Using checkPhaseThreadLimitHook Running phase: unpackPhase unpacking source archive /nix/store/m71fhyklgn4wx3w8li6pqas83bi0whf7-source source root is source Running phase: patchPhase patching script interpreter paths in lib/foldseek/lib/mmseqs/cmake/xxdi.pl lib/foldseek/lib/mmseqs/cmake/xxdi.pl: interpreter directive changed from "#!/usr/bin/env perl" to "/nix/store/kfqbfq23lafkrbhxxblzf65baqz5p1ia-perl-5.42.3/bin/perl" Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase cmake flags: -DCMAKE_FIND_USE_SYSTEM_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF -DCMAKE_INSTALL_LOCALEDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/share/locale -DCMAKE_INSTALL_LIBEXECDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/libexec -DCMAKE_INSTALL_LIBDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/lib -DCMAKE_INSTALL_DOCDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/share/doc/foldseek -DCMAKE_INSTALL_INFODIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/share/info -DCMAKE_INSTALL_MANDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/share/man -DCMAKE_INSTALL_INCLUDEDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/include -DCMAKE_INSTALL_SBINDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/sbin -DCMAKE_INSTALL_BINDIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin -DCMAKE_INSTALL_NAME_DIR=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/lib -DCMAKE_STRIP=/nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/strip -DCMAKE_RANLIB=/nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/ranlib -DCMAKE_AR=/nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/ar -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_INSTALL_PREFIX=/nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DHAVE_AVX2=1 -- The C compiler identification is GNU 15.3.0 -- The CXX compiler identification is GNU 15.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/gcc - 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: /nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Source Directory: /build/source/lib/foldseek/lib/mmseqs -- Project Directory: /build/source/lib/foldseek/lib/mmseqs -- Compiler is GNU -- ZSTD VERSION 1.3.8 -- xxd not found, using xxdi.pl instead -- 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_NATIVE -- Performing Test ATOMIC_NATIVE - Failed -- Performing Test ATOMIC_WITH_LIB -- Performing Test ATOMIC_WITH_LIB - Success -- Found Atomic: -latomic -- 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 -- xxd not found, using xxdi.pl instead -- ShellCheck not found -- Rust Target: x86_64-unknown-linux-gnu -- Determining required link libraries for target x86_64-unknown-linux-gnu -- Required static libs for target x86_64-unknown-linux-gnu: gcc_s;util;rt;pthread;m;dl;c -- Required link flags for target x86_64-unknown-linux-gnu: -- Found Rust: /nix/store/yaa1sq5g4jar7rvlspy7kk2wd98nj6qh-rustc-wrapper-1.97.1/bin/rustc (found version "1.97.1") -- Using Corrosion as a subdirectory -- Rust Feature: simd_avx2 -- xxd not found, using xxdi.pl instead -- ShellCheck not found -- Configuring done (2.8s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: BUILD_TESTING CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_BINDIR CMAKE_INSTALL_DOCDIR CMAKE_INSTALL_INCLUDEDIR CMAKE_INSTALL_INFODIR CMAKE_INSTALL_LIBEXECDIR CMAKE_INSTALL_LOCALEDIR CMAKE_INSTALL_MANDIR CMAKE_INSTALL_SBINDIR -- Build files have been written to: /build/source/build cmake: enabled parallel building cmake: enabled parallel installing Running phase: buildPhase build flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash [ 0%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o [ 0%] Building C object 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lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o [ 15%] Generating ../generated/encoder_weights_3di.kerasify.h [ 15%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o [ 15%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o [ 15%] Generating ../generated/CovSeqidQscPercMinDiagTargetCov.lib.h [ 15%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o [ 15%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o [ 16%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o [ 16%] Generating ../generated/evalue_nn.kerasify.h [ 16%] Generating ../generated/main.js.h [ 16%] Generating ../generated/vendor.js.zst.h [ 16%] Built target version [ 16%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o [ 17%] Generating ../generated/ExpOpt3_8_polished.cs32.lib.h [ 18%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o [ 18%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o [ 18%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o [ 18%] Linking C static library libmicrotar.a [ 18%] Generating ../generated/Library255_may17.lib.h /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base': /build/source/lib/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 /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:372:19: /build/source/lib/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 /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19: /build/source/lib/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; | ~~~~~~~~~~^~~~~~ /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc' 