Tests fail with @@ substitution error

[nemequ]

I'm trying to track down an issue with HMMER and SIMDe, but on my (Fedora 33, x86_64) a bunch of tests just fail with "FAILED [@@ substitution]" when I try to run the test suite.

This is with a fresh, unmodified checkout (no SIMDe usage yet) of 3.3.2 (03bf3c7767233e45cb969bfeda910545b80f2da8), with Easel 0.48 (281c81377595ef781dff962d9572240406a5e364).

Here is the log, starting right after cloning Easel:

nemequ@peltast:~/local/src/hmmer$ git:(master) autoconf
nemequ@peltast:~/local/src/hmmer$ git:(master) 1A ./configure
configure: Configuring HMMER3 for your system.
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking whether to compile using MPI... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking for a BSD-compatible install... /usr/bin/install -c
checking for strip... strip
checking for ranlib... ranlib
checking for ar... /usr/bin/ar
checking whether ln -s works... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking whether gcc can compile our Altivec/VMX code... no
checking whether gcc can compile our SSE code... yes
configure: Activating Intel/AMD SSE vector DP implementation
checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes
checking compiler support --start-group... yes
checking for gzip... /usr/bin/gzip
checking for python3... yes
checking for library containing clock_gettime... none required
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... no
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for off_t... yes
checking whether byte ordering is bigendian... no
checking for __attribute__((noreturn))... yes
checking for __attribute__((format))... yes
checking for mkstemp... yes
checking for popen... yes
checking for putenv... yes
checking for strcasecmp... yes
checking for strsep... yes
checking for times... yes
checking for getpid... yes
checking for sysctl... no
checking for sysconf... yes
checking for getcwd... yes
checking for chmod... yes
checking for stat... yes
checking for fstat... yes
checking for erfc... no
checking for library containing ntohs... none required
checking for library containing ntohl... none required
checking for library containing htons... none required
checking for library containing htonl... none required
checking for library containing socket... none required
checking for library containing inet_pton... none required
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating profmark/Makefile
config.status: creating src/impl_sse/Makefile
config.status: creating documentation/Makefile
config.status: creating documentation/man/Makefile
config.status: creating documentation/userguide/Makefile
config.status: creating documentation/userguide/inclusions/Makefile
config.status: creating libdivsufsort/Makefile
config.status: creating easel/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/documentation/Makefile
config.status: creating documentation/userguide/titlepage.tex
config.status: creating documentation/userguide/titlepage_daemon.tex
config.status: creating documentation/userguide/copyright.tex
config.status: creating documentation/man/alimask.man
config.status: creating documentation/man/hmmalign.man
config.status: creating documentation/man/hmmbuild.man
config.status: creating documentation/man/hmmc2.man
config.status: creating documentation/man/hmmconvert.man
config.status: creating documentation/man/hmmemit.man
config.status: creating documentation/man/hmmer.man
config.status: creating documentation/man/hmmfetch.man
config.status: creating documentation/man/hmmlogo.man
config.status: creating documentation/man/hmmpgmd.man
config.status: creating documentation/man/hmmpgmd_shard.man
config.status: creating documentation/man/hmmpress.man
config.status: creating documentation/man/hmmscan.man
config.status: creating documentation/man/hmmsearch.man
config.status: creating documentation/man/hmmsim.man
config.status: creating documentation/man/hmmstat.man
config.status: creating documentation/man/jackhmmer.man
config.status: creating documentation/man/makehmmerdb.man
config.status: creating documentation/man/nhmmer.man
config.status: creating documentation/man/nhmmscan.man
config.status: creating documentation/man/phmmer.man
config.status: creating easel/miniapps/esl-afetch.man
config.status: creating easel/miniapps/esl-alimanip.man
config.status: creating easel/miniapps/esl-alimap.man
config.status: creating easel/miniapps/esl-alimask.man
config.status: creating easel/miniapps/esl-alimerge.man
config.status: creating easel/miniapps/esl-alipid.man
config.status: creating easel/miniapps/esl-alirev.man
config.status: creating easel/miniapps/esl-alistat.man
config.status: creating easel/miniapps/esl-compalign.man
config.status: creating easel/miniapps/esl-compstruct.man
config.status: creating easel/miniapps/esl-construct.man
config.status: creating easel/miniapps/esl-histplot.man
config.status: creating easel/miniapps/esl-mask.man
config.status: creating easel/miniapps/esl-mixdchlet.man
config.status: creating easel/miniapps/esl-reformat.man
config.status: creating easel/miniapps/esl-selectn.man
config.status: creating easel/miniapps/esl-seqrange.man
config.status: creating easel/miniapps/esl-seqstat.man
config.status: creating easel/miniapps/esl-sfetch.man
config.status: creating easel/miniapps/esl-shuffle.man
config.status: creating easel/miniapps/esl-ssdraw.man
config.status: creating easel/miniapps/esl-translate.man
config.status: creating easel/miniapps/esl-weight.man
config.status: creating easel/decoy_config.h
config.status: creating src/p7_config.h
config.status: creating easel/esl_config.h
config.status: creating libdivsufsort/divsufsort.h
config.status: linking src/impl_sse to src/impl

