Failed Reason

Failed to install dependency package :
------------------------------------------------
Stage: 1.94s. Configure: 0.98s. Build: 1.82s. Install: 1.25s. Post-install: 1.06s. Total: 7.71s
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-file-homedir-1.006-a6urgecmerymj55ons3ji5pznf7ouijm
==> Installing perl-hash-merge-0.300-esfx27z5ggajhvr22swdmhs2t4s64kks [45/67]
==> No binary for perl-hash-merge-0.300-esfx27z5ggajhvr22swdmhs2t4s64kks found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/40/402fd52191d51415bb7163b7673fb4a108e3156493d7df931b8db4b2af757c40.tar.gz
==> No patches needed for perl-hash-merge
==> perl-hash-merge: Executing phase: 'configure'
==> perl-hash-merge: Executing phase: 'build'
==> perl-hash-merge: Executing phase: 'install'
==> perl-hash-merge: Successfully installed perl-hash-merge-0.300-esfx27z5ggajhvr22swdmhs2t4s64kks
Stage: 1.92s. Configure: 1.04s. Build: 1.10s. Install: 0.72s. Post-install: 0.91s. Total: 6.67s
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-hash-merge-0.300-esfx27z5ggajhvr22swdmhs2t4s64kks
==> Installing perl-exception-class-1.45-oreecz43ydjxhzuelywz3wnlykkh5i6w [46/67]
==> No binary for perl-exception-class-1.45-oreecz43ydjxhzuelywz3wnlykkh5i6w found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/54/5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249.tar.gz
==> No patches needed for perl-exception-class
==> perl-exception-class: Executing phase: 'configure'
==> perl-exception-class: Executing phase: 'build'
==> perl-exception-class: Executing phase: 'install'
==> perl-exception-class: Successfully installed perl-exception-class-1.45-oreecz43ydjxhzuelywz3wnlykkh5i6w
Stage: 2.18s. Configure: 1.09s. Build: 1.43s. Install: 0.84s. Post-install: 0.94s. Total: 7.09s
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-exception-class-1.45-oreecz43ydjxhzuelywz3wnlykkh5i6w
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-pillow-10.0.0-ywh46f5x74warwd5tthvjqvzvtanusm5
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-cython-3.0.4-7sdgkmtvjntri7top7bfm2hd5u7drmyc
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-wheel-0.41.2-uecnqi7ns7hm2wehm3fwrq4fyygklprs
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/libdeflate-1.18-wdq7uvwnauvzqysy24aknbmredmsjh5r
==> Installing diamond-2.1.7-xcg7kgxuq7imozzuvhxmg7v7smjd7nh5 [51/67]
==> No binary for diamond-2.1.7-xcg7kgxuq7imozzuvhxmg7v7smjd7nh5 found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/2d/2dcaba0e79ecb02c3d2a6816d317e714767118a9a056721643abff4c586ca95b.tar.gz
==> No patches needed for diamond
==> diamond: Executing phase: 'cmake'
==> diamond: Executing phase: 'build'
==> diamond: Executing phase: 'install'
==> diamond: Successfully installed diamond-2.1.7-xcg7kgxuq7imozzuvhxmg7v7smjd7nh5
Stage: 28.70s. Cmake: 15.16s. Build: 6m 19.37s. Install: 6.89s. Post-install: 1.71s. Total: 7m 13.22s
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/diamond-2.1.7-xcg7kgxuq7imozzuvhxmg7v7smjd7nh5
==> Installing genemark-et-4.69-uztrdevyfrcowfrakvzdqsbtvz3us7hn [52/67]
==> No binary for genemark-et-4.69-uztrdevyfrcowfrakvzdqsbtvz3us7hn found: installing from source
==> Error: FetchError: Manual download is required for genemark-et. Refer to http://topaz.gatech.edu/GeneMark for download instructions.
==> Installing perl-object-insideout-4.05-ewfawz2qtbbn2dpykgbuceec2gso4nbg [53/67]
==> No binary for perl-object-insideout-4.05-ewfawz2qtbbn2dpykgbuceec2gso4nbg found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/9d/9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4.tar.gz
==> No patches needed for perl-object-insideout
==> perl-object-insideout: Executing phase: 'configure'
==> perl-object-insideout: Executing phase: 'build'
==> perl-object-insideout: Executing phase: 'install'
==> perl-object-insideout: Successfully installed perl-object-insideout-4.05-ewfawz2qtbbn2dpykgbuceec2gso4nbg
Stage: 3.63s. Configure: 1.37s. Build: 2.33s. Install: 1.35s. Post-install: 1.12s. Total: 10.81s
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-object-insideout-4.05-ewfawz2qtbbn2dpykgbuceec2gso4nbg
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-pyparsing-3.0.9-x5syhgdsq2rgfco4tamxymq5hxzr2z42
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-six-1.16.0-ztq6x5ahyilyk723qkmrff772hjcllpa
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-packaging-23.1-yxzztmamwtgtkjqep4mb57ht6ztozn7a
==> Installing htslib-1.16-6n5zcm7iofcvxaebwu2q5yztkqh66y7j [57/67]
==> No binary for htslib-1.16-6n5zcm7iofcvxaebwu2q5yztkqh66y7j found: installing from source
==> Using cached archive: /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/var/spack/cache/_source-cache/archive/60/606b7c7aff73734cf033ecd156f40529fa5792f54524952a28938ca0890d7924.tar.bz2
==> No patches needed for htslib
==> htslib: Executing phase: 'autoreconf'
==> htslib: Executing phase: 'configure'
==> htslib: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16' 'V=1'

1 error found in build log:
84 ==> [2024-03-10-22:06:34.171363] Find (recursive): /data/rccs-sdt/a0
1008/tmpdir/spack-stage/spack-stage-htslib-1.16-6n5zcm7iofcvxaebwu2q
5yztkqh66y7j/spack-src ['libtool']
85 ==> [2024-03-10-22:06:34.249906] Find complete: /data/rccs-sdt/a0100
8/tmpdir/spack-stage/spack-stage-htslib-1.16-6n5zcm7iofcvxaebwu2q5yz
tkqh66y7j/spack-src ['libtool']
86 ==> htslib: Executing phase: 'build'
87 ==> [2024-03-10-22:06:34.305533] 'make' '-j16' 'V=1'
88 make: Makefile: Too many levels of symbolic links
89 make: stat: Makefile: Too many levels of symbolic links
>> 90 make: *** No rule to make target 'Makefile'. Stop.