88 | te_expr *ret = malloc(size); | ^~~~~~~~~~~~ /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base': /build/source/lib/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 /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19: /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc' 88 | te_expr *ret = malloc(size); | ^~~~~~~~~~~~ /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base': /build/source/lib/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 /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:444:19: /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc' 88 | te_expr *ret = malloc(size); | ^~~~~~~~~~~~ [ 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Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o [ 24%] Generating ../generated/result2structprofile.sh.h [ 24%] Generating ../generated/K4000.crf.h [ 25%] Generating ../generated/createstructsubdb.sh.h /build/source/lib/foldseek/lib/foldcomp/src/database_writer.cpp: In function 'void free_writer(void*)': /build/source/lib/foldseek/lib/foldcomp/src/database_writer.cpp:65:35: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int64_t' {aka 'long int'} [-Wformat=] 65 | fprintf(w->index, "%d\t%llu\t%d\n", w->entries[i].id, w->entries[i].offset, (uint32_t)w->entries[i].length); | ~~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int int64_t {aka long int} | %lu [ 25%] Generating ../generated/multimersearch.sh.h [ 25%] Generating ../generated/easymultimersearch.sh.h [ 25%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o [ 25%] Generating ../generated/easysearch.sh.h [ 25%] Generating ../generated/multimercluster.sh.h [ 25%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o [ 26%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o [ 26%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o [ 26%] Generating ../generated/easycluster.sh.h [ 26%] Generating ../generated/easymultimercluster.sh.h warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:32:12 | 32 | pub unsafe extern fn block_new_simple_aamatrix(match_score: i8, mismatch_score: i8) -> *mut AAMatrix { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` | = note: `#[warn(missing_abi)]` on by default warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:39:12 | 39 | pub unsafe extern fn block_set_aamatrix(matrix: *mut AAMatrix, a: u8, b: u8, score: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:46:12 | 46 | pub unsafe extern fn block_free_aamatrix(matrix: *mut AAMatrix) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:61:12 | 61 | pub unsafe extern fn block_new_aaprofile(str_len: usize, block_size: usize, gap_extend: i8) -> *mut AAProfile { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:68:12 | 68 | pub unsafe extern fn block_len_aaprofile(profile: *const AAProfile) -> usize { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:76:12 | 76 | pub unsafe extern fn block_clear_aaprofile(profile: *mut AAProfile, str_len: usize) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:86:12 | 86 | pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u8, score: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:97:12 | 97 | pub unsafe extern fn block_set_gap_open_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:108:12 | 108 | pub unsafe extern fn block_set_gap_close_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:119:12 | 119 | pub unsafe extern fn block_set_gap_open_R_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:126:12 | 126 | pub unsafe extern fn block_get_aaprofile(profile: *const AAProfile, i: usize, b: u8) -> i8 { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:133:12 | 133 | pub unsafe extern fn block_get_gap_extend_aaprofile(profile: *const AAProfile) -> i8 { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:140:12 | 140 | pub unsafe extern fn block_free_aaprofile(profile: *mut AAProfile) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:149:12 | 149 | pub unsafe extern fn block_new_cigar(query_len: usize, reference_len: usize) -> *mut Cigar { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:156:12 | 156 | pub unsafe extern fn block_get_cigar(cigar: *const Cigar, i: usize) -> OpLen { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:163:12 | 163 | pub unsafe extern fn block_len_cigar(cigar: *const Cigar) -> usize { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:170:12 | 170 | pub unsafe extern fn block_free_cigar(cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:179:12 | 179 | pub unsafe extern fn block_new_padded_aa(len: usize, max_size: usize) -> *mut PaddedBytes { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:186:12 | 186 | pub unsafe extern fn block_set_bytes_padded_aa(padded: *mut PaddedBytes, s: *const u8, len: usize, max_size: usize) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:194:12 | 194 | pub unsafe extern fn block_free_padded_aa(padded: *mut PaddedBytes) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:203:12 | 203 | pub unsafe extern fn block_new_pos_bias(len: usize, max_size: usize) -> *mut PosBias { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:210:12 | 210 | pub unsafe extern fn block_set_pos_bias(bias: *mut PosBias, b: *const i16, len: usize) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:218:12 | 