foldmason-4-dd3c235
checks.x86_64-linux.pkgs-foldmason
· build #95
· 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/8g4dmf7l8q1mf9w4wfmlcl8gvdgmhb8v-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/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/share/locale -DCMAKE_INSTALL_LIBEXECDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/libexec -DCMAKE_INSTALL_LIBDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/lib -DCMAKE_INSTALL_DOCDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/share/doc/foldseek -DCMAKE_INSTALL_INFODIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/share/info -DCMAKE_INSTALL_MANDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/share/man -DCMAKE_INSTALL_INCLUDEDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/include -DCMAKE_INSTALL_SBINDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/sbin -DCMAKE_INSTALL_BINDIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/bin -DCMAKE_INSTALL_NAME_DIR=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/lib -DCMAKE_STRIP=/nix/store/j1938gsbvbhkyz4kbmvjk56r479mkw3s-gcc-wrapper-16.2.0/bin/strip -DCMAKE_RANLIB=/nix/store/j1938gsbvbhkyz4kbmvjk56r479mkw3s-gcc-wrapper-16.2.0/bin/ranlib -DCMAKE_AR=/nix/store/j1938gsbvbhkyz4kbmvjk56r479mkw3s-gcc-wrapper-16.2.0/bin/ar -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_INSTALL_PREFIX=/nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235 -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DHAVE_AVX2=17-- The C compiler identification is GNU 16.2.08-- The CXX compiler identification is GNU 16.2.09-- Detecting C compiler ABI info10-- Detecting C compiler ABI info - done11-- Check for working C compiler: /nix/store/j1938gsbvbhkyz4kbmvjk56r479mkw3s-gcc-wrapper-16.2.0/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/j1938gsbvbhkyz4kbmvjk56r479mkw3s-gcc-wrapper-16.2.0/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 - Success31-- IPS4O sorting works32-- Found ZLIB33-- Performing Test HAVE_ZLIB_CHECK34-- Performing Test HAVE_ZLIB_CHECK - Success35-- ZLIB works36-- Found BZLIB37-- Performing Test HAVE_BZLIB_CHECK38-- Performing Test HAVE_BZLIB_CHECK - Success39-- BZLIB works40-- Found OpenMP41-- xxd not found, using xxdi.pl instead42-- ShellCheck not found43-- Rust Target: x86_64-unknown-linux-gnu44-- Determining required link libraries for target x86_64-unknown-linux-gnu45-- Required static libs for target x86_64-unknown-linux-gnu: gcc_s;util;rt;pthread;m;dl;c46-- Required link flags for target x86_64-unknown-linux-gnu: 47-- Found Rust: /nix/store/hr3npzrq9l029s5hf948by203m6qz3lw-rustc-wrapper-1.98.1/bin/rustc (found version "1.98.1")48-- Using Corrosion as a subdirectory49-- Rust Feature: simd_avx250-- xxd not found, using xxdi.pl instead51-- ShellCheck not found52-- Configuring done (4.4s)53-- Generating done (0.1s)54CMake Warning (unused-cli):55 Manually-specified variables were not used by the project:5657 BUILD_TESTING58 CMAKE_EXPORT_NO_PACKAGE_REGISTRY59 CMAKE_INSTALL_BINDIR60 CMAKE_INSTALL_DOCDIR61 CMAKE_INSTALL_INCLUDEDIR62 CMAKE_INSTALL_INFODIR63 CMAKE_INSTALL_LIBEXECDIR64 CMAKE_INSTALL_LOCALEDIR65 CMAKE_INSTALL_MANDIR66 CMAKE_INSTALL_SBINDIR676869-- Build files have been written to: /build/source/build70cmake: enabled parallel building71cmake: enabled parallel installingbuildPhase
72build flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/bash73[ 1%] Generating ../generated/easymsa.sh.h74[ 1%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o75[ 1%] Generating ../generated/vendor_foldmason.js.zst.h76[ 1%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o77[ 1%] Building CXX object src/version/CMakeFiles/version.dir/Version.cpp.o78[ 1%] Building CXX object lib/foldseek/lib/mmseqs/lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o79[ 3%] Built target cargo-prebuild_block_aligner_c80[ 3%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_random.cpp.o81[ 3%] Generating ../generated/structureindex.sh.h82[ 3%] Generating ../generated/main_foldmason.js.h83[ 3%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o84[ 4%] Generating ../generated/easystructuresearch.sh.h85[ 4%] Generating ../generated/nucleotide.out.h86[ 4%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o87[ 4%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o88[ 5%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o89[ 5%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o90[ 5%] Generating ../generated/blosum62.out.h91[ 5%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o92[ 5%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o93[ 6%] Building C 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lib/foldseek/lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o113[ 9%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/database_reader.cpp.o114[ 9%] Generating ../generated/structurecluster.sh.h115[ 9%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/atom_coordinate.cpp.o116[ 9%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o117[ 12%] Generating ../generated/mat3di.out.h118[ 9%] Generating ../generated/VTML80.out.h119[ 9%] Building CXX object lib/foldseek/lib/mmseqs/lib/tantan/CMakeFiles/tantan.dir/tantan.cpp.o120[ 12%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/amino_acid.cpp.o121[ 12%] Generating ../generated/VTML40.out.h122[ 12%] Generating ../generated/CovSeqidQscPercMinDiag.lib.h123[ 12%] Generating ../generated/CovSeqidQscPercMinDiagTargetCov.lib.h124[ 13%] Generating 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lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/nerf.cpp.o135[ 17%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o136[ 17%] Generating ../generated/libPolished_8.lib.h137[ 17%] Generating ../generated/Library255_may17.lib.h138[ 17%] Generating ../generated/evalue_nn.kerasify.h139[ 17%] Generating ../generated/cs219.lib.h140[ 17%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o141[ 17%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o142[ 17%] Built target version143[ 17%] Generating ../generated/main.js.h144[ 17%] Generating ../generated/vendor.js.zst.h145[ 17%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o146[ 18%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o147[ 19%] Generating ../generated/krona_prelude.html.h148[ 20%] Generating ../generated/makepaddeddb.sh.h149[ 21%] Generating ../generated/result_viz_prelude.html.zst.h150[ 21%] Linking C static library libmicrotar.a151[ 21%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o152[ 22%] Generating ../generated/result2structprofile.sh.h153[ 22%] Generating ../generated/K4000.crf.h154[ 23%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/sidechain.cpp.o155[ 23%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o156[ 23%] Built target microtar157[ 24%] Generating ../generated/createstructsubdb.sh.h158/build/source/lib/foldseek/lib/foldcomp/src/database_writer.cpp: In function 'void free_writer(void*)':159/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=]160 65 | fprintf(w->index, "%d\t%llu\t%d\n", w->entries[i].id, w->entries[i].offset, (uint32_t)w->entries[i].length);161 | ~~~^ ~~~~~~~~~~~~~~~~~~~~162 | | |163 | long long unsigned int int64_t {aka long int}164 | %lu165[ 24%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o166/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':167/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=]168 373 | ret->bound = s->bound;169 | ^~170In function 'new_expr',171 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:372:19:172/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'173 88 | te_expr *ret = malloc(size);174 | ^~~~~~~~~~~~175In function 'new_expr',176 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:177/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=]178 93 | ret->type = type;179 | ~~~~~~~~~~^~~~~~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/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':184/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=]185 367 | ret->value = s->value;186 | ^~187In function 'new_expr',188 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:189/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'190 88 | te_expr *ret = malloc(size);191 | ^~~~~~~~~~~~192/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':193/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=]194 446 | ret->value = NAN;195 | ^~196In function 'new_expr',197 inlined from 'base' at /build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:444:19:198/build/source/lib/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'199 88 | te_expr *ret = malloc(size);200 | ^~~~~~~~~~~~201[ 24%] Generating ../generated/multimersearch.sh.h202[ 25%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o203[ 25%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o204[ 25%] Generating ../generated/easymultimersearch.sh.h205[ 25%] Generating ../generated/easysearch.sh.h206[ 25%] Generating ../generated/multimercluster.sh.h207[ 25%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o208 Compiling block_aligner_c v0.4.0 (/build/source/lib/foldseek/lib/block-aligner/c)209[ 25%] Generating ../generated/easymultimercluster.sh.h210[ 25%] Generating ../generated/easycluster.sh.h211[ 25%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/torsion_angle.cpp.o212[ 26%] Generating ../generated/easytaxonomy.sh.h213[ 26%] Building CXX object lib/foldseek/lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o214[ 26%] Generating ../generated/easyrbh.sh.h215[ 26%] Linking C static library libtinyexpr.a216[ 26%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o217[ 27%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o218[ 27%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o219[ 28%] Building CXX object lib/foldseek/lib/foldcomp/CMakeFiles/foldcomp.dir/src/utility.cpp.o220[ 28%] Building C object lib/foldseek/lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o221[ 28%] Generating ../generated/blastp.sh.h222[ 28%] Generating ../generated/blastpgp.sh.h223[ 28%] Built target tinyexpr224[ 29%] Generating ../generated/map.sh.h225[ 29%] Generating ../generated/rbh.sh.h226[ 29%] Generating ../generated/linclust.sh.h227[ 30%] Generating ../generated/clustering.sh.h228[ 30%] Generating ../generated/cascaded_clustering.sh.h229[ 30%] Generating ../generated/update_clustering.sh.h230[ 30%] Generating ../generated/createindex.sh.h231[ 30%] Generating ../generated/searchtargetprofile.sh.h232[ 30%] Generating ../generated/createtaxdb.sh.h233[ 30%] Generating ../generated/translated_search.sh.h234[ 31%] Generating ../generated/taxpercontig.sh.h235[ 31%] Generating ../generated/multihitdb.sh.h236[ 31%] Generating ../generated/multihitsearch.sh.h237warning: `extern` declarations without an explicit ABI are deprecated238 --> ../src/ffi.rs:32:12239 |24032 | pub unsafe extern fn block_new_simple_aamatrix(match_score: i8, mismatch_score: i8) -> *mut AAMatrix {241 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`242 |243 = note: `#[warn(missing_abi)]` on by default244245warning: `extern` declarations without an explicit ABI are deprecated246 --> ../src/ffi.rs:39:12247 |24839 | pub unsafe extern fn block_set_aamatrix(matrix: *mut AAMatrix, a: u8, b: u8, score: i8) {249 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`250251warning: `extern` declarations without an explicit ABI are deprecated252 --> ../src/ffi.rs:46:12253 |25446 | pub unsafe extern fn block_free_aamatrix(matrix: *mut AAMatrix) {255 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`256257warning: `extern` declarations without an explicit ABI are deprecated258 --> ../src/ffi.rs:61:12259 |26061 | pub unsafe extern fn block_new_aaprofile(str_len: usize, block_size: usize, gap_extend: i8) -> *mut AAProfile {261 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`262263warning: `extern` declarations without an explicit ABI are deprecated264 --> ../src/ffi.rs:68:12265 |26668 | pub unsafe extern fn block_len_aaprofile(profile: *const AAProfile) -> usize {267 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`268269warning: `extern` declarations without an explicit ABI are deprecated270 --> ../src/ffi.rs:76:12271 |27276 | pub unsafe extern fn block_clear_aaprofile(profile: *mut AAProfile, str_len: usize) {273 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`274275warning: `extern` declarations without an explicit ABI are deprecated276 --> ../src/ffi.rs:86:12277 |27886 | pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u8, score: i8) {279 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`280281warning: `extern` declarations without an explicit ABI are deprecated282 --> ../src/ffi.rs:97:12283 |28497 | pub unsafe extern fn block_set_gap_open_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {285 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`286287warning: `extern` declarations without an explicit ABI are deprecated288 --> ../src/ffi.rs:108:12289 |290108 | pub unsafe extern fn block_set_gap_close_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {291 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`292293warning: `extern` declarations without an explicit ABI are deprecated294 --> ../src/ffi.rs:119:12295 |296119 | pub unsafe extern fn block_set_gap_open_R_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {297 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`298299warning: `extern` declarations without an explicit ABI are deprecated300 --> ../src/ffi.rs:126:12301 |302126 | pub unsafe extern fn block_get_aaprofile(profile: *const AAProfile, i: usize, b: u8) -> i8 {303 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`304305warning: `extern` declarations without an explicit ABI are deprecated306 --> ../src/ffi.rs:133:12307 |308133 | pub unsafe extern fn block_get_gap_extend_aaprofile(profile: *const AAProfile) -> i8 {309 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`310311warning: `extern` declarations without an explicit ABI are deprecated312 --> ../src/ffi.rs:140:12313 |314140 | pub unsafe extern fn block_free_aaprofile(profile: *mut AAProfile) {315 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`316317warning: `extern` declarations without an explicit ABI are deprecated318 --> ../src/ffi.rs:149:12319 |320149 | pub unsafe extern fn block_new_cigar(query_len: usize, reference_len: usize) -> *mut Cigar {321 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`322323warning: `extern` declarations without an explicit ABI are deprecated324 --> ../src/ffi.rs:156:12325 |326156 | pub unsafe extern fn block_get_cigar(cigar: *const Cigar, i: usize) -> OpLen {327 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`328329warning: `extern` declarations without an explicit ABI are deprecated330 --> ../src/ffi.rs:163:12331 |332163 | pub unsafe extern fn block_len_cigar(cigar: *const Cigar) -> usize {333 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`334335warning: `extern` declarations without an explicit ABI are deprecated336 --> ../src/ffi.rs:170:12337 |338170 | pub unsafe extern fn block_free_cigar(cigar: *mut Cigar) {339 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`340341warning: `extern` declarations without an explicit ABI are deprecated342 --> ../src/ffi.rs:179:12343 |344179 | pub unsafe extern fn block_new_padded_aa(len: usize, max_size: usize) -> *mut PaddedBytes {345 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`346347warning: `extern` declarations without an explicit ABI are deprecated348 --> ../src/ffi.rs:186:12349 |350186 | pub unsafe extern fn block_set_bytes_padded_aa(padded: *mut PaddedBytes, s: *const u8, len: usize, max_size: usize) {351 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`352353warning: `extern` declarations without an explicit ABI are deprecated354 --> ../src/ffi.rs:194:12355 |356194 | pub unsafe extern fn block_free_padded_aa(padded: *mut PaddedBytes) {357 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`358359warning: `extern` declarations without an explicit ABI are deprecated360 --> ../src/ffi.rs:203:12361 |362203 | pub unsafe extern fn block_new_pos_bias(len: usize, max_size: usize) -> *mut PosBias {363 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`364365warning: `extern` declarations without an explicit ABI are deprecated366 --> ../src/ffi.rs:210:12367 |368210 | pub unsafe extern fn block_set_pos_bias(bias: *mut PosBias, b: *const i16, len: usize) {369 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`370371warning: `extern` declarations without an explicit ABI are deprecated372 --> ../src/ffi.rs:218:12373 |374218 | pub unsafe extern fn block_free_pos_bias(bias: *mut PosBias) {375 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`376377warning: `extern` declarations without an explicit ABI are deprecated378 --> ../src/ffi.rs:237:20379 |380237 | pub unsafe extern fn $new_name(query_len: usize,381 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`382...383315 | / gen_functions!(384316 | | block_new_aa,385317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",386318 | | block_align_aa,387... |388332 | | AAMatrix, AAProfile, false, false389333 | | );390 | |_- in this macro invocation391 |392 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)393394warning: `extern` declarations without an explicit ABI are deprecated395 --> ../src/ffi.rs:246:20396 |397246 | pub unsafe extern fn $align_name(b: BlockHandle,398 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`399...400315 | / gen_functions!(401316 | | block_new_aa,402317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",403318 | | block_align_aa,404... |405332 | | AAMatrix, AAProfile, false, false406333 | | );407 | |_- in this macro invocation408 |409 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)410411warning: `extern` declarations without an explicit ABI are deprecated412 --> ../src/ffi.rs:259:20413 |414259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,415 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`416...417315 | / gen_functions!(418316 | | block_new_aa,419317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",420318 | | block_align_aa,421... |422332 | | AAMatrix, AAProfile, false, false423333 | | );424 | |_- in this macro invocation425 |426 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)427428warning: `extern` declarations without an explicit ABI are deprecated429 --> ../src/ffi.rs:270:20430 |431270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,432 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`433...434315 | / gen_functions!(435316 | | block_new_aa,436317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",437318 | | block_align_aa,438... |439332 | | AAMatrix, AAProfile, false, false440333 | | );441 | |_- in this macro invocation442 |443 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)444445warning: `extern` declarations without an explicit ABI are deprecated446 --> ../src/ffi.rs:288:20447 |448288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {449 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`450...451315 | / gen_functions!(452316 | | block_new_aa,453317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",454318 | | block_align_aa,455... |456332 | | AAMatrix, AAProfile, false, false457333 | | );458 | |_- in this macro invocation459 |460 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)461462warning: `extern` declarations without an explicit ABI are deprecated463 --> ../src/ffi.rs:295:20464 |465295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {466 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`467...468315 | / gen_functions!(469316 | | block_new_aa,470317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",471318 | | block_align_aa,472... |473332 | | AAMatrix, AAProfile, false, false474333 | | );475 | |_- in this macro invocation476 |477 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)478479warning: `extern` declarations without an explicit ABI are deprecated480 --> ../src/ffi.rs:302:20481 |482302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...483 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`484...485315 | / gen_functions!(486316 | | block_new_aa,487317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",488318 | | block_align_aa,489... |490332 | | AAMatrix, AAProfile, false, false491333 | | );492 | |_- in this macro invocation493 |494 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)495496warning: `extern` declarations without an explicit ABI are deprecated497 --> ../src/ffi.rs:309:20498 |499309 | pub unsafe extern fn $free_name(b: BlockHandle) {500 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`501...502315 | / gen_functions!(503316 | | block_new_aa,504317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",505318 | | block_align_aa,506... |507332 | | AAMatrix, AAProfile, false, false508333 | | );509 | |_- in this macro invocation510 |511 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)512513warning: `extern` declarations without an explicit ABI are deprecated514 --> ../src/ffi.rs:237:20515 |516237 | pub unsafe extern fn $new_name(query_len: usize,517 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`518...519335 | / gen_functions!(520336 | | block_new_aa_xdrop,521337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",522338 | | block_align_aa_xdrop,523... |524352 | | AAMatrix, AAProfile, false, true525353 | | );526 | |_- in this macro invocation527 |528 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)529530warning: `extern` declarations without an explicit ABI are deprecated531 --> ../src/ffi.rs:246:20532 |533246 | pub unsafe extern fn $align_name(b: BlockHandle,534 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`535...536335 | / gen_functions!(537336 | | block_new_aa_xdrop,538337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",539338 | | block_align_aa_xdrop,540... |541352 | | AAMatrix, AAProfile, false, true542353 | | );543 | |_- in this macro invocation544 |545 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)546547warning: `extern` declarations without an explicit ABI are deprecated548 --> ../src/ffi.rs:259:20549 |550259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,551 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`552...553335 | / gen_functions!(554336 | | block_new_aa_xdrop,555337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",556338 | | block_align_aa_xdrop,557... |558352 | | AAMatrix, AAProfile, false, true559353 | | );560 | |_- in this macro invocation561 |562 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)563564warning: `extern` declarations without an explicit ABI are deprecated565 --> ../src/ffi.rs:270:20566 |567270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,568 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`569...570335 | / gen_functions!