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.