Version Bump

Package-Manager: portage-2.2.0_alpha26/cvs/Linux x86_64

5 files changed, 214 insertions, 30 deletions

diff --git a/sci-libs/mmdb/ChangeLog b/sci-libs/mmdb/ChangeLog
index f11c3a4fce39..31002b0c6503 100644
--- a/sci-libs/mmdb/ChangeLog
+++ b/sci-libs/mmdb/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/mmdb
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/mmdb/ChangeLog,v 1.12 2010/07/15 20:11:13 maekke Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/mmdb/ChangeLog,v 1.13 2011/03/03 20:30:51 jlec Exp $
+
+*mmdb-1.23.2 (03 Mar 2011)
+
+  03 Mar 2011; Justin Lecher <jlec@gentoo.org> +files/1.23.2-allignment.patch,
+  -mmdb-1.21.ebuild, +mmdb-1.23.2.ebuild:
+  Version Bump
 
   15 Jul 2010; Markus Meier <maekke@gentoo.org> mmdb-1.21-r3.ebuild:
   x86 stable, bug #326031
diff --git a/sci-libs/mmdb/Manifest b/sci-libs/mmdb/Manifest
index 412cc168a56f..7459a6ae4190 100644
--- a/sci-libs/mmdb/Manifest
+++ b/sci-libs/mmdb/Manifest
@@ -2,15 +2,17 @@
 Hash: SHA1
 
 AUX 1.21-allignment.patch 6654 RMD160 b0044a35aeaf63f125250279fc9d2ae8d9c6301d SHA1 7806b608ddd9a498eb9b3437d662df297f1957f2 SHA256 748d95718018b84f0b1938ec553256177642b1ee5c8394994f2131c3e1c1129d
+AUX 1.23.2-allignment.patch 4280 RMD160 6a64dc726f59ab8fa2f581b14db8671c04b40242 SHA1 27ae7847eb7a07251d206ada02e8b02bb3161618 SHA256 7d04b9821b14a73475fb963af26b3453ccee273ce54450a906eafd7dd11d2cf5
 DIST mmdb-1.21.tar.gz 675301 RMD160 9feb5660ffb79289a796bde5e5effffc3e81a4af SHA1 cc17a4f12448e21ce9d0c772b269b42d417113fb SHA256 508dcb4bc3a8f9552d930edf019cd2a3750c5fa794d8a95e6a22eaeaeb5ab0be
+DIST mmdb-1.23.2.tar.gz 677024 RMD160 04400aef3c0fe0ec42e5a7c19be966b8c3f00bab SHA1 8a9bfa8cac5c56cc748f67eda4f541add8baddf1 SHA256 ade8a6197a34ede045924626fb8aa0fc0d8767fe1ecd2808579c3ac6c75192f7
 EBUILD mmdb-1.21-r3.ebuild 1200 RMD160 2753551928a11d104de4f91c8460a2221d6735b9 SHA1 1ad47c469239883057ce571939e38f14892416d4 SHA256 63c327ab074fb4060af09e1c6db43abffbca5ea6985ac4dd8b4e8059e450795c
-EBUILD mmdb-1.21.ebuild 663 RMD160 ee59666e91338ab493ad110e5329f3162a0ef80d SHA1 8c26daf1cf95cce8cdbf45fb2bf85d1548557b7a SHA256 4e21977ec66ff3b01a4993238a8f9c71fcfc089179641b2dff541442cf016080
-MISC ChangeLog 1955 RMD160 2e04bab167916820f4c7c95bcebbd28025ee7e87 SHA1 642fcfc03eeaf71933214e211c1449dcca43a746 SHA256 901a69a815926b25d25616d9b80c21a3d7def9083b4f87dd40f444ee267ea37e
+EBUILD mmdb-1.23.2.ebuild 1229 RMD160 dfa2186d609481cac16349b7854cc73dcb65de55 SHA1 c51da5f8054e79714c775db025ca51d04cbd844e SHA256 9399dbb70930d74857583b58fc8d4947531f37bbeb2d9aa8ff327e1652f3f979
+MISC ChangeLog 2118 RMD160 315954c68087de0ad5c9d26bfa6e7a8ef0689545 SHA1 7489db1102aa70b051ed1bee22771734d1cb152a SHA256 275844703d628ea10cd6527afa2ea0be828349ad4c7cbf55c73d2595aadf36c4
 MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAkw/awAACgkQkKaRLQcq0GJQxwCeJGqYzkMIHwbRFxFlbsuc2Xbc
-AcsAnjytOUB6Z2Xdb2KhJtDi5kEe22kh
-=MnvA
+iEYEARECAAYFAk1v+oAACgkQgAnW8HDreRam3gCgsf1gHIznHog5FjoyXRmJTqhA
+9tcAnjfETtWM2f6z8umQtq2+1arav0ZR
+=q6c4
 -----END PGP SIGNATURE-----
diff --git a/sci-libs/mmdb/files/1.23.2-allignment.patch b/sci-libs/mmdb/files/1.23.2-allignment.patch
new file mode 100644
index 000000000000..7d7c159e7daa
--- /dev/null
+++ b/sci-libs/mmdb/files/1.23.2-allignment.patch
@@ -0,0 +1,150 @@
+diff --git a/src/machine_.h b/src/machine_.h
+index 804bc6d..6ed52a6 100644
+--- a/src/machine_.h
++++ b/src/machine_.h
+@@ -127,8 +127,12 @@
+ # define CALL_LIKE_VMS  1

