foldmason-4-dd3c235
checks.x86_64-linux.pkgs-foldmason
· build #63
· raw
1Using checkPhaseThreadLimitHook
unpackPhase
2unpacking source archive /nix/store/m71fhyklgn4wx3w8li6pqas83bi0whf7-source3source root is sourcepatchPhase
4patching script interpreter paths in lib/foldseek/lib/mmseqs/cmake/xxdi.pl5lib/foldseek/lib/mmseqs/cmake/xxdi.pl: interpreter directive changed from "#!/usr/bin/env perl" to "/nix/store/kfqbfq23lafkrbhxxblzf65baqz5p1ia-perl-5.42.3/bin/perl"configurePhase
6cmake 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=17-- The C compiler identification is GNU 15.3.08-- The CXX compiler identification is GNU 15.3.09-- Detecting C compiler ABI info10-- Detecting C compiler ABI info - done11-- Check for working C compiler: /nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/gcc - skipped12-- Detecting C compile features13-- Detecting C compile features - done14-- Detecting CXX compiler ABI info15-- Detecting CXX compiler ABI info - done16-- Check for working CXX compiler: /nix/store/w88q44gqd1qg5wmkk7v0h97rpiqvam0l-gcc-wrapper-15.3.0/bin/g++ - skipped17-- Detecting CXX compile features18-- Detecting CXX compile features - done19-- Source Directory: /build/source/lib/foldseek/lib/mmseqs20-- Project Directory: /build/source/lib/foldseek/lib/mmseqs21-- Compiler is GNU 22-- ZSTD VERSION 1.3.823-- xxd not found, using xxdi.pl instead24-- ShellCheck disabled25-- Performing Test HAVE_POSIX_FADVISE26-- Performing Test HAVE_POSIX_FADVISE - Success27-- Performing Test HAVE_POSIX_MADVISE28-- Performing Test HAVE_POSIX_MADVISE - Success29-- Performing Test ATOMIC_NATIVE30-- Performing Test ATOMIC_NATIVE - Failed31-- Performing Test ATOMIC_WITH_LIB32-- Performing Test ATOMIC_WITH_LIB - Success33-- Found Atomic: -latomic34-- IPS4O sorting works35-- Found ZLIB36-- Performing Test HAVE_ZLIB_CHECK37-- Performing Test HAVE_ZLIB_CHECK - Success38-- ZLIB works39-- Found BZLIB40-- Performing Test HAVE_BZLIB_CHECK41-- Performing Test HAVE_BZLIB_CHECK - Success42-- BZLIB works43-- Found OpenMP44-- xxd not found, using xxdi.pl instead45-- ShellCheck not found46-- Rust Target: x86_64-unknown-linux-gnu47-- Determining required link libraries for target x86_64-unknown-linux-gnu48-- Required static libs for target x86_64-unknown-linux-gnu: gcc_s;util;rt;pthread;m;dl;c49-- Required link flags for target x86_64-unknown-linux-gnu: 50-- Found Rust: /nix/store/yaa1sq5g4jar7rvlspy7kk2wd98nj6qh-rustc-wrapper-1.97.1/bin/rustc (found version "1.97.1")51-- Using Corrosion as a subdirectory52-- Rust Feature: simd_avx253-- xxd not found, using xxdi.pl instead54-- ShellCheck not found55-- Configuring done (2.8s)56-- Generating done (0.1s)57CMake Warning:58 Manually-specified variables were not used by the project:5960 BUILD_TESTING61 CMAKE_EXPORT_NO_PACKAGE_REGISTRY62 CMAKE_INSTALL_BINDIR63 CMAKE_INSTALL_DOCDIR64 CMAKE_INSTALL_INCLUDEDIR65 CMAKE_INSTALL_INFODIR66 CMAKE_INSTALL_LIBEXECDIR67 CMAKE_INSTALL_LOCALEDIR68 CMAKE_INSTALL_MANDIR69 CMAKE_INSTALL_SBINDIR707172-- Build files have been written to: /build/source/build73cmake: enabled parallel building74cmake: enabled parallel installingbuildPhase
75build flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash76[ 0%] Building CXX object src/version/CMakeFiles/version.dir/Version.cpp.o77[ 1%] Building C object lib/foldseek/lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o78[ 1%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o79[ 1%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o80[ 1%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o81[ 1%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/amino_acid.cpp.o82[ 1%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/atom_coordinate.cpp.o83[ 1%] Generating ../generated/main_foldmason.js.h84[ 1%] Built target cargo-prebuild_block_aligner_c85[ 2%] 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lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o147[ 18%] Generating ../generated/encoder_weights_3di.kerasify.h148/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':149/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=]150 373 | ret->bound = s->bound;151 | ^~152In function 'new_expr',153 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:372:19:154/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'155 88 | te_expr *ret = malloc(size);156 | ^~~~~~~~~~~~157In function 'new_expr',158 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:159/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=]160 93 | ret->type = type;161 | ~~~~~~~~~~^~~~~~162/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'163 88 | te_expr *ret = malloc(size);164 | ^~~~~~~~~~~~165/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':166/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=]167 367 | ret->value = s->value;168 | ^~169In function 'new_expr',170 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:171/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'172 88 | te_expr *ret = malloc(size);173 | ^~~~~~~~~~~~174/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':175/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=]176 446 | ret->value = NAN;177 | ^~178In function 'new_expr',179 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:444:19:180/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'181 88 | te_expr *ret = malloc(size);182 | ^~~~~~~~~~~~183[ 18%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o184[ 18%] Generating ../generated/evalue_nn.kerasify.h185[ 18%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/utility.cpp.o186[ 18%] Generating ../generated/main.js.h187[ 19%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o188[ 19%] Linking C static library libmicrotar.a189[ 20%] Generating ../generated/krona_prelude.html.h190[ 21%] Generating ../generated/result_viz_prelude.html.zst.h191[ 21%] Built target microtar192[ 21%] Generating ../generated/K4000.crf.h193[ 21%] Generating ../generated/vendor.js.zst.h194 Compiling block_aligner_c v0.4.0 (/build/source/lib/foldseek/lib/block-aligner/c)195[ 22%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o196[ 23%] Generating ../generated/makepaddeddb.sh.h197/build/source/lib/foldseek/lib/foldcomp/src/database_writer.cpp: In function 'void free_writer(void*)':198/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=]199 65 | fprintf(w->index, "%d\t%llu\t%d\n", w->entries[i].id, w->entries[i].offset, (uint32_t)w->entries[i].length);200 | ~~~^ ~~~~~~~~~~~~~~~~~~~~201 | | |202 | long long unsigned int int64_t {aka long int}203 | %lu204[ 23%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o205[ 23%] Linking C static library libtinyexpr.a206[ 24%] Generating ../generated/result2structprofile.sh.h207[ 24%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o208[ 24%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o209[ 24%] Built target tinyexpr210[ 24%] Generating ../generated/easysearch.sh.h211[ 25%] Generating ../generated/createstructsubdb.sh.h212[ 25%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o213[ 25%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o214[ 25%] Generating ../generated/easycluster.sh.h215[ 25%] 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Generating ../generated/rbh.sh.h229[ 29%] Generating ../generated/linclust.sh.h230[ 30%] Generating ../generated/clustering.sh.h231[ 30%] Generating ../generated/cascaded_clustering.sh.h232[ 30%] Generating ../generated/searchtargetprofile.sh.h233[ 30%] Generating ../generated/update_clustering.sh.h234warning: `extern` declarations without an explicit ABI are deprecated235 --> ../src/ffi.rs:32:12236 |23732 | pub unsafe extern fn block_new_simple_aamatrix(match_score: i8, mismatch_score: i8) -> *mut AAMatrix {238 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`239 |240 = note: `#[warn(missing_abi)]` on by default241242warning: `extern` declarations without an explicit ABI are deprecated243 --> ../src/ffi.rs:39:12244 |24539 | pub unsafe extern fn block_set_aamatrix(matrix: *mut AAMatrix, a: u8, b: u8, score: i8) {246 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`247248warning: `extern` declarations without an explicit ABI are deprecated249 --> ../src/ffi.rs:46:12250 |25146 | pub unsafe extern fn block_free_aamatrix(matrix: *mut AAMatrix) {252 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`253254warning: `extern` declarations without an explicit ABI are deprecated255 --> ../src/ffi.rs:61:12256 |25761 | pub unsafe extern fn block_new_aaprofile(str_len: usize, block_size: usize, gap_extend: i8) -> *mut AAProfile {258 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`259260warning: `extern` declarations without an explicit ABI are deprecated261 --> ../src/ffi.rs:68:12262 |26368 | pub unsafe extern fn block_len_aaprofile(profile: *const AAProfile) -> usize {264 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`265266warning: `extern` declarations without an explicit ABI are deprecated267 --> ../src/ffi.rs:76:12268 |26976 | pub unsafe extern fn block_clear_aaprofile(profile: *mut AAProfile, str_len: usize) {270 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`271272warning: `extern` declarations without an explicit ABI are deprecated273 --> ../src/ffi.rs:86:12274 |27586 | pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u8, score: i8) {276 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`277278warning: `extern` declarations without an explicit ABI are deprecated279 --> ../src/ffi.rs:97:12280 |28197 | pub unsafe extern fn block_set_gap_open_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {282 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`283284warning: `extern` declarations without an explicit ABI are deprecated285 --> ../src/ffi.rs:108:12286 |287108 | pub unsafe extern fn block_set_gap_close_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {288 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`289290warning: `extern` declarations without an explicit ABI are deprecated291 --> ../src/ffi.rs:119:12292 |293119 | pub unsafe extern fn block_set_gap_open_R_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {294 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`295296warning: `extern` declarations without an explicit ABI are deprecated297 --> ../src/ffi.rs:126:12298 |299126 | pub unsafe extern fn block_get_aaprofile(profile: *const AAProfile, i: usize, b: u8) -> i8 {300 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`301302warning: `extern` declarations without an explicit ABI are deprecated303 --> ../src/ffi.rs:133:12304 |305133 | pub unsafe extern fn block_get_gap_extend_aaprofile(profile: *const AAProfile) -> i8 {306 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`307308warning: `extern` declarations without an explicit ABI are deprecated309 --> ../src/ffi.rs:140:12310 |311140 | pub unsafe extern fn block_free_aaprofile(profile: *mut AAProfile) {312 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`313314warning: `extern` declarations without an explicit ABI are deprecated315 --> ../src/ffi.rs:149:12316 |317149 | pub unsafe extern fn block_new_cigar(query_len: usize, reference_len: usize) -> *mut Cigar {318 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`319320warning: `extern` declarations without an explicit ABI are deprecated321 --> ../src/ffi.rs:156:12322 |323156 | pub unsafe extern fn block_get_cigar(cigar: *const Cigar, i: usize) -> OpLen {324 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`325326warning: `extern` declarations without an explicit ABI are deprecated327 --> ../src/ffi.rs:163:12328 |329163 | pub unsafe extern fn block_len_cigar(cigar: *const Cigar) -> usize {330 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`331332warning: `extern` declarations without an explicit ABI are deprecated333 --> ../src/ffi.rs:170:12334 |335170 | pub unsafe extern fn block_free_cigar(cigar: *mut Cigar) {336 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`337338warning: `extern` declarations without an explicit ABI are deprecated339 --> ../src/ffi.rs:179:12340 |341179 | pub unsafe extern fn block_new_padded_aa(len: usize, max_size: usize) -> *mut PaddedBytes {342 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`343344warning: `extern` declarations without an explicit ABI are deprecated345 --> ../src/ffi.rs:186:12346 |347186 | pub unsafe extern fn block_set_bytes_padded_aa(padded: *mut PaddedBytes, s: *const u8, len: usize, max_size: usize) {348 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`349350warning: `extern` declarations without an explicit ABI are deprecated351 --> ../src/ffi.rs:194:12352 |353194 | pub unsafe extern fn block_free_padded_aa(padded: *mut PaddedBytes) {354 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`355356warning: `extern` declarations without an explicit ABI are deprecated357 --> ../src/ffi.rs:203:12358 |359203 | pub unsafe extern fn block_new_pos_bias(len: usize, max_size: usize) -> *mut PosBias {360 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`361362warning: `extern` declarations without an explicit ABI are deprecated363 --> ../src/ffi.rs:210:12364 |365210 | pub unsafe extern fn block_set_pos_bias(bias: *mut PosBias, b: *const i16, len: usize) {366 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`367368warning: `extern` declarations without an explicit ABI are deprecated369 --> ../src/ffi.rs:218:12370 |371218 | pub unsafe extern fn block_free_pos_bias(bias: *mut PosBias) {372 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`373374warning: `extern` declarations without an explicit ABI are deprecated375 --> ../src/ffi.rs:237:20376 |377237 | pub unsafe extern fn $new_name(query_len: usize,378 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`379...380315 | / gen_functions!(381316 | | block_new_aa,382317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",383318 | | block_align_aa,384... |385332 | | AAMatrix, AAProfile, false, false386333 | | );387 | |_- in this macro invocation388 |389 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)390391warning: `extern` declarations without an explicit ABI are deprecated392 --> ../src/ffi.rs:246:20393 |394246 | pub unsafe extern fn $align_name(b: BlockHandle,395 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`396...397315 | / gen_functions!(398316 | | block_new_aa,399317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",400318 | | block_align_aa,401... |402332 | | AAMatrix, AAProfile, false, false403333 | | );404 | |_- in this macro invocation405 |406 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)407408[ 30%] Generating ../generated/createindex.sh.h409warning: `extern` declarations without an explicit ABI are deprecated410 --> ../src/ffi.rs:259:20411 |412259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,413 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`414...415315 | / gen_functions!(416316 | | block_new_aa,417317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",418318 | | block_align_aa,419... |420332 | | AAMatrix, AAProfile, false, false421333 | | );422 | |_- in this macro invocation423 |424 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)425426warning: `extern` declarations without an explicit ABI are deprecated427 --> ../src/ffi.rs:270:20428 |429270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,430 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`431...432315 | / gen_functions!(433316 | | block_new_aa,434317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",435318 | | block_align_aa,436... |437332 | | AAMatrix, AAProfile, false, false438333 | | );439 | |_- in this macro invocation440 |441 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)442443warning: `extern` declarations without an explicit ABI are deprecated444 --> ../src/ffi.rs:288:20445 |446288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {447 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`448...449315 | / gen_functions!(450316 | | block_new_aa,451317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",452318 | | block_align_aa,453... |454332 | | AAMatrix, AAProfile, false, false455333 | | );456 | |_- in this macro invocation457 |458 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)459460warning: `extern` declarations without an explicit ABI are deprecated461 --> ../src/ffi.rs:295:20462 |463295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {464 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`465...466315 | / gen_functions!(467316 | | block_new_aa,468317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",469318 | | block_align_aa,470... |471332 | | AAMatrix, AAProfile, false, false472333 | | );473 | |_- in this macro invocation474 |475 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)476477warning: `extern` declarations without an explicit ABI are deprecated478 --> ../src/ffi.rs:302:20479 |480302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...481 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`482...483315 | / gen_functions!(484316 | | block_new_aa,485317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",486318 | | block_align_aa,487... |488332 | | AAMatrix, AAProfile, false, false489333 | | );490 | |_- in this macro invocation491 |492 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)493494warning: `extern` declarations without an explicit ABI are deprecated495 --> ../src/ffi.rs:309:20496 |497309 | pub unsafe extern fn $free_name(b: BlockHandle) {498 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`499...500315 | / gen_functions!(501316 | | block_new_aa,502317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",503318 | | block_align_aa,504... |505332 | | AAMatrix, AAProfile, false, false506333 | | );507 | |_- in this macro invocation508 |509 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)510511warning: `extern` declarations without an explicit ABI are deprecated512 --> ../src/ffi.rs:237:20513 |514237 | pub unsafe extern fn $new_name(query_len: usize,515 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`516...517335 | / gen_functions!(518336 | | block_new_aa_xdrop,519337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",520338 | | block_align_aa_xdrop,521... |522352 | | AAMatrix, AAProfile, false, true523353 | | );524 | |_- in this macro invocation525 |526 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)527528warning: `extern` declarations without an explicit ABI are deprecated529 --> ../src/ffi.rs:246:20530 |531246 | pub unsafe extern fn $align_name(b: BlockHandle,532 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`533...534335 | / gen_functions!(535336 | | block_new_aa_xdrop,536337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",537338 | | block_align_aa_xdrop,538... |539352 | | AAMatrix, AAProfile, false, true540353 | | );541 | |_- in this macro invocation542 |543 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)544545warning: `extern` declarations without an explicit ABI are deprecated546 --> ../src/ffi.rs:259:20547 |548259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,549 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`550...551335 | / gen_functions!(552336 | | block_new_aa_xdrop,553337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",554338 | | block_align_aa_xdrop,555... |556352 | | AAMatrix, AAProfile, false, true557353 | | );558 | |_- in this macro invocation559 |560 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)561562warning: `extern` declarations without an explicit ABI are deprecated563 --> ../src/ffi.rs:270:20564 |565270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,566 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`567...568335 | / gen_functions!(569336 | | block_new_aa_xdrop,570337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",571338 | | block_align_aa_xdrop,572... |573352 | | AAMatrix, AAProfile, false, true574353 | | );575 | |_- in this macro invocation576 |577 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)578579warning: `extern` declarations without an explicit ABI are deprecated580 --> ../src/ffi.rs:288:20581 |582288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {583 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`584...585335 | / gen_functions!(586336 | | block_new_aa_xdrop,587337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",588338 | | block_align_aa_xdrop,589... |590352 | | AAMatrix, AAProfile, false, true591353 | | );592 | |_- in this macro invocation593 |594 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)595596warning: `extern` declarations without an explicit ABI are deprecated597 --> ../src/ffi.rs:295:20598 |599295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {600 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`601...602335 | / gen_functions!(603336 | | block_new_aa_xdrop,604337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",605338 | | block_align_aa_xdrop,606... |607352 | | AAMatrix, AAProfile, false, true608353 | | );609 | |_- in this macro invocation610 |611 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)612613warning: `extern` declarations without an explicit ABI are deprecated614 --> ../src/ffi.rs:302:20615 |616302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...617 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`618...619335 | / gen_functions!(620336 | | block_new_aa_xdrop,621337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",622338 | | block_align_aa_xdrop,623... |624352 | | AAMatrix, AAProfile, false, true625353 | | );626 | |_- in this macro invocation627 |628 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)629630warning: `extern` declarations without an explicit ABI are deprecated631 --> ../src/ffi.rs:309:20632 |633309 | pub unsafe extern fn $free_name(b: BlockHandle) {634 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`635...636335 | / gen_functions!(637336 | | block_new_aa_xdrop,638337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",639338 | | block_align_aa_xdrop,640... |641352 | | AAMatrix, AAProfile, false, true642353 | | );643 | |_- in this macro invocation644 |645 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)646647warning: `extern` declarations without an explicit ABI are deprecated648 --> ../src/ffi.rs:237:20649 |650237 | pub unsafe extern fn $new_name(query_len: usize,651 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`652...653355 | / gen_functions!(654356 | | block_new_aa_trace,655357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",656358 | | block_align_aa_trace,657... |658372 | | AAMatrix, AAProfile, true, false659373 | | );660 | |_- in this macro invocation661 |662 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)663664warning: `extern` declarations without an explicit ABI are deprecated665 --> ../src/ffi.rs:246:20666 |667246 | pub unsafe extern fn $align_name(b: BlockHandle,668 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`669...670355 | / gen_functions!(671356 | | block_new_aa_trace,672357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",673358 | | block_align_aa_trace,674... |675372 | | AAMatrix, AAProfile, true, false676373 | | );677 | |_- in this macro invocation678 |679 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)680681warning: `extern` declarations without an explicit ABI are deprecated682 --> ../src/ffi.rs:259:20683 |684259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,685 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`686...687355 | / gen_functions!(688356 | | block_new_aa_trace,689357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",690358 | | block_align_aa_trace,691... |692372 | | AAMatrix, AAProfile, true, false693373 | | );694 | |_- in this macro invocation695 |696 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)697698warning: `extern` declarations without an explicit ABI are deprecated699 --> ../src/ffi.rs:270:20700 |701270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,702 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`703...704355 | / gen_functions!(705356 | | block_new_aa_trace,706357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",707358 | | block_align_aa_trace,708... |709372 | | AAMatrix, AAProfile, true, false710373 | | );711 | |_- in this macro invocation712 |713 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)714715warning: `extern` declarations without an explicit ABI are deprecated716 --> ../src/ffi.rs:288:20717 |718288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {719 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`720...721355 | / gen_functions!