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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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Compilation issues #248

Closed shayandoust closed 5 years ago

shayandoust commented 5 years ago

Hello,

My name is Shayan and I am a contributor for the Debian-Med packaging team1. More specifically, this software is being packaged for Debian2, however I am hitting some slight issues.

Generally, pbuilder3 is used to build the package within a chroot / clean environment and to test if the package builds successfully. Pbuilder builds within sid. Unfortunately, there is an error during the compilation step which I cannot seem to figure out a patch or fix for4. Any suggestions or help would be much appreciated.

Kind regards, Shayan Doust

voutcn commented 5 years ago

I encountered this with gcc8 too. And it has been fixed in v1.2.9 or the latest master branch. Could you try the latest source code?

Thank you for your help to pack Megahit to Debian-Med!

voutcn commented 5 years ago

I also reviewed the Debian-Med repo for Megahit. I think this patch is incorrect and breaks the correctness of the function. We just need to remove the __attribute__((packed)) as shown here.

shayandoust commented 5 years ago

Hello,

And it has been fixed in v1.2.9 or the latest master branch. Could you try the latest source code?

Yes it has. Thanks!

I also reviewed the Debian-Med repo for Megahit. I think this patch is incorrect and breaks the correctness of the function. We just need to remove the attribute((packed)) as shown here.

The patch was more of an experimentation to try figure out why it was failing with relation to the compiler's output. As the latest upstream tarball has fixed this issue, I'll remove the patch.

Thanks once again.