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<title>[117813] trunk/dports/science/ce</title>
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<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/117813">117813</a></dd>
<dt>Author</dt> <dd>mmoll@macports.org</dd>
<dt>Date</dt> <dd>2014-03-13 10:04:32 -0700 (Thu, 13 Mar 2014)</dd>
</dl>
<h3>Log Message</h3>
<pre>science/ce: use patches instead of reinplace to fix code</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportssciencecePortfile">trunk/dports/science/ce/Portfile</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li><a href="#trunkdportssciencecefilespatchMakefilesdiff">trunk/dports/science/ce/files/patch-Makefiles.diff</a></li>
<li><a href="#trunkdportssciencecefilespatchnonstandardcodediff">trunk/dports/science/ce/files/patch-nonstandardcode.diff</a></li>
</ul>
<h3>Removed Paths</h3>
<ul>
<li><a href="#trunkdportssciencecefilespatchMakefilediff">trunk/dports/science/ce/files/patch-Makefile.diff</a></li>
<li><a href="#trunkdportssciencecefilespatchceCdiff">trunk/dports/science/ce/files/patch-ce.C.diff</a></li>
<li><a href="#trunkdportssciencecefilespatchpomhdiff">trunk/dports/science/ce/files/patch-pom.h.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportssciencecePortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/ce/Portfile (117812 => 117813)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/ce/Portfile 2014-03-13 16:02:35 UTC (rev 117812)
+++ trunk/dports/science/ce/Portfile 2014-03-13 17:04:32 UTC (rev 117813)
</span><span class="lines">@@ -3,6 +3,7 @@
</span><span class="cx"> PortSystem 1.0
</span><span class="cx"> name ce
</span><span class="cx"> version 2004-07-06
</span><ins>+revision 1
</ins><span class="cx"> categories science
</span><span class="cx"> maintainers mmoll
</span><span class="cx"> description Combinatorial Extension (CE) Method for 3D protein \
</span><span class="lines">@@ -16,11 +17,12 @@
</span><span class="cx"> sha1 cb1d7507a931e2635f302cad523c3082ba63596b \
</span><span class="cx"> rmd160 5475e00ff66d95fbe61e433d85067f5830259d0d
</span><span class="cx"> worksrcdir ${name}_distr_${version}
</span><del>-patchfiles patch-ce.C.diff patch-Makefile.diff patch-pom.h.diff
</del><ins>+#patchfiles patch-ce.C.diff patch-Makefile.diff patch-pom.h.diff
+patchfiles patch-Makefiles.diff patch-nonstandardcode.diff
</ins><span class="cx"> post-patch {
</span><del>- reinplace "s|g++|${configure.cxx}|g" ${worksrcpath}/ce/Makefile ${worksrcpath}/pom/Makefile
- reinplace "s|main(int argc|int main(int argc|g" ${worksrcpath}/ce/ce.C ${worksrcpath}/pom/ipdb.C
- reinplace "s|iostream.h|iostream|g" ${worksrcpath}/pom/calc.C
</del><ins>+ reinplace "s|@CXX@|${configure.cxx}|g" ${worksrcpath}/ce/Makefile ${worksrcpath}/pom/Makefile
+# reinplace "s|main(int argc|int main(int argc|g" ${worksrcpath}/ce/ce.C ${worksrcpath}/pom/ipdb.C
+# reinplace "s|iostream.h|iostream|g" ${worksrcpath}/pom/calc.C
</ins><span class="cx"> }
</span><span class="cx"> use_configure no
</span><span class="cx"> destroot.env-append PREFIX=${prefix}
</span></span></pre></div>
<a id="trunkdportssciencecefilespatchMakefilediff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/ce/files/patch-Makefile.diff (117812 => 117813)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/ce/files/patch-Makefile.diff 2014-03-13 16:02:35 UTC (rev 117812)
+++ trunk/dports/science/ce/files/patch-Makefile.diff 2014-03-13 17:04:32 UTC (rev 117813)
</span><span class="lines">@@ -1,16 +0,0 @@