HMMER configuration:
   compiler:             gcc -O3   -pthread 
   host:                 x86_64-pc-linux-gnu
   linker:               
   libraries:              
   DP implementation:    sse

Now do 'make'  to build HMMER, and optionally:
       'make check'  to run self tests,
       'make install'  to install programs and man pages,
       '(cd easel; make install)'  to install Easel tools.

nemequ@peltast:~/local/src/hmmer$ git:(master) 2A make -j
     SUBDIR easel
     CC easel.o
     CC esl_alloc.o
     CC esl_alphabet.o
     CC esl_arr2.o
     CC esl_bitfield.o
     CC esl_arr3.o
     CC esl_buffer.o
     CC esl_cluster.o
     CC esl_composition.o
     CC esl_cpu.o
     CC esl_dirichlet.o
     CC esl_distance.o
     CC esl_dmatrix.o
     CC esl_dsqdata.o
     CC esl_exponential.o
     CC esl_fileparser.o
     CC esl_gamma.o
     CC esl_gencode.o
     CC esl_getopts.o
     CC esl_gev.o
     CC esl_graph.o
     CC esl_gumbel.o
     CC esl_heap.o
     CC esl_histogram.o
     CC esl_hmm.o
     CC esl_huffman.o
     CC esl_hyperexp.o
     CC esl_json.o
     CC esl_keyhash.o
     CC esl_matrixops.o
     CC esl_mem.o
     CC esl_minimizer.o
     CC esl_mixdchlet.o
     CC esl_mixgev.o
     CC esl_mpi.o
     CC esl_msa.o
     CC esl_msacluster.o
     CC esl_msafile.o
     CC esl_msafile2.o
     CC esl_msafile_a2m.o
     CC esl_msafile_afa.o
     CC esl_msafile_clustal.o
     CC esl_msafile_phylip.o
     CC esl_msafile_psiblast.o
     CC esl_msafile_selex.o
     CC esl_msafile_stockholm.o
     CC esl_msashuffle.o
     CC esl_msaweight.o
     CC esl_normal.o
     CC esl_paml.o
     CC esl_quicksort.o
     CC esl_random.o
     CC esl_rand64.o
     CC esl_randomseq.o
     CC esl_ratematrix.o
     CC esl_recorder.o
     CC esl_red_black.o
     CC esl_regexp.o
     CC esl_rootfinder.o
     CC esl_scorematrix.o
     CC esl_sq.o
     CC esl_sqio.o
     CC esl_sqio_ascii.o
     CC esl_sqio_ncbi.o
     CC esl_stack.o
     CC esl_stats.o
     CC esl_ssi.o
     CC esl_stopwatch.o
     CC esl_stretchexp.o
     CC esl_subcmd.o
     CC esl_threads.o
     CC esl_tree.o
     CC esl_varint.o
     CC esl_vectorops.o
     CC esl_weibull.o
     CC esl_workqueue.o
     CC esl_wuss.o
     CC esl_sse.o
     CC esl_avx.o
     CC esl_avx512.o
     CC esl_neon.o
     CC esl_vmx.o
     AR libeasel.a
     SUBDIR miniapps
     GEN esl-afetch
     GEN esl-alimanip
     GEN esl-alimap
     GEN esl-alimask
     GEN esl-alipid
     GEN esl-alimerge
     GEN esl-alirev
     GEN esl-alistat
     GEN esl-compalign
     GEN esl-compstruct
     GEN esl-construct
     GEN esl-histplot
     GEN esl-mask
     GEN esl-mixdchlet
     GEN esl-reformat
     GEN esl-selectn
     GEN esl-seqrange
     GEN esl-seqstat
     GEN esl-sfetch
     GEN esl-shuffle
     GEN esl-ssdraw
     GEN esl-translate
