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Allow more than 2^32 sequences to be clustered #1039

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Cirrus CI / FreeBSD failed Sep 29, 2025 in 50s

Task Summary

Instruction compile failed in 00:19

Details

⚠️ Not enough compute credits to prioritize tasks!

✅ 00:08 clone
✅ 00:20 install
❌ 00:19 compile

[ 28%] Building C object lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o
[ 28%] Building C object lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o
[ 29%] Linking C static library libzstd.a
[ 29%] Built target libzstd_static
[ 29%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o
[ 29%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o
/tmp/cirrus-ci-build/src/alignment/CompressedA3M.cpp:205:40: error: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Werror,-Wshorten-64-to-32]
  205 |             match.qLen = match.dbLen = qLen;
      |                                      ~ ^~~~
/tmp/cirrus-ci-build/src/alignment/CompressedA3M.cpp:207:26: error: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Werror,-Wshorten-64-to-32]
  207 |             match.qLen = qLen;
      |                        ~ ^~~~
/tmp/cirrus-ci-build/src/alignment/CompressedA3M.cpp:208:42: error: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Werror,-Wshorten-64-to-32]
  208 |             match.dbLen = sequenceReader.getSeqLen(entryIndex);
      |                         ~ ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
3 errors generated.
--- src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o ---
*** [src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o] Error code 1

make[2]: stopped in /tmp/cirrus-ci-build/build
In file included from /tmp/cirrus-ci-build/src/alignment/Alignment.cpp:10:
/tmp/cirrus-ci-build/src/commons/SubstitutionMatrixProfileStates.h:83:34: error: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Werror,-Wshorten-64-to-32]
   83 |         this->alphabetSize = ps->getAlphSize();
      |                            ~ ~~~~^~~~~~~~~~~~~
/tmp/cirrus-ci-build/src/alignment/Alignment.cpp:128:25: error: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Werror,-Wshorten-64-to-32]
  128 |         threads = qdbr->getSize();
      |                 ~ ~~~~~~^~~~~~~~~
/tmp/cirrus-ci-build/src/alignment/Alignment.cpp:295:58: error: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Werror,-Wshorten-64-to-32]
  295 |             Matcher matcher(querySeqType, targetSeqType, maxMatcherSeqLen, m, &evaluer, compBiasCorrection, compBiasCorrectionScale, gapOpen, gapExtend, correlationScoreWeight, zdrop);
      |                     ~~~~~~~                              ^~~~~~~~~~~~~~~~
/tmp/cirrus-ci-build/src/alignment/Alignment.cpp:303:74: error: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Werror,-Wshorten-64-to-32]
  303 |                     realigner = new Matcher(querySeqType, targetSeqType, maxMatcherSeqLen, realign_m, &evaluer, compBiasCorrection, compBiasCorrectionScale, gapOpen, gapExtend, 0.0, zdrop);
      |                                     ~~~~~~~                              ^~~~~~~~~~~~~~~~
4 errors generated.
--- src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o ---
*** [src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o] Error code 1

make[2]: stopped in /tmp/cirrus-ci-build/build
2 errors

make[2]: stopped in /tmp/cirrus-ci-build/build
--- src/CMakeFiles/mmseqs-framework.dir/all ---
*** [src/CMakeFiles/mmseqs-framework.dir/all] Error code 2

make[1]: stopped in /tmp/cirrus-ci-build/build
1 error

make[1]: stopped in /tmp/cirrus-ci-build/build
*** [all] Error code 2

make: stopped in /tmp/cirrus-ci-build/build
1 error

make: stopped in /tmp/cirrus-ci-build/build

Exit status: 2