Package evaluation of BioTools on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:17:18.704


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.45s


################################################################################
# Installation
#

Installing BioTools...
   Resolving package versions...
    Updating `~/.julia/environments/v1.11/Project.toml`
  [fa51a905] + BioTools v1.2.0
    Updating `~/.julia/environments/v1.11/Manifest.toml`
⌅ [67c07d97] + Automa v0.7.0
  [28d598bf] + BGZFStreams v0.3.2
⌅ [00701ae9] + BioAlignments v1.0.1
  [37cfa864] + BioCore v2.0.5
⌅ [7e6ae17a] + BioSequences v1.1.0
⌅ [3c28c6f8] + BioSymbols v3.1.0
  [fa51a905] + BioTools v1.2.0
  [e1450e63] + BufferedStreams v1.2.2
  [944b1d66] + CodecZlib v0.7.8
⌅ [3da002f7] + ColorTypes v0.9.1
⌅ [861a8166] + Combinatorics v0.7.0
⌅ [864edb3b] + DataStructures v0.17.20
  [8f5d6c58] + EzXML v1.2.1
⌅ [53c48c17] + FixedPointNumbers v0.7.1
⌅ [899a7d2d] + GenomicFeatures v1.0.4
  [1cb3b9ac] + IndexableBitVectors v1.0.0
  [524e6230] + IntervalTrees v1.1.0
  [692b3bcd] + JLLWrappers v1.7.0
  [2ec943e9] + Libz v1.0.1
  [bac558e1] + OrderedCollections v1.8.0
⌅ [f27b6e38] + Polynomials v0.6.1
  [21216c6a] + Preferences v1.4.3
⌅ [3cdcf5f2] + RecipesBase v0.8.0
  [69024149] + StringEncodings v0.3.7
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [7200193e] + Twiddle v1.1.2
  [30578b45] + URIParser v0.4.1
  [ddb6d928] + YAML v0.4.13
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [02c8fc9c] + XML2_jll v2.13.6+1
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [fa267f1f] + TOML v1.0.3
  [8dfed614] + Test v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 2.59s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 106.21s


################################################################################
# Testing
#

