[INFO] fetching crate hmmer-rs 0.2.0... [INFO] checking hmmer-rs-0.2.0 against master#350d0ef0ec0493e6d21cfb265cb8211a0e74d766 for pr-145342-1 [INFO] extracting crate hmmer-rs 0.2.0 into /workspace/builds/worker-3-tc1/source [INFO] started tweaking crates.io crate hmmer-rs 0.2.0 [INFO] finished tweaking crates.io crate hmmer-rs 0.2.0 [INFO] tweaked toml for crates.io crate hmmer-rs 0.2.0 written to /workspace/builds/worker-3-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate hmmer-rs 0.2.0 on toolchain 350d0ef0ec0493e6d21cfb265cb8211a0e74d766 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 72 packages to latest compatible versions [INFO] [stderr] Adding libhmmer-sys v0.3.0 (available: v0.4.0) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded libhmmer-sys v0.3.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] ba56bcf7dd38aed632cd0a2f95501493e32a5b4e6c360317c6e35e17644235ae [INFO] running `Command { std: "docker" "start" "-a" "ba56bcf7dd38aed632cd0a2f95501493e32a5b4e6c360317c6e35e17644235ae", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "ba56bcf7dd38aed632cd0a2f95501493e32a5b4e6c360317c6e35e17644235ae", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ba56bcf7dd38aed632cd0a2f95501493e32a5b4e6c360317c6e35e17644235ae", kill_on_drop: false }` [INFO] [stdout] ba56bcf7dd38aed632cd0a2f95501493e32a5b4e6c360317c6e35e17644235ae [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8c81c54a99527e07f795372ea483babee4ef275e10541d5d4bdb11869a3478eb [INFO] running `Command { std: "docker" "start" "-a" "8c81c54a99527e07f795372ea483babee4ef275e10541d5d4bdb11869a3478eb", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.175 [INFO] [stderr] Compiling memchr v2.7.5 [INFO] [stderr] Compiling glob v0.3.3 [INFO] [stderr] Compiling regex-syntax v0.8.6 [INFO] [stderr] Compiling proc-macro2 v1.0.101 [INFO] [stderr] Compiling rustix v0.38.44 [INFO] [stderr] Compiling unicode-width v0.1.14 [INFO] [stderr] Compiling linux-raw-sys v0.4.15 [INFO] [stderr] Compiling bitflags v2.9.3 [INFO] [stderr] Compiling unicode-ident v1.0.18 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling cfg-if v1.0.3 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Compiling termcolor v1.4.1 [INFO] [stderr] Compiling humantime v2.2.0 [INFO] [stderr] Compiling log v0.4.27 [INFO] [stderr] Compiling libloading v0.8.8 [INFO] [stderr] Compiling home v0.5.11 [INFO] [stderr] Compiling bindgen v0.59.2 [INFO] [stderr] Compiling ansi_term v0.12.1 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling either v1.15.0 [INFO] [stderr] Compiling shlex v1.3.0 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling fs_extra v1.3.0 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling quote v1.0.40 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling num_cpus v1.17.0 [INFO] [stderr] Compiling clap v2.34.0 [INFO] [stderr] Compiling regex-automata v0.4.10 [INFO] [stderr] Compiling which v4.4.2 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling regex v1.11.2 [INFO] [stderr] Compiling env_logger v0.9.3 [INFO] [stderr] Compiling libhmmer-sys v0.3.0 [INFO] [stderr] error: failed to run custom build command for `libhmmer-sys v0.3.0` [INFO] [stderr] note: To improve backtraces for build dependencies, set the CARGO_PROFILE_DEV_BUILD_OVERRIDE_DEBUG=true environment variable to enable debug information