[Debian-med-packaging] Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)

[Matthew Fernandez]

> On Apr 29, 2020, at 09:04, Andreas Tille <tille at debian.org> wrote:
> 
> On Wed, Apr 29, 2020 at 07:14:30AM -0700, Matthew Fernandez wrote:
> 
>> For those on this thread who have access to mipsel hardware or can shell in to one of the mipsel build machines, I would suggest running an ASan-instrumented test there (`export CFLAGS="-g -fsanitize=address"; export CXXFLAGS="-g -fsanitize=address"`) and see what we learn.
> 
> I tried on real hardware.  Unfortunately I'm running into
> 
> 
> 
> configure:3720: $? = 0
> configure:3709: gcc -v >&5
> Using built-in specs.
> COLLECT_GCC=gcc
> COLLECT_LTO_WRAPPER=/usr/lib/gcc/mipsel-linux-gnu/9/lto-wrapper
> Target: mipsel-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Debian 9.3.0-10' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=mipsel-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libsanitizer --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-multiarch --disable-werror --enable-multilib --with-arch-32=mips32r2 --with-fp-32=xx --with-madd4=no --with-lxc1-sxc1=no --enable-targets=all --with-arch-64=mips64r2 --enable-checking=release --build=mipsel-linux-gnu --host=mipsel-linux-gnu --target=mipsel-linux-gnu
> Thread model: posix
> gcc version 9.3.0 (Debian 9.3.0-10) 
> configure:3720: $? = 0
> configure:3709: gcc -V >&5
> gcc: error: unrecognized command line option '-V'
> gcc: fatal error: no input files
> compilation terminated.
> configure:3720: $? = 1
> configure:3709: gcc -qversion >&5
> gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
> gcc: fatal error: no input files
> compilation terminated.
> configure:3720: $? = 1
> configure:3740: checking whether the C compiler works
> configure:3762: gcc -g -O2 -fdebug-prefix-map=/home/tille/clustalo=. -fstack-protector-strong -Wformat -Werror=format-security -fsanitize=address -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c  >&5
> /usr/bin/ld: cannot find libasan_preinit.o: No such file or directory
> /usr/bin/ld: cannot find -lasan
> collect2: error: ld returned 1 exit status
> configure:3766: $? = 1
> configure:3804: result: no
> configure: failed program was:
> 
> 
> 
> I have no idea why libasan_preinit.o and libasan.a are not installed.
> The package libgcc-9-dev is installed for sure and on amd64 both files
> are included here.  It seems the sudo command on eller does not permit
> me executing `apt-file update` in a chroot so I have no idea where these
> files are on mipsel (if they exist at all).
> 
> Any more help from debian-mipsel is really appreciated.

Hm yes, “--disable-libsanitizer” is rather ominous. I guess the mipsel GCC package has been built without ASan support. Surprising that it fails so messily (the front end seems to think -fsanitize=address is an accepted command line option), but libasan does indeed seem not available on mipsel [0]. The other option I suggested was Valgrind, but if you can’t run apt-file you probably can’t install Valgrind either. If anyone spectating has ideas, please chime in.

  [0]: https://packages.debian.org/search?searchon=contents&keywords=libasan.so&mode=exactfilename&suite=sid&arch=mipsel