(571336 | | block_new_aa_xdrop,572337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",573338 | | block_align_aa_xdrop,574... |575352 | | AAMatrix, AAProfile, false, true576353 | | );577 | |_- in this macro invocation578 |579 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)580581warning: `extern` declarations without an explicit ABI are deprecated582 --> ../src/ffi.rs:288:20583 |584288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {585 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`586...587335 | / gen_functions!(588336 | | block_new_aa_xdrop,589337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",590338 | | block_align_aa_xdrop,591... |592352 | | AAMatrix, AAProfile, false, true593353 | | );594 | |_- in this macro invocation595 |596 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)597598warning: `extern` declarations without an explicit ABI are deprecated599 --> ../src/ffi.rs:295:20600 |601295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {602 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`603...604335 | / gen_functions!(605336 | | block_new_aa_xdrop,606337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",607338 | | block_align_aa_xdrop,608... |609352 | | AAMatrix, AAProfile, false, true610353 | | );611 | |_- in this macro invocation612 |613 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)614615warning: `extern` declarations without an explicit ABI are deprecated616 --> ../src/ffi.rs:302:20617 |618302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...619 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`620...621335 | / gen_functions!(622336 | | block_new_aa_xdrop,623337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",624338 | | block_align_aa_xdrop,625... |626352 | | AAMatrix, AAProfile, false, true627353 | | );628 | |_- in this macro invocation629 |630 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)631632warning: `extern` declarations without an explicit ABI are deprecated633 --> ../src/ffi.rs:309:20634 |635309 | pub unsafe extern fn $free_name(b: BlockHandle) {636 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`637...638335 | / gen_functions!(639336 | | block_new_aa_xdrop,640337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",641338 | | block_align_aa_xdrop,642... |643352 | | AAMatrix, AAProfile, false, true644353 | | );645 | |_- in this macro invocation646 |647 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)648649warning: `extern` declarations without an explicit ABI are deprecated650 --> ../src/ffi.rs:237:20651 |652237 | pub unsafe extern fn $new_name(query_len: usize,653 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`654...655355 | / gen_functions!(656356 | | block_new_aa_trace,657357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",658358 | | block_align_aa_trace,659... |660372 | | AAMatrix, AAProfile, true, false661373 | | );662 | |_- in this macro invocation663 |664 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)665666warning: `extern` declarations without an explicit ABI are deprecated667 --> ../src/ffi.rs:246:20668 |669246 | pub unsafe extern fn $align_name(b: BlockHandle,670 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`671...672355 | / gen_functions!(673356 | | block_new_aa_trace,674357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",675358 | | block_align_aa_trace,676... |677372 | | AAMatrix, AAProfile, true, false678373 | | );679 | |_- in this macro invocation680 |681 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)682683warning: `extern` declarations without an explicit ABI are deprecated684 --> ../src/ffi.rs:259:20685 |686259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,687 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`688...689355 | / gen_functions!(690356 | | block_new_aa_trace,691357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",692358 | | block_align_aa_trace,693... |694372 | | AAMatrix, AAProfile, true, false695373 | | );696 | |_- in this macro invocation697 |698 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)699700warning: `extern` declarations without an explicit ABI are deprecated701 --> ../src/ffi.rs:270:20702 |703270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,704 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`705...706355 | / gen_functions!(707356 | | block_new_aa_trace,708357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",709358 | | block_align_aa_trace,710... |711372 | | AAMatrix, AAProfile, true, false712373 | | );713 | |_- in this macro invocation714 |715 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)716717warning: `extern` declarations without an explicit ABI are deprecated718 --> ../src/ffi.rs:288:20719 |720288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {721 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`722...723355 | / gen_functions!(724356 | | block_new_aa_trace,725357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",726358 | | block_align_aa_trace,727... |728372 | | AAMatrix, AAProfile, true, false729373 | | );730 | |_- in this macro invocation731 |732 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)733734warning: `extern` declarations without an explicit ABI are deprecated735 --> ../src/ffi.rs:295:20736 |737295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {738 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`739...740355 | / gen_functions!(741356 | | block_new_aa_trace,742357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",743358 | | block_align_aa_trace,744... |745372 | | AAMatrix, AAProfile, true, false746373 | | );747 | |_- in this macro invocation748 |749 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)750751warning: `extern` declarations without an explicit ABI are deprecated752 --> ../src/ffi.rs:302:20753 |754302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...755 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`756...757355 | / gen_functions!(758356 | | block_new_aa_trace,759357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",760358 | | block_align_aa_trace,761... |762372 | | AAMatrix, AAProfile, true, false763373 | | );764 | |_- in this macro invocation765 |766 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)767768warning: `extern` declarations without an explicit ABI are deprecated769 --> ../src/ffi.rs:309:20770 |771309 | pub unsafe extern fn $free_name(b: BlockHandle) {772 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`773...774355 | / gen_functions!(775356 | | block_new_aa_trace,776357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",777358 | | block_align_aa_trace,778... |779372 | | AAMatrix, AAProfile, true, false780373 | | );781 | |_- in this macro invocation782 |783 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)784785warning: `extern` declarations without an explicit ABI are deprecated786 --> ../src/ffi.rs:237:20787 |788237 | pub unsafe extern fn $new_name(query_len: usize,789 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`790...791375 | / gen_functions!(792376 | | block_new_aa_trace_xdrop,793377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",794378 | | block_align_aa_trace_xdrop,795... |796392 | | AAMatrix, AAProfile, true, true797393 | | );798 | |_- in this macro invocation799 |800 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)801802warning: `extern` declarations without an explicit ABI are deprecated803 --> ../src/ffi.rs:246:20804 |805246 | pub unsafe extern fn $align_name(b: BlockHandle,806 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`807...808375 | / gen_functions!(809376 | | block_new_aa_trace_xdrop,810377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",811378 | | block_align_aa_trace_xdrop,812... |813392 | | AAMatrix, AAProfile, true, true814393 | | );815 | |_- in this macro invocation816 |817 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)818819warning: `extern` declarations without an explicit ABI are deprecated820 --> ../src/ffi.rs:259:20821 |822259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,823 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`824...825375 | / gen_functions!(826376 | | block_new_aa_trace_xdrop,827377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",828378 | | block_align_aa_trace_xdrop,829... |830392 | | AAMatrix, AAProfile, true, true831393 | | );832 | |_- in this macro invocation833 |834 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)835836warning: `extern` declarations without an explicit ABI are deprecated837 --> ../src/ffi.rs:270:20838 |839270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,840 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`841...842375 | / gen_functions!(843376 | | block_new_aa_trace_xdrop,844377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",845378 | | block_align_aa_trace_xdrop,846... |847392 | | AAMatrix, AAProfile, true, true848393 | | );849 | |_- in this macro invocation850 |851 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)852853warning: `extern` declarations without an explicit ABI are deprecated854 --> ../src/ffi.rs:288:20855 |856288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {857 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`858...859375 | / gen_functions!(860376 | | block_new_aa_trace_xdrop,861377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",862378 | | block_align_aa_trace_xdrop,863... |864392 | | AAMatrix, AAProfile, true, true865393 | | );866 | |_- in this macro invocation867 |868 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)869870warning: `extern` declarations without an explicit ABI are deprecated871 --> ../src/ffi.rs:295:20872 |873295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {874 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`875...876375 | / gen_functions!(877376 | | block_new_aa_trace_xdrop,878377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",879378 | | block_align_aa_trace_xdrop,880... |881392 | | AAMatrix, AAProfile, true, true882393 | | );883 | |_- in this macro invocation884 |885 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)886887warning: `extern` declarations without an explicit ABI are deprecated888 --> ../src/ffi.rs:302:20889 |890302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...891 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`892...893375 | / gen_functions!(894376 | | block_new_aa_trace_xdrop,895377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",896378 | | block_align_aa_trace_xdrop,897... |898392 | | AAMatrix, AAProfile, true, true899393 | | );900 | |_- in this macro invocation901 |902 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)903904warning: `extern` declarations without an explicit ABI are deprecated905 --> ../src/ffi.rs:309:20906 |907309 | pub unsafe extern fn $free_name(b: BlockHandle) {908 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`909...910375 | / gen_functions!