generation. [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/build/libhmmer-sys-092af47d343aa2bf/build-script-build` (exit status: 101) [INFO] [stderr] --- stdout [INFO] [stderr] configure: Configuring HMMER3 for your system. [INFO] [stderr] checking build system type... x86_64-pc-linux-gnu [INFO] [stderr] checking host system type... x86_64-pc-linux-gnu [INFO] [stderr] checking whether to compile using MPI... no [INFO] [stderr] checking for gcc... gcc [INFO] [stderr] checking whether the C compiler works... yes [INFO] [stderr] checking for C compiler default output file name... a.out [INFO] [stderr] checking for suffix of executables... [INFO] [stderr] checking whether we are cross compiling... no [INFO] [stderr] checking for suffix of object files... o [INFO] [stderr] checking whether the compiler supports GNU C... yes [INFO] [stderr] checking whether gcc accepts -g... yes [INFO] [stderr] checking for gcc option to enable C11 features... none needed [INFO] [stderr] checking how to run the C preprocessor... gcc -E [INFO] [stderr] checking for a BSD-compatible install... /usr/bin/install -c [INFO] [stderr] checking for strip... strip [INFO] [stderr] checking for ranlib... ranlib [INFO] [stderr] checking for ar... /usr/bin/ar [INFO] [stderr] checking whether ln -s works... yes [INFO] [stderr] checking for a sed that does not truncate output... /usr/bin/sed [INFO] [stderr] checking for grep that handles long lines and -e... /usr/bin/grep [INFO] [stderr] checking for egrep... /usr/bin/grep -E [INFO] [stderr] checking whether gcc is Clang... no [INFO] [stderr] checking whether pthreads work with -pthread... yes [INFO] [stderr] checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE [INFO] [stderr] checking whether more special flags are required for pthreads... no [INFO] [stderr] checking for PTHREAD_PRIO_INHERIT... yes [INFO] [stderr] checking whether gcc can compile our Altivec/VMX code... no [INFO] [stderr] checking whether gcc can compile our SSE code... yes [INFO] [stderr] configure: Activating Intel/AMD SSE vector DP implementation [INFO] [stderr] checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes [INFO] [stderr] checking compiler support --start-group... yes [INFO] [stderr] checking for gzip... /usr/bin/gzip [INFO] [stderr] checking for python3... yes [INFO] [stderr] checking for library containing clock_gettime... none required [INFO] [stderr] checking for stdio.h... yes [INFO] [stderr] checking for stdlib.h... yes [INFO] [stderr] checking for string.h... yes [INFO] [stderr] checking for inttypes.h... yes [INFO] [stderr] checking for stdint.h... yes [INFO] [stderr] checking for strings.h... yes [INFO] [stderr] checking for sys/stat.h... yes [INFO] [stderr] checking for sys/types.h... yes [INFO] [stderr] checking for unistd.h... yes [INFO] [stderr] checking for endian.h... yes [INFO] [stderr] checking for inttypes.h... (cached) yes [INFO] [stderr] checking for stdint.h... (cached) yes [INFO] [stderr] checking for unistd.h... (cached) yes [INFO] [stderr] checking for sys/types.h... (cached) yes [INFO] [stderr] checking for netinet/in.h... yes [INFO] [stderr] checking for sys/param.h... yes [INFO] [stderr] checking for sys/sysctl.h... no [INFO] [stderr] checking for uint8_t... yes [INFO] [stderr] checking for uint16_t... yes [INFO] [stderr] checking for uint32_t... yes [INFO] [stderr] checking