     GEN esl-weight
     CC cmd_alistat.o
     CC cmd_downsample.o
     CC cmd_filter.o
     CC cmd_index.o
     GEN easel
     SUBDIR libdivsufsort
     CC divsufsort.o
     AR libdivsufsort.a
     SUBDIR src
     CC alimask.o
     CC build.o
     CC cachedb.o
     CC cachedb_shard.o
     CC emit.o
     CC errors.o
     CC evalues.o
     CC eweight.o
     CC generic_decoding.o
     CC generic_fwdback.o
     CC generic_fwdback_chk.o
     CC generic_fwdback_banded.o
     CC generic_null2.o
     CC generic_msv.o
     CC generic_optacc.o
     CC generic_stotrace.o
     CC generic_viterbi.o
     CC generic_vtrace.o
     CC h2_io.o
     CC heatmap.o
     CC hmmlogo.o
     CC hmmdmstr.o
     CC hmmdmstr_shard.o
     CC hmmd_search_status.o
     CC hmmdwrkr.o
     CC hmmdwrkr_shard.o
     CC hmmdutils.o
     CC hmmer.o
     CC logsum.o
     CC modelconfig.o
     CC modelstats.o
     CC mpisupport.o
     CC seqmodel.o
     CC tracealign.o
     CC p7_alidisplay.o
     CC p7_bg.o
     CC p7_builder.o
     CC p7_domain.o
     CC p7_domaindef.o
     CC p7_gbands.o
     CC p7_gmx.o
     CC p7_gmxb.o
     CC p7_gmxchk.o
     CC p7_hit.o
     CC p7_hmm.o
     CC p7_hmmcache.o
     CC p7_hmmd_search_stats.o
     CC p7_hmmfile.o
     CC p7_hmmwindow.o
     CC p7_pipeline.o
     CC p7_prior.o
     CC p7_profile.o
     CC p7_spensemble.o
     CC p7_tophits.o
     CC p7_trace.o
     CC p7_scoredata.o
     CC hmmpgmd2msa.o
     CC fm_alphabet.o
     CC fm_general.o
     CC fm_sse.o
     CC fm_ssv.o
     CC hmmalign.o
     CC hmmbuild.o
     CC hmmconvert.o
     CC hmmemit.o
     CC hmmfetch.o
     CC hmmpgmd.o
     CC hmmpgmd_shard.o
     CC hmmpress.o
     CC hmmscan.o
     CC hmmsearch.o
     CC hmmsim.o
     CC hmmstat.o
     CC jackhmmer.o
     CC phmmer.o
     CC nhmmer.o
     CC nhmmscan.o
     CC makehmmerdb.o
     CC hmmc2.o
     CC hmmerfm-exactmatch.o
     AR libhmmer-src.stamp
     SUBDIR impl_sse
     CC decoding.o
     CC fwdback.o
     CC io.o
     CC ssvfilter.o
     CC msvfilter.o
     CC null2.o
     CC optacc.o
     CC stotrace.o
     CC vitfilter.o
     CC p7_omx.o
     CC p7_oprofile.o
     CC mpi.o
     AR libhmmer-impl.stamp
     GEN alimask
     GEN hmmalign
     GEN hmmbuild
     GEN hmmconvert
     GEN hmmemit
     GEN hmmfetch
     GEN hmmlogo
     GEN hmmpgmd
     GEN hmmpgmd_shard
     GEN hmmpress
     GEN hmmscan
     GEN hmmsearch
     GEN hmmsim
     GEN hmmstat
     GEN jackhmmer
     GEN phmmer
     GEN nhmmer
     GEN nhmmscan
     GEN makehmmerdb
     GEN hmmc2
     GEN hmmerfm-exactmatch
     SUBDIR profmark
     CC create-profmark.o
     CC rocplot.o
     GEN rocplot
     GEN create-profmark
nemequ@peltast:~/local/src/hmmer$ git:(master) 2A cd testsuite/
nemequ@peltast:~/local/src/hmmer/testsuite$ git:(master) 2A make V=1