(722356 | | block_new_aa_trace,723357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",724358 | | block_align_aa_trace,725... |726372 | | AAMatrix, AAProfile, true, false727373 | | );728 | |_- in this macro invocation729 |730 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)731732warning: `extern` declarations without an explicit ABI are deprecated733 --> ../src/ffi.rs:295:20734 |735295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {736 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`737...738355 | / gen_functions!(739356 | | block_new_aa_trace,740357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",741358 | | block_align_aa_trace,742... |743372 | | AAMatrix, AAProfile, true, false744373 | | );745 | |_- in this macro invocation746 |747 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)748749warning: `extern` declarations without an explicit ABI are deprecated750 --> ../src/ffi.rs:302:20751 |752302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...753 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`754...755355 | / gen_functions!(756356 | | block_new_aa_trace,757357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",758358 | | block_align_aa_trace,759... |760372 | | AAMatrix, AAProfile, true, false761373 | | );762 | |_- in this macro invocation763 |764 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)765766warning: `extern` declarations without an explicit ABI are deprecated767 --> ../src/ffi.rs:309:20768 |769309 | pub unsafe extern fn $free_name(b: BlockHandle) {770 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`771...772355 | / gen_functions!(773356 | | block_new_aa_trace,774357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",775358 | | block_align_aa_trace,776... |777372 | | AAMatrix, AAProfile, true, false778373 | | );779 | |_- in this macro invocation780 |781 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)782783warning: `extern` declarations without an explicit ABI are deprecated784 --> ../src/ffi.rs:237:20785 |786237 | pub unsafe extern fn $new_name(query_len: usize,787 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`788...789375 | / gen_functions!(790376 | | block_new_aa_trace_xdrop,791377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",792378 | | block_align_aa_trace_xdrop,793... |794392 | | AAMatrix, AAProfile, true, true795393 | | );796 | |_- in this macro invocation797 |798 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)799800warning: `extern` declarations without an explicit ABI are deprecated801 --> ../src/ffi.rs:246:20802 |803246 | pub unsafe extern fn $align_name(b: BlockHandle,804 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`805...806375 | / gen_functions!(807376 | | block_new_aa_trace_xdrop,808377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",809378 | | block_align_aa_trace_xdrop,810... |811392 | | AAMatrix, AAProfile, true, true812393 | | );813 | |_- in this macro invocation814 |815 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)816817warning: `extern` declarations without an explicit ABI are deprecated818 --> ../src/ffi.rs:259:20819 |820259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,821 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`822...823375 | / gen_functions!(824376 | | block_new_aa_trace_xdrop,825377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",826378 | | block_align_aa_trace_xdrop,827... |828392 | | AAMatrix, AAProfile, true, true829393 | | );830 | |_- in this macro invocation831 |832 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)833834warning: `extern` declarations without an explicit ABI are deprecated835 --> ../src/ffi.rs:270:20836 |837270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,838 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`839...840375 | / gen_functions!(841376 | | block_new_aa_trace_xdrop,842377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",843378 | | block_align_aa_trace_xdrop,844... |845392 | | AAMatrix, AAProfile, true, true846393 | | );847 | |_- in this macro invocation848 |849 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)850851warning: `extern` declarations without an explicit ABI are deprecated852 --> ../src/ffi.rs:288:20853 |854288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {855 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`856...857375 | / gen_functions!(858376 | | block_new_aa_trace_xdrop,859377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",860378 | | block_align_aa_trace_xdrop,861... |862392 | | AAMatrix, AAProfile, true, true863393 | | );864 | |_- in this macro invocation865 |866 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)867868warning: `extern` declarations without an explicit ABI are deprecated869 --> ../src/ffi.rs:295:20870 |871295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {872 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`873...874375 | / gen_functions!(875376 | | block_new_aa_trace_xdrop,876377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",877378 | | block_align_aa_trace_xdrop,878... |879392 | | AAMatrix, AAProfile, true, true880393 | | );881 | |_- in this macro invocation882 |883 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)884885warning: `extern` declarations without an explicit ABI are deprecated886 --> ../src/ffi.rs:302:20887 |888302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...889 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`890...891375 | / gen_functions!(892376 | | block_new_aa_trace_xdrop,893377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",894378 | | block_align_aa_trace_xdrop,895... |896392 | | AAMatrix, AAProfile, true, true897393 | | );898 | |_- in this macro invocation899 |900 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)901902warning: `extern` declarations without an explicit ABI are deprecated903 --> ../src/ffi.rs:309:20904 |905309 | pub unsafe extern fn $free_name(b: BlockHandle) {906 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`907...908375 | / gen_functions!(909376 | | block_new_aa_trace_xdrop,910377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",911378 | | block_align_aa_trace_xdrop,912... |913392 | | AAMatrix, AAProfile, true, true914393 | | );915 | |_- in this macro invocation916 |917 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)918919[ 30%] Generating ../generated/translated_search.sh.h920[ 30%] Generating ../generated/multihitdb.sh.h921[ 31%] Generating ../generated/taxpercontig.sh.h922[ 31%] Generating ../generated/createtaxdb.sh.h923[ 31%] Generating ../generated/multihitsearch.sh.h924[ 31%] Generating ../generated/enrich.sh.h925[ 31%] Generating ../generated/blastn.sh.h926[ 31%] Generating ../generated/searchslicedtargetprofile.sh.h927[ 31%] Generating ../generated/linsearch.sh.h928[ 31%] Generating ../generated/taxonomy.sh.h929[ 32%] Generating ../generated/databases.sh.h930[ 32%] Generating ../generated/pickconsensusrep.sh.h931[ 32%] Generating ../generated/tsv2exprofiledb.sh.h932[ 33%] Generating ../generated/nucleotide_clustering.sh.h933[ 33%] Generating ../generated/iterativepp.sh.h934[ 33%] Built target local-generated935[ 33%] Built target foldmason-generated936[ 34%] Linking CXX static library libtantan.a937[ 34%] Built target tantan938[ 34%] Built target ksw2939[ 34%] Built target alp940warning: `block_aligner_c` (lib) generated 55 warnings (run `cargo fix --lib -p block_aligner_c` to apply 55 suggestions)941 Finished `release` profile [optimized] target(s) in 5.54s942Copying byproducts `libblock_aligner_c.a` to /build/source/build/lib/foldseek943[ 34%] Built target _cargo-build_block_aligner_c944[ 34%] Built target cargo-build_block_aligner_c945[ 34%] Built target generated946[ 34%] Linking CXX static library libfoldcomp.a947[ 34%] Built target foldcomp948[ 35%] Building CXX object lib/foldseek/src/strucclustutils/CMakeFiles/gemmiwrapper.dir/GemmiWrapper.cpp.o949[ 35%] Linking C static library libzstd.a950[ 35%] Built target libzstd_static951[ 35%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o952[ 