bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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Build failure on FreeBSD CURRENT after import of llvm/clang v17 #769

Open Jehops opened 6 months ago

Jehops commented 6 months ago

Hello Benjamin,

On FreeBSD's main branch, we recently updated llvm/clang to version 17.

root@15amd64-default:~ # clang -v
FreeBSD clang version 17.0.6 (https://github.com/llvm/llvm-project.git llvmorg-17.0.6-0-g6009708b4367)
Target: x86_64-unknown-freebsd15.0
Thread model: posix
InstalledDir: /usr/bin

Since that change, diamond fails to build. The error reported is

In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/table.cpp:21:
In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/global_ranking.h:21:
In file included from /wrkdirs/usr/ports/biology/diamond/work/diamond-2.1.8/src/align/global_ranking/../../output/output.h:25:
In file included from /usr/include/c++/v1/map:2529:
In file included from /usr/include/c++/v1/functional:526:
In file included from /usr/include/c++/v1/__functional/boyer_moore_searcher.h:25:
In file included from /usr/include/c++/v1/array:547:
In file included from /usr/include/c++/v1/algorithm:1803:
In file included from /usr/include/c++/v1/__algorithm/nth_element.h:15:
/usr/include/c++/v1/__algorithm/sort.h:564:11: error: no viable overloaded '-='
  564 |     __lm1 -= (__right_bitset == 0) ? difference_type(__detail::__block_size) : difference_type(0);
      |     ~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Here is a full build log.

Please let me know if there is any other information I can provide, or there is anything I can test.

Thanks,

Joe

Jehops commented 6 months ago

Proposed solution in https://github.com/bbuchfink/diamond/pull/771.

bbuchfink commented 5 months ago

Thanks, merged.