[coot] * Sat Jan 14 2012 Tim Fenn <tim.fenn at gmail.com> - 0.6.2-12.20110715svn3566 - patches to fix unistd.h

[Timothy Fenn]

commit 01409c1dd94dfb9720c977d6cf00f295384038db
Author: Tim Fenn <fenn at stanford.edu>
Date:   Sat Jan 14 19:29:22 2012 -0800

    * Sat Jan 14 2012 Tim Fenn <tim.fenn at gmail.com> - 0.6.2-12.20110715svn3566
    - patches to fix unistd.h issue and compilation errors

 coot-fixes.patch  |   34 ++++++++++++++++++++++++++++++++++
 coot-unistd.patch |   12 ++++++++++++
 coot.spec         |    9 ++++++++-
 3 files changed, 54 insertions(+), 1 deletions(-)
---
diff --git a/coot-fixes.patch b/coot-fixes.patch
new file mode 100644
index 0000000..bc6c5c4
--- /dev/null
+++ b/coot-fixes.patch
@@ -0,0 +1,34 @@
+--- coot-utils/coot-coord-utils.cc_orig	2012-01-14 15:37:13.659012534 -0800
++++ coot-utils/coot-coord-utils.cc	2012-01-14 15:37:25.340287814 -0800
+@@ -180,7 +180,8 @@
+       clipper::Coord_frac cf = coot::util::shift_to_origin(mol);
+       clipper::Coord_orth co = cf.coord_orth(csp.first);
+       for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
+-	 int imod = 1;
++	// int imod = 1;
++	imod = 1;
+ 	 CModel *model_p = mol->GetModel(imod);
+ 	 CChain *chain_p;
+ 	 int nchains = model_p->GetNumberOfChains();
+@@ -2644,7 +2645,8 @@
+    short int whole_res_flag = 1;
+ 
+    for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) {
+-     int imod = 1;
++     // int imod = 1;
++     imod = 1;
+      CModel *model_p = mol_in->GetModel(imod);
+      CModel *new_model_p = new CModel;
+      int nchains = model_p->GetNumberOfChains();
+--- src/molecule-class-info-residues.cc_orig	2012-01-14 15:58:26.111024446 -0800
++++ src/molecule-class-info-residues.cc	2012-01-14 15:57:44.284039047 -0800
+@@ -131,7 +131,8 @@
+ 
+    int r = 0;
+    for(int imod = 1; imod<=atom_sel.mol->GetNumberOfModels(); imod++) {
+-      int imod = 1;
++     // int imod = 1;
++     imod = 1;
+       CModel *model_p = atom_sel.mol->GetModel(imod);
+       CChain *chain_p;
+       // run over chains of the existing mol
diff --git a/coot-unistd.patch b/coot-unistd.patch
new file mode 100644
index 0000000..352386f
--- /dev/null
+++ b/coot-unistd.patch
@@ -0,0 +1,12 @@
+--- utils/coot-utils.cc_orig	2012-01-14 14:55:00.076247314 -0800
++++ utils/coot-utils.cc	2012-01-14 14:55:16.310628650 -0800
+@@ -47,9 +47,7 @@
+ 
+ #include <sys/stat.h>   // for mkdir
+ #include <sys/types.h>
+-#if defined WINDOWS_MINGW
+ #include <unistd.h>   // BL says: in windows needed for mkdir
+-#endif // MINGW
+ 
+ // #include "clipper/core/hkl_compute.h"
+ 
diff --git a/coot.spec b/coot.spec
index bb771ec..6febc93 100644
--- a/coot.spec
+++ b/coot.spec
@@ -5,7 +5,7 @@ Name: coot
 Summary: The crystallographic object-oriented toolkit
 URL: http://www.biop.ox.ac.uk/coot/
 Version: 0.6.2
-Release: 11.20110715svn3566%{?dist}
+Release: 12.20110715svn3566%{?dist}
 # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown)
 License: GPLv3+ and LGPLv2+
 Group: Applications/Engineering
@@ -23,6 +23,8 @@ Source6: __init__.py
 Patch0: coot-configure.in.patch
 Patch1: coot-user-manual.texi.patch
 Patch2: coot-libpng15.patch
+Patch3: coot-unistd.patch
+Patch4: coot-fixes.patch
 BuildRequires: autoconf
 BuildRequires: automake
 BuildRequires: clipper-devel >= 2.1-7
@@ -86,6 +88,8 @@ package.
 %patch0 -p0
 %patch1 -p0
 %patch2 -p0
+%patch3 -p0
+%patch4 -p0
 
 cp %{SOURCE2} ./src/
 cp %{SOURCE3} ./src/
@@ -175,6 +179,9 @@ make check
 %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf
 
 %changelog
+* Sat Jan 14 2012 Tim Fenn <tim.fenn at gmail.com> - 0.6.2-12.20110715svn3566
+- patches to fix unistd.h issue and compilation errors
+
 * Thu Jan 12 2012 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 0.6.2-11.20110715svn3566
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild