sci-biology/ncbi-tools: Fix typo in sed construct, #459920; add patch to fix buffer overflows

Package-Manager: portage-2.2.0_alpha164/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

4 files changed, 116 insertions, 26 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 927835767fd8..f8e6825a481f 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,10 @@
 # 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 1.91 2013/03/01 19:34:47 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.92 2013/03/02 13:09:15 jlec Exp $
+
+  02 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-2.2.26-r2.ebuild,
+  +files/ncbi-tools-2.2.26-bfr-overflow.patch:
+  Fix typo in sed construct, #459920; add patch to fix buffer overflows
 
   01 Mar 2013; Agostino Sarubbo <ago@gentoo.org> ncbi-tools-2.2.26-r2.ebuild:
   Stable for x86, wrt bug #458112
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 77e4bd751033..8d5de6b144be 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,7 +1,5 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
 AUX 21ncbi-r1 232 SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 SHA512 cddde027eb42ce34862c35ad0d809de3738301ea57aec2f84a447efa00eeedbeb528df29390041a1f947dd955d43cabac525316d343aafef001f1de21f5da2d9 WHIRLPOOL d70b9bc3a2b1cdec9c6d2def8b06c70dc0f847992a0720f036a7d2d1e0c90bd8a6a390c7f87c24edd2b0f6326a1d9e0fd0059db20ede0e791cc6ff0c46b8cc70
+AUX ncbi-tools-2.2.26-bfr-overflow.patch 3712 SHA256 65418ea20b92561b1811bec0cd63d79c645afe86ce60f72b852c4860ff4ffe2f SHA512 f88ffb38ca70ffc200943ee9c44d0d3828eec2c681622c8a6eae90f0a59bf6de0e0f609b5a24b42803a39bf0b6d7d203a323a18cead749120e84affbe7405397 WHIRLPOOL a5cc4399a377a0436b30991ae21c9bb385763942ba8df169d70898fdbf206c1cfb910bd63d34f94d55ca2ef607e5abf0b1571a72ef94e44531492ef8cfdc8ea3
 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
@@ -12,24 +10,7 @@ DIST ncbi-tools-20080302.tar.gz 17294669 SHA256 93a30ec0a6e408858c6364039a4eb240
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
 EBUILD ncbi-tools-0.20080302.ebuild 7172 SHA256 0cb4afa52072d210070446bbf5087488c8ec5d9606552cc12fb600429461acff SHA512 c01be3c1468862020b9d43bc3e14bd5a165058e33cb507ae7ddaafa7c0df5ea06df04306dea4c082b00b2a3aa910a8b60db82185de2e57ae37b5d08a3a34dca7 WHIRLPOOL 7a5d5f83c033b45a9456af36c80a2a8c9be3eff253709aabb2251209463bf1b5999b650d9aeba4563715691ae8052fbe8afaeb513f7303e3e60c84747ddd5949
 EBUILD ncbi-tools-0.20090809.ebuild 6154 SHA256 5ca2bff0d8ec0883db98f2b855e1a58adb63bda490a0572c52adbe8455837444 SHA512 b5f10ce32bdce79c8b4d6faecc5d1c7b9930011a4f0f0c8f5bb7453e874e9b461176cbb684e04b925a95e0bbc615c8c349eac72a25c85ac42b16810b0fe91af4 WHIRLPOOL 07487e7f2fe84c5850c4af595a744fd55335c736be08f6651053c2ec9eef2e4968e50a12ff98d0da18b7ab8464f5a3d1cee260d9626843fbdc40dc8e34a9960c
-EBUILD ncbi-tools-2.2.26-r2.ebuild 4478 SHA256 163d938b00da8e04f3227c84f6e281544f9ae8e4e070c995a82730adb7793dac SHA512 1fa951b6cef82752945238473da194540f3f58e1ebb8082224555099912de9e36aae32f101c144ef7ee089ce809dbc8d97799a63b7de31132139d9435cc41c63 WHIRLPOOL 36de4e5ed575adec4b32c336eb2580788a9322012cfa81699912c446bbe159835d6e14d47e4b63be7a2d2c0f759466091bf8ed47eae4feafc90a5ae267bfd2be
+EBUILD ncbi-tools-2.2.26-r2.ebuild 4522 SHA256 4e6e9dc1f5742bb80ada8607c0054c83f31179348e876e7ee7dc3e235b9c9223 SHA512 cad4cf940aa1efbb2f970432fedd410d633e7b4b582a9630431aa18f6b961f150001fed49624c585da75e710b6e87d79c52fc488d5a9c8b48e3b619a24a400b3 WHIRLPOOL 7c06489236acdc6b7d7ed2214e7e303bd225fe91e01c00aadca4115f4b9ad31120fae3704d52a07e9fe231c7e108453566255e668b39f76f7f2544853944f45d
 EBUILD ncbi-tools-2.2.26.ebuild 4571 SHA256 8a345ab1cbf762aebb79fbe3fd07b5026060184db8ad364c62442b4f341f6abe SHA512 58f838b40ed9f24c12ec6a744055b538bb84e55315ba5b2f9c8e56b9f507f307f00ed0b8e6dd3cf18020c0e8ce9aaa51a84bd02874ba4ae7df88a86830c0986f WHIRLPOOL 121f00ef6075162a84b5eb1dc571443d26a81ff2dc27d4500ad970a640a40e1deeba6b95259a5a738fad2e5e68654ab352a59a118958ea4c58755d8ab1376dc9
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diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch
new file mode 100644
index 000000000000..e6763214a6e5
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch
@@ -0,0 +1,103 @@
+ cdromlib/cdnewlib.c | 6 +++---
+ corelib/ncbierr.c   | 2 +-
+ corelib/ncbisgml.c  | 8 ++++----
+ demo/errhdr.c       | 2 +-
+ 4 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c