Running HMMER test suite...

    exercise    1 [                hmmer] ...     FAILED [@@ substitution]
    exercise    2 [                build] ...     FAILED [@@ substitution]
    exercise    3 [      generic_fwdback] ...     FAILED [@@ substitution]
    exercise    4 [          generic_msv] ...     FAILED [@@ substitution]
    exercise    5 [     generic_stotrace] ...     FAILED [@@ substitution]
    exercise    6 [      generic_viterbi] ...     FAILED [@@ substitution]
    exercise    7 [   hmmd_search_status] ...     FAILED [@@ substitution]
    exercise    8 [               logsum] ...     FAILED [@@ substitution]
    exercise    9 [          modelconfig] ...     FAILED [@@ substitution]
    exercise   10 [             seqmodel] ...     FAILED [@@ substitution]
    exercise   11 [        p7_alidisplay] ...     FAILED [@@ substitution]
    exercise   12 [                p7_bg] ...     FAILED [@@ substitution]
    exercise   13 [            p7_domain] ...     FAILED [@@ substitution]
    exercise   14 [               p7_gmx] ...     FAILED [@@ substitution]
    exercise   15 [               p7_hit] ...     FAILED [@@ substitution]
    exercise   16 [               p7_hmm] ...     FAILED [@@ substitution]
    exercise   17 [           p7_hmmfile] ...     FAILED [@@ substitution]
    exercise   18 [ p7_hmmd_search_stats] ...     FAILED [@@ substitution]
    exercise   19 [           p7_profile] ...     FAILED [@@ substitution]
    exercise   20 [           p7_tophits] ...     FAILED [@@ substitution]
    exercise   21 [             p7_trace] ...     FAILED [@@ substitution]
    exercise   22 [         p7_scoredata] ...     FAILED [@@ substitution]
    exercise   23 [             decoding] ...     FAILED [@@ substitution]
    exercise   24 [              fwdback] ...     FAILED [@@ substitution]
    exercise   25 [                   io] ...     FAILED [@@ substitution]
    exercise   26 [            msvfilter] ...     FAILED [@@ substitution]
    exercise   27 [                null2] ...     FAILED [@@ substitution]
    exercise   28 [               optacc] ...     FAILED [@@ substitution]
    exercise   29 [             stotrace] ...     FAILED [@@ substitution]
    exercise   30 [            vitfilter] ...     FAILED [@@ substitution]
    exercise   31 [          hmmpgmd2msa] ...     FAILED [@@ substitution]
    exercise   32 [             hmmalign] ...     ok.
    exercise   33 [          hmmalign/-h] ...     ok.
    exercise   34 [          hmmalign/-o] ...     ok.
    exercise   35 [    hmmalign/--mapali] ...     ok.
    exercise   36 [      hmmalign/--trim] ...     ok.
    exercise   37 [     hmmalign/--amino] ...     ok.
    exercise   38 [  hmmalign/--informat] ...     ok.
    exercise   39 [ hmmalign/--outformat] ...     ok.
    exercise   40 [             hmmbuild] ...     ok.
    exercise   41 [             build/-h] ...     ok.
    exercise   42 [             build/-n] ...     ok.
    exercise   43 [             build/-o] ...     ok.
    exercise   44 [             build/-O] ...     ok.
    exercise   45 [        build/--amino] ...     ok.
    exercise   46 [          build/--dna] ...     ok.
    exercise   47 [          build/--rna] ...     ok.
    exercise   48 [         build/--fast] ...     ok.
    exercise   49 [         build/--hand] ...     ok.
    exercise   50 [      build/--symfrac] ...     ok.
    exercise   51 [   build/--fragthresh] ...     ok.
    exercise   52 [          build/--wpb] ...     ok.
    exercise   53 [         build/--wgsc] ...     ok.
    exercise   54 [      build/--wblosum] ...     ok.
    exercise   55 [        build/--wnone] ...     ok.
    exercise   56 [          build/--wid] ...     ok.
    exercise   57 [         build/--eent] ...     ok.
    exercise   58 [       build/--eclust] ...     ok.
    exercise   59 [        build/--enone] ...     ok.
    exercise   60 [         build/--eset] ...     ok.
    exercise   61 [          build/--ere] ...     ok.
    exercise   62 [       build/--esigma] ...     ok.
    exercise   63 [          build/--eid] ...     ok.
    exercise   64 [        build/--pnone] ...     ok.
    exercise   65 [     build/--plaplace] ...     ok.
    exercise   66 [          build/--EmL] ...     ok.
    exercise   67 [          build/--EmN] ...     ok.
