Comments (9)
gitozi
commented on June 10, 2024
1
I can confirm that I can now build without the workaround. Thanks again!
from foldseek.
milot-mirdita
commented on June 10, 2024
You need to have either xxd (usually from a vim or vim-common package) or perl installed to generate the header during build. Can you post the whole cmake output?
from foldseek.
gitozi
commented on June 10, 2024
I could not see any hints regarding the dependencies you are mentioning, neither from the install instructions nor from the cmake output:
[user@server build]$ cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Source Directory: /home/user/packages/foldseek/foldseek/lib/mmseqs
-- Project Directory: /home/user/packages/foldseek/foldseek/lib/mmseqs
-- Compiler is GNU
-- Performing Test HAVE_AVX2_EXTENSIONS
-- Performing Test HAVE_AVX2_EXTENSIONS - Success
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
-- Performing Test HAVE_SSE4_2_EXTENSIONS
-- Performing Test HAVE_SSE4_2_EXTENSIONS - Success
-- Performing Test HAVE_SSE4_1_EXTENSIONS
-- Performing Test HAVE_SSE4_1_EXTENSIONS - Success
-- Performing Test HAVE_SSE3_EXTENSIONS
-- Performing Test HAVE_SSE3_EXTENSIONS - Success
-- Performing Test HAVE_SSE2_EXTENSIONS
-- Performing Test HAVE_SSE2_EXTENSIONS - Success
-- Performing Test HAVE_SSE_EXTENSIONS
-- Performing Test HAVE_SSE_EXTENSIONS - Success
-- ZSTD VERSION 1.3.8
-- ShellCheck disabled
-- Performing Test HAVE_POSIX_FADVISE
-- Performing Test HAVE_POSIX_FADVISE - Success
-- Performing Test HAVE_POSIX_MADVISE
-- Performing Test HAVE_POSIX_MADVISE - Success
-- Performing Test ATOMIC_LIBRARY_NATIVE
-- Performing Test ATOMIC_LIBRARY_NATIVE - Failed
-- Performing Test ATOMIC_LIBRARY_LIB
-- Performing Test ATOMIC_LIBRARY_LIB - Success
-- Found Atomic: atomic
-- IPS4O sorting works
-- Found ZLIB
-- Performing Test HAVE_ZLIB_CHECK
-- Performing Test HAVE_ZLIB_CHECK - Success
-- ZLIB works
-- Found BZLIB
-- Performing Test HAVE_BZLIB_CHECK
-- Performing Test HAVE_BZLIB_CHECK - Success
-- BZLIB works
-- Found OpenMP
-- ShellCheck not found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/user/packages/foldseek/foldseek/build
from foldseek.
milot-mirdita
commented on June 10, 2024
Can you post the make output please too
from foldseek.
gitozi
commented on June 10, 2024
[user@server build]$ make -j1
[ 0%] Generating ../generated/VTML80.out.h
[ 1%] Generating ../generated/VTML40.out.h
[ 2%] Generating ../generated/nucleotide.out.h
[ 2%] Generating ../generated/blosum62.out.h
[ 2%] Generating ../generated/PAM30.out.h
[ 3%] Generating ../generated/CovSeqidQscPercMinDiag.lib.h
[ 3%] Generating ../generated/CovSeqidQscPercMinDiagTargetCov.lib.h
[ 3%] Generating ../generated/ExpOpt3_8_polished.cs32.lib.h
[ 3%] Generating ../generated/Library255_may17.lib.h
[ 4%] Generating ../generated/libPolished_8.lib.h
[ 4%] Generating ../generated/cs219.lib.h
[ 4%] Generating ../generated/krona_prelude.html.h
[ 5%] Generating ../generated/result_viz_prelude.html.zst.h
[ 6%] Generating ../generated/K4000.crf.h
[ 6%] Generating ../generated/easysearch.sh.h
[ 7%] Generating ../generated/easycluster.sh.h
[ 8%] Generating ../generated/easytaxonomy.sh.h
[ 8%] Generating ../generated/easyrbh.sh.h
[ 9%] Generating ../generated/blastp.sh.h
[ 9%] Generating ../generated/blastpgp.sh.h
[ 10%] Generating ../generated/map.sh.h
[ 10%] Generating ../generated/rbh.sh.h
[ 10%] Generating ../generated/linclust.sh.h
[ 10%] Generating ../generated/clustering.sh.h
[ 11%] Generating ../generated/cascaded_clustering.sh.h
[ 11%] Generating ../generated/update_clustering.sh.h
[ 11%] Generating ../generated/searchtargetprofile.sh.h
[ 11%] Generating ../generated/createindex.sh.h
[ 12%] Generating ../generated/createtaxdb.sh.h
[ 12%] Generating ../generated/translated_search.sh.h
[ 12%] Generating ../generated/taxpercontig.sh.h
[ 12%] Generating ../generated/multihitdb.sh.h
[ 12%] Generating ../generated/multihitsearch.sh.h
[ 12%] Generating ../generated/enrich.sh.h
[ 12%] Generating ../generated/blastn.sh.h
[ 12%] Generating ../generated/searchslicedtargetprofile.sh.h
[ 13%] Generating ../generated/taxonomy.sh.h
[ 13%] Generating ../generated/linsearch.sh.h
[ 13%] Generating ../generated/databases.sh.h
[ 13%] Generating ../generated/nucleotide_clustering.sh.h
[ 13%] Generating ../generated/iterativepp.sh.h
[ 14%] Generating ../generated/tsv2exprofiledb.sh.h
[ 14%] Built target generated
[ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o
[ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o
[ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o
[ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o
[ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o
[ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o
[ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o
[ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o
[ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o
[ 19%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o
[ 19%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o
[ 19%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o
[ 22%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o
[ 22%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o
[ 22%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o
[ 24%] Linking C static library libzstd.a
[ 24%] Built target libzstd_static
[ 25%] Building C object lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:373:16: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
373 | ret->bound = s->bound;
| ^~
In function 'new_expr',
inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:372:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
88 | te_expr *ret = malloc(size);
| ^~~~~~~~~~~~
In function 'new_expr',
inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:93:15: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
93 | ret->type = type;
| ~~~~~~~~~~^~~~~~
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
88 | te_expr *ret = malloc(size);
| ^~~~~~~~~~~~
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:367:16: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
367 | ret->value = s->value;
| ^~
In function 'new_expr',
inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
88 | te_expr *ret = malloc(size);
| ^~~~~~~~~~~~
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:446:16: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
446 | ret->value = NAN;
| ^~
In function 'new_expr',
inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:444:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
88 | te_expr *ret = malloc(size);
| ^~~~~~~~~~~~
[ 25%] Linking C static library libtinyexpr.a
[ 25%] Built target tinyexpr
[ 26%] Building C object lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/microtar.c.o
[ 26%] Linking C static library libmicrotar.a
[ 26%] Built target microtar
[ 27%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lambda_calculator.cpp.o
[ 27%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lubksb.cpp.o
[ 27%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/ludcmp.cpp.o
[ 28%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/nrutil.cpp.o
[ 28%] Built target cacode
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_random.cpp.o
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o
[ 30%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o
[ 30%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o
[ 30%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o
[ 31%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o
[ 31%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o
[ 31%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o
[ 32%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o
[ 32%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp.cpp.o
[ 32%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o
[ 33%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o
[ 33%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o
[ 33%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o
[ 33%] Built target alp
[ 33%] Building CXX object lib/mmseqs/lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o
[ 33%] Built target ksw2
[ 33%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o
[ 34%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o
[ 34%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o
[ 34%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o
[ 34%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o
[ 35%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o
[ 35%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o
[ 35%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/StripedSmithWaterman.cpp.o
[ 36%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/BandedNucleotideAligner.cpp.o
[ 36%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/rescorediagonal.cpp.o
[ 36%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Main.cpp.o
[ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/AlignmentSymmetry.cpp.o
[ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Clustering.cpp.o
[ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/ClusteringAlgorithms.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CSProfile.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/A3MReader.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Application.cpp.o
[ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/BaseMatrix.cpp.o
[ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Command.cpp.o
[ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CommandCaller.cpp.o
[ 40%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBConcat.cpp.o
[ 40%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBReader.cpp.o
[ 40%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBWriter.cpp.o
[ 41%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Debug.cpp.o
[ 41%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ExpressionParser.cpp.o
[ 41%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/FileUtil.cpp.o
[ 42%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/HeaderSummarizer.cpp.o
[ 42%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/KSeqWrapper.cpp.o
[ 42%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MemoryMapped.cpp.o
[ 43%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MemoryTracker.cpp.o
[ 43%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MMseqsMPI.cpp.o
[ 43%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MultiParam.cpp.o
[ 44%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/NucleotideMatrix.cpp.o
[ 44%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Orf.cpp.o
[ 44%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Parameters.cpp.o
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ProfileStates.cpp.o
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/LibraryReader.cpp.o
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Sequence.cpp.o
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/SubstitutionMatrix.cpp.o
[ 46%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/tantan.cpp.o
[ 46%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/UniprotKB.cpp.o
[ 46%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Util.cpp.o
[ 47%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/CacheFriendlyOperations.cpp.o
[ 47%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ExtendedSubstitutionMatrix.cpp.o
[ 47%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Indexer.cpp.o
[ 48%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/IndexBuilder.cpp.o
[ 48%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/KmerGenerator.cpp.o
[ 48%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Main.cpp.o
[ 49%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Prefiltering.cpp.o
[ 49%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/PrefilteringIndexReader.cpp.o
[ 49%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/QueryMatcher.cpp.o
[ 50%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ReducedMatrix.cpp.o
[ 50%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/SequenceLookup.cpp.o
[ 50%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/UngappedAlignment.cpp.o
[ 51%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ungappedprefilter.cpp.o
[ 51%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/besthitperset.cpp.o
[ 51%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/combinepvalperset.cpp.o
[ 52%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/Aggregation.cpp.o
[ 52%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/MultiHitDb.cpp.o
[ 52%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/MultiHitSearch.cpp.o
[ 53%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/lca.cpp.o
[ 53%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/addtaxonomy.cpp.o
[ 53%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/NcbiTaxonomy.cpp.o
[ 54%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/filtertaxdb.cpp.o
[ 54%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/filtertaxseqdb.cpp.o
[ 54%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/aggregatetax.cpp.o
[ 55%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createtaxdb.cpp.o
[ 55%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createbintaxonomy.cpp.o
[ 55%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createbintaxmapping.cpp.o
[ 56%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/taxonomyreport.cpp.o
[ 56%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmermatcher.cpp.o
[ 56%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmerindexdb.cpp.o
[ 56%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmersearch.cpp.o
[ 57%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/LinsearchIndexReader.cpp.o
[ 57%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/alignall.cpp.o
[ 57%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/alignbykmer.cpp.o
[ 58%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/appenddbtoindex.cpp.o
[ 58%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/apply.cpp.o
[ 58%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/clusthash.cpp.o
[ 59%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/compress.cpp.o
[ 59%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convert2fasta.cpp.o
[ 59%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertalignments.cpp.o
[ 60%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertca3m.cpp.o
[ 60%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertkb.cpp.o
[ 60%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertmsa.cpp.o
[ 61%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertprofiledb.cpp.o
[ 61%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createdb.cpp.o
[ 61%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/dbtype.cpp.o
[ 62%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/db2tar.cpp.o
[ 62%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/indexdb.cpp.o
[ 62%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/offsetalignment.cpp.o
[ 63%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createseqfiledb.cpp.o
[ 63%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createsubdb.cpp.o
[ 63%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/view.cpp.o
[ 64%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createtsv.cpp.o
[ 64%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/diffseqdbs.cpp.o
[ 64%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/expandaln.cpp.o
[ 65%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractalignedregion.cpp.o
[ 65%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractdomains.cpp.o
[ 65%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractorfs.cpp.o
[ 66%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/orftocontig.cpp.o
[ 66%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/touchdb.cpp.o
[ 66%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/filterdb.cpp.o
[ 67%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/gff2db.cpp.o
[ 67%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/renamedbkeys.cpp.o
[ 67%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/masksequence.cpp.o
[ 67%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/maskbygff.cpp.o
[ 68%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/mergeclusters.cpp.o
[ 68%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/mergeresultsbyset.cpp.o
[ 68%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/mergedbs.cpp.o
[ 69%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/msa2profile.cpp.o
[ 69%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/msa2result.cpp.o
[ 69%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/nrtotaxmapping.cpp.o
[ 70%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/countkmer.cpp.o
[ 70%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/pairaln.cpp.o
[ 70%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/prefixid.cpp.o
[ 71%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/profile2pssm.cpp.o
[ 71%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/profile2seq.cpp.o
[ 71%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2dnamsa.cpp.o
[ 72%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2flat.cpp.o
[ 72%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2msa.cpp.o
[ 72%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2rbh.cpp.o
[ 73%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2profile.cpp.o
