660baefb8c0ded1da8ed4f922c5a362c10984 WHIRLPOOL b9827439440bf5f2fb87c9c30e99fa9b95fd4a50d47f7aacf05bbf1e0c5e7ae8d09641a1bbc27013c7cff244954c0adb8b575e897d2cf9c8e493f40c96168371
+MISC ChangeLog 19264 SHA256 d06eed970f62b9fd228571b80aa5595729969dfae68b28762c66c0d51b85781f SHA512 1955b97482ec5b34953707fab31b81ee41209dca9034bce326a7f7ba31ee745dcdf75cbe06c8529a2b593198254c10bc5797d24023e7059dfb5ca6ec3180c30f WHIRLPOOL b129ceeb190673c7c6cb0ec2979061b557a952f6715e471c2c87979980974c20b928a1201afcc7e9878bfab44779bb24c632521c00bedffbcd02633a9b4d1074
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.20 (GNU/Linux)
+Version: GnuPG v2.0
 
-iEYEAREKAAYFAlG4XCcACgkQgAnW8HDreRaoxQCghQ6O/15FZatZG7SckC9Oh4Py
-ZqgAn38ipfCXsA/eJzzZuNdOzNaMCrqF
-=KDBz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+=YsDI
 -----END PGP SIGNATURE-----
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 (file)
index 0000000..bbc4623
--- /dev/null
@@ -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 (file)
index 0000000..c12feff
--- /dev/null
@@ -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;
index 5a170d413b4b445d517bf94fdf549f964de514e6..5a3f1ca33f32774df1b88b339b3b944dfb7dd1b0 100644 (file)
@@ -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