Well, it used to work 5 days ago, but today the compilation fails, even if I go back to the commit I did just after it had worked:
┌ Error: Error building `QafDemux`:
│ [ Info: Smallest distance between barcodes: 3
│ ┌ Info: Fastq files have been written:
│ │ outfile_paths_dict =
│ │ Dict{String,String} with 13 entries:
│ │ "GCAGAGAGGAAT" => "test_run/GCAGAGAGGAAT.fastq.gz"
│ │ "GCAGAGAGAGAC" => "test_run/GCAGAGAGAGAC.fastq.gz"
│ │ "GCAGAGATGTTG" => "test_run/GCAGAGATGTTG.fastq.gz"
│ │ "GCAGAGACCAAC" => "test_run/GCAGAGACCAAC.fastq.gz"
│ │ "Undetermined" => "test_run/Undetermined.fastq.gz"
│ │ "GCAGAGAGGCTA" => "test_run/GCAGAGAGGCTA.fastq.gz"
│ │ "GCAGAGACAACT" => "test_run/GCAGAGACAACT.fastq.gz"
│ └ ⋮ => ⋮
│ ┌ Warning: Snoop file errored. Precompile statements were recorded untill error!
│ │ exception =
│ │ LoadError: MethodError: no method matching make_record_reader(::SubString{String}, ::Array{String,1}, ::getfield(QafDemux, Symbol("#seq_qual_extractor#7")){UnitRange{Int64}}, ::Bool)
│ │ Closest candidates are:
│ │ make_record_reader(!Matched::String, ::Array{String,1}, ::Any, ::Any) at /home/bli/src/qaf_demux/Julia/QafDemux/src/QafDemux.jl:216
│ │ make_record_reader(!Matched::String, ::Array{String,1}, ::Any) at /home/bli/src/qaf_demux/Julia/QafDemux/src/QafDemux.jl:216
│ │ in expression starting at /home/bli/src/qaf_demux/Julia/QafDemux/bin/snoop.jl:16
│ └ @ Main ~/.julia/packages/PackageCompiler/CJQcs/sysimg/run_julia_code.jl:7
│ ERROR: Unable to find compatible target in system image.
│ [ Info: used 266 out of 266 precompile statements
│ ERROR: LoadError: failed process: Process(`/home/bli/src/julia/usr/bin/julia --cpu-target=x86_64 --output-o=qaf_demux.a --track-allocation=none --code-coverage=none --inline=yes --math-mode=ieee --startup-file=no --compile=yes --track-allocation=none --sysimage-native-code=yes --sysimage=/home/bli/src/julia/usr/lib/julia/sys.so --compiled-modules=yes --optimize=0 /home/bli/.julia/packages/PackageCompiler/CJQcs/sysimg/run_julia_code.jl`, ProcessExited(1)) [1]
│
│ Stacktrace:
│ [1] pipeline_error at ./process.jl:813 [inlined]
│ [2] #run#536(::Bool, ::typeof(run), ::Cmd) at ./process.jl:728
│ [3] run at ./process.jl:726 [inlined]
│ [4] #run_julia#1 at /home/bli/.julia/packages/PackageCompiler/CJQcs/src/compiler_flags.jl:225 [inlined]
│ [5] #run_julia at ./none:0 [inlined]
│ [6] (::getfield(PackageCompiler, Symbol("##13#14")){Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,String,Nothing,Nothing,Nothing,Nothing,Nothing}}},String})() at /home/bli/.julia/packages/PackageCompiler/CJQcs/src/static_julia.jl:263
│ [7] cd(::getfield(PackageCompiler, Symbol("##13#14")){Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,String,Nothing,Nothing,Nothing,Nothing,Nothing}}},String}, ::String) at ./file.jl:96
│ [8] #build_object#12(::Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,String,Nothing,Nothing,Nothing,Nothing,Nothing}}}, ::typeof(PackageCompiler.build_object), ::String, ::String, ::String, ::Bool) at /home/bli/.julia/packages/PackageCompiler/CJQcs/src/static_julia.jl:262
│ [9] #build_object at ./none:0 [inlined]
│ [10] build_object(::String, ::String, ::String, ::Bool, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing) at /home/bli/.julia/packages/PackageCompiler/CJQcs/src/static_julia.jl:241