218 | pub unsafe extern fn block_free_pos_bias(bias: *mut PosBias) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) [ 27%] Generating ../generated/easytaxonomy.sh.h [ 27%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o [ 27%] Linking C static library libtinyexpr.a [ 27%] Generating ../generated/easyrbh.sh.h [ 28%] Generating ../generated/blastp.sh.h [ 28%] Generating ../generated/blastpgp.sh.h [ 28%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o [ 29%] Generating ../generated/map.sh.h [ 29%] Generating ../generated/rbh.sh.h [ 29%] Built target tinyexpr [ 29%] Generating ../generated/linclust.sh.h [ 30%] Generating ../generated/clustering.sh.h [ 30%] Generating ../generated/cascaded_clustering.sh.h [ 30%] Generating ../generated/update_clustering.sh.h [ 30%] Generating ../generated/searchtargetprofile.sh.h [ 30%] Generating ../generated/createindex.sh.h [ 30%] Generating ../generated/createtaxdb.sh.h [ 31%] Generating ../generated/taxpercontig.sh.h [ 31%] Generating ../generated/multihitdb.sh.h [ 31%] Generating ../generated/translated_search.sh.h [ 31%] Generating ../generated/enrich.sh.h [ 31%] Generating ../generated/multihitsearch.sh.h [ 31%] Generating ../generated/searchslicedtargetprofile.sh.h [ 31%] Generating ../generated/blastn.sh.h [ 31%] Generating ../generated/taxonomy.sh.h [ 31%] Generating ../generated/linsearch.sh.h [ 32%] Generating ../generated/databases.sh.h [ 32%] Generating ../generated/pickconsensusrep.sh.h [ 33%] Generating ../generated/nucleotide_clustering.sh.h [ 33%] Generating ../generated/tsv2exprofiledb.sh.h [ 33%] Generating ../generated/iterativepp.sh.h [ 33%] Built target ksw2 [ 33%] Built target local-generated [ 33%] Built target foldmason-generated [ 34%] Linking CXX static library libtantan.a [ 34%] Built target tantan [ 34%] Built target alp warning: `block_aligner_c` (lib) generated 55 warnings (run `cargo fix --lib -p block_aligner_c` to apply 55 suggestions) Finished `release` profile [optimized] target(s) in 5.22s Copying byproducts `libblock_aligner_c.a` to /build/source/build/lib/foldseek [ 34%] Built target _cargo-build_block_aligner_c [ 34%] Built target cargo-build_block_aligner_c [ 34%] Built target generated [ 34%] Linking CXX static library libfoldcomp.a [ 34%] Built target foldcomp [ 35%] Building CXX object lib/foldseek/src/strucclustutils/CMakeFiles/gemmiwrapper.dir/GemmiWrapper.cpp.o [ 35%] Linking C static library libzstd.a [ 35%] Built target libzstd_static [ 36%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o [ 36%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o [ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o [ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o [ 37%] Building CXX object 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lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2repseq.cpp.o [ 72%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2stats.cpp.o [ 72%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/reverseseq.cpp.o [ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractframes.cpp.o [ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sequence2profile.cpp.o [ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/cpmvrmlndb.cpp.o [ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/setextendeddbtype.cpp.o [ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitdb.cpp.o [ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sortresult.cpp.o [ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitsequence.cpp.o [ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/subtractdbs.cpp.o [ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizealis.cpp.o [ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeheaders.cpp.o [ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeresult.cpp.o [ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizetabs.cpp.o /build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp: In function 'int result2flat(int, const char**, const Command&)': /build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp:65:37: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 65 | dbKeyBuffer.size(); | ~~~~~~~~~~~~~~~~^~ In file included from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/string:56, from /build/source/lib/foldseek/lib/mmseqs/src/commons/Parameters.h:7, from /build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp:2: /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/bits/basic_string.h:1163:7: note: declared here 1163 | size() const _GLIBCXX_NOEXCEPT | ^~~~ [ 76%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/swapresults.cpp.o [ 76%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/transitivealign.cpp.o [ 76%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/translatenucs.cpp.o [ 76%] Building CXX 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lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/EasyMultimerCluster.cpp.o [ 96%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/FoldseekBase.cpp.o [ 96%] Linking CXX static library libfoldseek-framework.a [ 96%] Built target foldseek-framework [ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/FoldmasonParameters.cpp.o [ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/FMStructureSmithWaterman.cpp.o [ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/SimpleGotoh.cpp.o [ 98%] Building CXX object src/CMakeFiles/foldmason.dir/commons/MSA.cpp.o [ 98%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/structuremsa.cpp.o [ 98%] Building CXX object src/CMakeFiles/foldmason.dir/commons/newick.cpp.o [ 98%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/refinemsa.cpp.o [100%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/msa2lddt.cpp.o [100%] Building CXX object src/CMakeFiles/foldmason.dir/workflow/EasyMSA.cpp.o [100%] Building CXX object src/CMakeFiles/foldmason.dir/foldmason.cpp.o /build/source/src/strucclustutils/structuremsa.cpp: In function 'Matcher::result_t pairwiseAlignment(unsigned int, Sequence*, Sequence*, Sequence*, Sequence*, int, int, SubstitutionMatrix*, SubstitutionMatrix*, int, float**)': /build/source/src/strucclustutils/structuremsa.cpp:177:65: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 177 | short **target_profile_scores_aa = new short * [alphabetSize]; | ^ In file included from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/bits/new_allocator.h:34, from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/x86_64-unknown-linux-gnu/bits/c++allocator.h:33, from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/bits/allocator.h:46, from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/vector:65, from /build/source/lib/foldseek/lib/mmseqs/src/commons/DBReader.h:11, from /build/source/lib/foldseek/lib/mmseqs/src/commons/IndexReader.h:4, from /build/source/lib/foldseek/lib/mmseqs/src/alignment/Alignment.h:4, from /build/source/src/strucclustutils/structuremsa.cpp:1: /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/new:140:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here 140 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) | ^~~~~~~~ /build/source/src/strucclustutils/structuremsa.cpp:178:66: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 178 | short **target_profile_scores_3di = new short * [alphabetSize]; | ^ /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/new:140:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here 140 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) | ^~~~~~~~ In file included from /nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/string.h:548, from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/cstring:48, from /build/source/lib/foldseek/lib/mmseqs/src/commons/MultiParam.h:10, from /build/source/lib/foldseek/lib/mmseqs/src/commons/Parameters.h:16, from /build/source/lib/foldseek/lib/mmseqs/src/commons/Sequence.h:10, from /build/source/lib/foldseek/lib/mmseqs/src/commons/DBReader.h:13: In function 'void* memset(void*, int, size_t)', inlined from '_Z12structuremsaiPPKcRK7Commandb._omp_fn.0' at /build/source/src/strucclustutils/structuremsa.cpp:1952:27: /nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:59:33: warning: 'void* __builtin_memset(void*, int, long unsigned int)' specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void* memset(void*, int, size_t)', inlined from '_Z12structuremsaiPPKcRK7Commandb._omp_fn.0' at /build/source/src/strucclustutils/structuremsa.cpp:1953:27: /nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:59:33: warning: 'void* __builtin_memset(void*, int, long unsigned int)' specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable foldmason [100%] Built target foldmason buildPhase completed in 1 minutes 34 seconds Running phase: installPhase install flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash install [ 0%] Built target cargo-prebuild_block_aligner_c [ 6%] Built target local-generated [ 7%] Built target foldmason-generated [ 8%] Built target version [ 8%] Built target tinyexpr [ 8%] Built target microtar [ 19%] Built target generated [ 19%] Built target ksw2 [ 26%] Built target libzstd_static [ 27%] Built target tantan [ 30%] Built target foldcomp [ 34%] Built target alp warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:32:12 | 32 | pub unsafe extern fn block_new_simple_aamatrix(match_score: i8, mismatch_score: i8) -> *mut AAMatrix { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` | = note: `#[warn(missing_abi)]` on by default warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:39:12 | 39 | pub unsafe extern fn block_set_aamatrix(matrix: *mut AAMatrix, a: u8, b: u8, score: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:46:12 | 46 | pub unsafe extern fn block_free_aamatrix(matrix: *mut AAMatrix) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:61:12 | 61 | pub unsafe extern fn block_new_aaprofile(str_len: usize, block_size: usize, gap_extend: i8) -> *mut AAProfile { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:68:12 | 68 | pub unsafe extern fn block_len_aaprofile(profile: *const AAProfile) -> usize { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:76:12 | 76 | pub unsafe extern fn block_clear_aaprofile(profile: *mut AAProfile, str_len: usize) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:86:12 | 86 | pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u8, score: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:97:12 | 97 | pub unsafe extern fn block_set_gap_open_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:108:12 | 108 | pub unsafe extern fn block_set_gap_close_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:119:12 | 119 | pub unsafe extern fn block_set_gap_open_R_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:126:12 | 126 | pub unsafe extern fn block_get_aaprofile(profile: *const AAProfile, i: usize, b: u8) -> i8 { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:133:12 | 133 | pub unsafe extern fn block_get_gap_extend_aaprofile(profile: *const AAProfile) -> i8 { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:140:12 | 140 | pub unsafe extern fn block_free_aaprofile(profile: *mut AAProfile) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:149:12 | 149 | pub unsafe extern fn block_new_cigar(query_len: usize, reference_len: usize) -> *mut Cigar { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:156:12 | 156 | pub unsafe extern fn block_get_cigar(cigar: *const Cigar, i: usize) -> OpLen { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:163:12 | 163 | pub unsafe extern fn block_len_cigar(cigar: *const Cigar) -> usize { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:170:12 | 170 | pub unsafe extern fn block_free_cigar(cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:179:12 | 179 | pub unsafe extern fn block_new_padded_aa(len: usize, max_size: usize) -> *mut PaddedBytes { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:186:12 | 186 | pub unsafe extern fn block_set_bytes_padded_aa(padded: *mut PaddedBytes, s: *const u8, len: usize, max_size: usize) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:194:12 | 194 | pub unsafe extern fn block_free_padded_aa(padded: *mut PaddedBytes) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:203:12 | 203 | pub unsafe extern fn block_new_pos_bias(len: usize, max_size: usize) -> *mut PosBias { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:210:12 | 210 | pub unsafe extern fn block_set_pos_bias(bias: *mut PosBias, b: *const i16, len: usize) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:218:12 | 218 | pub unsafe extern fn block_free_pos_bias(bias: *mut PosBias) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 315 | / gen_functions!( 316 | | block_new_aa, 317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).", 318 | | block_align_aa, ... | 332 | | AAMatrix, AAProfile, false, false 333 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 335 | / gen_functions!( 336 | | block_new_aa_xdrop, 337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).", 338 | | block_align_aa_xdrop, ... | 352 | | AAMatrix, AAProfile, false, true 353 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 355 | / gen_functions!( 356 | | block_new_aa_trace, 357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.", 358 | | block_align_aa_trace, ... | 372 | | AAMatrix, AAProfile, true, false 373 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:237:20 | 237 | pub unsafe extern fn $new_name(query_len: usize, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:246:20 | 246 | pub unsafe extern fn $align_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:259:20 | 259 | pub unsafe extern fn $align_profile_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:270:20 | 270 | pub unsafe extern fn $align_3di_name(b: BlockHandle, | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:288:20 | 288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:295:20 | 295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:302:20 | 302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer... | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `extern` declarations without an explicit ABI are deprecated --> ../src/ffi.rs:309:20 | 309 | pub unsafe extern fn $free_name(b: BlockHandle) { | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"` ... 375 | / gen_functions!( 376 | | block_new_aa_trace_xdrop, 377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.", 378 | | block_align_aa_trace_xdrop, ... | 392 | | AAMatrix, AAProfile, true, true 393 | | ); | |_- in this macro invocation | = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info) warning: `block_aligner_c` (lib) generated 55 warnings (run `cargo fix --lib -p block_aligner_c` to apply 55 suggestions) Finished `release` profile [optimized] target(s) in 0.00s [ 35%] Built target gemmiwrapper Copying byproducts `libblock_aligner_c.a` to /build/source/build/lib/foldseek [ 35%] Built target _cargo-build_block_aligner_c [ 35%] Built target cargo-build_block_aligner_c [ 84%] Built target mmseqs-framework [ 84%] Built target pulchra [ 84%] Built target 3di [ 85%] Built target tmalign [ 86%] Built target kerasify [ 96%] Built target foldseek-framework [100%] Built target foldmason Install the project... -- Install configuration: "Release" -- Installing: /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin/foldmason Running phase: fixupPhase shrinking RPATHs of ELF executables and libraries in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235 shrinking /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin/foldmason checking for references to /build/ in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235... patching script interpreter paths in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235 stripping (with command strip and flags -S -p) in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin