The AMD64 build (for the scubuntu-dev PPA) of staden-1-7-0 0-1ubuntu21 fails.
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Log extract:
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cp ../mutlib/mutlib.def 2>&-
make[3]: [../lib/debian-binaries/libmutlib.so] Error 1 (ignored)
g++ -L../../lib/debian-binaries -L../lib/debian-binaries -L/lib/debian-binaries -shared -o ../lib/debian-binaries/libmutlib.so debian-binaries/align.o debian-binaries/basecall.o debian-binaries/caller.o debian-binaries/caller_snr.o debian-binaries/caller_base.o debian-binaries/caller_level.o debian-binaries/dnatable.o debian-binaries/muttag.o debian-binaries/mutationtag.o debian-binaries/mutationtag_utils.o debian-binaries/pathutil.o debian-binaries/peakcall.o debian-binaries/stringlist.o debian-binaries/tagarray.o debian-binaries/trace.o debian-binaries/validate.o debian-binaries/read_matrix.o debian-binaries/sp_align_lib.o debian-binaries/sp_alignment.o debian-binaries/sp_hash_lib.o debian-binaries/sp_matrix.o debian-binaries/tracediff.o debian-binaries/tracediff_helper.o debian-binaries/tracediff_mutations.o debian-binaries/tracediff_parameters.o debian-binaries/tracediff_validate.o debian-binaries/tracealign.o debian-binaries/tracealign_cache.o debian-binaries/tracealign_helper.o debian-binaries/tracealign_interpolate.o debian-binaries/tracealign_preprocess.o debian-binaries/tracealign_validate.o debian-binaries/mutscan.o debian-binaries/mutscan_helper.o debian-binaries/mutscan_validate.o debian-binaries/mutscan_analysis.o debian-binaries/mutscan_preprocess.o debian-binaries/mutscan_parameters.o -lseq_utils -ltk_utils -lread -lmisc -lm
/usr/bin/ld: debian-binaries/align.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
debian-binaries/align.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [../lib/debian-binaries/libmutlib.so] Error 1
make[3]: Leaving directory `/build/buildd/staden-1-7-0-0/src/mutlib'
make[2]: *** [mutlib] Error 2
make[2]: Leaving directory `/build/buildd/staden-1-7-0-0/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/build/buildd/staden-1-7-0-0'
make: *** [build-stamp] Error 2
dpkg-buildpackage: failure: debian/rules build gave error exit status 2
see: https://launchpad.net/~scubuntu-dev/+archive/+build/752259
The change suggested by the build process ("-fPIC") does not seem to be taking effect. Since the flag is now present for all g++ invocations I would need to test this on an actual AuthenticAMD cpu to reproduce this bug.