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Installation issue: diamond #26261

Closed omsai closed 2 years ago

omsai commented 3 years ago

Steps to reproduce the issue

$ spack install braker
...
==> Installing diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7
==> No binary for diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7 found: installing from source
==> Using cached archive: /home/FCAM/pnanda/spackpm/var/spack/cache/_source-cache/archive/41/41f3197aaafff9c42763fb7658b67f730ebc6dd3c0533c9c3d54bd
3166e93f24.tar.gz
==> No patches needed for diamond
==> diamond: Executing phase: 'cmake'
==> diamond: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' '-j2'

7 errors found in build log:
     394    [ 99%] Building CXX object CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o
     395    /home/FCAM/pnanda/spackpm/lib/spack/env/gcc/g++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/home/FCAM/pnanda
            /spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/zlib-1.2.11-icltdvyu4qcjmarmsrmu4huh3aflx4ds/include -I/tmp/pnanda/spack-stage/s
            pack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-src/src/lib -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wn
            o-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O2 -g -DNDEBU
            G -std=gnu++14 -MD -MT CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o
            .d -o CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o -c /tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sase
            ar2xestle3f7/spack-src/src/output/daa/daa_write.cpp
     396    [100%] Linking CXX executable diamond
     397    /isg/shared/apps/cmake/3.20.2/bin/cmake -E cmake_link_script CMakeFiles/diamond.dir/link.txt --verbose=1
     398    /home/FCAM/pnanda/spackpm/lib/spack/env/gcc/g++  -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-paramet
            er -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O2 -g -DNDEBUG -rdynamic CMakeFiles/diamo
            nd.dir/src/run/main.cpp.o CMakeFiles/diamond.dir/src/basic/config.cpp.o CMakeFiles/diamond.dir/src/stats/score_matrix.cpp.o CMakeFiles
            /diamond.dir/src/data/queries.cpp.o CMakeFiles/diamond.dir/src/data/reference.cpp.o CMakeFiles/diamond.dir/src/data/seed_histogram.cpp
            .o CMakeFiles/diamond.dir/src/output/daa/daa_record.cpp.o CMakeFiles/diamond.dir/src/util/command_line_parser.cpp.o CMakeFiles/diamond
            .dir/src/util/seq_file_format.cpp.o CMakeFiles/diamond.dir/src/util/util.cpp.o CMakeFiles/diamond.dir/src/basic/basic.cpp.o CMakeFiles
            /diamond.dir/src/basic/hssp.cpp.o CMakeFiles/diamond.dir/src/dp/ungapped_align.cpp.o CMakeFiles/diamond.dir/src/run/tools.cpp.o CMakeF
            iles/diamond.dir/src/chaining/greedy_align.cpp.o CMakeFiles/diamond.dir/src/output/output_format.cpp.o CMakeFiles/diamond.dir/src/outp
            ut/clustering_variables.cpp.o CMakeFiles/diamond.dir/src/output/clustering_format.cpp.o CMakeFiles/diamond.dir/src/output/join_blocks.
            cpp.o CMakeFiles/diamond.dir/src/data/frequent_seeds.cpp.o CMakeFiles/diamond.dir/src/align/legacy/query_mapper.cpp.o CMakeFiles/diamo
            nd.dir/src/output/blast_tab_format.cpp.o CMakeFiles/diamond.dir/src/dp/needleman_wunsch.cpp.o CMakeFiles/diamond.dir/src/output/blast_
            pairwise_format.cpp.o CMakeFiles/diamond.dir/src/run/double_indexed.cpp.o CMakeFiles/diamond.dir/src/output/sam_format.cpp.o CMakeFile
            s/diamond.dir/src/align/align.cpp.o CMakeFiles/diamond.dir/src/search/setup.cpp.o CMakeFiles/diamond.dir/src/data/taxonomy.cpp.o CMake
            Files/diamond.dir/src/basic/masking.cpp.o CMakeFiles/diamond.dir/src/dp/banded_sw.cpp.o CMakeFiles/diamond.dir/src/data/seed_set.cpp.o
             CMakeFiles/diamond.dir/src/util/simd.cpp.o CMakeFiles/diamond.dir/src/output/taxon_format.cpp.o CMakeFiles/diamond.dir/src/output/vie
            w.cpp.o CMakeFiles/diamond.dir/src/output/output_sink.cpp.o CMakeFiles/diamond.dir/src/output/target_culling.cpp.o CMakeFiles/diamond.
            dir/src/align/legacy/banded_swipe_pipeline.cpp.o CMakeFiles/diamond.dir/src/util/io/compressed_stream.cpp.o CMakeFiles/diamond.dir/src