for uint64_t... yes [INFO] [stderr] checking for off_t... yes [INFO] [stderr] checking whether byte ordering is bigendian... no [INFO] [stderr] checking for __attribute__((noreturn))... yes [INFO] [stderr] checking for __attribute__((format))... yes [INFO] [stderr] checking for mkstemp... yes [INFO] [stderr] checking for popen... yes [INFO] [stderr] checking for putenv... yes [INFO] [stderr] checking for strcasecmp... yes [INFO] [stderr] checking for strsep... yes [INFO] [stderr] checking for times... yes [INFO] [stderr] checking for getpid... yes [INFO] [stderr] checking for sysctl... no [INFO] [stderr] checking for sysconf... yes [INFO] [stderr] checking for getcwd... yes [INFO] [stderr] checking for chmod... yes [INFO] [stderr] checking for stat... yes [INFO] [stderr] checking for fstat... yes [INFO] [stderr] checking for erfc... no [INFO] [stderr] checking for library containing ntohs... none required [INFO] [stderr] checking for library containing ntohl... none required [INFO] [stderr] checking for library containing htons... none required [INFO] [stderr] checking for library containing htonl... none required [INFO] [stderr] checking for library containing socket... none required [INFO] [stderr] checking for library containing inet_pton... none required [INFO] [stderr] checking for _LARGEFILE_SOURCE value needed for large files... no [INFO] [stderr] checking for special C compiler options needed for large files... no [INFO] [stderr] checking for _FILE_OFFSET_BITS value needed for large files... no [INFO] [stderr] configure: creating ./config.status [INFO] [stderr] config.status: creating Makefile [INFO] [stderr] config.status: creating src/Makefile [INFO] [stderr] config.status: creating testsuite/Makefile [INFO] [stderr] config.status: creating profmark/Makefile [INFO] [stderr] config.status: creating src/impl_sse/Makefile [INFO] [stderr] config.status: creating documentation/Makefile [INFO] [stderr] config.status: creating documentation/man/Makefile [INFO] [stderr] config.status: creating documentation/userguide/Makefile [INFO] [stderr] config.status: creating documentation/userguide/inclusions/Makefile [INFO] [stderr] config.status: creating libdivsufsort/Makefile [INFO] [stderr] config.status: creating easel/Makefile [INFO] [stderr] config.status: creating easel/miniapps/Makefile [INFO] [stderr] config.status: creating easel/testsuite/Makefile [INFO] [stderr] config.status: creating easel/documentation/Makefile [INFO] [stderr] config.status: creating documentation/userguide/titlepage.tex [INFO] [stderr] config.status: creating documentation/userguide/titlepage_daemon.tex [INFO] [stderr] config.status: creating documentation/userguide/copyright.tex [INFO] [stderr] config.status: creating documentation/man/alimask.man [INFO] [stderr] config.status: creating documentation/man/hmmalign.man [INFO] [stderr] config.status: creating documentation/man/hmmbuild.man [INFO] [stderr] config.status: creating documentation/man/hmmc2.man [INFO] [stderr] config.status: creating documentation/man/hmmconvert.man [INFO] [stderr] config.status: creating documentation/man/hmmemit.man [INFO] [stderr] config.status: creating documentation/man/hmmer.man [INFO] [stderr] config.status: creating documentation/man/hmmfetch.man [INFO] [stderr] config.status: creating documentation/man/hmmlogo.man [INFO] [stderr] config.status: creating documentation/man/hmmpgmd.man [INFO] [stderr] config.status: creating documentation/man/hmmpgmd_shard.man [INFO] [stderr] config.status: creating documentation/man/hmmpress.man [INFO] [stderr] config.status: creating documentation/man/hmmscan.man [INFO] [stderr] config.status: creating documentation/man/hmmsearch.man [INFO] [stderr] config.status: creating documentation/man/hmmsim.man [INFO] [stderr] config.status: creating documentation/man/hmmstat.man [INFO] [stderr] config.status: creating documentation/man/jackhmmer.man [INFO] [stderr] config.status: creating documentation/man/makehmmerdb.man [INFO] [stderr] config.status: creating documentation/man/nhmmer.man [INFO] [stderr] config.status: creating documentation/man/nhmmscan.man [INFO] [stderr] config.status: creating documentation/man/phmmer.man [INFO] [stderr] config.status: creating easel/miniapps/esl-afetch.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alimanip.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alimap.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alimask.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alimerge.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alipid.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alirev.man [INFO] [stderr] config.status: creating easel/miniapps/esl-alistat.man [INFO] [stderr] config.status: creating easel/miniapps/esl-compalign.man [INFO] [stderr] config.status: creating easel/miniapps/esl-compstruct.man [INFO] [stderr] config.status: creating easel/miniapps/esl-construct.man [INFO] [stderr] config.status: creating easel/miniapps/esl-histplot.man [INFO] [stderr] config.status: creating easel/miniapps/esl-mask.man [INFO] [stderr] config.status: creating easel/miniapps/esl-mixdchlet.man [INFO] [stderr] config.status: creating easel/miniapps/esl-reformat.man [INFO] [stderr] config.status: creating easel/miniapps/esl-selectn.man [INFO] [stderr] config.status: creating easel/miniapps/esl-seqrange.man [INFO] [stderr] config.status: creating easel/miniapps/esl-seqstat.man [INFO] [stderr] config.status: creating easel/miniapps/esl-sfetch.man [INFO] [stderr] config.status: creating easel/miniapps/esl-shuffle.man [INFO] [stderr] config.status: creating easel/miniapps/esl-ssdraw.man [INFO] [stderr] config.status: creating easel/miniapps/esl-translate.man [INFO] [stderr] config.status: creating easel/miniapps/esl-weight.man [INFO] [stderr] config.status: creating easel/decoy_config.h [INFO] [stderr] config.status: creating src/p7_config.h [INFO] [stderr] config.status: creating easel/esl_config.h [INFO] [stderr] config.status: creating libdivsufsort/divsufsort.h [INFO] [stderr] config.status: linking src/impl_sse to src/impl [INFO] [stderr] [INFO] [stderr] [INFO] [stderr] HMMER configuration: [INFO] [stderr] compiler: gcc -O3 -pthread [INFO] [stderr] host: x86_64-pc-linux-gnu [INFO] [stderr] linker: [INFO] [stderr] libraries: [INFO] [stderr] DP implementation: sse [INFO] [stderr] [INFO] [stderr] Now do 'make' to build HMMER, and optionally: [INFO] [stderr] 'make check' to run self tests, [INFO] [stderr] 'make install' to install programs and man pages, [INFO] [stderr] '(cd easel; make install)' to install Easel tools. [INFO] [stderr] [INFO] [stderr] CC build.o [INFO] [stderr] CC cachedb.o [INFO] [stderr] CC cachedb_shard.o [INFO] [stderr] CC emit.o [INFO] [stderr] CC evalues.o [INFO] [stderr] CC errors.o [INFO] [stderr] CC eweight.o [INFO] [stderr] CC generic_decoding.o [INFO] [stderr] CC generic_fwdback.o [INFO] [stderr] CC generic_fwdback_chk.o [INFO] [stderr] CC generic_fwdback_banded.o [INFO] [stderr] CC generic_null2.o [INFO] [stderr] CC generic_msv.o [INFO] [stderr] CC generic_optacc.o [INFO] [stderr] CC generic_viterbi.o [INFO] [stderr] CC generic_stotrace.o [INFO] [stderr] CC h2_io.o [INFO] [stderr] CC generic_vtrace.o [INFO] [stderr] CC heatmap.o [INFO] [stderr] CC hmmdmstr.o [INFO] [stderr] CC hmmd_search_status.o [INFO] [stderr] CC hmmdmstr_shard.o [INFO] [stderr] CC hmmdwrkr.o [INFO] [stderr] CC hmmdwrkr_shard.o [INFO] [stderr] CC hmmdutils.o [INFO] [stderr] CC hmmer.o [INFO] [stderr] CC modelconfig.o [INFO] [stderr] CC logsum.o [INFO] [stderr] CC modelstats.o [INFO] [stderr] CC mpisupport.o [INFO] [stderr] CC seqmodel.o [INFO] [stderr] CC tracealign.o [INFO] [stderr] CC p7_alidisplay.o [INFO] [stderr] CC p7_bg.o [INFO] [stderr] CC p7_builder.o [INFO] [stderr] CC p7_domain.o [INFO] [stderr] CC p7_domaindef.o [INFO] [stderr] CC p7_gbands.o [INFO] [stderr] CC p7_gmx.o [INFO] [stderr] CC p7_gmxb.o [INFO] [stderr] CC p7_gmxchk.o [INFO] [stderr] CC p7_hit.o [INFO] [stderr] CC p7_hmm.o [INFO] [stderr] CC p7_hmmcache.o [INFO] [stderr] CC p7_hmmd_search_stats.o [INFO] [stderr] CC p7_hmmfile.o [INFO] [stderr] CC p7_hmmwindow.o [INFO] [stderr] CC p7_pipeline.o [INFO] [stderr] CC p7_prior.o [INFO] [stderr] CC p7_profile.o [INFO] [stderr] CC p7_spensemble.o [INFO] [stderr] CC p7_tophits.o [INFO] [stderr] CC p7_trace.o [INFO] [stderr] CC p7_scoredata.o [INFO] [stderr] CC hmmpgmd2msa.o [INFO] [stderr] CC fm_alphabet.o [INFO] [stderr] CC fm_general.o [INFO] [stderr] CC fm_sse.o [INFO] [stderr] CC fm_ssv.o [INFO] [stderr] AR libhmmer-src.stamp [INFO] [stderr] SUBDIR impl_sse [INFO] [stderr] CC decoding.o [INFO] [stderr] CC io.o [INFO] [stderr] CC ssvfilter.o [INFO] [stderr] CC msvfilter.o [INFO] [stderr] CC null2.o [INFO] [stderr] CC optacc.o [INFO] [stderr] CC stotrace.o [INFO] [stderr] CC vitfilter.o [INFO] [stderr] CC p7_omx.o [INFO] [stderr] CC fwdback.o [INFO] [stderr] CC mpi.o [INFO] [stderr] CC p7_oprofile.o [INFO] [stderr] AR libhmmer-impl.stamp [INFO] [stderr] CC easel.o [INFO] [stderr] CC esl_alloc.o [INFO] [stderr] CC esl_arr2.o [INFO] [stderr] CC esl_alphabet.o [INFO] [stderr] CC esl_arr3.o [INFO] [stderr] CC esl_bitfield.o [INFO] [stderr] CC esl_buffer.o [INFO] [stderr] CC esl_cluster.o [INFO] [stderr] CC esl_composition.o [INFO] [stderr] CC esl_cpu.o [INFO] [stderr] CC esl_dirichlet.o [INFO] [stderr] CC esl_distance.o [INFO] [stderr] CC esl_dmatrix.o [INFO] [stderr] CC esl_dsqdata.o [INFO] [stderr] CC esl_exponential.o [INFO] [stderr] CC esl_fileparser.o [INFO] [stderr] CC esl_gamma.o [INFO] [stderr] CC esl_gencode.o [INFO] [stderr] CC esl_getopts.o [INFO] [stderr] CC esl_gev.o [INFO] [stderr] CC esl_graph.o [INFO] [stderr] CC esl_gumbel.o [INFO] [stderr] CC esl_heap.o [INFO] [stderr] CC esl_histogram.o [INFO] [stderr] CC esl_hmm.o [INFO] [stderr] CC esl_huffman.o [INFO] [stderr] CC esl_hyperexp.o [INFO] [stderr] CC esl_json.o [INFO] [stderr] CC esl_keyhash.o [INFO] [stderr] CC esl_matrixops.o [INFO] [stderr] CC esl_mem.o [INFO] [stderr] CC esl_minimizer.o [INFO] [stderr] CC esl_mixdchlet.o [INFO] [stderr] CC esl_mixgev.o [INFO] [stderr] CC esl_mpi.o [INFO] [stderr] CC esl_msa.o [INFO] [stderr] CC esl_msacluster.o [INFO] [stderr] CC esl_msafile.o [INFO] [stderr] CC esl_msafile2.o [INFO] [stderr] CC esl_msafile_a2m.o [INFO] [stderr] CC esl_msafile_afa.o [INFO] [stderr] CC esl_msafile_clustal.o [INFO] [stderr] CC esl_msafile_phylip.o [INFO] [stderr] CC esl_msafile_psiblast.o [INFO] [stderr] CC esl_msafile_selex.o [INFO] [stderr] CC esl_msafile_stockholm.o [INFO] [stderr] CC esl_msashuffle.o [INFO] [stderr] CC esl_msaweight.o [INFO] [stderr] CC esl_normal.o [INFO] [stderr] CC esl_paml.o [INFO] [stderr] CC esl_quicksort.o [INFO] [stderr] CC esl_random.o [INFO] [stderr] CC esl_rand64.o [INFO] [stderr] CC esl_randomseq.o [INFO] [stderr] CC esl_ratematrix.o [INFO] [stderr] CC esl_recorder.o [INFO] [stderr] CC esl_red_black.o [INFO] [stderr] CC esl_regexp.o [INFO] [stderr] CC esl_rootfinder.o [INFO] [stderr] CC esl_scorematrix.o [INFO] [stderr] CC esl_sq.o [INFO] [stderr] CC esl_sqio.o [INFO] [stderr] CC esl_sqio_ascii.o [INFO] [stderr] CC esl_sqio_ncbi.o [INFO] [stderr] CC esl_ssi.o [INFO] [stderr] CC esl_stack.o [INFO] [stderr] CC esl_stats.o [INFO] [stderr] CC esl_stopwatch.o [INFO] [stderr] CC esl_stretchexp.o [INFO] [stderr] CC esl_subcmd.o [INFO] [stderr] CC esl_threads.o [INFO] [stderr] CC esl_tree.o [INFO] [stderr] CC esl_varint.o [INFO] [stderr] CC esl_vectorops.o [INFO] [stderr] CC esl_weibull.o [INFO] [stderr] CC esl_workqueue.o [INFO] [stderr] CC esl_wuss.o [INFO] [stderr] CC esl_sse.o [INFO] [stderr] CC esl_avx.o [INFO] [stderr] CC esl_avx512.o [INFO] [stderr] CC esl_neon.o [INFO] [stderr] CC esl_vmx.o [INFO] [stderr] AR libeasel.a [INFO] [stderr] [INFO] [stderr] --- stderr [INFO] [stderr] configure.ac:238: warning: The macro `AC_PROG_CC_STDC' is obsolete. [INFO] [stderr] configure.ac:238: You should run autoupdate. [INFO] [stderr] ./lib/autoconf/c.m4:1666: AC_PROG_CC_STDC is expanded from... [INFO] [stderr] configure.ac:238: the top level [INFO] [stderr] configure.ac:278: warning: $as_echo is obsolete; use AS_ECHO(["message"]) instead [INFO] [stderr] lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... [INFO] [stderr] lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... [INFO] [stderr] ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... [INFO] [stderr] ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... [INFO] [stderr] easel/m4/ax_pthread.m4:88: AX_PTHREAD is expanded from... [INFO] [stderr] configure.ac:278: the top level [INFO] [stderr] In file included from /usr/include/string.h:548, [INFO] [stderr] from hmmdmstr.c:10: [INFO] [stderr] In function 'memset', [INFO] [stderr] inlined from 'destroy_worker' at hmmdmstr.c:948:5, [INFO] [stderr] inlined from 'update_workers' at hmmdmstr.c:285:7, [INFO] [stderr] inlined from 'update_workers' at hmmdmstr.c:240:1: [INFO] [stderr] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull] [INFO] [stderr] 59 | return __builtin___memset_chk (__dest, __ch, __len, [INFO] [stderr] | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] 60 | __glibc_objsize0 (__dest)); [INFO] [stderr] | ~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: note: in a call to built-in function '__builtin_memset' [INFO] [stderr] In file included from /usr/include/string.h:548, [INFO] [stderr] from hmmdmstr_shard.c:10: [INFO] [stderr] In function 'memset', [INFO] [stderr] inlined