</span><del>---- Makefile.orig 2000-05-25 20:26:03.000000000 -0500
-+++ Makefile 2010-01-13 08:49:40.000000000 -0600
-@@ -1,4 +1,4 @@
--all: make_pom make_ce make_copy
-+all: make_pom make_ce
-
- make_ce:
- $(MAKE) -C ce
-@@ -16,3 +16,7 @@
- use_exe_sgi:
- cp ce/ce_sgi ./CE
- cp pom/mkDB_sgi pom/mkDB
-+
-+install:
-+ cp ce/ce ${DESTDIR}/${PREFIX}/bin/ce
-+ cp pom/mkDB ${DESTDIR}/${PREFIX}/bin/mkDB
</del></span></pre></div>
<a id="trunkdportssciencecefilespatchMakefilesdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/ce/files/patch-Makefiles.diff (0 => 117813)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/ce/files/patch-Makefiles.diff (rev 0)
+++ trunk/dports/science/ce/files/patch-Makefiles.diff 2014-03-13 17:04:32 UTC (rev 117813)
</span><span class="lines">@@ -0,0 +1,38 @@
</span><ins>+--- Makefile.orig 2000-05-25 20:26:03.000000000 -0500
++++ Makefile 2010-01-13 08:49:40.000000000 -0600
+@@ -1,4 +1,4 @@
+-all: make_pom make_ce make_copy
++all: make_pom make_ce
+
+ make_ce:
+ $(MAKE) -C ce
+@@ -16,3 +16,7 @@
+ use_exe_sgi:
+ cp ce/ce_sgi ./CE
+ cp pom/mkDB_sgi pom/mkDB
++
++install:
++ cp ce/ce ${DESTDIR}/${PREFIX}/bin/ce
++ cp pom/mkDB ${DESTDIR}/${PREFIX}/bin/mkDB
+--- ce/Makefile.orig 2014-03-13 11:48:06.000000000 -0500
++++ ce/Makefile 2014-03-13 11:52:06.000000000 -0500
+@@ -7,7 +7,7 @@
+ LINTFILES=$(SOURCES:.C=.ln)
+ INCLUDE_DIR=
+
+-CC = g++ ${INCLUDE_DIR} -DREAD_WRITE
++CC = @CXX@ ${INCLUDE_DIR} -DREAD_WRITE
+ CFLAGS = -DFUNCPROTO
+
+
+--- pom/Makefile.orig 2014-03-13 11:49:41.000000000 -0500
++++ pom/Makefile 2014-03-13 11:52:06.000000000 -0500
+@@ -23,7 +23,7 @@
+ calc.h \
+ linkedid.h
+
+-CC = g++
++CC = @CXX@
+
+ MKOBJS = $(MKSRCS:.C=.o)
+
</ins></span></pre></div>
<a id="trunkdportssciencecefilespatchceCdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/ce/files/patch-ce.C.diff (117812 => 117813)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/ce/files/patch-ce.C.diff 2014-03-13 16:02:35 UTC (rev 117812)
+++ trunk/dports/science/ce/files/patch-ce.C.diff 2014-03-13 17:04:32 UTC (rev 117813)
</span><span class="lines">@@ -1,20 +0,0 @@
</span><del>---- ce/ce.C.orig 2003-03-13 18:42:38.000000000 -0600
-+++ ce/ce.C 2010-01-07 12:12:40.000000000 -0600
-@@ -79,7 +79,7 @@
- char *user_file1, *entity_id1;
- setText(&user_file1, pdb_file1);
-
-- setText(&mkdb_command, "pom/mkDB");
-+ setText(&mkdb_command, "mkDB");
- addText(&mkdb_command, " scratch ");
- addText(&mkdb_command, db_tmp_path);
- addText(&mkdb_command, " ");
-@@ -96,7 +96,7 @@
- setText(&user_file2, pdb_file2);
-
-
-- setText(&mkdb_command, "pom/mkDB");
-+ setText(&mkdb_command, "mkDB");
- addText(&mkdb_command, " scratch ");
- addText(&mkdb_command, db_tmp_path);
- addText(&mkdb_command, " ");
</del></span></pre></div>
<a id="trunkdportssciencecefilespatchnonstandardcodediff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/ce/files/patch-nonstandardcode.diff (0 => 117813)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/ce/files/patch-nonstandardcode.diff (rev 0)
+++ trunk/dports/science/ce/files/patch-nonstandardcode.diff 2014-03-13 17:04:32 UTC (rev 117813)
</span><span class="lines">@@ -0,0 +1,90 @@
</span><ins>+--- ce/ce.C.orig 2014-03-13 11:50:40.000000000 -0500
++++ ce/ce.C 2014-03-13 11:52:06.000000000 -0500
+@@ -47,7 +47,7 @@
+ };
+ double vecDist(XYZ *o1, XYZ *e1, XYZ *o2, XYZ *e2);
+ ////////////////////////////////////////////////////////////////////
+-main(int argc, char **argv) {
++int main(int argc, char **argv) {
+ if(argc<2) exit(0);
+
+ CE ce;
+@@ -79,7 +79,7 @@