36%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o953[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o954[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o955[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o956[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o957[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Fwbw.cpp.o958[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/rescorediagonal.cpp.o959[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o960[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/StripedSmithWaterman.cpp.o961[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/BandedNucleotideAligner.cpp.o962[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/AlignmentSymmetry.cpp.o963[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/ClusteringAlgorithms.cpp.o964[ 39%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Main.cpp.o965[ 39%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Clustering.cpp.o966[ 40%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CSProfile.cpp.o967[ 40%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/A3MReader.cpp.o968[ 40%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Application.cpp.o969[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/BaseMatrix.cpp.o970[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Command.cpp.o971[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBWriter.cpp.o972[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBConcat.cpp.o973[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CommandCaller.cpp.o974[ 42%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBReader.cpp.o975[ 43%] 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lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MemoryTracker.cpp.o984[ 44%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/NucleotideMatrix.cpp.o985[ 44%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MultiParam.cpp.o986[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MMseqsMPI.cpp.o987[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Orf.cpp.o988[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ProfileStates.cpp.o989[ 46%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Parameters.cpp.o990[ 46%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/LibraryReader.cpp.o991[ 46%] Building CXX object 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lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sortresult.cpp.o1091[ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitdb.cpp.o1092[ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitsequence.cpp.o1093[ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/subtractdbs.cpp.o1094[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizealis.cpp.o1095[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeheaders.cpp.o1096/build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp: In function 'int result2flat(int, const char**, const Command&)':1097/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<char>; _Alloc = std::allocator<char>; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result]1098 65 | dbKeyBuffer.size();1099 | ~~~~~~~~~~~~~~~~^~1100In file included from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/string:56,1101 from /build/source/lib/foldseek/lib/mmseqs/src/commons/Parameters.h:7,1102 from /build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp:2:1103/nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/bits/basic_string.h:1163:7: note: declared here1104 1163 | size() const _GLIBCXX_NOEXCEPT1105 | ^~~~1106[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeresult.cpp.o1107[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizetabs.cpp.o1108[ 76%] Building CXX object 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Linking CXX static library libfoldseek-framework.a1192[ 96%] Built target foldseek-framework1193[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/FoldmasonParameters.cpp.o1194[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/SimpleGotoh.cpp.o1195[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/FMStructureSmithWaterman.cpp.o1196[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/structuremsa.cpp.o1197[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/refinemsa.cpp.o1198[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/newick.cpp.o1199[ 98%] Building CXX object src/CMakeFiles/foldmason.dir/commons/MSA.cpp.o1200[ 98%] Building CXX object src/CMakeFiles/foldmason.dir/foldmason.cpp.o1201[100%] Building CXX object src/CMakeFiles/foldmason.dir/workflow/EasyMSA.cpp.o1202[100%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/msa2lddt.cpp.o1203/build/source/src/strucclustutils/structuremsa.cpp: In function 'Matcher::result_t pairwiseAlignment(unsigned int, Sequence*, Sequence*, Sequence*, Sequence*, int, int, SubstitutionMatrix*, SubstitutionMatrix*, int, float**)':1204/build/source/src/strucclustutils/structuremsa.cpp:177:65: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]1205 177 | short **target_profile_scores_aa = new short * [alphabetSize];1206 | ^1207In file included from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/bits/new_allocator.h:34,1208 from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/x86_64-unknown-linux-gnu/bits/c++allocator.h:33,1209 from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/bits/allocator.h:46,1210 from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/vector:65,1211 from /build/source/lib/foldseek/lib/mmseqs/src/commons/DBReader.h:11,1212 from /build/source/lib/foldseek/lib/mmseqs/src/commons/IndexReader.h:4,1213 from /build/source/lib/foldseek/lib/mmseqs/src/alignment/Alignment.h:4,1214 from /build/source/src/strucclustutils/structuremsa.cpp:1:1215/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 here1216 140 | _GLIBCXX_NODISCARD void* operator new[](std::size_t)1217 | ^~~~~~~~1218/build/source/src/strucclustutils/structuremsa.cpp:178:66: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]1219 178 | short **target_profile_scores_3di = new short * [alphabetSize];1220 | ^1221/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 here1222 140 | _GLIBCXX_NODISCARD void* operator new[](std::size_t)1223 | ^~~~~~~~1224In file included from /nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/string.h:548,1225 from /nix/store/4yxdxw3kppr2pbic95p4mri520rkdag2-gcc-15.3.0/include/c++/15.3.0/cstring:48,1226 from /build/source/lib/foldseek/lib/mmseqs/src/commons/MultiParam.h:10,1227 from /build/source/lib/foldseek/lib/mmseqs/src/commons/Parameters.h:16,1228 from /build/source/lib/foldseek/lib/mmseqs/src/commons/Sequence.h:10,1229 from /build/source/lib/foldseek/lib/mmseqs/src/commons/DBReader.h:13:1230In function 'void* memset(void*, int, size_t)',1231 inlined from '_Z12structuremsaiPPKcRK7Commandb._omp_fn.0' at /build/source/src/strucclustutils/structuremsa.cpp:1952:27:1232/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=]1233 59 | return __builtin___memset_chk (__dest, __ch, __len,1234 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~1235 60 | __glibc_objsize0 (__dest));1236 | ~~~~~~~~~~~~~~~~~~~~~~~~~~1237In function 'void* memset(void*, int, size_t)',1238 inlined from '_Z12structuremsaiPPKcRK7Commandb._omp_fn.0' at /build/source/src/strucclustutils/structuremsa.cpp:1953:27:1239/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=]1240 59 | return __builtin___memset_chk (__dest, __ch, __len,1241 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~1242 60 | __glibc_objsize0 (__dest));1243 | ~~~~~~~~~~~~~~~~~~~~~~~~~~1244[100%] Linking CXX executable foldmason1245[100%] Built target foldmason1246buildPhase completed in 1 minutes 45 secondsinstallPhase