from 'destroy_worker' at hmmdmstr_shard.c:987:5, [INFO] [stderr] inlined from 'update_workers' at hmmdmstr_shard.c:306:7, [INFO] [stderr] inlined from 'update_workers' at hmmdmstr_shard.c:260:1: [INFO] [stderr] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull] [INFO] [stderr] 59 | return __builtin___memset_chk (__dest, __ch, __len, [INFO] [stderr] | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] 60 | __glibc_objsize0 (__dest)); [INFO] [stderr] | ~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: note: in a call to built-in function '__builtin_memset' [INFO] [stderr] [INFO] [stderr] thread 'main' (711) panicked at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/bindgen-0.59.2/src/ir/ty.rs:1135:22: [INFO] [stderr] Not able to resolve vector element?: Continue [INFO] [stderr] stack backtrace: [INFO] [stderr] 0: 0x635c71c923f2 - std::backtrace_rs::backtrace::libunwind::trace::h0fb8082ca5562a61 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stderr] 1: 0x635c71c923f2 - std::backtrace_rs::backtrace::trace_unsynchronized::hfaa258994374a3cd [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stderr] 2: 0x635c71c923f2 - std::sys::backtrace::_print_fmt::h11496fe34963a885 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/sys/backtrace.rs:66:9 [INFO] [stderr] 3: 0x635c71c923f2 - ::fmt::hff1a9408d012ee89 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/sys/backtrace.rs:39:26 [INFO] [stderr] 4: 0x635c71cb51df - core::fmt::rt::Argument::fmt::hf11195b61445f5d1 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/core/src/fmt/rt.rs:173:76 [INFO] [stderr] 5: 0x635c71cb51df - core::fmt::write::h2f1fc679f228cc52 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/core/src/fmt/mod.rs:1468:25 [INFO] [stderr] 6: 0x635c71c827c3 - std::io::default_write_fmt::hdd5e6d67566e664d [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/io/mod.rs:639:11 [INFO] [stderr] 7: 0x635c71c827c3 - std::io::Write::write_fmt::haa2231cbd9aebf95 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/io/mod.rs:1954:13 [INFO] [stderr] 8: 0x635c71c92242 - std::sys::backtrace::BacktraceLock::print::h28bfdbcac6d3828b [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/sys/backtrace.rs:42:9 [INFO] [stderr] 9: 0x635c71c7f36c - std::panicking::default_hook::{{closure}}::h1f968e3a24b0e3b4 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:301:27 [INFO] [stderr] 10: 0x635c71c7f1b3 - std::panicking::default_hook::h43da101644971931 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:328:9 [INFO] [stderr] 11: 0x635c71c7f8aa - std::panicking::panic_with_hook::hb4e916c3e65eccec [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:834:13 [INFO] [stderr] 12: 0x635c71c91dca - std::panicking::panic_handler::{{closure}}::hbff715d0475cf1bd [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:707:13 [INFO] [stderr] 13: 0x635c71c91d29 - std::sys::backtrace::__rust_end_short_backtrace::hd6f43484e45a4955 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/sys/backtrace.rs:174:18 [INFO] [stderr] 14: 0x635c71c7fd9d - __rustc[b29d3319de9a3146]::rust_begin_unwind [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:698:5 [INFO] [stderr] 15: 0x635c71cbd790 - core::panicking::panic_fmt::h5f8d281875be5ff1 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/core/src/panicking.rs:75:14 [INFO] [stderr] 16: 