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| author | Kei Kebreau <kkebreau@posteo.net> | 2018-07-21 12:47:34 -0400 |
|---|---|---|
| committer | Kei Kebreau <kkebreau@posteo.net> | 2018-07-21 22:28:51 -0400 |
| commit | eb5ece73a84439d21219a802c0dcb88d54046371 (patch) | |
| tree | 98c5f0d4ce0b3979d2d7d80f6d918171211c5889 | |
| parent | 889e7fab3c04be98a59b880bf44fbdaa6ddf0a4e (diff) | |
| download | guix-eb5ece73a84439d21219a802c0dcb88d54046371.tar guix-eb5ece73a84439d21219a802c0dcb88d54046371.tar.gz | |
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.
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/chemistry.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/patches/openbabel-fix-crash-on-nwchem-output.patch | 34 |
3 files changed, 38 insertions, 1 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index e55c2bf3ba..8ad81e6935 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 a81c14b43c..418b4be2f4 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 0000000000..879df026a1 --- /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 <daniel.hogan@usask.ca> +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); + } + |