[ 73%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2repseq.cpp.o
[ 73%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2stats.cpp.o
[ 74%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/reverseseq.cpp.o
[ 74%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/cpmvrmlndb.cpp.o
[ 74%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractframes.cpp.o
[ 75%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sequence2profile.cpp.o
[ 75%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sortresult.cpp.o
[ 75%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitdb.cpp.o
[ 76%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitsequence.cpp.o
[ 76%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/subtractdbs.cpp.o
[ 76%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizealis.cpp.o
[ 77%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeheaders.cpp.o
[ 77%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeresult.cpp.o
[ 77%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizetabs.cpp.o
[ 78%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/swapresults.cpp.o
[ 78%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/transitivealign.cpp.o
[ 78%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/translatenucs.cpp.o
[ 78%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/translateaa.cpp.o
[ 79%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/tsv2db.cpp.o
[ 79%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/tsv2exprofiledb.cpp.o
[ 79%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/tar2db.cpp.o
[ 80%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/unpackdb.cpp.o
[ 80%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/proteinaln2nucl.cpp.o
[ 80%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/versionstring.cpp.o
[ 81%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/diskspaceavail.cpp.o
[ 81%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Cluster.cpp.o
[ 81%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/ClusterUpdate.cpp.o
[ 82%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Databases.cpp.o
[ 82%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Linclust.cpp.o
[ 82%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasySearch.cpp.o
[ 83%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyRbh.cpp.o
[ 83%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyCluster.cpp.o
[ 83%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyLinclust.cpp.o
[ 84%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Enrich.cpp.o
[ 84%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Linsearch.cpp.o
[ 84%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Map.cpp.o
[ 85%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Rbh.cpp.o
[ 85%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Search.cpp.o
[ 85%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Taxonomy.cpp.o
[ 86%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyTaxonomy.cpp.o
[ 86%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/CreateIndex.cpp.o
[ 86%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/MMseqsBase.cpp.o
[ 87%] Linking CXX static library libmmseqs-framework.a
[ 87%] Built target mmseqs-framework
[ 87%] Building CXX object lib/3di/CMakeFiles/3di.dir/structureto3di.cpp.o
/home/user/packages/foldseek/foldseek/lib/3di/structureto3di.cpp:7:10: fatal error: encoder_weights_3di.kerasify.h: No such file or directory
7 | #include "encoder_weights_3di.kerasify.h"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [lib/3di/CMakeFiles/3di.dir/build.make:76: lib/3di/CMakeFiles/3di.dir/structureto3di.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:880: lib/3di/CMakeFiles/3di.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
from foldseek.
milot-mirdita
commented on June 10, 2024
Can you try as a workaround to call:
make local-generated
make
Not sure why the dependency resolution is going wrong. I saw this before but have no idea what’s causing it.
from foldseek.
gitozi
commented on June 10, 2024
Thanks a lot! The workaround worked!
FYI:
I suspected that it might be because shellcheck was not installed on my system. But even after having shellcheck installed it failed at the same point.
from foldseek.
gitozi
commented on June 10, 2024
PS: I am using cmake version 3.24.3
from foldseek.
milot-mirdita
commented on June 10, 2024
I pushed a fix that should fix the issue without the workaround.
from foldseek.
Related Issues (20)
- Backbone only search returns no hit. HOT 4
- easy-search hangs on scop40 test HOT 9
- precomputed pdb lookup and sequence don't line up HOT 1
- `--taxon-list` option not accepting multiple taxonomy IDs correctly HOT 5
- Can't find exact match in PDB HOT 2
- 3di for multi-chain protein HOT 2
- Comparison of specified structure fragments HOT 1
- Job kept being stucked in the pending state HOT 7
- How to conduct clusters based on global structures instead of local substructures? HOT 1
- Create human-readable taxonomy lookup table from precomputed database HOT 3
- Potential permission issue when trying to create foldseek db HOT 1
- Error std::out_of_range when creating database with specific cif files HOT 4
- Cannot use createdb to merge two existing db HOT 1
- (core dumped) "$MMSEQS" createcomplexreport "${QUERY}" "${TARGET}" "${SCORECOMPLEX_RESULT}" "${REPORT}" ${REPORT_PAR} HOT 18
- No 3D alignment shown in webserver viewer HOT 9
- Retrain Foldseek's VQ-VAE and compile it with the main program. HOT 1
- How to convert the 3D descriptors back to PDB file? HOT 3
- Foldseek-multimer returns non-interacting chains HOT 3
- How to download AFDB clusters? HOT 3
- Input taxonomy database is missing when using createdb HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from foldseek.