            /util/io/deserializer.cpp.o CMakeFiles/diamond.dir/src/util/io/file_sink.cpp.o CMakeFiles/diamond.dir/src/util/io/file_source.cpp.o CM
            akeFiles/diamond.dir/src/util/io/input_file.cpp.o CMakeFiles/diamond.dir/src/util/io/input_stream_buffer.cpp.o CMakeFiles/diamond.dir/
            src/util/io/output_file.cpp.o CMakeFiles/diamond.dir/src/util/io/output_stream_buffer.cpp.o CMakeFiles/diamond.dir/src/util/io/seriali
            zer.cpp.o CMakeFiles/diamond.dir/src/util/io/temp_file.cpp.o CMakeFiles/diamond.dir/src/util/io/text_input_file.cpp.o CMakeFiles/diamo
            nd.dir/src/data/taxon_list.cpp.o CMakeFiles/diamond.dir/src/data/taxonomy_nodes.cpp.o CMakeFiles/diamond.dir/src/util/algo/MurmurHash3
            .cpp.o CMakeFiles/diamond.dir/src/search/stage0.cpp.o CMakeFiles/diamond.dir/src/data/seed_array.cpp.o CMakeFiles/diamond.dir/src/outp
            ut/paf_format.cpp.o CMakeFiles/diamond.dir/src/util/system/system.cpp.o CMakeFiles/diamond.dir/src/util/algo/greedy_vertex_cover.cpp.o
             CMakeFiles/diamond.dir/src/util/sequence/sequence.cpp.o CMakeFiles/diamond.dir/src/tools/tsv_record.cpp.o CMakeFiles/diamond.dir/src/
            tools/tools.cpp.o CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o CMakeFiles/diamond.dir/src/lib/tantan/LambdaCalculator.cc.o CMak
            eFiles/diamond.dir/src/util/algo/upgma.cpp.o CMakeFiles/diamond.dir/src/util/algo/upgma_mc.cpp.o CMakeFiles/diamond.dir/src/util/algo/
            edge_vec.cpp.o CMakeFiles/diamond.dir/src/util/string/string.cpp.o CMakeFiles/diamond.dir/src/align/extend.cpp.o CMakeFiles/diamond.di
            r/src/test/simulate.cpp.o CMakeFiles/diamond.dir/src/test/test.cpp.o CMakeFiles/diamond.dir/src/align/ungapped.cpp.o CMakeFiles/diamon
            d.dir/src/align/gapped.cpp.o CMakeFiles/diamond.dir/src/align/culling.cpp.o CMakeFiles/diamond.dir/src/cluster/medoid.cpp.o CMakeFiles
            /diamond.dir/src/cluster/cluster_registry.cpp.o CMakeFiles/diamond.dir/src/cluster/multi_step_cluster.cpp.o CMakeFiles/diamond.dir/src
            /cluster/mcl.cpp.o CMakeFiles/diamond.dir/src/align/output.cpp.o CMakeFiles/diamond.dir/src/tools/roc.cpp.o CMakeFiles/diamond.dir/src
            /test/data.cpp.o CMakeFiles/diamond.dir/src/test/test_cases.cpp.o CMakeFiles/diamond.dir/src/chaining/smith_waterman.cpp.o CMakeFiles/
            diamond.dir/src/basic/value.cpp.o CMakeFiles/diamond.dir/src/tools/merge_tsv.cpp.o CMakeFiles/diamond.dir/src/output/xml_format.cpp.o
            CMakeFiles/diamond.dir/src/align/gapped_filter.cpp.o CMakeFiles/diamond.dir/src/util/parallel/filestack.cpp.o CMakeFiles/diamond.dir/s
            rc/util/parallel/parallelizer.cpp.o CMakeFiles/diamond.dir/src/util/parallel/multiprocessing.cpp.o CMakeFiles/diamond.dir/src/tools/be
            nchmark_io.cpp.o CMakeFiles/diamond.dir/src/align/memory.cpp.o CMakeFiles/diamond.dir/src/lib/alp/njn_dynprogprob.cpp.o CMakeFiles/dia
            mond.dir/src/lib/alp/njn_dynprogproblim.cpp.o CMakeFiles/diamond.dir/src/lib/alp/njn_dynprogprobproto.cpp.o CMakeFiles/diamond.dir/src
            /lib/alp/njn_ioutil.cpp.o CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstat.cpp.o CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxsta
            tmatrix.cpp.o CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatutil.cpp.o CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o CMakeF
            iles/diamond.dir/src/lib/alp/sls_alignment_evaluer.cpp.o CMakeFiles/diamond.dir/src/lib/alp/sls_alp.cpp.o CMakeFiles/diamond.dir/src/l
            ib/alp/sls_alp_data.cpp.o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_sim.c
            pp.o CMakeFiles/diamond.dir/src/lib/alp/sls_basic.cpp.o CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o CMakeFiles/diamond.dir/sr
            c/align/global_ranking/global_ranking.cpp.o CMakeFiles/diamond.dir/src/align/global_ranking/extend.cpp.o CMakeFiles/diamond.dir/src/to
            ols/rocid.cpp.o CMakeFiles/diamond.dir/src/lib/blast/blast_seg.cpp.o CMakeFiles/diamond.dir/src/lib/blast/blast_filter.cpp.o CMakeFile
            s/diamond.dir/src/lib/blast/nlm_linear_algebra.cpp.o CMakeFiles/diamond.dir/src/stats/matrices/blosum45.cpp.o CMakeFiles/diamond.dir/s
            rc/stats/matrices/blosum50.cpp.o CMakeFiles/diamond.dir/src/stats/matrices/blosum62.cpp.o CMakeFiles/diamond.dir/src/stats/matrices/bl