+ char *user_file1, *entity_id1;
+ setText(&user_file1, pdb_file1);
+
+- setText(&mkdb_command, "pom/mkDB");
++ setText(&mkdb_command, "mkDB");
+ addText(&mkdb_command, " scratch ");
+ addText(&mkdb_command, db_tmp_path);
+ addText(&mkdb_command, " ");
+@@ -96,7 +96,7 @@
+ setText(&user_file2, pdb_file2);
+
+
+- setText(&mkdb_command, "pom/mkDB");
++ setText(&mkdb_command, "mkDB");
+ addText(&mkdb_command, " scratch ");
+ addText(&mkdb_command, db_tmp_path);
+ addText(&mkdb_command, " ");
+--- pom/ipdb.C.orig 2014-03-13 11:50:14.000000000 -0500
++++ pom/ipdb.C 2014-03-13 11:52:06.000000000 -0500
+@@ -2947,7 +2947,7 @@
+ //////////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////////
+ int main(int, char**, char **env=NULL);
+-main(int argc, char **argv, char **env)
++int main(int argc, char **argv, char **env)
+ {
+
+ Tlpdb tlpdb;
+--- pom/calc.C.orig 2014-03-13 11:50:30.000000000 -0500
++++ pom/calc.C 2014-03-13 11:52:06.000000000 -0500
+@@ -1,5 +1,5 @@
+ #include <math.h>
+-#include <iostream.h>
++#include <iostream>
+ #include "contour.h"
+ #include "calc.h"
+
+--- pom/pom.h.orig 2000-05-25 16:38:55.000000000 -0500
++++ pom/pom.h 2010-01-07 12:04:24.000000000 -0600
+@@ -410,11 +410,11 @@
+ };
+ ////////////////////////////////////////////////////////////////////
+ class Entities {
+- friend IEntity;
+- friend ISubentity;
+- friend IAtom;
+- friend IMonomer;
+- friend IBond;
++ friend class IEntity;
++ friend class ISubentity;
++ friend class IAtom;
++ friend class IMonomer;
++ friend class IBond;
+ public:
+ static DB *db_default;
+ DB *db;
+@@ -502,7 +502,7 @@
+ };
+ ////////////////////////////////////////////////////////////////////
+ class ISubentity {
+- friend IMonomer;
++ friend class IMonomer;
+ int iE;
+ int iS;
+ int iM;
+@@ -576,9 +576,9 @@
+ };
+ ////////////////////////////////////////////////////////////////////
+ class IAtom {
+- friend ISubentity;
+- friend IMonomer;
+- friend IBond;
++ friend class ISubentity;
++ friend class IMonomer;
++ friend class IBond;
+ int iE;
+ int iS;
+ int iA;
</ins></span></pre></div>
<a id="trunkdportssciencecefilespatchpomhdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/ce/files/patch-pom.h.diff (117812 => 117813)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/ce/files/patch-pom.h.diff 2014-03-13 16:02:35 UTC (rev 117812)
+++ trunk/dports/science/ce/files/patch-pom.h.diff 2014-03-13 17:04:32 UTC (rev 117813)
</span><span class="lines">@@ -1,41 +0,0 @@
</span><del>---- pom/pom.h.orig 2000-05-25 16:38:55.000000000 -0500
-+++ pom/pom.h 2010-01-07 12:04:24.000000000 -0600
-@@ -410,11 +410,11 @@
- };
- ////////////////////////////////////////////////////////////////////
- class Entities {
-- friend IEntity;
-- friend ISubentity;
-- friend IAtom;
-- friend IMonomer;
-- friend IBond;
-+ friend class IEntity;
-+ friend class ISubentity;
-+ friend class IAtom;
-+ friend class IMonomer;
-+ friend class IBond;
- public:
- static DB *db_default;
- DB *db;
-@@ -502,7 +502,7 @@
- };
- ////////////////////////////////////////////////////////////////////
- class ISubentity {
-- friend IMonomer;
-+ friend class IMonomer;
- int iE;
- int iS;
- int iM;
-@@ -576,9 +576,9 @@
- };
- ////////////////////////////////////////////////////////////////////
- class IAtom {
-- friend ISubentity;
-- friend IMonomer;
-- friend IBond;
-+ friend class ISubentity;
-+ friend class IMonomer;
-+ friend class IBond;
- int iE;
- int iS;
- int iA;
</del></span></pre>
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