user debian-sp...@lists.debian.org usertags sparc64 thanks (You missed the User: pseudoheader)
> On 2 Feb 2018, at 14:46, David Matthew Mattli <d...@mattli.us> wrote: > > Package: abyss > Severity: normal > Tags: patch upstream > Usertags: sparc64 > > Dear Maintainer, > > This package currently FTBFS on sparc64 due to the > PairedDBG_LoadAlgorithm test failing with a SIGBUS. The Kmer.load and > Kmer.storeReverse methods in the Common/Kmer.cpp file cast a uint8_t* > to a size_t* without ensuring the pointer value has the proper > alignment. > > To fix this I added an aligned stack allocated buffer and memcpy to > that. Stack allocated is appropriate because the buffer size is > small(32 bytes) and known at compile time. Hi, As a sparc64 porter, thanks for fixing packages! Just a couple of comments on the patch. > --- a/Common/Kmer.cpp > +++ b/Common/Kmer.cpp > @@ -188,9 +188,10 @@ > Seq seq; > #if MAX_KMER > 96 > # if WORDS_BIGENDIAN > - const size_t *s = reinterpret_cast<const size_t*>(src); > + size_t buf[Kmer::NUM_BYTES]; Should be divided by sizeof(size_t). Also, why not call it s? That should reduce the number of changes. > + memcpy(buf, src, Kmer::NUM_BYTES); > size_t *d = reinterpret_cast<size_t*>(&seq + 1); > - copy(s, s + Kmer::NUM_BYTES/sizeof(size_t), > reverse_iterator<size_t*>(d)); > + copy(buf, buf + Kmer::NUM_BYTES/sizeof(size_t), > reverse_iterator<size_t*>(d)); > # else > uint8_t *d = reinterpret_cast<uint8_t*>(&seq); > memcpy(d, src, sizeof seq); > @@ -235,9 +236,10 @@ > #if MAX_KMER > 96 > # if WORDS_BIGENDIAN > const size_t *s = reinterpret_cast<const size_t*>(&seq); > - size_t *d = reinterpret_cast<size_t*>(dest); > + size_t d[Kmer::NUM_BYTES]; Ditto for the size (this time you used the same name as before). > copy(s, s + Kmer::NUM_BYTES/sizeof(size_t), > reverse_iterator<size_t*>(d + > Kmer::NUM_BYTES/sizeof(size_t))); > + memcpy(dest, d, Kmer::NUM_BYTES); > reverse(dest, dest + Kmer::NUM_BYTES); > # else > memcpy(dest, &seq, Kmer::NUM_BYTES); Regards, James