(911376 | | block_new_aa_trace_xdrop,912377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",913378 | | block_align_aa_trace_xdrop,914... |915392 | | AAMatrix, AAProfile, true, true916393 | | );917 | |_- in this macro invocation918 |919 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)920921[ 31%] Generating ../generated/taxonomy.sh.h922[ 31%] Generating ../generated/enrich.sh.h923[ 31%] Generating ../generated/searchslicedtargetprofile.sh.h924[ 32%] Generating ../generated/databases.sh.h925[ 32%] Generating ../generated/linsearch.sh.h926[ 32%] Generating ../generated/blastn.sh.h927[ 32%] Generating ../generated/pickconsensusrep.sh.h928[ 33%] Generating ../generated/nucleotide_clustering.sh.h929[ 33%] Generating ../generated/iterativepp.sh.h930[ 33%] Generating ../generated/tsv2exprofiledb.sh.h931[ 33%] Built target foldmason-generated932[ 33%] Built target local-generated933[ 33%] Built target ksw2934[ 34%] Linking CXX static library libtantan.a935[ 34%] Built target tantan936[ 34%] Built target alp937warning: `block_aligner_c` (lib) generated 55 warnings (run `cargo fix --lib -p block_aligner_c` to apply 55 suggestions)938 Finished `release` profile [optimized] target(s) in 3.94s939Copying byproducts `libblock_aligner_c.a` to /build/source/build/lib/foldseek940[ 34%] Built target _cargo-build_block_aligner_c941[ 34%] Built target cargo-build_block_aligner_c942[ 34%] Built target generated943[ 34%] Linking CXX static library libfoldcomp.a944[ 34%] Built target foldcomp945[ 35%] Building CXX object lib/foldseek/src/strucclustutils/CMakeFiles/gemmiwrapper.dir/GemmiWrapper.cpp.o946[ 35%] Linking C static library libzstd.a947[ 35%] Built target libzstd_static948[ 36%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o949[ 36%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o950[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o951[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o952[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o953[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o954[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o955[ 37%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/BandedNucleotideAligner.cpp.o956[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/StripedSmithWaterman.cpp.o957[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/rescorediagonal.cpp.o958[ 38%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/AlignmentSymmetry.cpp.o959[ 39%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Main.cpp.o960[ 39%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Fwbw.cpp.o961[ 39%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Clustering.cpp.o962[ 39%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/ClusteringAlgorithms.cpp.o963[ 40%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/BaseMatrix.cpp.o964[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CSProfile.cpp.o965[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/A3MReader.cpp.o966[ 41%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Application.cpp.o967[ 42%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CommandCaller.cpp.o968[ 42%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Command.cpp.o969[ 42%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBConcat.cpp.o970[ 42%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBWriter.cpp.o971[ 42%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBReader.cpp.o972[ 43%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/FileUtil.cpp.o973[ 43%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Debug.cpp.o974[ 43%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/HeaderSummarizer.cpp.o975[ 43%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ExpressionParser.cpp.o976[ 43%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/GpuUtil.cpp.o977[ 43%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MultiParam.cpp.o978[ 44%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/KSeqWrapper.cpp.o979[ 44%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MemoryMapped.cpp.o980[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MMseqsMPI.cpp.o981[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Masker.cpp.o982[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MemoryTracker.cpp.o983[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/LibraryReader.cpp.o984[ 45%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Orf.cpp.o985[ 46%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Parameters.cpp.o986[ 46%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ProfileStates.cpp.o987[ 46%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/NucleotideMatrix.cpp.o988[ 47%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Sequence.cpp.o989[ 47%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/SubstitutionMatrix.cpp.o990[ 47%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/SequenceWeights.cpp.o991[ 47%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/UniprotKB.cpp.o992[ 47%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ExtendedSubstitutionMatrix.cpp.o993[ 47%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/CacheFriendlyOperations.cpp.o994[ 48%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Util.cpp.o995[ 48%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Indexer.cpp.o996[ 49%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/IndexBuilder.cpp.o997[ 49%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/KmerGenerator.cpp.o998[ 49%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Main.cpp.o999[ 50%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Prefiltering.cpp.o1000[ 50%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/PrefilteringIndexReader.cpp.o1001[ 50%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/QueryMatcher.cpp.o1002[ 50%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ReducedMatrix.cpp.o1003[ 51%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/SequenceLookup.cpp.o1004[ 51%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/UngappedAlignment.cpp.o1005[ 51%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ungappedprefilter.cpp.o1006[ 51%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/besthitperset.cpp.o1007[ 52%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/combinepvalperset.cpp.o1008[ 52%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/Aggregation.cpp.o1009[ 52%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/MultiHitDb.cpp.o1010[ 53%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/MultiHitSearch.cpp.o1011[ 53%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/lca.cpp.o1012[ 53%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/addtaxonomy.cpp.o1013[ 53%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/NcbiTaxonomy.cpp.o1014[ 54%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/filtertaxdb.cpp.o1015[ 54%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/filtertaxseqdb.cpp.o1016[ 54%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/aggregatetax.cpp.o1017[ 54%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createtaxdb.cpp.o1018[ 55%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createbintaxonomy.cpp.o1019[ 55%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createbintaxmapping.cpp.o1020[ 55%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/taxonomyreport.cpp.o1021[ 56%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmermatcher.cpp.o1022[ 56%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmerindexdb.cpp.o1023[ 56%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmersearch.cpp.o1024[ 56%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/LinsearchIndexReader.cpp.o1025[ 57%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/alignall.cpp.o1026[ 57%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/alignbykmer.cpp.o1027[ 57%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/appenddbtoindex.cpp.o1028[ 57%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/apply.cpp.o1029[ 58%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/clusthash.cpp.o1030[ 58%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/compress.cpp.o1031[ 58%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convert2fasta.cpp.o1032[ 59%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertalignments.cpp.o1033[ 59%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertca3m.cpp.o1034In file included from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/algorithm:62,1035 from /build/source/lib/foldseek/lib/mmseqs/lib/simd/simd.h:9,1036 from /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.h:9,1037 from /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:5:1038In function 'void std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]',1039 inlined from 'void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = float*; _Tp = double]' at /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/stl_algobase.h:977:21,1040 inlined from 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]' at /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/stl_algobase.h:1008:20,1041 inlined from 'float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 2]' at /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:383:14,1042 inlined from 'float* CSProfile::computeProfileCs(int, float*, float*, float, float)' at /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:350:58:1043/nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/stl_algobase.h:923:18: warning: 'void* __builtin_memset(void*, int, long unsigned int)' specified size between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]1044 923 | *__first = __val;1045 | ~~~~~~~~~^~~~~~~1046In member function 'float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 2]',1047 inlined from 'float* CSProfile::computeProfileCs(int, float*, float*, float, float)' at /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:350:58:1048/build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:383:21: note: destination object allocated here1049 383 | std::fill(sums, sums + seqLen, 0.0);1050 | ^~~~1051[ 59%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertkb.cpp.o1052[ 59%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertmsa.cpp.o1053[ 60%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertprofiledb.cpp.o1054/build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp: In function 'void runFilterOnCpu(Parameters&, BaseMatrix*, int8_t*, DBReader<unsigned int>*, DBReader<unsigned int>*, SequenceLookup*, bool, DBWriter&, EvalueComputation*, QueryMatcherTaxonomyHook*, int)':1055/build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:460:19: warning: 'master' construct deprecated since OpenMP 5.1, use 'masked' [-Wdeprecated-openmp]1056 460 | #pragma omp master1057 | ^1058In function 'void std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]',1059 inlined from 'void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = float*; _Tp = double]' at /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/stl_algobase.h:977:21,1060 inlined from 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]' at /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/stl_algobase.h:1008:20,1061 inlined from 'float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 0]' at /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:383:14,1062 inlined from 'float* CSProfile::computeSequenceCs(unsigned char*, int, float)' at /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:354:58:1063/nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/stl_algobase.h:923:18: warning: 'void* __builtin_memset(void*, int, long unsigned int)' specified size between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]1064 923 | *__first = __val;1065 | ~~~~~~~~~^~~~~~~1066In member function 'float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 0]',1067 inlined from 'float* CSProfile::computeSequenceCs(unsigned char*, int, float)' at /build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:354:58:1068/build/source/lib/foldseek/lib/mmseqs/src/commons/CSProfile.cpp:383:21: note: destination object allocated here1069 383 | std::fill(sums, sums + seqLen, 0.0);1070 | ^~~~1071[ 60%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createdb.cpp.o1072[ 60%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/dbtype.cpp.o1073[ 60%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/db2tar.cpp.o1074[ 61%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/indexdb.cpp.o1075[ 61%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/offsetalignment.cpp.o1076[ 61%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createseqfiledb.cpp.o1077[ 62%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createsubdb.cpp.o1078[ 62%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/view.cpp.o1079[ 62%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createtsv.cpp.o1080[ 62%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/diffseqdbs.cpp.o1081[ 63%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/expandaln.cpp.o1082[ 63%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractalignedregion.cpp.o1083[ 63%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractdomains.cpp.o1084[ 63%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractorfs.cpp.o1085[ 64%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/orftocontig.cpp.o1086[ 64%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/touchdb.cpp.o1087[ 64%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/filtera3m.cpp.o1088[ 64%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/filterdb.cpp.o1089[ 65%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/gff2db.cpp.o1090[ 65%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/gpuserver.cpp.o1091[ 65%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/renamedbkeys.cpp.o1092[ 66%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/makepaddedseqdb.cpp.o1093[ 66%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/masksequence.cpp.o1094[ 66%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/maskbygff.cpp.o1095[ 66%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/mergeclusters.cpp.o1096[ 67%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/mergeresultsbyset.cpp.o1097[ 67%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/mergedbs.cpp.o1098[ 67%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createclusterdb.cpp.o1099[ 67%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/msa2profile.cpp.o1100[ 68%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/msa2result.cpp.o1101[ 68%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/nrtotaxmapping.cpp.o1102[ 68%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/countkmer.cpp.o1103[ 69%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/pairaln.cpp.o1104[ 69%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/prefixid.cpp.o1105[ 69%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/profile2pssm.cpp.o1106[ 69%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/profile2neff.cpp.o1107[ 70%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/profile2seq.cpp.o1108[ 70%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/recoverlongestorf.cpp.o1109In file included from /build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:15:1110In destructor 'virtual SubstitutionMatrixProfileStates::~SubstitutionMatrixProfileStates()',1111 inlined from 'virtual SubstitutionMatrixProfileStates::~SubstitutionMatrixProfileStates()' at /build/source/lib/foldseek/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:90:5,1112 inlined from 'int prefilterInternal(int, const char**, const Command&, int)' at /build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:579:12:1113/build/source/lib/foldseek/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:90:5: warning: array subscript 'SubstitutionMatrixProfileStates[0]' is partly outside array bounds of 'BaseMatrix [1]' [-Warray-bounds=]1114 90 | };1115 | ^1116/build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp: In function 'int prefilterInternal(int, const char**, const Command&, int)':1117/build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:526:98: note: object of size 160 allocated by 'operator new'1118 526 | subMat = new NucleotideMatrix(par.scoringMatrixFile.values.nucleotide().c_str(), 1.0, 0.0);1119 | ^1120/build/source/lib/foldseek/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:536:99: note: object of size 152 allocated by 'operator new'1121 536 | subMat = new SubstitutionMatrix(par.scoringMatrixFile.values.aminoacid().c_str(), 2.0, 0.0);1122 | ^1123[ 70%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2dnamsa.cpp.o1124[ 70%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2flat.cpp.o1125[ 71%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2msa.cpp.o1126[ 71%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2rbh.cpp.o1127[ 71%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2profile.cpp.o1128[ 72%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2repseq.cpp.o1129[ 72%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/result2stats.cpp.o1130[ 72%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/reverseseq.cpp.o1131[ 72%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/cpmvrmlndb.cpp.o1132[ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/extractframes.cpp.o1133[ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sequence2profile.cpp.o1134[ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/setextendeddbtype.cpp.o1135[ 73%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/sortresult.cpp.o1136[ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitdb.cpp.o1137[ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/splitsequence.cpp.o1138[ 74%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/subtractdbs.cpp.o1139[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizealis.cpp.o1140/build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp: In function 'int result2flat(int, const char**, const Command&)':1141/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]1142 65 | dbKeyBuffer.size();1143 | ~~~~~~~~~~~~~~~~^~1144In file included from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/string:58,1145 from /build/source/lib/foldseek/lib/mmseqs/src/commons/Parameters.h:7,1146 from /build/source/lib/foldseek/lib/mmseqs/src/util/result2flat.cpp:2:1147/nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/basic_string.h:1187:7: note: declared here1148 1187 | size() const _GLIBCXX_NOEXCEPT1149 | ^~~~1150[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeheaders.cpp.o1151[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizeresult.cpp.o1152[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/summarizetabs.cpp.o1153[ 75%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/transitivealign.cpp.o1154[ 76%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/swapresults.cpp.o1155[ 76%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/translatenucs.cpp.o1156[ 76%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/translateaa.cpp.o1157[ 77%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/tsv2db.cpp.o1158[ 77%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/tsv2exprofiledb.cpp.o1159[ 77%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/tar2db.cpp.o1160[ 78%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/unpackdb.cpp.o1161[ 78%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/proteinaln2nucl.cpp.o1162[ 78%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/versionstring.cpp.o1163[ 78%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/diskspaceavail.cpp.o1164[ 79%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Cluster.cpp.o1165[ 79%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/ClusterUpdate.cpp.o1166[ 79%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Databases.cpp.o1167[ 79%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Linclust.cpp.o1168[ 80%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasySearch.cpp.o1169[ 80%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyRbh.cpp.o1170[ 80%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyCluster.cpp.o1171[ 81%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyLinclust.cpp.o1172[ 81%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Enrich.cpp.o1173[ 81%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Linsearch.cpp.o1174[ 81%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Map.cpp.o1175[ 82%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Rbh.cpp.o1176[ 82%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Search.cpp.o1177[ 82%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/Taxonomy.cpp.o1178[ 83%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/EasyTaxonomy.cpp.o1179[ 83%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/PickConsensusRep.cpp.o1180[ 83%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/workflow/CreateIndex.cpp.o1181[ 83%] Building CXX object lib/foldseek/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/MMseqsBase.cpp.o1182[ 83%] Linking CXX static library libgemmiwrapper.a1183[ 83%] Built target gemmiwrapper1184[ 84%] Linking CXX static library libmmseqs-framework.a1185[ 84%] Built target mmseqs-framework1186[ 84%] Building CXX object lib/foldseek/lib/pulchra/CMakeFiles/pulchra.dir/pulchra.cpp.o1187[ 84%] Building CXX object lib/foldseek/lib/3di/CMakeFiles/3di.dir/structureto3diseqdist.cpp.o1188[ 84%] Building CXX object lib/foldseek/lib/3di/CMakeFiles/3di.dir/structureto3di.cpp.o1189[ 84%] Building CXX object lib/foldseek/lib/tmalign/CMakeFiles/tmalign.dir/affineneedlemanwunsch.cpp.o1190[ 85%] Building CXX object lib/foldseek/lib/kerasify/CMakeFiles/kerasify.dir/keras_model.cpp.o1191[ 86%] Building CXX object lib/foldseek/lib/tmalign/CMakeFiles/tmalign.dir/TMalign.cpp.o1192[ 86%] Linking CXX static library libpulchra.a1193[ 86%] Built target pulchra1194[ 86%] Linking CXX static library lib3di.a1195[ 86%] Built target 3di1196[ 86%] Linking CXX static library libkerasify.a1197[ 86%] Built target kerasify1198[ 86%] Linking CXX static library libtmalign.a1199[ 86%] Built target tmalign1200[ 86%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/commons/StructureSmithWaterman.cpp.o1201[ 86%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/commons/LDDT.cpp.o1202[ 87%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/commons/LocalParameters.cpp.o1203[ 87%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/structurealign.cpp.o1204[ 87%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/EvalueNeuralNet.cpp.o1205[ 87%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/commons/TMaligner.cpp.o1206[ 89%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/aln2tmscore.cpp.o1207[ 89%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/tmalign.cpp.o1208[ 89%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/samplemulambda.cpp.o1209[ 89%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/convert2pdb.cpp.o1210[ 90%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/compressca.cpp.o1211[ 91%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/PulchraWrapper.cpp.o1212[ 91%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/structureto3didescriptor.cpp.o1213[ 91%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/scoremultimer.cpp.o1214[ 91%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/structureconvertalis.cpp.o1215[ 91%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/structcreatedb.cpp.o1216[ 91%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/filtermultimer.cpp.o1217[ 92%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/expandmultimer.cpp.o1218[ 92%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/createmultimerreport.cpp.o1219[ 92%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/structurerescorediagonal.cpp.o1220[ 92%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/makepaddeddb.cpp.o1221[ 92%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/createstructsubdb.cpp.o1222[ 92%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/result2structprofile.cpp.o1223[ 93%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/strucclustutils/LoLAlign.cpp.o1224[ 93%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/StructureCluster.cpp.o1225[ 93%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/StructureRbh.cpp.o1226[ 94%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/StructureIndex.cpp.o1227[ 94%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/StructureSearch.cpp.o1228[ 94%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/EasyStructureRbh.cpp.o1229[ 94%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/EasyStructureSearch.cpp.o1230[ 95%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/EasyStructureCluster.cpp.o1231[ 95%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/EasyMultimerSearch.cpp.o1232[ 95%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/MultimerSearch.cpp.o1233[ 95%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/MultimerCluster.cpp.o1234[ 95%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/FoldseekBase.cpp.o1235[ 96%] Building CXX object lib/foldseek/src/CMakeFiles/foldseek-framework.dir/workflow/EasyMultimerCluster.cpp.o1236/build/source/lib/foldseek/src/strucclustutils/structureto3didescriptor.cpp: In function 'int structureto3didescriptor(int, const char**, const Command&)':1237/build/source/lib/foldseek/src/strucclustutils/structureto3didescriptor.cpp:62:12: warning: variable 'incorrectFiles' set but not used [-Wunused-but-set-variable=]1238 62 | size_t incorrectFiles = 0;1239 | ^~~~~~~~~~~~~~1240/build/source/lib/foldseek/src/strucclustutils/structureto3didescriptor.cpp:63:12: warning: variable 'toShort' set but not used [-Wunused-but-set-variable=]1241 63 | size_t toShort = 0;1242 | ^~~~~~~1243[ 96%] Linking CXX static library libfoldseek-framework.a1244[ 96%] Built target foldseek-framework1245[ 96%] Building CXX object src/CMakeFiles/foldmason.dir/commons/FMStructureSmithWaterman.cpp.o1246[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/SimpleGotoh.cpp.o1247[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/refinemsa.cpp.o1248[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/FoldmasonParameters.cpp.o1249[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/workflow/EasyMSA.cpp.o1250[ 97%] Building CXX object src/CMakeFiles/foldmason.dir/commons/newick.cpp.o1251[ 98%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/structuremsa.cpp.o1252[ 98%] Building CXX object src/CMakeFiles/foldmason.dir/commons/MSA.cpp.o1253[100%] Building CXX object src/CMakeFiles/foldmason.dir/strucclustutils/msa2lddt.cpp.o1254[100%] Building CXX object src/CMakeFiles/foldmason.dir/foldmason.cpp.o1255/build/source/src/strucclustutils/structuremsa.cpp: In function 'int structuremsa(int, const char**, const Command&, bool)':1256/build/source/src/strucclustutils/structuremsa.cpp:2096:19: warning: 'master' construct deprecated since OpenMP 5.1, use 'masked' [-Wdeprecated-openmp]1257 2096 | #pragma omp master1258 | ^1259/build/source/src/strucclustutils/structuremsa.cpp:2106:19: warning: 'master' construct deprecated since OpenMP 5.1, use 'masked' [-Wdeprecated-openmp]1260 2106 | #pragma omp master1261 | ^1262/build/source/src/strucclustutils/structuremsa.cpp: In function 'Matcher::result_t pairwiseAlignment(unsigned int, Sequence*, Sequence*, Sequence*, Sequence*, int, int, SubstitutionMatrix*, SubstitutionMatrix*, int, float**)':1263/build/source/src/strucclustutils/structuremsa.cpp:177:65: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]1264 177 | short **target_profile_scores_aa = new short * [alphabetSize];1265 | ^1266In file included from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/new_allocator.h:34,1267 from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/x86_64-unknown-linux-gnu/bits/c++allocator.h:33,1268 from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/bits/allocator.h:46,1269 from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/vector:65,1270 from /build/source/lib/foldseek/lib/mmseqs/src/commons/DBReader.h:11,1271 from /build/source/lib/foldseek/lib/mmseqs/src/commons/IndexReader.h:4,1272 from /build/source/lib/foldseek/lib/mmseqs/src/alignment/Alignment.h:4,1273 from /build/source/src/strucclustutils/structuremsa.cpp:1:1274/nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/new:102:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here1275 102 | _GLIBCXX_NODISCARD void* operator new[](std::size_t)1276 | ^~~~~~~~1277/build/source/src/strucclustutils/structuremsa.cpp:178:66: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]1278 178 | short **target_profile_scores_3di = new short * [alphabetSize];1279 | ^1280/nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/new:102:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here1281 102 | _GLIBCXX_NODISCARD void* operator new[](std::size_t)1282 | ^~~~~~~~1283In file included from /nix/store/m38wglsqnh1mrmj2cmqa3pjb6w4yjxdi-glibc-2.44-25-dev/include/string.h:580,1284 from /nix/store/5q6bdxkp7lc70gn9mnf4yiybrx8ry5xq-gcc-16.2.0/include/c++/16.2.0/cstring:48,1285 from /build/source/lib/foldseek/lib/mmseqs/src/commons/MultiParam.h:10,1286 from /build/source/lib/foldseek/lib/mmseqs/src/commons/Parameters.h:16,1287 from /build/source/lib/foldseek/lib/mmseqs/src/commons/Sequence.h:10,1288 from /build/source/lib/foldseek/lib/mmseqs/src/commons/DBReader.h:13:1289In function 'void* memset(void*, int, size_t)',1290 inlined from '_Z12structuremsaiPPKcRK7Commandb._omp_fn.0' at /build/source/src/strucclustutils/structuremsa.cpp:1952:27:1291/nix/store/m38wglsqnh1mrmj2cmqa3pjb6w4yjxdi-glibc-2.44-25-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=]1292 59 | return __builtin___memset_chk (__dest, __ch, __len,1293 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~1294 60 | __glibc_objsize0 (__dest));1295 | ~~~~~~~~~~~~~~~~~~~~~~~~~~1296In function 'void* memset(void*, int, size_t)',1297 inlined from '_Z12structuremsaiPPKcRK7Commandb._omp_fn.0' at /build/source/src/strucclustutils/structuremsa.cpp:1953:27:1298/nix/store/m38wglsqnh1mrmj2cmqa3pjb6w4yjxdi-glibc-2.44-25-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=]1299 59 | return __builtin___memset_chk (__dest, __ch, __len,1300 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~1301 60 | __glibc_objsize0 (__dest));1302 | ~~~~~~~~~~~~~~~~~~~~~~~~~~1303[100%] Linking CXX executable foldmason1304[100%] Built target foldmason1305buildPhase completed in 1 minutes 41 secondsinstallPhase
1306install flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/bash install1307[ 2%] Built target foldmason-generated1308[ 7%] Built target local-generated1309[ 7%] Built target cargo-prebuild_block_aligner_c1310[ 8%] Built target version1311[ 8%] Built target tinyexpr1312[ 8%] Built target microtar1313[ 19%] Built target generated1314[ 19%] Built target ksw21315[ 20%] Built target tantan1316[ 27%] Built target libzstd_static1317[ 30%] Built target foldcomp1318[ 34%] Built target alp1319warning: `extern` declarations without an explicit ABI are deprecated1320 --> ../src/ffi.rs:32:121321 |132232 | pub unsafe extern fn block_new_simple_aamatrix(match_score: i8, mismatch_score: i8) -> *mut AAMatrix {1323 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1324 |1325 = note: `#[warn(missing_abi)]` on by default13261327warning: `extern` declarations without an explicit ABI are deprecated1328 --> ../src/ffi.rs:39:121329 |133039 | pub unsafe extern fn block_set_aamatrix(matrix: *mut AAMatrix, a: u8, b: u8, score: i8) {1331 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13321333warning: `extern` declarations without an explicit ABI are deprecated1334 --> ../src/ffi.rs:46:121335 |133646 | pub unsafe extern fn block_free_aamatrix(matrix: *mut AAMatrix) {1337 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13381339warning: `extern` declarations without an explicit ABI are deprecated1340 --> ../src/ffi.rs:61:121341 |134261 | pub unsafe extern fn block_new_aaprofile(str_len: usize, block_size: usize, gap_extend: i8) -> *mut AAProfile {1343 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13441345warning: `extern` declarations without an explicit ABI are deprecated1346 --> ../src/ffi.rs:68:121347 |134868 | pub unsafe extern fn block_len_aaprofile(profile: *const AAProfile) -> usize {1349 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13501351warning: `extern` declarations without an explicit ABI are deprecated1352 --> ../src/ffi.rs:76:121353 |135476 | pub unsafe extern fn block_clear_aaprofile(profile: *mut AAProfile, str_len: usize) {1355 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13561357warning: `extern` declarations without an explicit ABI are deprecated1358 --> ../src/ffi.rs:86:121359 |136086 | pub unsafe extern fn block_set_aaprofile(profile: *mut AAProfile, i: usize, b: u8, score: i8) {1361 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13621363warning: `extern` declarations without an explicit ABI are deprecated1364 --> ../src/ffi.rs:97:121365 |136697 | pub unsafe extern fn block_set_gap_open_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {1367 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13681369warning: `extern` declarations without an explicit ABI are deprecated1370 --> ../src/ffi.rs:108:121371 |1372108 | pub unsafe extern fn block_set_gap_close_C_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {1373 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13741375warning: `extern` declarations without an explicit ABI are deprecated1376 --> ../src/ffi.rs:119:121377 |1378119 | pub unsafe extern fn block_set_gap_open_R_aaprofile(profile: *mut AAProfile, i: usize, gap: i8) {1379 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13801381warning: `extern` declarations without an explicit ABI are deprecated1382 --> ../src/ffi.rs:126:121383 |1384126 | pub unsafe extern fn block_get_aaprofile(profile: *const AAProfile, i: usize, b: u8) -> i8 {1385 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13861387warning: `extern` declarations without an explicit ABI are deprecated1388 --> ../src/ffi.rs:133:121389 |1390133 | pub unsafe extern fn block_get_gap_extend_aaprofile(profile: *const AAProfile) -> i8 {1391 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13921393warning: `extern` declarations without an explicit ABI are deprecated1394 --> ../src/ffi.rs:140:121395 |1396140 | pub unsafe extern fn block_free_aaprofile(profile: *mut AAProfile) {1397 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`13981399warning: `extern` declarations without an explicit ABI are deprecated1400 --> ../src/ffi.rs:149:121401 |1402149 | pub unsafe extern fn block_new_cigar(query_len: usize, reference_len: usize) -> *mut Cigar {1403 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14041405warning: `extern` declarations without an explicit ABI are deprecated1406 --> ../src/ffi.rs:156:121407 |1408156 | pub unsafe extern fn block_get_cigar(cigar: *const Cigar, i: usize) -> OpLen {1409 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14101411warning: `extern` declarations without an explicit ABI are deprecated1412 --> ../src/ffi.rs:163:121413 |1414163 | pub unsafe extern fn block_len_cigar(cigar: *const Cigar) -> usize {1415 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14161417warning: `extern` declarations without an explicit ABI are deprecated1418 --> ../src/ffi.rs:170:121419 |1420170 | pub unsafe extern fn block_free_cigar(cigar: *mut Cigar) {1421 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14221423warning: `extern` declarations without an explicit ABI are deprecated1424 --> ../src/ffi.rs:179:121425 |1426179 | pub unsafe extern fn block_new_padded_aa(len: usize, max_size: usize) -> *mut PaddedBytes {1427 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14281429warning: `extern` declarations without an explicit ABI are deprecated1430 --> ../src/ffi.rs:186:121431 |1432186 | pub unsafe extern fn block_set_bytes_padded_aa(padded: *mut PaddedBytes, s: *const u8, len: usize, max_size: usize) {1433 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14341435warning: `extern` declarations without an explicit ABI are deprecated1436 --> ../src/ffi.rs:194:121437 |1438194 | pub unsafe extern fn block_free_padded_aa(padded: *mut PaddedBytes) {1439 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14401441warning: `extern` declarations without an explicit ABI are deprecated1442 --> ../src/ffi.rs:203:121443 |1444203 | pub unsafe extern fn block_new_pos_bias(len: usize, max_size: usize) -> *mut PosBias {1445 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14461447warning: `extern` declarations without an explicit ABI are deprecated1448 --> ../src/ffi.rs:210:121449 |1450210 | pub unsafe extern fn block_set_pos_bias(bias: *mut PosBias, b: *const i16, len: usize) {1451 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14521453warning: `extern` declarations without an explicit ABI are deprecated1454 --> ../src/ffi.rs:218:121455 |1456218 | pub unsafe extern fn block_free_pos_bias(bias: *mut PosBias) {1457 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`14581459warning: `extern` declarations without an explicit ABI are deprecated1460 --> ../src/ffi.rs:237:201461 |1462237 | pub unsafe extern fn $new_name(query_len: usize,1463 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1464...1465315 | / gen_functions!(1466316 | | block_new_aa,1467317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1468318 | | block_align_aa,1469... |1470332 | | AAMatrix, AAProfile, false, false1471333 | | );1472 | |_- in this macro invocation1473 |1474 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14751476warning: `extern` declarations without an explicit ABI are deprecated1477 --> ../src/ffi.rs:246:201478 |1479246 | pub unsafe extern fn $align_name(b: BlockHandle,1480 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1481...1482315 | / gen_functions!(1483316 | | block_new_aa,1484317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1485318 | | block_align_aa,1486... |1487332 | | AAMatrix, AAProfile, false, false1488333 | | );1489 | |_- in this macro invocation1490 |1491 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)14921493warning: `extern` declarations without an explicit ABI are deprecated1494 --> ../src/ffi.rs:259:201495 |1496259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1497 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1498...1499315 | / gen_functions!(1500316 | | block_new_aa,1501317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1502318 | | block_align_aa,1503... |1504332 | | AAMatrix, AAProfile, false, false1505333 | | );1506 | |_- in this macro invocation1507 |1508 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15091510warning: `extern` declarations without an explicit ABI are deprecated1511 --> ../src/ffi.rs:270:201512 |1513270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1514 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1515...1516315 | / gen_functions!(1517316 | | block_new_aa,1518317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1519318 | | block_align_aa,1520... |1521332 | | AAMatrix, AAProfile, false, false1522333 | | );1523 | |_- in this macro invocation1524 |1525 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15261527warning: `extern` declarations without an explicit ABI are deprecated1528 --> ../src/ffi.rs:288:201529 |1530288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1531 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1532...1533315 | / gen_functions!(1534316 | | block_new_aa,1535317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1536318 | | block_align_aa,1537... |1538332 | | AAMatrix, AAProfile, false, false1539333 | | );1540 | |_- in this macro invocation1541 |1542 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15431544warning: `extern` declarations without an explicit ABI are deprecated1545 --> ../src/ffi.rs:295:201546 |1547295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1548 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1549...1550315 | / gen_functions!(1551316 | | block_new_aa,1552317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1553318 | | block_align_aa,1554... |1555332 | | AAMatrix, AAProfile, false, false1556333 | | );1557 | |_- in this macro invocation1558 |1559 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15601561warning: `extern` declarations without an explicit ABI are deprecated1562 --> ../src/ffi.rs:302:201563 |1564302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1565 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1566...1567315 | / gen_functions!(1568316 | | block_new_aa,1569317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1570318 | | block_align_aa,1571... |1572332 | | AAMatrix, AAProfile, false, false1573333 | | );1574 | |_- in this macro invocation1575 |1576 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15771578warning: `extern` declarations without an explicit ABI are deprecated1579 --> ../src/ffi.rs:309:201580 |1581309 | pub unsafe extern fn $free_name(b: BlockHandle) {1582 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1583...1584315 | / gen_functions!(1585316 | | block_new_aa,1586317 | | "Create a new block aligner instance for global alignment of amino acid strings (no traceback).",1587318 | | block_align_aa,1588... |1589332 | | AAMatrix, AAProfile, false, false1590333 | | );1591 | |_- in this macro invocation1592 |1593 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)15941595warning: `extern` declarations without an explicit ABI are deprecated1596 --> ../src/ffi.rs:237:201597 |1598237 | pub unsafe extern fn $new_name(query_len: usize,1599 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1600...1601335 | / gen_functions!(1602336 | | block_new_aa_xdrop,1603337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1604338 | | block_align_aa_xdrop,1605... |1606352 | | AAMatrix, AAProfile, false, true1607353 | | );1608 | |_- in this macro invocation1609 |1610 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16111612warning: `extern` declarations without an explicit ABI are deprecated1613 --> ../src/ffi.rs:246:201614 |1615246 | pub unsafe extern fn $align_name(b: BlockHandle,1616 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1617...1618335 | / gen_functions!(1619336 | | block_new_aa_xdrop,1620337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1621338 | | block_align_aa_xdrop,1622... |1623352 | | AAMatrix, AAProfile, false, true1624353 | | );1625 | |_- in this macro invocation1626 |1627 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16281629warning: `extern` declarations without an explicit ABI are deprecated1630 --> ../src/ffi.rs:259:201631 |1632259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1633 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1634...1635335 | / gen_functions!(1636336 | | block_new_aa_xdrop,1637337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1638338 | | block_align_aa_xdrop,1639... |1640352 | | AAMatrix, AAProfile, false, true1641353 | | );1642 | |_- in this macro invocation1643 |1644 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16451646warning: `extern` declarations without an explicit ABI are deprecated1647 --> ../src/ffi.rs:270:201648 |1649270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1650 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1651...1652335 | / gen_functions!(1653336 | | block_new_aa_xdrop,1654337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1655338 | | block_align_aa_xdrop,1656... |1657352 | | AAMatrix, AAProfile, false, true1658353 | | );1659 | |_- in this macro invocation1660 |1661 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16621663warning: `extern` declarations without an explicit ABI are deprecated1664 --> ../src/ffi.rs:288:201665 |1666288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1667 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1668...1669335 | / gen_functions!(1670336 | | block_new_aa_xdrop,1671337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1672338 | | block_align_aa_xdrop,1673... |1674352 | | AAMatrix, AAProfile, false, true1675353 | | );1676 | |_- in this macro invocation1677 |1678 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16791680warning: `extern` declarations without an explicit ABI are deprecated1681 --> ../src/ffi.rs:295:201682 |1683295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1684 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1685...1686335 | / gen_functions!(1687336 | | block_new_aa_xdrop,1688337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1689338 | | block_align_aa_xdrop,1690... |1691352 | | AAMatrix, AAProfile, false, true1692353 | | );1693 | |_- in this macro invocation1694 |1695 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)16961697warning: `extern` declarations without an explicit ABI are deprecated1698 --> ../src/ffi.rs:302:201699 |1700302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1701 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1702...1703335 | / gen_functions!