1247install flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash install1248[ 1%] Built target foldmason-generated1249[ 1%] Built target cargo-prebuild_block_aligner_c1250[ 2%] Built target version1251[ 8%] Built target local-generated1252[ 19%] Built target generated1253[ 19%] Built target microtar1254[ 19%] Built target tinyexpr1255[ 19%] Built target ksw21256[ 20%] Built target tantan1257[ 27%] Built target libzstd_static1258[ 30%] Built target foldcomp1259[ 34%] Built target alp1260warning: `extern` declarations without an explicit ABI are deprecated1261 --> ../src/ffi.rs:32:121262 |126332 | pub unsafe extern fn block_new_simple_aamatrix(match_score: i8, mismatch_score: i8) -> *mut AAMatrix {1264 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1265 |1266 = note: `#[warn(missing_abi)]` on by default12671268warning: `extern` declarations without an explicit ABI are deprecated1269 --> ../src/ffi.rs:39:121270 |127139 | pub unsafe extern fn block_set_aamatrix(matrix: *mut AAMatrix, a: u8, b: u8, score: i8) {1272 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`12731274warning: `extern` declarations without an explicit ABI are deprecated1275 --> ../src/ffi.rs:46:121276 |127746 | pub unsafe extern fn block_free_aamatrix(matrix: *mut AAMatrix) {1278 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`12791280warning: `extern` declarations without an explicit ABI are deprecated1281 --> ../src/ffi.rs:61:121282 |128361 | pub unsafe extern fn block_new_aaprofile(str_len: usize, block_size: usize, gap_extend: i8) -> *mut AAProfile {1284 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`12851286warning: `extern` declarations without an explicit ABI are deprecated1287 --> ../src/ffi.rs:68:121288 |128968 | pub unsafe extern fn block_len_aaprofile(profile: *const AAProfile) -> usize {1290 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`12911292warning: `extern` declarations without an explicit ABI are deprecated1293 --> ../src/ffi.rs:76:121294 |129576 | pub unsafe extern fn block_clear_aaprofile(profile: *mut AAProfile, str_len: usize) {1296 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`12971298warning: `extern` declarations without an explicit ABI are deprecated1299 --> ../src/ffi.rs:86:121300 |130186 | pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u8, score: i8) {1302 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13031304warning: `extern` declarations without an explicit ABI are deprecated1305 --> ../src/ffi.rs:97:121306 |130797 | pub unsafe extern fn block_set_gap_open_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {1308 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13091310warning: `extern` declarations without an explicit ABI are deprecated1311 --> ../src/ffi.rs:108:121312 |1313108 | pub unsafe extern fn block_set_gap_close_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {1314 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13151316warning: `extern` declarations without an explicit ABI are deprecated1317 --> ../src/ffi.rs:119:121318 |1319119 | pub unsafe extern fn block_set_gap_open_R_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {1320 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13211322warning: `extern` declarations without an explicit ABI are deprecated1323 --> ../src/ffi.rs:126:121324 |1325126 | pub unsafe extern fn block_get_aaprofile(profile: *const AAProfile, i: usize, b: u8) -> i8 {1326 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13271328warning: `extern` declarations without an explicit ABI are deprecated1329 --> ../src/ffi.rs:133:121330 |1331133 | pub unsafe extern fn block_get_gap_extend_aaprofile(profile: *const AAProfile) -> i8 {1332 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13331334warning: `extern` declarations without an explicit ABI are deprecated1335 --> ../src/ffi.rs:140:121336 |1337140 | pub unsafe extern fn block_free_aaprofile(profile: *mut AAProfile) {1338 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13391340warning: `extern` declarations without an explicit ABI are deprecated1341 --> ../src/ffi.rs:149:121342 |1343149 | pub unsafe extern fn block_new_cigar(query_len: usize, reference_len: usize) -> *mut Cigar {1344 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13451346warning: `extern` declarations without an explicit ABI are deprecated1347 --> ../src/ffi.rs:156:121348 |1349156 | pub unsafe extern fn block_get_cigar(cigar: *const Cigar, i: usize) -> OpLen {1350 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13511352warning: `extern` declarations without an explicit ABI are deprecated1353 --> ../src/ffi.rs:163:121354 |1355163 | pub unsafe extern fn block_len_cigar(cigar: *const Cigar) -> usize {1356 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13571358warning: `extern` declarations without an explicit ABI are deprecated1359 --> ../src/ffi.rs:170:121360 |1361170 | pub unsafe extern fn block_free_cigar(cigar: *mut Cigar) {1362 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13631364warning: `extern` declarations without an explicit ABI are deprecated1365 --> ../src/ffi.rs:179:121366 |1367179 | pub unsafe extern fn block_new_padded_aa(len: usize, max_size: usize) -> *mut PaddedBytes {1368 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13691370warning: `extern` declarations without an explicit ABI are deprecated1371 --> ../src/ffi.rs:186:121372 |1373186 | pub unsafe extern fn block_set_bytes_padded_aa(padded: *mut PaddedBytes, s: *const u8, len: usize, max_size: usize) {1374 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13751376warning: `extern` declarations without an explicit ABI are deprecated1377 --> ../src/ffi.rs:194:121378 |1379194 | pub unsafe extern fn block_free_padded_aa(padded: *mut PaddedBytes) {1380 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13811382warning: `extern` declarations without an explicit ABI are deprecated1383 --> ../src/ffi.rs:203:121384 |1385203 | pub unsafe extern fn block_new_pos_bias(len: usize, max_size: usize) -> *mut PosBias {1386 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13871388warning: `extern` declarations without an explicit ABI are deprecated1389 --> ../src/ffi.rs:210:121390 |1391210 | pub unsafe extern fn block_set_pos_bias(bias: *mut PosBias, b: *const i16, len: usize) {1392 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13931394warning: `extern` declarations without an explicit ABI are deprecated1395 --> ../src/ffi.rs:218:121396 |1397218 | pub unsafe extern fn block_free_pos_bias(bias: *mut PosBias) {1398 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13991400warning: `extern` declarations without an explicit ABI are deprecated1401 --> ../src/ffi.rs:237:201402 |1403237 | pub unsafe extern fn $new_name(query_len: usize,1404 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1405...1406315 | / gen_functions!(1407316 | | block_new_aa,1408317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1409318 | | block_align_aa,1410... |1411332 | | AAMatrix, AAProfile, false, false1412333 | | );1413 | |_- in this macro invocation1414 |1415 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14161417warning: `extern` declarations without an explicit ABI are deprecated1418 --> ../src/ffi.rs:246:201419 |1420246 | pub unsafe extern fn $align_name(b: BlockHandle,1421 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1422...1423315 | / gen_functions!(1424316 | | block_new_aa,1425317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1426318 | | block_align_aa,1427... |1428332 | | AAMatrix, AAProfile, false, false1429333 | | );1430 | |_- in this macro invocation1431 |1432 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14331434warning: `extern` declarations without an explicit ABI are deprecated1435 --> ../src/ffi.rs:259:201436 |1437259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1438 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1439...1440315 | / gen_functions!(1441316 | | block_new_aa,1442317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1443318 | | block_align_aa,1444... |1445332 | | AAMatrix, AAProfile, false, false1446333 | | );1447 | |_- in this macro invocation1448 |1449 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14501451warning: `extern` declarations without an explicit ABI are deprecated1452 --> ../src/ffi.rs:270:201453 |1454270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1455 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1456...1457315 | / gen_functions!(1458316 | | block_new_aa,1459317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1460318 | | block_align_aa,1461... |1462332 | | AAMatrix, AAProfile, false, false1463333 | | );1464 | |_- in this macro invocation1465 |1466 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14671468warning: `extern` declarations without an explicit ABI are deprecated1469 --> ../src/ffi.rs:288:201470 |1471288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1472 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1473...1474315 | / gen_functions!