Package: openbabel / 2.3.2+dfsg-3

Metadata

Package Version Patches format
openbabel 2.3.2+dfsg-3 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
perl_hardening.patch | (download)

scripts/CMakeLists.txt | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 build perl module using flags set by debian/rules.
libinchi_static.patch | (download)

src/formats/libinchi/CMakeLists.txt | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 force static build of the inchi library.
 We currently don't want to ship a separate source package nor
 should libinchi be shipped as shared library with openbabel.
 The -fPIC switch is explicitely added to avoid an FTBFS on
 amd64 by relocation error. More information about the latter
 at http://www.cmake.org/pipermail/cmake/2006-March/008482.html.
fix_ftbfs.patch | (download)

scripts/CMakeLists.txt | 4 2 + 2 - 0 !
scripts/python/setup.py | 2 1 + 1 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 fix several ftbfses by cmake and make.
715668_fix_babel_segfault.patch | (download)

tools/babel.cpp | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 fix a potential crash reported by the mayhem project.
gcc5.diff | (download)

include/openbabel/shared_ptr.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---
gcc version.diff | (download)

CMakeLists.txt | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---
862517_initialise.patch | (download)

src/ops/loader.cpp | 14 12 + 2 - 0 !
1 file changed, 12 insertions(+), 2 deletions(-)

 [patch] fix garbage plugin strings bug with libc++

With libc++, using OBDefine to load descriptors from plugindefines.txt would result in some plugin IDs and descriptions becoming garbage.

This was because plugins use const char* pointers for their ID and description, which point towards strings stored in a vector by OBDefine. The problem was that as new strings were read from plugindefines.txt and added to the vector, reallocations can occur to expand the vector capacity, invalidating any existing const char* created from the previously added strings using c_str().

This commit fixes this bug by reading in all descriptors from plugindefines.txt before creating the plugin instances. This ensures no changes are made the string vector once a plugin instance has been created.

https://github.com/openbabel/openbabel/pull/62