+ 

+ // MVS stands for Microsoft Visual Studio

+-#elif defined(_MVS) 

++#elif defined(_MSC_VER)
++# if (_MSC_VER) >= 800
++# define CALL_LIKE_MVS  2
++# else
+ # define CALL_LIKE_MVS  1

++# endif
+ 

+ #elif defined(F2C) || defined(G77)

+ # define CALL_LIKE_SUN  8

+@@ -400,11 +404,41 @@ typedef  double     apireal;    // FORTRAN  real*8
+ 

+ #elif defined(CALL_LIKE_MVS)

+ 

++# if ( CALL_LIKE_MVS == 2 )
++
+   typedef pstr fpstr;

+ 

+ # define FTN_STR(s)  s

+ # define FTN_LEN(s)  s##_len

+ 

++# define char_struct(s)           \
++    pstr  s;                      \
++    int   s##_len;
++# define fill_char_struct(s,str)  \
++    s  = str;                     \
++    s##_len = strlen(str);
++
++# ifdef __cplusplus
++#   define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
++    extern "C" void NAME p_sun
++# else
++#   define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
++    void NAME p_sun
++# endif
++
++# define FORTRAN_EXTERN(NAME,name,p_sun,p_stardent,p_mvs) \
++    extern "C" void NAME p_sun
++
++# define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
++    NAME p_sun
++
++# else 
++
++  typedef pstr fpstr;
++
++# define FTN_STR(s)  s
++# define FTN_LEN(s)  s##_len
++
+ # define char_struct(s)  \

+     pstr  s;             \

+     int   s##_len;

+@@ -425,7 +459,7 @@ typedef  double     apireal;    // FORTRAN  real*8
+ 

+ # define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \

+     NAME p_mvs

+-

++# endif
+ #else

+ 

+ # error  Unknown machine!!!

+diff --git a/src/mmdb_atom.h b/src/mmdb_atom.h
+index 61bafaa..c860e30 100644
+--- a/src/mmdb_atom.h
++++ b/src/mmdb_atom.h
+@@ -312,7 +312,7 @@ class CAtom : public CUDData  {
+ 

+     realtype GetDist2 ( PCAtom a );

+     realtype GetDist2 ( PCAtom a, mat44 & tm );  // tm applies to A

+-    realtype GetDist2 ( PCAtom a, mat33 & r, vect3 & t );// tm applies to A

++    realtype GetDist2 ( PCAtom a, mat33 & r, vect3 & t );  // tm applies to A

+     realtype GetDist2 ( realtype ax, realtype ay, realtype az );

+ 

+     // GetCosine(a1,a2) calculates cosine of angle a1-this-a2,

+diff --git a/src/mmdb_chain.cpp b/src/mmdb_chain.cpp
+index 95023b7..fcf602f 100644
+--- a/src/mmdb_chain.cpp
++++ b/src/mmdb_chain.cpp
+@@ -679,7 +679,7 @@ int  i,k,sN;
+     i  = 0;

+     sN = 1;

+     while (i<numRes)  {

+-      PutInteger ( &(S[8]),sN,2 );

++      PutInteger ( &(S[7]),sN,3 );

+       k = 19;

+       while ((i<numRes) && (k<70))  {

+         if (resName[i][0])

+diff --git a/src/mmdb_selmngr.cpp b/src/mmdb_selmngr.cpp
+index 20261c7..87b4bef 100644
+--- a/src/mmdb_selmngr.cpp
++++ b/src/mmdb_selmngr.cpp
+@@ -1158,7 +1158,7 @@ void  CMMDBSelManager::Select (
+              int   selKey    // selection key