            osum80.cpp.o CMakeFiles/diamond.dir/src/stats/matrices/blosum90.cpp.o CMakeFiles/diamond.dir/src/stats/matrices/pam250.cpp.o CMakeFile
            s/diamond.dir/src/stats/matrices/pam30.cpp.o CMakeFiles/diamond.dir/src/stats/matrices/pam70.cpp.o CMakeFiles/diamond.dir/src/stats/st
            ats.cpp.o CMakeFiles/diamond.dir/src/stats/cbs.cpp.o CMakeFiles/diamond.dir/src/stats/comp_based_stats.cpp.o CMakeFiles/diamond.dir/sr
            c/stats/hauser_correction.cpp.o CMakeFiles/diamond.dir/src/stats/matrix_adjust.cpp.o CMakeFiles/diamond.dir/src/stats/matrix_adjust_ei
            gen.cpp.o CMakeFiles/diamond.dir/src/data/index.cpp.o CMakeFiles/diamond.dir/src/data/dmnd/dmnd.cpp.o CMakeFiles/diamond.dir/src/data/
            sequence_file.cpp.o CMakeFiles/diamond.dir/src/tools/find_shapes.cpp.o CMakeFiles/diamond.dir/src/data/block.cpp.o CMakeFiles/diamond.
            dir/src/run/config.cpp.o CMakeFiles/diamond.dir/src/data/sequence_set.cpp.o CMakeFiles/diamond.dir/src/align/global_ranking/table.cpp.
            o CMakeFiles/diamond.dir/src/output/daa/daa_write.cpp.o CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o CMakeFiles/
            arch_generic.dir/src/dp/swipe/swipe.cpp.o CMakeFiles/arch_generic.dir/src/dp/swipe/banded_swipe.cpp.o CMakeFiles/arch_generic.dir/src/
            search/stage2.cpp.o CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o
             CMakeFiles/arch_generic.dir/src/util/tantan.cpp.o CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o CMakeFiles/arch_generic.dir/src
            /dp/ungapped_simd.cpp.o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swip
            e.cpp.o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_swipe.cpp.o CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o CMakeFiles/arch_
            sse4_1.dir/src/tools/benchmark.cpp.o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o CMakeFiles/arch_sse4_1.dir/src/util/t
            antan.cpp.o CMakeFiles/arch_sse4_1.dir/src/dp/scan_diags.cpp.o CMakeFiles/arch_sse4_1.dir/src/dp/ungapped_simd.cpp.o CMakeFiles/arch_a
            vx2.dir/src/dp/swipe/banded_3frame_swipe.cpp.o CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe.cpp.o CMakeFiles/arch_avx2.dir/src/dp/swipe
            /banded_swipe.cpp.o CMakeFiles/arch_avx2.dir/src/search/stage2.cpp.o CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o CMakeFiles/arc
            h_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o CMakeFiles/arch_avx2.dir/src/util/tantan.cpp.o CMakeFiles/arch_avx2.dir/src/dp/scan_diags.
            cpp.o CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o -o diamond  -Wl,-rpath,/home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-bro
            adwell/gcc-10.2.0/zlib-1.2.11-icltdvyu4qcjmarmsrmu4huh3aflx4ds/lib::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            :::::::::::::::::::::::::::::::::::::::::::::: /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/zlib-1.2.11-iclt
            dvyu4qcjmarmsrmu4huh3aflx4ds/lib/libz.so -lpthread
     399    CMakeFiles/diamond.dir/src/align/align.cpp.o: In function `ExtensionPipeline::Swipe::Pipeline::~Pipeline()':
  >> 400    /tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-src/src/align/align.h:57: undefined referenc
            e to `vtable for ExtensionPipeline::Swipe::Pipeline'
  >> 401    /tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-src/src/align/align.h:57: undefined referenc
            e to `vtable for ExtensionPipeline::Swipe::Pipeline'
     402    CMakeFiles/diamond.dir/src/align/align.cpp.o: In function `ExtensionPipeline::Swipe::Pipeline::~Pipeline()':
  >> 403    /tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-src/src/align/align.h:57: undefined referenc
            e to `vtable for ExtensionPipeline::Swipe::Pipeline'
  >> 404    collect2: error: ld returned 1 exit status
  >> 405    make[2]: *** [diamond] Error 1
     406    make[2]: Leaving directory `/tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-build-xvjit3c'
  >> 407    make[1]: *** [CMakeFiles/diamond.dir/all] Error 2
     408    make[1]: Leaving directory `/tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-build-xvjit3c'
  >> 409    make: *** [all] Error 2

