[Debian-med-packaging] Bug#833538: ncbi-blast+: FTBFS on s390x and sparc64: run_with_lock crashes

[Aaron M. Ucko]

Source: ncbi-blast+
Version: 2.4.0-2
Severity: serious
Justification: fails to build from source

The s390x and sparc64 builds of BLAST+ 2.4.0 have been failing:

  make[2]: Entering directory '/.../ncbi-blast+-2.4.0/c++/BUILD/build/corelib'
  /.../ncbi-blast+-2.4.0/c++/src/build-system/Makefile.meta_l:260: recipe for target 'sources.usr.locked' failed
  make[2]: *** [sources.usr.locked] Segmentation fault
  make[2]: Leaving directory '/.../ncbi-blast+-2.4.0/c++/BUILD/build/corelib'

The problem turned out to be that the build system, as patched by
Debian, winds up linking an optional helper tool named run_with_lock
with -pie but not compiling it with -fPIE.  On most platforms, this
inconsistency results in a linker error, and the build system proceeds
to fall back on a shell script.  However, on these two architectures,
the linker nominally succeeds but produces an executable that
immediately segfaults.

It should be possible to address the problem by supplying hardened
CFLAGS and LDFLAGS to configure as {C,LD}FLAGS_FOR_BUILD respectively;
we will then also want to add run_with_lock to the blacklist in
override_dh_install-arch.  I'll take care of these changes when I get
a chance, but am looking at a busy weekend.