(1475316 | | block_new_aa,1476317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1477318 | | block_align_aa,1478... |1479332 | | AAMatrix, AAProfile, false, false1480333 | | );1481 | |_- in this macro invocation1482 |1483 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14841485warning: `extern` declarations without an explicit ABI are deprecated1486 --> ../src/ffi.rs:295:201487 |1488295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1489 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1490...1491315 | / gen_functions!(1492316 | | block_new_aa,1493317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1494318 | | block_align_aa,1495... |1496332 | | AAMatrix, AAProfile, false, false1497333 | | );1498 | |_- in this macro invocation1499 |1500 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15011502warning: `extern` declarations without an explicit ABI are deprecated1503 --> ../src/ffi.rs:302:201504 |1505302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1506 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1507...1508315 | / gen_functions!(1509316 | | block_new_aa,1510317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1511318 | | block_align_aa,1512... |1513332 | | AAMatrix, AAProfile, false, false1514333 | | );1515 | |_- in this macro invocation1516 |1517 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15181519warning: `extern` declarations without an explicit ABI are deprecated1520 --> ../src/ffi.rs:309:201521 |1522309 | pub unsafe extern fn $free_name(b: BlockHandle) {1523 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1524...1525315 | / gen_functions!(1526316 | | block_new_aa,1527317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1528318 | | block_align_aa,1529... |1530332 | | AAMatrix, AAProfile, false, false1531333 | | );1532 | |_- in this macro invocation1533 |1534 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15351536warning: `extern` declarations without an explicit ABI are deprecated1537 --> ../src/ffi.rs:237:201538 |1539237 | pub unsafe extern fn $new_name(query_len: usize,1540 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1541...1542335 | / gen_functions!(1543336 | | block_new_aa_xdrop,1544337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1545338 | | block_align_aa_xdrop,1546... |1547352 | | AAMatrix, AAProfile, false, true1548353 | | );1549 | |_- in this macro invocation1550 |1551 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15521553warning: `extern` declarations without an explicit ABI are deprecated1554 --> ../src/ffi.rs:246:201555 |1556246 | pub unsafe extern fn $align_name(b: BlockHandle,1557 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1558...1559335 | / gen_functions!(1560336 | | block_new_aa_xdrop,1561337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1562338 | | block_align_aa_xdrop,1563... |1564352 | | AAMatrix, AAProfile, false, true1565353 | | );1566 | |_- in this macro invocation1567 |1568 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15691570warning: `extern` declarations without an explicit ABI are deprecated1571 --> ../src/ffi.rs:259:201572 |1573259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1574 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1575...1576335 | / gen_functions!(1577336 | | block_new_aa_xdrop,1578337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1579338 | | block_align_aa_xdrop,1580... |1581352 | | AAMatrix, AAProfile, false, true1582353 | | );1583 | |_- in this macro invocation1584 |1585 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15861587warning: `extern` declarations without an explicit ABI are deprecated1588 --> ../src/ffi.rs:270:201589 |1590270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1591 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1592...1593335 | / gen_functions!(1594336 | | block_new_aa_xdrop,1595337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1596338 | | block_align_aa_xdrop,1597... |1598352 | | AAMatrix, AAProfile, false, true1599353 | | );1600 | |_- in this macro invocation1601 |1602 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16031604warning: `extern` declarations without an explicit ABI are deprecated1605 --> ../src/ffi.rs:288:201606 |1607288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1608 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1609...1610335 | / gen_functions!(1611336 | | block_new_aa_xdrop,1612337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1613338 | | block_align_aa_xdrop,1614... |1615352 | | AAMatrix, AAProfile, false, true1616353 | | );1617 | |_- in this macro invocation1618 |1619 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16201621warning: `extern` declarations without an explicit ABI are deprecated1622 --> ../src/ffi.rs:295:201623 |1624295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1625 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1626...1627335 | / gen_functions!(1628336 | | block_new_aa_xdrop,1629337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1630338 | | block_align_aa_xdrop,1631... |1632352 | | AAMatrix, AAProfile, false, true1633353 | | );1634 | |_- in this macro invocation1635 |1636 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16371638warning: `extern` declarations without an explicit ABI are deprecated1639 --> ../src/ffi.rs:302:201640 |1641302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1642 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1643...1644335 | / gen_functions!(1645336 | | block_new_aa_xdrop,1646337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1647338 | | block_align_aa_xdrop,1648... |1649352 | | AAMatrix, AAProfile, false, true1650353 | | );1651 | |_- in this macro invocation1652 |1653 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16541655warning: `extern` declarations without an explicit ABI are deprecated1656 --> ../src/ffi.rs:309:201657 |1658309 | pub unsafe extern fn $free_name(b: BlockHandle) {1659 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1660...1661335 | / gen_functions!(1662336 | | block_new_aa_xdrop,1663337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1664338 | | block_align_aa_xdrop,1665... |1666352 | | AAMatrix, AAProfile, false, true1667353 | | );1668 | |_- in this macro invocation1669 |1670 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16711672warning: `extern` declarations without an explicit ABI are deprecated1673 --> ../src/ffi.rs:237:201674 |1675237 | pub unsafe extern fn $new_name(query_len: usize,1676 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1677...1678355 | / gen_functions!(1679356 | | block_new_aa_trace,1680357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1681358 | | block_align_aa_trace,1682... |1683372 | | AAMatrix, AAProfile, true, false1684373 | | );1685 | |_- in this macro invocation1686 |1687 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16881689warning: `extern` declarations without an explicit ABI are deprecated1690 --> ../src/ffi.rs:246:201691 |1692246 | pub unsafe extern fn $align_name(b: BlockHandle,1693 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1694...1695355 | / gen_functions!(1696356 | | block_new_aa_trace,1697357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1698358 | | block_align_aa_trace,1699... |1700372 | | AAMatrix, AAProfile, true, false1701373 | | );1702 | |_- in this macro invocation1703 |1704 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17051706warning: `extern` declarations without an explicit ABI are deprecated1707 --> ../src/ffi.rs:259:201708 |1709259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1710 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1711...1712355 | / gen_functions!(1713356 | | block_new_aa_trace,1714357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1715358 | | block_align_aa_trace,1716... |1717372 | | AAMatrix, AAProfile, true, false1718373 | | );1719 | |_- in this macro invocation1720 |1721 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17221723warning: `extern` declarations without an explicit ABI are deprecated1724 --> ../src/ffi.rs:270:201725 |1726270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1727 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1728...1729355 | / gen_functions!