Debian Patches

Status for terraphast/0.1.0+dfsg-2

Patch Description Author Forwarded Bugs Origin Last update
dynamic_lib.patch Attempt to create shared library This patch is deactivated since the build fails with it.
Thus we simply stick to the existing static library		 Andreas Tille <tille@debian.org>, no 2021-10-20
fix-memory-limit-corruption.patch Fix heap corruption when the multitree memory limit is reached In the memory limited multitree callback, begin_iteration() returns an
"unexplored" node when the alternative array cannot be allocated (e.g.
because the memory limit was reached). The loop in
tree_enumerator::iterate() then kept iterating over the bipartitions and
called accumulate() on that unexplored node as if it were an alternative
array, writing a full multitree_node into the leaf array of the unexplored
node. This corrupted the heap and could lead to a "realloc(): invalid
pointer" abort inside GMP, making the unittests fail randomly.
.
Fix this by marking the memory limit as hit whenever begin_iteration()
has to fall back to an unexplored node, so that continue_iteration()
stops the iteration and accumulate() is never called on an unexplored
node.		 Andreas Tille <tille@debian.org> yes 2026-10-17
fix-c-api-test-corruption.patch Fix heap corruption in the c_api_error_num_partitions test The test created a missing-data matrix with zero partitions and then
called setDataMatrix() on it. initializeMissingData() allocates a
zero-sized matrix (new unsigned char[0]) for zero partitions, so the
setDataMatrix() calls wrote past the end of the allocation, corrupting
the heap. terraceAnalysis() returns TERRACE_NUM_PARTITIONS_ERROR as soon
as numberOfPartitions < 2, before it reads the matrix, so the
setDataMatrix() calls are not needed at all; drop them.		 Andreas Tille <tille@debian.org> not-needed 2026-10-17
site-gen-root-species.patch site_gen: fix root species off-by-one generating invalid data The root species index was drawn from the inclusive range 0..num_species,
so it could equal num_species, which is out of range. In that case no
species was present in every site and a site column could end up without a
single 1. Downstream tools (e.g. validated_run) require every site to
have at least one occurrence and abort with
"subtree_extraction.cpp:45: induced_lca: Assertion 'present(lca)' failed".
Draw the index from 0..num_species-1 so that one species is always present
in every site, and reject num_species == 0 to avoid an underflow.		 Andreas Tille <tille@debian.org> yes 2026-10-17

All known versions for source package 'terraphast'

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