+                     )  {

+ int       i,j,k,n,m1,m2,c, sk,nsel;

+-Boolean   noRes,modelSel,chainSel,resSel,selAND;

++Boolean   noRes,modelSel(False),chainSel,resSel,selAND;

+ PCModel   model;

+ PCChain   chain;

+ PCResidue res;

+diff --git a/src/mmdb_title.cpp b/src/mmdb_title.cpp
+index 3dd7925..eb6de74 100644
+--- a/src/mmdb_title.cpp
++++ b/src/mmdb_title.cpp
+@@ -1381,6 +1381,10 @@ MakeStreamFunctions(CRemark)
+ #define  R350_CHAINS         2

+ #define  R350_BIOMT          3

+ 

++#ifdef _WIN32
++#define  strcasestr(s, t) strstr(strupr(s), t)
++#endif
++
+ void getRemarkKey ( RPCRemark rem, int & lkey )  {

+   if (rem)  {

+     if (rem->remarkNum!=350)  lkey = R350_END;

+@@ -1458,7 +1462,7 @@ int      l,lkey,nAdd,j;
+ 

+   while ((i<l) && (lkey==R350_NONE))  {

+ 

+-    p = strcasestr ( rem->Remark,"CHAINS:" );

++    p = strcasestr( rem->Remark,"CHAINS:" );
+     if (p)  p += 7;

+     else  {

+       p = rem->Remark;

+@@ -1513,7 +1517,7 @@ pstr p1,p2;
+ int  l,j,lkey;

+ 

+   sprintf ( PN,"BIOMT%1i",biomtNo );

+-  p1 = strcasestr ( rem->Remark,PN );

++  p1 = strcasestr( rem->Remark,PN );
+   if (!p1)  return R350_ERRBIOMT;

+ 

+   p1 += 6;

+@@ -1976,7 +1980,7 @@ int      i,l;
+     if (rem)  {

+       if (rem->remarkNum==2)  {

+         if (rem->Remark)  {

+-          p = strcasestr ( rem->Remark,"RESOLUTION" );

++          p = strcasestr( rem->Remark,"RESOLUTION" );
+           if (p)  {

+             while ((*p) && (*p!=' '))  p++;

+             if (*p)  {

diff --git a/sci-libs/mmdb/mmdb-1.21.ebuild b/sci-libs/mmdb/mmdb-1.21.ebuild
deleted file mode 100644
index b716d141f750..000000000000
--- a/sci-libs/mmdb/mmdb-1.21.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/mmdb/mmdb-1.21.ebuild,v 1.5 2010/06/28 21:36:43 angelos Exp $
-
-EAPI="2"
-
-DESCRIPTION="The Coordinate Library is designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="http://www.ebi.ac.uk/~keb/cldoc/"
-SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
-
-src_install() {
-	emake DESTDIR="${D}" install || die "emake install failed"
-}
diff --git a/sci-libs/mmdb/mmdb-1.23.2.ebuild b/sci-libs/mmdb/mmdb-1.23.2.ebuild
new file mode 100644
index 000000000000..cd695468c680
--- /dev/null
+++ b/sci-libs/mmdb/mmdb-1.23.2.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/mmdb/mmdb-1.23.2.ebuild,v 1.1 2011/03/03 20:30:51 jlec Exp $
+
+EAPI="3"
+
+inherit autotools eutils
+
+DESCRIPTION="The Coordinate Library is designed to assist CCP4 developers in working with coordinate files"
+HOMEPAGE="http://www.ebi.ac.uk/~keb/cldoc/ http://www.biop.ox.ac.uk/coot"
+SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz"
+
+LICENSE="GPL-2 LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="!<sci-libs/ccp4-libs-6.1.3"
+RDEPEND=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-allignment.patch
+	eautoreconf
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "emake install failed"
+
+	# create missing mmdb.pc
+	cat >> "${T}"/mmdb.pc <<- EOF
+	prefix=${EPREFIX}/usr
+	exec_prefix=${EPREFIX}/usr
+	libdir=${EPREFIX}/usr/$(get_libdir)
+	includedir=${EPREFIX}/usr/include
+
+	Name: ${PN}
+	Description: Macromolecular coordinate library
+	Version: ${PV}
+	Requires:
+	Conflicts:
+	Libs: -L${EPREFIX}/usr/$(get_libdir) -lmmdb
+	Cflags: -I${EPREFIX}/usr/include
+
+	EOF
+
+	insinto /usr/$(get_libdir)/pkgconfig
+	doins "${T}"/mmdb.pc || die
+}