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authorJustin Lecher <jlec@gentoo.org>2011-03-03 20:30:51 +0000
committerJustin Lecher <jlec@gentoo.org>2011-03-03 20:30:51 +0000
commitf2965ee4856f56efc7442189c0aca89897360043 (patch)
treea6eaeb3e8fede7814682bd6c4cae16006a7e49d2 /sci-libs/mmdb
parentCheck chroot on restart. (diff)
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Version Bump
(Portage version: 2.2.0_alpha26/cvs/Linux x86_64)
Diffstat (limited to 'sci-libs/mmdb')
-rw-r--r--sci-libs/mmdb/ChangeLog10
-rw-r--r--sci-libs/mmdb/files/1.23.2-allignment.patch150
-rw-r--r--sci-libs/mmdb/mmdb-1.21.ebuild22
-rw-r--r--sci-libs/mmdb/mmdb-1.23.2.ebuild48
4 files changed, 206 insertions, 24 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/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
+}