See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-htslib-1.16-6n5zcm7iofcvxaebwu2q5yztkqh66y7j/spack-build-out.txt

==> Warning: Skipping build of bcftools-1.16-kus44edq22dsvhax7jb4qfand5uuzbqt since htslib-1.16-6n5zcm7iofcvxaebwu2q5yztkqh66y7j failed
==> Warning: Skipping build of augustus-3.3.2-beudgnk2w5awyyrfx5uyxojlsnk6yz5d since bcftools-1.16-kus44edq22dsvhax7jb4qfand5uuzbqt failed
==> Warning: Skipping build of samtools-1.16.1-fetxy3tvmw24a2b5yghpvc4rtk7lq2t7 since htslib-1.16-6n5zcm7iofcvxaebwu2q5yztkqh66y7j failed
==> Installing perl-logger-simple-2.0-eqni4ymmsf2alf2sbz4emywe7w73j3si [58/67]
==> No binary for perl-logger-simple-2.0-eqni4ymmsf2alf2sbz4emywe7w73j3si found: installing from source
==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/2e/2e63fd3508775b5902132ba1bfb03b42bee468dfaf35dfe42e1909ff6d291b2d.tar.gz
==> No patches needed for perl-logger-simple
==> perl-logger-simple: Executing phase: 'configure'
==> perl-logger-simple: Executing phase: 'build'
==> perl-logger-simple: Executing phase: 'install'
==> perl-logger-simple: Successfully installed perl-logger-simple-2.0-eqni4ymmsf2alf2sbz4emywe7w73j3si
Stage: 1.52s. Configure: 0.86s. Build: 1.04s. Install: 0.66s. Post-install: 1.06s. Total: 6.03s
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-logger-simple-2.0-eqni4ymmsf2alf2sbz4emywe7w73j3si
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-python-dateutil-2.5.2-hnnnls4s3lrlztmuojqkwkrylheinba2
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-pyproject-metadata-0.7.1-fs3vme4uqputh5py6ykygic6maqw3tlh
==> Installing py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3yw [61/67]
==> No binary for py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3yw found: installing from source
==> Using cached archive: /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/var/spack/cache/_source-cache/archive/c8/c8c6c72d4a9f831f328efb1312642a1cafafaa88981d9ab76368d50d07d93cbe.tar.gz
==> Applied patch /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/var/spack/repos/builtin/packages/py-numpy/check_executables.patch
==> py-numpy: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
'/vol0004/apps/oss/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q66snjvhvy7im57hncbgpirmddrb5sk/bin/python3.10' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3yw' '--config-settings=builddir=build' '--config-settings=compile-args=-j16' '--config-settings=setup-args=-Dblas=fjlapackexsve' '--config-settings=setup-args=-Dlapack=fjlapackexsve' '.'

2 errors found in build log:
64
65 Library m found: YES
66 Found CMake: /usr/bin/cmake (3.20.2)
67 WARNING: CMake Toolchain: Failed to determine CMake compilers stat
e
68 Run-time dependency fjlapackexsve found: NO (tried pkgconfig and c
make)
69
>> 70 ../numpy/meson.build:169:4: ERROR: Problem encountered: No BLAS libr
ary detected! Install one, or use the `allow-noblas` build option (n
ote, this may be up to 100x slower for some linear algebra operation
s).
71
72 A full log can be found at /vol0003/rccs-sdt/data/a01008/tmpdir/sp
ack-stage/spack-stage-py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3
yw/spack-src/build/meson-logs/meson-log.txt
73 error: subprocess-exited-with-error
74
75 × Preparing metadata (pyproject.toml) did not run successfully.
76 │ exit code: 1
77 ╰─> See above for output.
78
79 note: This error originates from a subprocess, and is likely not a
problem with pip.
80 full command: /vol0004/apps/oss/spack-v0.19/opt/spack/linux-rhel8-
a64fx/fj-4.8.1/python-3.10.8-7q66snjvhvy7im57hncbgpirmddrb5sk/bin/py
thon3.10 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/s
pack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/py-pip-23.1.2-e5mqkkojghz
4zpl6zboxzql3mko55ccd/lib/python3.10/site-packages/pip/_vendor/pypro
ject_hooks/_in_process/_in_process.py prepare_metadata_for_build_whe
el /data/rccs-sdt/a01008/tmpdir/tmpg4ewk21_
81 cwd: /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3yw/spack-src
82 Preparing metadata (pyproject.toml): finished with status 'error'
>> 83 error: metadata-generation-failed
84
85 × Encountered error while generating package metadata.
86 ╰─> See above for output.
87
88 note: This is an issue with the package mentioned above, not pip.
89 hint: See above for details.

See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3yw/spack-build-out.txt

==> Warning: Skipping build of py-matplotlib-3.3.4-uvahwxwwhsx7vox3nce33czaojh3nai6 since py-numpy-1.26.1-brmrviclbqnhu4f3swabbqjwk5pjz3yw failed
==> Error: braker-2.1.6-kog6cjht3xqawh6zokdbw4b3vf5ztzir: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).