    exercise   68 [          build/--EvL] ...     ok.
    exercise   69 [          build/--EvN] ...     ok.
    exercise   70 [          build/--EfL] ...     ok.
    exercise   71 [          build/--EfN] ...     ok.
    exercise   72 [          build/--Eft] ...     ok.
    exercise   73 [     build/--informat] ...     ok.
    exercise   74 [         build/--seed] ...     ok.
    exercise   75 [               search] ...     ok.
    exercise   76 [            search/-h] ...     ok.
    exercise   77 [            search/-o] ...     ok.
    exercise   78 [            search/-A] ...     ok.
    exercise   79 [      search/--tblout] ...     ok.
    exercise   80 [   search/--domtblout] ...     ok.
    exercise   81 [  search/--pfamtblout] ...     ok.
    exercise   82 [         search/--acc] ...     ok.
    exercise   83 [       search/--noali] ...     ok.
    exercise   84 [     search/--notextw] ...     ok.
    exercise   85 [       search/--textw] ...     ok.
    exercise   86 [            search/-E] ...     ok.
    exercise   87 [            search/-T] ...     ok.
    exercise   88 [        search/--domE] ...     ok.
    exercise   89 [        search/--domT] ...     ok.
    exercise   90 [        search/--incE] ...     ok.
    exercise   91 [        search/--incT] ...     ok.
    exercise   92 [     search/--incdomE] ...     ok.
    exercise   93 [     search/--incdomT] ...     ok.
    exercise   94 [      search/--cut_ga] ...     ok.
    exercise   95 [      search/--cut_nc] ...     ok.
    exercise   96 [      search/--cut_tc] ...     ok.
    exercise   97 [         search/--max] ...     ok.
    exercise   98 [          search/--F1] ...     ok.
    exercise   99 [          search/--F2] ...     ok.
    exercise  100 [          search/--F3] ...     ok.
    exercise  101 [      search/--nobias] ...     ok.
    exercise  102 [     search/--nonull2] ...     ok.
    exercise  103 [            search/-Z] ...     ok.
    exercise  104 [        search/--domZ] ...     ok.
    exercise  105 [        search/--seed] ...     ok.
    exercise  106 [     search/--tformat] ...     ok.
    exercise  107 [              hmmscan] ...     ok.
    exercise  108 [              scan/-h] ...     ok.
    exercise  109 [              scan/-o] ...     ok.
    exercise  110 [        scan/--tblout] ...     ok.
    exercise  111 [     scan/--domtblout] ...     ok.
    exercise  112 [    scan/--pfamtblout] ...     ok.
    exercise  113 [           scan/--acc] ...     ok.
    exercise  114 [         scan/--noali] ...     ok.
    exercise  115 [       scan/--notextw] ...     ok.
    exercise  116 [         scan/--textw] ...     ok.
    exercise  117 [              scan/-E] ...     ok.
    exercise  118 [              scan/-T] ...     ok.
    exercise  119 [          scan/--domE] ...     ok.
    exercise  120 [          scan/--domT] ...     ok.
    exercise  121 [          scan/--incE] ...     ok.
    exercise  122 [          scan/--incT] ...     ok.
    exercise  123 [       scan/--incdomE] ...     ok.
    exercise  124 [       scan/--incdomT] ...     ok.
    exercise  125 [       scan/--incdomT] ...     ok.
    exercise  126 [        scan/--cut_ga] ...     ok.
    exercise  127 [        scan/--cut_nc] ...     ok.
    exercise  128 [        scan/--cut_tc] ...     ok.
    exercise  129 [           scan/--max] ...     ok.
    exercise  130 [            scan/--F1] ...     ok.
    exercise  131 [            scan/--F2] ...     ok.
    exercise  132 [            scan/--F3] ...     ok.
    exercise  133 [        scan/--nobias] ...     ok.
    exercise  134 [       scan/--nonull2] ...     ok.
    exercise  135 [              scan/-Z] ...     ok.
    exercise  136 [          scan/--domZ] ...     ok.
    exercise  137 [          scan/--seed] ...     ok.
    exercise  138 [       scan/--qformat] ...     ok.
    exercise  139 [           scan/--cpu] ...     ok.
    exercise  140 [            jackhmmer] ...     ok.
    exercise  141 [                 j/-h] ...     ok.
    exercise  142 [                 j/-N] ...     ok.
    exercise  143 [                 j/-o] ...     ok.
    exercise  144 [                 j/-A] ...     ok.
    exercise  145 [           j/--tblout] ...     ok.
    exercise  146 [        j/--domtblout] ...     ok.
    exercise  147 [           j/--chkhmm] ...     ok.
