[Debian-med-packaging] Bug#919778: Bug#919778: mash FTBFS on armhf when built on arm64 hardware

[Sascha Steinbiss]

tags 919778 help
forwarded 919778 https://github.com/marbl/Mash/issues/108
thanks

Hi,

thanks for reporting this issue!
I have forwarded this upstream but I'm afraid I won't be able to do much
about it in the near future. With the upcoming freeze in mind, and given
the fact that upstream doesn't seem to be too active about our recent
bug reports, TBH I would be tempted to remove support for the
architectures with missing builds from the mash package and file RM for
the old binary packages until there is a solution.
Some other packages depend on mash so I would like to see it in buster,
since (as always, in my own humble opinion) the problematic
architectures (arm, s390, mips) are not within the typical target
audience of mash.

Also tagging this as help -- so if there's anyone with expertise in this
kind of porting work, I would surely appreciate help :)
BTW Fabian, did you get any further with #918566 as this may be related?

Cheers
Sascha


On 19.01.19 15:42, Adrian Bunk wrote:
> Source: mash
> Version: 2.1-2
> Severity: serious
> Tags: ftbfs
> 
> https://buildd.debian.org/status/fetch.php?pkg=mash&arch=armhf&ver=2.1-2&stamp=1545838322&raw=0
> 
> ...
>    dh_auto_test -a
> 	make -j8 test VERBOSE=1
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> cd test ; ../mash sketch -o genomes.msh genome1.fna genome2.fna genome3.fna
> cd test ; ../mash sketch -r -I reads reads1.fastq reads2.fastq -o reads.msh
> Sketching genome1.fna...
> Sketching genome2.fna...
> Sketching genome3.fna...
> Bus error
> make[1]: *** [Makefile:94: test/reads.msh] Error 135
> 
> 
> Backtrace:
> 
> #0  0x00638d2e in MurmurHash3_x64_128 (key=0xf523a009, len=len at entry=21, seed=<optimized out>, out=out at entry=0xf6b2dbd4)
>     at src/mash/MurmurHash3.cpp:277
> #1  0x00635b4c in getHash (seq=<optimized out>, length=length at entry=21, seed=<optimized out>, use64=true)
>     at src/mash/hash.cpp:23
> #2  0x00639a50 in addMinHashes (minHashHeap=..., 
>     seq=0xf523a008 "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT"..., 
>     length=<optimized out>, parameters=...) at src/mash/Sketch.cpp:601
> #3  0x0063a7d6 in sketchFile (input=0x692268) at src/mash/Sketch.cpp:1264
> #4  0x006400a0 in ThreadPool<Sketch::SketchInput, Sketch::SketchOutput>::thread (arg=0xffeea370)
>     at src/mash/ThreadPool.hxx:182
> #5  0xf6cd2bbe in start_thread () from /lib/arm-linux-gnueabihf/libpthread.so.0
> #6  0xf6bc94dc in ?? () from /lib/arm-linux-gnueabihf/libc.so.6
> 
> 
> 
> void MurmurHash3_x64_128 ( const void * key, const int len,
>                            const uint32_t seed, void * out )
> {
>   const uint8_t * data = (const uint8_t*)key;
> ...
>   const uint64_t * blocks = (const uint64_t *)(data);
> ...
> 
> 
> key=0xf523a009 is not properly aligned for that.
> 
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