+index 461292c..be4a2d6 100644
+--- a/cdromlib/cdnewlib.c
++++ b/cdromlib/cdnewlib.c
+@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi
+ 			char volname[16];
+ 			volname[0] = '\0';
+ 			if (cddev->volume != NULL)
+-				strncat(volname,cddev->volume->volume_name,sizeof volname);
++				strncat(volname,cddev->volume->volume_name,sizeof volname - 1);
+ 			else
+ 				sprintf(volname,"entrez%d",cddev->hint);
+ 			if (!FileBuildPath(fpath,volname,NULL))
+@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev)
+ 	memset((void*)&info,0,sizeof info);
+ 	fpath[0] = '\0';
+ 	if (cddev->inf.root !=NULL)
+-		strncat(fpath,cddev->inf.root,sizeof fpath);
++		strncat(fpath,cddev->inf.root,sizeof fpath - 1);
+ 		
+ 	if (cddev->ins_volname)
+ 	{
+@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev)
+ 			{
+ 				fpath[0] = '\0';
+ 				if (cddev->inf.root !=NULL)
+-					strncat(fpath,cddev->inf.root,sizeof fpath);
++					strncat(fpath,cddev->inf.root,sizeof fpath - 1);
+ 				sprintf(volname,"entrez%d",j+1);
+ 				FileBuildPath(fpath,volname,NULL);
+ 				if (CdTestPath(fpath,&info))
+diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c
+index 0429d86..7b96a2e 100644
+--- a/corelib/ncbierr.c
++++ b/corelib/ncbierr.c
+@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx)
+ 	if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL)
+           {
+             strcpy(path,info->msgpath);
+-            strncat(path,file,sizeof(path));
++            strncat(path,file,sizeof(path) - 1);
+             fd = FileOpen(path,s_msg_mode);
+           }
+ 
+diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c
+index 99412be..a653aef 100644
+--- a/corelib/ncbisgml.c
++++ b/corelib/ncbisgml.c
+@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL  Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t
+ 			}
+ 			if (i >= num_sgml_entity)
+ 			{
+-				char bad[SGML_ERROR_MSG_LIM];
++				char bad[SGML_ERROR_MSG_LIM + 2];
+ 				bad[0] = '\0';
+ 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ 				ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad);
+@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL  Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t
+ 				from++;
+ 			if (*from == '\0')
+ 			{
+-				char bad[SGML_ERROR_MSG_LIM];
++				char bad[SGML_ERROR_MSG_LIM + 2];
+ 				bad[0] = '\0';
+ 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ 				ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad);
+@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL  Nlm_Sgml2AsciiLen (const char *sgml)
+ 			}
+ 			if (i >= num_sgml_entity)
+ 			{
+-				char bad[SGML_ERROR_MSG_LIM];
++				char bad[SGML_ERROR_MSG_LIM + 2];
+ 				bad[0] = '\0';
+ 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ 				ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad);
+@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL  Nlm_Sgml2AsciiLen (const char *sgml)
+ 				from++;
+ 			if (*from == '\0')
+ 			{
+-				char bad[SGML_ERROR_MSG_LIM];
++				char bad[SGML_ERROR_MSG_LIM + 2];
+ 				bad[0] = '\0';
+ 				strncat(bad,sgml,SGML_ERROR_MSG_LIM);
+ 				ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad);
+diff --git a/demo/errhdr.c b/demo/errhdr.c
+index 01cd955..5081489 100644
+--- a/demo/errhdr.c
++++ b/demo/errhdr.c
+@@ -41,7 +41,7 @@ int main (int argc, char **argv)
+ 		else if (mod[0] == '\0')
+ 		{
+ 			char *p;
+-			strncat(mod,argv[i],sizeof mod);
++			strncat(mod,argv[i],sizeof mod - 1);
+ 			if ((p = strstr(argv[i],".msg")) != NULL)
+ 				*p = '\0';
+ 		}
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 a8306b411b8e..336fda013397 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
 # 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 1.3 2013/03/01 19:34:47 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild,v 1.4 2013/03/02 13:09:15 jlec Exp $
 
 EAPI=5
 
@@ -37,7 +37,9 @@ pkg_setup() {
 }
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PN}-extra_vib.patch
+	epatch \
+		"${FILESDIR}"/${PN}-extra_vib.patch \
+		"${FILESDIR}"/${P}-bfr-overflow.patch
 
 	if use ppc || use ppc64; then
 		epatch "${FILESDIR}"/${PN}-lop.patch
@@ -56,7 +58,7 @@ src_prepare() {
 	# Apply user C flags...
 	cd "${S}"/platform
 	sed \
-		-e "s:-O[s0-9]\?:asd:g" \
+		-e "s:-O[s0-9]\?::g" \
 		-e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
 		-e 's:-x[A-Z]*::g' \
 		-e 's:-pipe::g' \