01/01: gnu: openbabel: Fix crash when opening NWChem output files.

[Kei Kebreau]

kkebreau pushed a commit to branch master
in repository guix.

commit eb5ece73a84439d21219a802c0dcb88d54046371
Author: Kei Kebreau <address@hidden>
Date:   Sat Jul 21 12:47:34 2018 -0400

    gnu: openbabel: Fix crash when opening NWChem output files.
    
    * gnu/packages/patches/openbabel-fix-crash-on-nwchem-output.patch: New file.
    * gnu/local.mk (dist_patch_DATA): Register it.
    * gnu/packages/chemistry.scm (openbabel)[source]: Use it.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/chemistry.scm                         |  4 ++-
 .../openbabel-fix-crash-on-nwchem-output.patch     | 34 ++++++++++++++++++++++
 3 files changed, 38 insertions(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index e55c2bf..8ad81e6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -979,6 +979,7 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/ocaml-graph-honor-source-date-epoch.patch       \
   %D%/packages/patches/omake-fix-non-determinism.patch \
   %D%/packages/patches/ola-readdir-r.patch                     \
+  %D%/packages/patches/openbabel-fix-crash-on-nwchem-output.patch      \
   %D%/packages/patches/opencascade-oce-glibc-2.26.patch                \
   %D%/packages/patches/openblas-fix-tests-i686.patch           \
   %D%/packages/patches/openexr-missing-samples.patch           \
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index a81c14b..418b4be 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -213,7 +213,9 @@ NumPy < 1.9.")
                                   version "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))))
+                "1z3d6xm70dpfikhwdnbzc66j2l49vq105ch041wivrfz5ic3ch90"))
+              (patches
+               (search-patches "openbabel-fix-crash-on-nwchem-output.patch"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
diff --git a/gnu/packages/patches/openbabel-fix-crash-on-nwchem-output.patch 
b/gnu/packages/patches/openbabel-fix-crash-on-nwchem-output.patch
new file mode 100644
index 0000000..879df02
--- /dev/null
+++ b/gnu/packages/patches/openbabel-fix-crash-on-nwchem-output.patch
@@ -0,0 +1,34 @@
+From 52cea818bf68f8a2d3c48d55d00c2f8b7da25e4c Mon Sep 17 00:00:00 2001
+From: Daniel Hogan <address@hidden>
+Date: Tue, 28 Mar 2017 22:21:18 -0600
+Subject: [PATCH] Remove delete statement.
+
+When from_scratch is true, coordinates is not allocated. A separate if
+statement was added to handle the case when from_scratch is true that
+does not try to free coordinates.
+---
+ src/formats/nwchemformat.cpp | 9 ++++++---
+ 1 file changed, 6 insertions(+), 3 deletions(-)
+
+diff --git a/src/formats/nwchemformat.cpp b/src/formats/nwchemformat.cpp
+index 6f625ad5b..79298555f 100644
+--- a/src/formats/nwchemformat.cpp
++++ b/src/formats/nwchemformat.cpp
+@@ -232,11 +232,14 @@ static const char* OPTIMIZATION_END_PATTERN = "  
Optimization converged";
+           break;
+         tokenize(vs,buffer);
+     }
+-    if ((from_scratch)||(i != natoms))
+-      {
++    if (from_scratch) 
++    {
++        return;
++    }
++    if (i != natoms) {
+         delete[] coordinates;
+         return;
+-      }
++    }
+     molecule->AddConformer(coordinates);
+   }
+