    exercise  148 [           j/--chkali] ...     ok.
    exercise  149 [              j/--acc] ...     ok.
    exercise  150 [            j/--noali] ...     ok.
    exercise  151 [          j/--notextw] ...     ok.
    exercise  152 [            j/--textw] ...     ok.
    exercise  153 [            j/--popen] ...     ok.
    exercise  154 [          j/--pextend] ...     ok.
    exercise  155 [           j/--mxfile] ...     ok.
    exercise  156 [                 j/-E] ...     ok.
    exercise  157 [                 j/-T] ...     ok.
    exercise  158 [             j/--domE] ...     ok.
    exercise  159 [             j/--domT] ...     ok.
    exercise  160 [             j/--incE] ...     ok.
    exercise  161 [             j/--incT] ...     ok.
    exercise  162 [          j/--incdomE] ...     ok.
    exercise  163 [          j/--incdomT] ...     ok.
    exercise  164 [              j/--max] ...     ok.
    exercise  165 [               j/--F1] ...     ok.
    exercise  166 [               j/--F2] ...     ok.
    exercise  167 [               j/--F3] ...     ok.
    exercise  168 [           j/--nobias] ...     ok.
    exercise  169 [              j/--EmL] ...     ok.
    exercise  170 [              j/--EmN] ...     ok.
    exercise  171 [              j/--EvL] ...     ok.
    exercise  172 [              j/--EvN] ...     ok.
    exercise  173 [              j/--EfL] ...     ok.
    exercise  174 [              j/--EfN] ...     ok.
    exercise  175 [              j/--Eft] ...     ok.
    exercise  176 [          j/--nonull2] ...     ok.
    exercise  177 [                 j/-Z] ...     ok.
    exercise  178 [             j/--domZ] ...     ok.
    exercise  179 [             j/--seed] ...     ok.
    exercise  180 [          j/--qformat] ...     ok.
    exercise  181 [          j/--tformat] ...     ok.
    exercise  182 [               phmmer] ...     ok.
    exercise  183 [            phmmer/-h] ...     ok.
    exercise  184 [            phmmer/-o] ...     ok.
    exercise  185 [            phmmer/-A] ...     ok.
    exercise  186 [      phmmer/--tblout] ...     ok.
    exercise  187 [   phmmer/--domtblout] ...     ok.
    exercise  188 [  phmmer/--pfamtblout] ...     ok.
    exercise  189 [         phmmer/--acc] ...     ok.
    exercise  190 [       phmmer/--noali] ...     ok.
    exercise  191 [     phmmer/--notextw] ...     ok.
    exercise  192 [       phmmer/--textw] ...     ok.
    exercise  193 [       phmmer/--popen] ...     ok.
    exercise  194 [     phmmer/--pextend] ...     ok.
    exercise  195 [      phmmer/--mxfile] ...     ok.
    exercise  196 [            phmmer/-E] ...     ok.
    exercise  197 [            phmmer/-T] ...     ok.
    exercise  198 [        phmmer/--domE] ...     ok.
    exercise  199 [        phmmer/--domT] ...     ok.
    exercise  200 [        phmmer/--incE] ...     ok.
    exercise  201 [        phmmer/--incT] ...     ok.
    exercise  202 [     phmmer/--incdomE] ...     ok.
    exercise  203 [     phmmer/--incdomT] ...     ok.
    exercise  204 [         phmmer/--max] ...     ok.
    exercise  205 [          phmmer/--F1] ...     ok.
    exercise  206 [          phmmer/--F2] ...     ok.
    exercise  207 [          phmmer/--F3] ...     ok.
    exercise  208 [      phmmer/--nobias] ...     ok.
    exercise  209 [         phmmer/--EmL] ...     ok.
    exercise  210 [         phmmer/--EmN] ...     ok.
    exercise  211 [         phmmer/--EvL] ...     ok.
    exercise  212 [         phmmer/--EvN] ...     ok.
    exercise  213 [         phmmer/--EfL] ...     ok.
    exercise  214 [         phmmer/--EfN] ...     ok.
    exercise  215 [         phmmer/--Eft] ...     ok.
    exercise  216 [     phmmer/--nonull2] ...     ok.
    exercise  217 [            phmmer/-Z] ...     ok.
    exercise  218 [        phmmer/--domZ] ...     ok.
    exercise  219 [        phmmer/--seed] ...     ok.
    exercise  220 [     phmmer/--qformat] ...     ok.
    exercise  221 [     phmmer/--tformat] ...     ok.
    exercise  222 [               nhmmer] ...     ok.
    exercise  223 [            nhmmer/-h] ...     ok.
    exercise  224 [            nhmmer/-o] ...     ok.
    exercise  225 [            nhmmer/-A] ...     ok.
    exercise  226 [      nhmmer/--tblout] ...     ok.
    exercise  227 [  nhmmer/--dfamtblout] ...     ok.