(1730356 | | block_new_aa_trace,1731357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1732358 | | block_align_aa_trace,1733... |1734372 | | AAMatrix, AAProfile, true, false1735373 | | );1736 | |_- in this macro invocation1737 |1738 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17391740warning: `extern` declarations without an explicit ABI are deprecated1741 --> ../src/ffi.rs:288:201742 |1743288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1744 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1745...1746355 | / gen_functions!(1747356 | | block_new_aa_trace,1748357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1749358 | | block_align_aa_trace,1750... |1751372 | | AAMatrix, AAProfile, true, false1752373 | | );1753 | |_- in this macro invocation1754 |1755 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17561757warning: `extern` declarations without an explicit ABI are deprecated1758 --> ../src/ffi.rs:295:201759 |1760295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1761 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1762...1763355 | / gen_functions!(1764356 | | block_new_aa_trace,1765357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1766358 | | block_align_aa_trace,1767... |1768372 | | AAMatrix, AAProfile, true, false1769373 | | );1770 | |_- in this macro invocation1771 |1772 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17731774warning: `extern` declarations without an explicit ABI are deprecated1775 --> ../src/ffi.rs:302:201776 |1777302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1778 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1779...1780355 | / gen_functions!(1781356 | | block_new_aa_trace,1782357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1783358 | | block_align_aa_trace,1784... |1785372 | | AAMatrix, AAProfile, true, false1786373 | | );1787 | |_- in this macro invocation1788 |1789 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17901791warning: `extern` declarations without an explicit ABI are deprecated1792 --> ../src/ffi.rs:309:201793 |1794309 | pub unsafe extern fn $free_name(b: BlockHandle) {1795 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1796...1797355 | / gen_functions!(1798356 | | block_new_aa_trace,1799357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1800358 | | block_align_aa_trace,1801... |1802372 | | AAMatrix, AAProfile, true, false1803373 | | );1804 | |_- in this macro invocation1805 |1806 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18071808warning: `extern` declarations without an explicit ABI are deprecated1809 --> ../src/ffi.rs:237:201810 |1811237 | pub unsafe extern fn $new_name(query_len: usize,1812 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1813...1814375 | / gen_functions!(1815376 | | block_new_aa_trace_xdrop,1816377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1817378 | | block_align_aa_trace_xdrop,1818... |1819392 | | AAMatrix, AAProfile, true, true1820393 | | );1821 | |_- in this macro invocation1822 |1823 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18241825warning: `extern` declarations without an explicit ABI are deprecated1826 --> ../src/ffi.rs:246:201827 |1828246 | pub unsafe extern fn $align_name(b: BlockHandle,1829 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1830...1831375 | / gen_functions!(1832376 | | block_new_aa_trace_xdrop,1833377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1834378 | | block_align_aa_trace_xdrop,1835... |1836392 | | AAMatrix, AAProfile, true, true1837393 | | );1838 | |_- in this macro invocation1839 |1840 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18411842warning: `extern` declarations without an explicit ABI are deprecated1843 --> ../src/ffi.rs:259:201844 |1845259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1846 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1847...1848375 | / gen_functions!(1849376 | | block_new_aa_trace_xdrop,1850377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1851378 | | block_align_aa_trace_xdrop,1852... |1853392 | | AAMatrix, AAProfile, true, true1854393 | | );1855 | |_- in this macro invocation1856 |1857 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18581859warning: `extern` declarations without an explicit ABI are deprecated1860 --> ../src/ffi.rs:270:201861 |1862270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1863 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1864...1865375 | / gen_functions!(1866376 | | block_new_aa_trace_xdrop,1867377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1868378 | | block_align_aa_trace_xdrop,1869... |1870392 | | AAMatrix, AAProfile, true, true1871393 | | );1872 | |_- in this macro invocation1873 |1874 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18751876warning: `extern` declarations without an explicit ABI are deprecated1877 --> ../src/ffi.rs:288:201878 |1879288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1880 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1881...1882375 | / gen_functions!(1883376 | | block_new_aa_trace_xdrop,1884377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1885378 | | block_align_aa_trace_xdrop,1886... |1887392 | | AAMatrix, AAProfile, true, true1888393 | | );1889 | |_- in this macro invocation1890 |1891 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18921893warning: `extern` declarations without an explicit ABI are deprecated1894 --> ../src/ffi.rs:295:201895 |1896295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1897 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1898...1899375 | / gen_functions!(1900376 | | block_new_aa_trace_xdrop,1901377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1902378 | | block_align_aa_trace_xdrop,1903... |1904392 | | AAMatrix, AAProfile, true, true1905393 | | );1906 | |_- in this macro invocation1907 |1908 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19091910warning: `extern` declarations without an explicit ABI are deprecated1911 --> ../src/ffi.rs:302:201912 |1913302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1914 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1915...1916375 | / gen_functions!(1917376 | | block_new_aa_trace_xdrop,1918377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1919378 | | block_align_aa_trace_xdrop,1920... |1921392 | | AAMatrix, AAProfile, true, true1922393 | | );1923 | |_- in this macro invocation1924 |1925 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19261927warning: `extern` declarations without an explicit ABI are deprecated1928 --> ../src/ffi.rs:309:201929 |1930309 | pub unsafe extern fn $free_name(b: BlockHandle) {1931 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1932...1933375 | / gen_functions!(1934376 | | block_new_aa_trace_xdrop,1935377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1936378 | | block_align_aa_trace_xdrop,1937... |1938392 | | AAMatrix, AAProfile, true, true1939393 | | );1940 | |_- in this macro invocation1941 |1942 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19431944warning: `block_aligner_c` (lib) generated 55 warnings (run `cargo fix --lib -p block_aligner_c` to apply 55 suggestions)1945 Finished `release` profile [optimized] target(s) in 0.00s1946[ 35%] Built target gemmiwrapper1947Copying byproducts `libblock_aligner_c.a` to /build/source/build/lib/foldseek1948[ 35%] Built target _cargo-build_block_aligner_c1949[ 35%] Built target cargo-build_block_aligner_c1950[ 84%] Built target mmseqs-framework1951[ 84%] Built target pulchra1952[ 84%] Built target 3di1953[ 85%] Built target kerasify1954[ 86%] Built target tmalign1955[ 96%] Built target foldseek-framework1956[100%] Built target foldmason1957Install the project...1958-- Install configuration: "Release"1959-- Installing: /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin/foldmasonfixupPhase
1960shrinking RPATHs of ELF executables and libraries in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c2351961shrinking /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin/foldmason1962checking for references to /build/ in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235...1963patching script interpreter paths in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c2351964stripping (with command strip and flags -S -p) in /nix/store/w5jrl7mcwbkk448a2fxni4v68axp0jbs-foldmason-4-dd3c235/bin