     Testing BioTools
      Status `/tmp/jl_Bwzfwg/Project.toml`
⌅ [00701ae9] BioAlignments v1.0.1
  [37cfa864] BioCore v2.0.5
⌅ [7e6ae17a] BioSequences v1.1.0
  [fa51a905] BioTools v1.2.0
  [8f5d6c58] EzXML v1.2.1
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_Bwzfwg/Manifest.toml`
⌅ [67c07d97] Automa v0.7.0
  [28d598bf] BGZFStreams v0.3.2
⌅ [00701ae9] BioAlignments v1.0.1
  [37cfa864] BioCore v2.0.5
⌅ [7e6ae17a] BioSequences v1.1.0
⌅ [3c28c6f8] BioSymbols v3.1.0
  [fa51a905] BioTools v1.2.0
  [e1450e63] BufferedStreams v1.2.2
  [944b1d66] CodecZlib v0.7.8
⌅ [3da002f7] ColorTypes v0.9.1
⌅ [861a8166] Combinatorics v0.7.0
⌅ [864edb3b] DataStructures v0.17.20
  [8f5d6c58] EzXML v1.2.1
⌅ [53c48c17] FixedPointNumbers v0.7.1
⌅ [899a7d2d] GenomicFeatures v1.0.4
  [1cb3b9ac] IndexableBitVectors v1.0.0
  [524e6230] IntervalTrees v1.1.0
  [692b3bcd] JLLWrappers v1.7.0
  [2ec943e9] Libz v1.0.1
  [bac558e1] OrderedCollections v1.8.0
⌅ [f27b6e38] Polynomials v0.6.1
  [21216c6a] Preferences v1.4.3
⌅ [3cdcf5f2] RecipesBase v0.8.0
  [69024149] StringEncodings v0.3.7
⌅ [3bb67fe8] TranscodingStreams v0.9.13
  [7200193e] Twiddle v1.1.2
  [30578b45] URIParser v0.4.1
  [ddb6d928] YAML v0.4.13
  [94ce4f54] Libiconv_jll v1.18.0+0
  [02c8fc9c] XML2_jll v2.13.6+1
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] OpenBLAS_jll v0.3.27+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Warning: This package has been depreceated, and should not be used for new projects. Please see BioTools.jl's repository README for more information.
└ @ BioTools ~/.julia/packages/BioTools/LY7H3/src/BioTools.jl:4
Cloning into '/home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens'...
Note: switching to 'v1.0.0-9-ga88ddc9'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at a88ddc9 Merge pull request #29 from jgreener64/mmtf
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:30
  Test threw exception
  Expression: typeof(blastn(na1, na2)) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_cqhcLv -subject /tmp/jl_WJgQUM -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:82 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:89 [inlined]
   [16] blastn(query::BioSequences.DNASequence, subject::BioSequences.DNASequence)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:88
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [18] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:30 [inlined]
   [19] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [20] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:31
  Test threw exception
  Expression: typeof(blastn(na1, [na1, na2])) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_QbRW3Q -subject /tmp/jl_5n3BWo -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:82 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:94 [inlined]
   [16] blastn(query::BioSequences.DNASequence, subject::Vector{BioSequences.DNASequence})
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:93
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [18] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:31 [inlined]
   [19] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [20] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:32
  Test threw exception
  Expression: typeof(blastn([na1, na2], [na1, na2])) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_kFh1dR -subject /tmp/jl_Wnttpn -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:82 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:108 [inlined]
   [16] blastn(query::Vector{BioSequences.DNASequence}, subject::Vector{BioSequences.DNASequence})
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:107
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [18] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:32 [inlined]
   [19] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [20] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:33
  Test threw exception
  Expression: typeof(blastn(na1, nucldb, db = true)) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_R1hCHp -db /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/BLASTDB/f002 -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:80 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] #blastn#4
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:100 [inlined]
   [16] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:97 [inlined]
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [18] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:33 [inlined]
   [19] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [20] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:34
  Test threw exception
  Expression: typeof(blastn(na1, fna)) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_9VvMTO -subject /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/FASTA/f002.fasta -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:82 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] #blastn#4
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:102 [inlined]
   [16] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:97 [inlined]
   [17] blastn(query::BioSequences.DNASequence, subject::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:97
   [18] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [19] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:34 [inlined]
   [20] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [21] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:35
  Test threw exception
  Expression: typeof(blastn(fna, nucldb, db = true)) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/FASTA/f002.fasta -db /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/BLASTDB/f002 -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:80 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [16] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:35 [inlined]
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [18] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:36
  Test threw exception
  Expression: typeof(blastn([na1, na2], nucldb, db = true)) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_0euRgB -db /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/BLASTDB/f002 -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:80 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] #blastn#5
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:114 [inlined]
   [16] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:111 [inlined]
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [18] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:36 [inlined]
   [19] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [20] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:37
  Test threw exception
  Expression: typeof(blastn([na1, na2], fna)) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /tmp/jl_COH1YZ -subject /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/FASTA/f002.fasta -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:82 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] #blastn#5
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:116 [inlined]
   [16] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:111 [inlined]
   [17] blastn(query::Vector{BioSequences.DNASequence}, subject::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:111
   [18] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [19] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:37 [inlined]
   [20] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [21] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
BLAST+ blastn: Error During Test at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:38
  Test threw exception
  Expression: typeof(blastn(fna, [na1, na2])) == Array{BLASTResult, 1}
  IOError: could not spawn `blastn -query /home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens/FASTA/f002.fasta -subject /tmp/jl_kLDlt5 -outfmt 5`: no such file or directory (ENOENT)
  Stacktrace:
    [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Memory{Union{RawFD, Base.SyncCloseFD, IO}})
      @ Base ./process.jl:140
    [2] _spawn
      @ ./process.jl:157 [inlined]
    [3] #883
      @ ./process.jl:149 [inlined]
    [4] setup_stdios(f::Base.var"#883#884"{Cmd}, stdios::Vector{Union{RawFD, Base.FileRedirect, IO}})
      @ Base ./process.jl:236
    [5] _spawn
      @ ./process.jl:148 [inlined]
    [6] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
      @ Base ./process.jl:407
    [7] open
      @ ./process.jl:397 [inlined]
    [8] open(cmds::Cmd, mode::String, stdio::Base.DevNull)
      @ Base ./process.jl:378
    [9] read(cmd::Cmd)
      @ Base ./process.jl:480
   [10] read
      @ ./process.jl:491 [inlined]
   [11] readblastXML(blastrun::Cmd; seqtype::String)
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:67
   [12] readblastXML
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:66 [inlined]
   [13] #blastn#3
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:82 [inlined]
   [14] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:78 [inlined]
   [15] blastn
      @ ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:122 [inlined]
   [16] blastn(query::String, subject::Vector{BioSequences.DNASequence})
      @ BioTools.BLAST ~/.julia/packages/BioTools/LY7H3/src/blast/blastcommandline.jl:121
   [17] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [18] macro expansion
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:38 [inlined]
   [19] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
   [20] top-level scope
      @ ~/.julia/packages/BioTools/LY7H3/test/runtests.jl:16
Test Summary: | Error  Total   Time
BLAST+ blastn |     9      9  33.9s
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 9 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/BioTools/LY7H3/test/runtests.jl:1

Testing failed after 23.0s

ERROR: LoadError: Package BioTools errored during testing
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68
 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
   @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2124
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined]
 [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined]
 [8] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:219
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 184.98s: package tests unexpectedly errored