0x635c71cbed26 - core::result::unwrap_failed::hbb243a6a8b53218d [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/core/src/result.rs:1852:5 [INFO] [stderr] 17: 0x635c718e65e5 - core::result::Result::expect::ha33344b8c6240a34 [INFO] [stderr] 18: 0x635c718b0db6 - bindgen::ir::ty::Type::from_clang_ty::hba5e37ca1e7fd33d [INFO] [stderr] 19: 0x635c717e5a03 - ::from_ty_with_id::h0c2c7d47e29a2a9b [INFO] [stderr] 20: 0x635c717df938 - ::from_ty::hc20c4fdf6fb48261 [INFO] [stderr] 21: 0x635c7182b8df - bindgen::ir::context::BindgenContext::resolve_typerefs::hb2a59d929ccb2855 [INFO] [stderr] 22: 0x635c7182c05a - bindgen::ir::context::BindgenContext::gen::h0e38a3906ba6a609 [INFO] [stderr] 23: 0x635c717c8e2d - bindgen::codegen::codegen::h90ec8255d628bd6f [INFO] [stderr] 24: 0x635c718f105f - bindgen::Bindings::generate::h2cf76c67740bcd7e [INFO] [stderr] 25: 0x635c718edd7b - bindgen::Builder::generate::hef87a89dc324a6db [INFO] [stderr] 26: 0x635c717a25e3 - build_script_build::main::h70b2db9caac7a674 [INFO] [stderr] 27: 0x635c717a13e3 - core::ops::function::FnOnce::call_once::h1a5f9f9d97600513 [INFO] [stderr] 28: 0x635c717a4556 - std::sys::backtrace::__rust_begin_short_backtrace::h372d699a01665970 [INFO] [stderr] 29: 0x635c717a38f9 - std::rt::lang_start::{{closure}}::h6e2e969fe81ab0c4 [INFO] [stderr] 30: 0x635c71c92a00 - core::ops::function::impls:: for &F>::call_once::h32dc2b2f49a48277 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/core/src/ops/function.rs:290:21 [INFO] [stderr] 31: 0x635c71c92a00 - std::panicking::catch_unwind::do_call::h3353546a38525559 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:590:40 [INFO] [stderr] 32: 0x635c71c92a00 - std::panicking::catch_unwind::h57fb70202d1ae368 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:553:19 [INFO] [stderr] 33: 0x635c71c92a00 - std::panic::catch_unwind::h4b724a52bb5803b4 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panic.rs:359:14 [INFO] [stderr] 34: 0x635c71c92a00 - std::rt::lang_start_internal::{{closure}}::h3724b3072c80532a [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/rt.rs:175:24 [INFO] [stderr] 35: 0x635c71c92a00 - std::panicking::catch_unwind::do_call::h4f6e90f858bd1c3f [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:590:40 [INFO] [stderr] 36: 0x635c71c92a00 - std::panicking::catch_unwind::h81c085c0d350991c [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panicking.rs:553:19 [INFO] [stderr] 37: 0x635c71c92a00 - std::panic::catch_unwind::h289049af1176d82a [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/panic.rs:359:14 [INFO] [stderr] 38: 0x635c71c92a00 - std::rt::lang_start_internal::h3c37ebeb799b11e1 [INFO] [stderr] at /rustc/350d0ef0ec0493e6d21cfb265cb8211a0e74d766/library/std/src/rt.rs:171:5 [INFO] [stderr] 39: 0x635c717a38e1 - std::rt::lang_start::ha7bd087002f5b6c2 [INFO] [stderr] 40: 0x635c717aa595 - main [INFO] [stderr] 41: 0x700cad3a51ca - [INFO] [stderr] 42: 0x700cad3a528b - __libc_start_main [INFO] [stderr] 43: 0x635c7179fd75 - _start [INFO] [stderr] 44: 0x0 - [INFO] running `Command { std: "docker" "inspect" "8c81c54a99527e07f795372ea483babee4ef275e10541d5d4bdb11869a3478eb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8c81c54a99527e07f795372ea483babee4ef275e10541d5d4bdb11869a3478eb", kill_on_drop: false }` [INFO] [stdout] 8c81c54a99527e07f795372ea483babee4ef275e10541d5d4bdb11869a3478eb