See build log for details:  
  /tmp/pnanda/spack-stage/spack-stage-diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7/spack-build-out.txt

==> Warning: Skipping build of braker-2.1.6-isd5dl735vsvoxodlbroju2exzd52fh2 since diamond-2.0.11-xvjit3coim5dohq3sasear2xestle3f7 failed
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/bamtools-2.5.1-m5il7nhmj2cuptxplsnx7hkxaqd2wmmd
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/diffutils-3.8-zkssnr2mvef3djsavlv4hdudb2qi7jsf
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-class-data-inheritable-0.08-eiduyurbqxefes6hf574nvnvm7uy5i7h
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-threads-2.21-flqehwivhxqflwbehh4ikas4mfbaeigl
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/openssl-1.1.1l-wc7keoo24sc5cig5e75clgxylbxmo43m
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-parallel-forkmanager-1.19-ir3d3373x2wviopopvmxahho2ncicrmt
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-module-build-0.4224-exd3cajwksgi5tstko5qw77zyowkg2zy
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-clone-choose-0.010-gb7g2dqy43crpmsbm4g6hhtg2r7ravgr
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-yaml-1.27-zqafcwdeopjs6zrdjvkrfxokki5m6hq6
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-scalar-list-utils-1.50-lugd6wzhh7om6tvtekjl2x4guc426avz
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-file-which-1.22-rdset447gkexru5rrrrxyi6zbno23ox2
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-mce-1.874-6oisai2f7tkczzdy4fxnkumjpttfw7nr
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-thread-queue-3.13-53c3rx7snoe5ln7vaytdxkxezakivmhp
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-devel-stacktrace-2.02-zl3flrn4upk44otsrbjkuhx3yhuxwc2a
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-scalar-util-numeric-0.40-u5fueuqs4uk3zhhjhzebruhpsgiahtcz
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/ncurses-6.2-ytenty4jsjxjiceqovigubalb5yvzdlc
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/bzip2-1.0.8-ivqelsdsklixapgh7kmvqxe6ahk47wkz
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/curl-7.79.0-fqjvdhc7lw3jqafl6jj7k3ux6uox5niq
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-hash-merge-0.300-prbdxpv23cvvbcpia7m53khen5hn445l
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-file-homedir-1.004-ojcnkuweduegjkkpjoe745hletcafp7c
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-exception-class-1.43-fw7cgxcg734tuzt3r2tic53b4yqvnko5
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/boost-1.77.0-3474rus75xyyp4luzpiz3pgprrrnszjn
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/htslib-1.13-4k34ymm2osmztfukmcbqbspv5djzhddb
==> Installing genemark-et-4.65-yzcaf67gls5mhlisg6s3wge4ci37l4a6
==> No binary for genemark-et-4.65-yzcaf67gls5mhlisg6s3wge4ci37l4a6 found: installing from source
==> Error: FetchError: Manual download is required for genemark-et. Refer to http://topaz.gatech.edu/GeneMark for download instructions.