(1704336 | | block_new_aa_xdrop,1705337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1706338 | | block_align_aa_xdrop,1707... |1708352 | | AAMatrix, AAProfile, false, true1709353 | | );1710 | |_- in this macro invocation1711 |1712 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17131714warning: `extern` declarations without an explicit ABI are deprecated1715 --> ../src/ffi.rs:309:201716 |1717309 | pub unsafe extern fn $free_name(b: BlockHandle) {1718 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1719...1720335 | / gen_functions!(1721336 | | block_new_aa_xdrop,1722337 | | "Create a new block aligner instance for X-drop alignment of amino acid strings (no traceback).",1723338 | | block_align_aa_xdrop,1724... |1725352 | | AAMatrix, AAProfile, false, true1726353 | | );1727 | |_- in this macro invocation1728 |1729 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17301731warning: `extern` declarations without an explicit ABI are deprecated1732 --> ../src/ffi.rs:237:201733 |1734237 | pub unsafe extern fn $new_name(query_len: usize,1735 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1736...1737355 | / gen_functions!(1738356 | | block_new_aa_trace,1739357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1740358 | | block_align_aa_trace,1741... |1742372 | | AAMatrix, AAProfile, true, false1743373 | | );1744 | |_- in this macro invocation1745 |1746 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17471748warning: `extern` declarations without an explicit ABI are deprecated1749 --> ../src/ffi.rs:246:201750 |1751246 | pub unsafe extern fn $align_name(b: BlockHandle,1752 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1753...1754355 | / gen_functions!(1755356 | | block_new_aa_trace,1756357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1757358 | | block_align_aa_trace,1758... |1759372 | | AAMatrix, AAProfile, true, false1760373 | | );1761 | |_- in this macro invocation1762 |1763 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17641765warning: `extern` declarations without an explicit ABI are deprecated1766 --> ../src/ffi.rs:259:201767 |1768259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1769 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1770...1771355 | / gen_functions!(1772356 | | block_new_aa_trace,1773357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1774358 | | block_align_aa_trace,1775... |1776372 | | AAMatrix, AAProfile, true, false1777373 | | );1778 | |_- in this macro invocation1779 |1780 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17811782warning: `extern` declarations without an explicit ABI are deprecated1783 --> ../src/ffi.rs:270:201784 |1785270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1786 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1787...1788355 | / gen_functions!(1789356 | | block_new_aa_trace,1790357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1791358 | | block_align_aa_trace,1792... |1793372 | | AAMatrix, AAProfile, true, false1794373 | | );1795 | |_- in this macro invocation1796 |1797 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)17981799warning: `extern` declarations without an explicit ABI are deprecated1800 --> ../src/ffi.rs:288:201801 |1802288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1803 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1804...1805355 | / gen_functions!(1806356 | | block_new_aa_trace,1807357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1808358 | | block_align_aa_trace,1809... |1810372 | | AAMatrix, AAProfile, true, false1811373 | | );1812 | |_- in this macro invocation1813 |1814 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18151816warning: `extern` declarations without an explicit ABI are deprecated1817 --> ../src/ffi.rs:295:201818 |1819295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1820 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1821...1822355 | / gen_functions!(1823356 | | block_new_aa_trace,1824357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1825358 | | block_align_aa_trace,1826... |1827372 | | AAMatrix, AAProfile, true, false1828373 | | );1829 | |_- in this macro invocation1830 |1831 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18321833warning: `extern` declarations without an explicit ABI are deprecated1834 --> ../src/ffi.rs:302:201835 |1836302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1837 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1838...1839355 | / gen_functions!(1840356 | | block_new_aa_trace,1841357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1842358 | | block_align_aa_trace,1843... |1844372 | | AAMatrix, AAProfile, true, false1845373 | | );1846 | |_- in this macro invocation1847 |1848 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18491850warning: `extern` declarations without an explicit ABI are deprecated1851 --> ../src/ffi.rs:309:201852 |1853309 | pub unsafe extern fn $free_name(b: BlockHandle) {1854 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1855...1856355 | / gen_functions!(1857356 | | block_new_aa_trace,1858357 | | "Create a new block aligner instance for global alignment of amino acid strings, with traceback.",1859358 | | block_align_aa_trace,1860... |1861372 | | AAMatrix, AAProfile, true, false1862373 | | );1863 | |_- in this macro invocation1864 |1865 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18661867warning: `extern` declarations without an explicit ABI are deprecated1868 --> ../src/ffi.rs:237:201869 |1870237 | pub unsafe extern fn $new_name(query_len: usize,1871 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1872...1873375 | / gen_functions!(1874376 | | block_new_aa_trace_xdrop,1875377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1876378 | | block_align_aa_trace_xdrop,1877... |1878392 | | AAMatrix, AAProfile, true, true1879393 | | );1880 | |_- in this macro invocation1881 |1882 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)18831884warning: `extern` declarations without an explicit ABI are deprecated1885 --> ../src/ffi.rs:246:201886 |1887246 | pub unsafe extern fn $align_name(b: BlockHandle,1888 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1889...1890375 | / gen_functions!(1891376 | | block_new_aa_trace_xdrop,1892377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1893378 | | block_align_aa_trace_xdrop,1894... |1895392 | | AAMatrix, AAProfile, true, true1896393 | | );1897 | |_- in this macro invocation1898 |1899 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19001901warning: `extern` declarations without an explicit ABI are deprecated1902 --> ../src/ffi.rs:259:201903 |1904259 | pub unsafe extern fn $align_profile_name(b: BlockHandle,1905 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1906...1907375 | / gen_functions!(1908376 | | block_new_aa_trace_xdrop,1909377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1910378 | | block_align_aa_trace_xdrop,1911... |1912392 | | AAMatrix, AAProfile, true, true1913393 | | );1914 | |_- in this macro invocation1915 |1916 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19171918warning: `extern` declarations without an explicit ABI are deprecated1919 --> ../src/ffi.rs:270:201920 |1921270 | pub unsafe extern fn $align_3di_name(b: BlockHandle,1922 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1923...1924375 | / gen_functions!(1925376 | | block_new_aa_trace_xdrop,1926377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1927378 | | block_align_aa_trace_xdrop,1928... |1929392 | | AAMatrix, AAProfile, true, true1930393 | | );1931 | |_- in this macro invocation1932 |1933 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19341935warning: `extern` declarations without an explicit ABI are deprecated1936 --> ../src/ffi.rs:288:201937 |1938288 | pub unsafe extern fn $res_name(b: BlockHandle) -> AlignResult {1939 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1940...1941375 | / gen_functions!(1942376 | | block_new_aa_trace_xdrop,1943377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1944378 | | block_align_aa_trace_xdrop,1945... |1946392 | | AAMatrix, AAProfile, true, true1947393 | | );1948 | |_- in this macro invocation1949 |1950 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19511952warning: `extern` declarations without an explicit ABI are deprecated1953 --> ../src/ffi.rs:295:201954 |1955295 | pub unsafe extern fn $trace_name(b: BlockHandle, query_idx: usize, reference_idx: usize, cigar: *mut Cigar) {1956 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1957...1958375 | / gen_functions!(1959376 | | block_new_aa_trace_xdrop,1960377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1961378 | | block_align_aa_trace_xdrop,1962... |1963392 | | AAMatrix, AAProfile, true, true1964393 | | );1965 | |_- in this macro invocation1966 |1967 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19681969warning: `extern` declarations without an explicit ABI are deprecated1970 --> ../src/ffi.rs:302:201971 |1972302 | pub unsafe extern fn $trace_eq_name(b: BlockHandle, q: *const PaddedBytes, r: *const PaddedBytes, query_idx: usize, refer...1973 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1974...1975375 | / gen_functions!(1976376 | | block_new_aa_trace_xdrop,1977377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1978378 | | block_align_aa_trace_xdrop,1979... |1980392 | | AAMatrix, AAProfile, true, true1981393 | | );1982 | |_- in this macro invocation1983 |1984 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)19851986warning: `extern` declarations without an explicit ABI are deprecated1987 --> ../src/ffi.rs:309:201988 |1989309 | pub unsafe extern fn $free_name(b: BlockHandle) {1990 | ^^^^^^ help: explicitly specify the "C" ABI: `extern "C"`1991...1992375 | / gen_functions!(1993376 | | block_new_aa_trace_xdrop,1994377 | | "Create a new block aligner instance for X-drop alignment of amino acid strings, with traceback.",1995378 | | block_align_aa_trace_xdrop,1996... |1997392 | | AAMatrix, AAProfile, true, true1998393 | | );1999 | |_- in this macro invocation2000 |2001 = note: this warning originates in the macro `gen_functions` (in Nightly builds, run with -Z macro-backtrace for more info)20022003warning: `block_aligner_c` (lib) generated 55 warnings (run `cargo fix --lib -p block_aligner_c` to apply 55 suggestions)2004 Finished `release` profile [optimized] target(s) in 0.00s2005[ 35%] Built target gemmiwrapper2006Copying byproducts `libblock_aligner_c.a` to /build/source/build/lib/foldseek2007[ 35%] Built target _cargo-build_block_aligner_c2008[ 35%] Built target cargo-build_block_aligner_c2009[ 84%] Built target mmseqs-framework2010[ 84%] Built target 3di2011[ 84%] Built target pulchra2012[ 85%] Built target kerasify2013[ 86%] Built target tmalign2014[ 96%] Built target foldseek-framework2015[100%] Built target foldmason2016Install the project...2017-- Install configuration: "Release"2018-- Installing: /nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/bin/foldmasonfixupPhase
2019shrinking RPATHs of ELF executables and libraries in /nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c2352020shrinking /nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/bin/foldmason2021checking for references to /build/ in /nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235...2022patching script interpreter paths in /nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c2352023stripping (with command strip and flags -S -p) in /nix/store/rjdimajz8fi4vyf832p3njyf7wnglj4b-foldmason-4-dd3c235/bin