    exercise  228 [         nhmmer/--acc] ...     ok.
    exercise  229 [       nhmmer/--noali] ...     ok.
    exercise  230 [     nhmmer/--notextw] ...     ok.
    exercise  231 [       nhmmer/--textw] ...     ok.
    exercise  232 [            nhmmer/-E] ...     ok.
    exercise  233 [            nhmmer/-T] ...     ok.
    exercise  234 [        nhmmer/--incE] ...     ok.
    exercise  235 [        nhmmer/--incT] ...     ok.
    exercise  236 [         nhmmer/--max] ...     ok.
    exercise  237 [          nhmmer/--F1] ...     ok.
    exercise  238 [          nhmmer/--F2] ...     ok.
    exercise  239 [          nhmmer/--F3] ...     ok.
    exercise  240 [      nhmmer/--nobias] ...     ok.
    exercise  241 [     nhmmer/--nonull2] ...     ok.
    exercise  242 [            nhmmer/-Z] ...     ok.
    exercise  243 [        nhmmer/--seed] ...     ok.
    exercise  244 [             nhmmscan] ...     ok.
    exercise  245 [          nhmmscan/-h] ...     ok.
    exercise  246 [          nhmmscan/-o] ...     ok.
    exercise  247 [    nhmmscan/--tblout] ...     ok.
    exercise  248 [nhmmscan/--dfamtblout] ...     ok.
    exercise  249 [       nhmmscan/--acc] ...     ok.
    exercise  250 [     nhmmscan/--noali] ...     ok.
    exercise  251 [   nhmmscan/--notextw] ...     ok.
    exercise  252 [     nhmmscan/--textw] ...     ok.
    exercise  253 [          nhmmscan/-E] ...     ok.
    exercise  254 [          nhmmscan/-T] ...     ok.
    exercise  255 [      nhmmscan/--incE] ...     ok.
    exercise  256 [      nhmmscan/--incT] ...     ok.
    exercise  257 [       nhmmscan/--max] ...     ok.
    exercise  258 [        nhmmscan/--F1] ...     ok.
    exercise  259 [        nhmmscan/--F2] ...     ok.
    exercise  260 [        nhmmscan/--F3] ...     ok.
    exercise  261 [    nhmmscan/--nobias] ...     ok.
    exercise  262 [   nhmmscan/--nonull2] ...     ok.
    exercise  263 [          nhmmscan/-Z] ...     ok.
    exercise  264 [      nhmmscan/--seed] ...     ok.
    exercise  265 [              hmmemit] ...     ok.
    exercise  266 [           hmmemit/-h] ...     ok.
    exercise  267 [           hmmemit/-c] ...     ok.
    exercise  268 [           hmmemit/-o] ...     ok.
    exercise  269 [           hmmemit/-p] ...     ok.
    exercise  270 [           hmmemit/-N] ...     ok.
    exercise  271 [           hmmemit/-L] ...     ok.
    exercise  272 [      hmmemit/--local] ...     ok.
    exercise  273 [   hmmemit/--unilocal] ...     ok.
    exercise  274 [     hmmemit/--glocal] ...     ok.
    exercise  275 [  hmmemit/--uniglocal] ...     ok.
    exercise  276 [             hmmfetch] ...     ok.
    exercise  277 [              hmmstat] ...     ok.
    exercise  278 [              hmmlogo] ...     ok.
    exercise  279 [           hmmconvert] ...     ok.
    exercise  280 [               hmmsim] ...     ok.
    exercise  281 [   hmmbuild_variation] ...     ok.
    exercise  282 [    hmmscan_variation] ...     ok.
    exercise  283 [  hmmsearch_variation] ...     ok.
    exercise  284 [     phmmer_variation] ...     ok.
    exercise  285 [               mapali] ...     ok.
    exercise  286 [            fragments] ...     ok.
    exercise  287 [          nonresidues] ...     ok.
    exercise  288 [       opt-annotation] ...     ok.
    exercise  289 [            dup-names] ...     ok.
    exercise  290 [         mapali-again] ...     ok.
    exercise  291 [    delete-corruption] ...     ok.
    exercise  292 [        msa-integrity] ...     ok.
    exercise  293 [    hmmemit-consensus] ...     ok.
    exercise  294 [           hmmconvert] ...     ok.
    exercise  295 [          stdin_pipes] ...     ok.
    exercise  296 [       nhmmer_generic] ...     ok.
    exercise  297 [           hmmpgmd_ga] ...     ok.
    exercise  298 [               rewind] ...     ok.
    exercise  299 [     hmmpgmd_shard_ga] ...     ok.
    exercise  300 [            bad-fasta] ...     ok.
    exercise  301 [          brute-itest] ...     FAILED [@@ substitution]
    exercise  302 [       hmmpress-itest] ...     ok.
    exercise  303 [                  h39] ...     ok.
    exercise  304 [                  h45] ...     ok.
    exercise  305 [                  h50] ...     ok.
    exercise  306 [                  h82] ...     ok.
    exercise  307 [               iss159] ...     ok.