/home/FCAM/pnanda/spackpm/lib/spack/spack/package.py:1376, in do_fetch:
       1373
       1374        self.stage.create()
       1375        err_msg = None if not self.manual_download else self.download_instr
  >>   1376        start_time = time.time()
       1377        self.stage.fetch(mirror_only, err_msg=err_msg)
       1378        self._fetch_time = time.time() - start_time
       1379

[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-object-insideout-4.05-wrghicdr5pqcy7q4ictp6igeeza2loqx
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/samtools-1.13-spzgwqlhda2p5i3vilpjbgonvxzalcmr
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/perl-logger-simple-2.0-2ilyupico3ym2sndopiovycx5c3rtqrd
[+] /home/FCAM/pnanda/spackpm/opt/spack/linux-centos7-broadwell/gcc-10.2.0/augustus-3.3.2-u6ewzfk4qk5mvdfkosqpebbm5qosfsj2
==> Error: braker-2.1.6-isd5dl735vsvoxodlbroju2exzd52fh2: Package was not installed
==> Error: Installation request failed.  Refer to reported errors for failing package(s).

Information on your system

$ spack debug report
* **Spack:** 0.16.3-4457-e90534d
* **Python:** 3.6.8
* **Platform:** linux-centos7-broadwell
* **Concretizer:** clingo

Contents of ~/.spack/packages.yaml

packages:
  cmake:
    externals:
    - spec: cmake@3.20.2
      prefix: /isg/shared/apps/cmake/3.20.2
    - spec: cmake@2.8.12.2
      prefix: /usr
  python:
    externals:
    - spec: python@2.7.5+bz2+ctypes+dbm+lzma+nis+pyexpat+readline+sqlite3+ssl~tix~tkinter+uuid+zlib
      prefix: /usr
    - spec: python@3.6.8+bz2+ctypes+dbm+lzma+nis+pyexpat+readline+sqlite3+ssl~tix~tkinter+uuid+zlib
      prefix: /usr
  perl:
    externals:
    - spec: perl@5.16.3+cpanm+shared+threads
      prefix: /usr
  bcftools:
    externals:
    - spec: bcftools@1.12
      prefix: /isg/shared/apps/bcftools/1.12

Additional information

General information

sethrj commented 3 years ago

@glennpj looks like this is a package you've worked with before? Have any ideas or should this be reported on the project's build site? Thanks!

Sorry the install line deceived me: the failure is in diamond, which @RemiLacroix-IDRIS and @erimar77 have worked with before.

RemiLacroix-IDRIS commented 3 years ago

I see undefined reference to vtable in the output, seems like a C++ issue with virtual method/constructor. Not sure if it's Spack related or if the problem is in the code.

sethrj commented 3 years ago

I would guess it's a problem in the code. @omsai can you try spack install diamond@2.0.12 and see if that fixes the error?