32 of 307 exercises at level <= 2 FAILED.

System information:
Fri Jan  8 04:14:48 PM PST 2021
Linux peltast 5.9.16-200.fc33.x86_64 #1 SMP Mon Dec 21 14:08:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
make: *** [Makefile:41: check] Error 1

I see that error message is generate from a Perl script in devkit/sqc, and that's where I stopped… sorry, I'm not willing to read through Perl code to try to find a fix ;). I'm happy to answer any questions to help debug, though.

[cryptogenomicon]

Thanks, I'll look into it, it shouldn't do that. But the workaround is simple. Just follow the instructions:

Now do 'make'  to build HMMER, and optionally:
       'make check'  to run self tests,
       'make install'  to install programs and man pages,
       '(cd easel; make install)'  to install Easel tools.

So don't cd testsuite; make, just make check.

[nemequ]

Sorry, I should have mentioned that the tests work when I run them like that. This is just something I ran into while trying to figure out how to isolate the problematic test, and I know if I were in your place I'd want to hear about it.

[cryptogenomicon]

OK, the problem is simpler than I thought. make works fine in testsuite provided that you build the package as documented. You didn't build the test programs first, and the test suite requires them to be built (usually by the top-level Makefile) before you navigate into the testsuite directory and start trying to run the suite from the subdirectory. The failures are coming from failures to find compiled test programs in other directories where they'd usually be built by the top-level Makefile. Although I'm sure we could find some way to make it fail more gracefully, I think the documentation is already pretty clear that you just need to make check in the top-level Makefile. So I'm going to leave it as is, but thanks for the report.