│ [11] #static_julia#5(::Nothing, ::Bool, ::Bool, ::Nothing, ::String, ::String, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Bool, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(static_julia), ::String) at /home/bli/.julia/packages/PackageCompiler/CJQcs/src/static_julia.jl:162
│ [12] #static_julia at ./tuple.jl:0 [inlined]
│ [13] #build_executable#31 at /home/bli/.julia/packages/PackageCompiler/CJQcs/src/api.jl:104 [inlined]
│ [14] #build_executable at ./none:0 [inlined] (repeats 2 times)
│ [15] top-level scope at /home/bli/src/qaf_demux/Julia/QafDemux/deps/build.jl:14
│ [16] include at ./boot.jl:328 [inlined]
│ [17] include_relative(::Module, ::String) at ./loading.jl:1094
│ [18] include(::Module, ::String) at ./Base.jl:31
│ [19] include(::String) at ./client.jl:431
│ [20] top-level scope at none:5
│ in expression starting at /home/bli/src/qaf_demux/Julia/QafDemux/deps/build.jl:14
│ Building qaf_demux
│ Updating registry at `~/.julia/registries/BioJuliaRegistry`
│ Updating git-repo `https://github.com/BioJulia/BioJuliaRegistry.git`
Updating registry at `~/.julia/registries/General`
│ Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
│ Updating `/tmp/jl_BKXKwA/Project.toml`
│ [3fa0cd96] + REPL
│ Updating `/tmp/jl_BKXKwA/Manifest.toml`
│ [2a0f44e3] ~ Base64 [`@stdlib/Base64`] ⇒
│ [ade2ca70] ~ Dates [`@stdlib/Dates`] ⇒
│ [8bb1440f] ~ DelimitedFiles [`@stdlib/DelimitedFiles`] ⇒
│ [8ba89e20] ~ Distributed [`@stdlib/Distributed`] ⇒
│ [b77e0a4c] ~ InteractiveUtils [`@stdlib/InteractiveUtils`] ⇒
│ [76f85450] ~ LibGit2 [`@stdlib/LibGit2`] ⇒
│ [8f399da3] ~ Libdl [`@stdlib/Libdl`] ⇒
│ [37e2e46d] ~ LinearAlgebra [`@stdlib/LinearAlgebra`] ⇒
│ [56ddb016] ~ Logging [`@stdlib/Logging`] ⇒
│ [d6f4376e] ~ Markdown [`@stdlib/Markdown`] ⇒
│ [a63ad114] ~ Mmap [`@stdlib/Mmap`] ⇒
│ [de0858da] ~ Printf [`@stdlib/Printf`] ⇒
│ [3fa0cd96] ~ REPL [`@stdlib/REPL`] ⇒
│ [9a3f8284] ~ Random [`@stdlib/Random`] ⇒
│ [ea8e919c] ~ SHA [`@stdlib/SHA`] ⇒
│ [9e88b42a] ~ Serialization [`@stdlib/Serialization`] ⇒
│ [1a1011a3] ~ SharedArrays [`@stdlib/SharedArrays`] ⇒
│ [6462fe0b] ~ Sockets [`@stdlib/Sockets`] ⇒
│ [2f01184e] ~ SparseArrays [`@stdlib/SparseArrays`] ⇒
│ [10745b16] ~ Statistics [`@stdlib/Statistics`] ⇒
│ [8dfed614] ~ Test [`@stdlib/Test`] ⇒
│ [cf7118a7] ~ UUIDs [`@stdlib/UUIDs`] ⇒
│ [4ec0a83e] ~ Unicode [`@stdlib/Unicode`] ⇒
│ Resolving package versions...
│ Updating `/tmp/jl_BKXKwA/Project.toml`
│ [no changes]
│ Updating `/tmp/jl_BKXKwA/Manifest.toml`
│ [no changes]
│ Julia program file:
│ "/home/bli/src/qaf_demux/Julia/QafDemux/bin/qaf_demux_to_compile.jl"
│ C program file:
│ "/home/bli/.julia/packages/PackageCompiler/CJQcs/examples/program.c"
│ Build directory:
│ "/home/bli/src/qaf_demux/Julia/QafDemux/deps/builddir"
└ @ Pkg.Operations ~/src/julia/usr/share/julia/stdlib/v1.2/Pkg/src/backwards_compatible_isolation.jl:647
My make_record_reader has the following declaration:
function make_record_reader(fq_filename::String, barcodes::Vector{String}, seq_qual_extractor, func_style=true)
And is called as follows:
make_record_reader(fq_filename, barcodes, seq_qual_extractor, true)
Where seq_qual_extractor is generated by the following piece of code:
if bc_start < 0
# bc_range has to be computed for each read based on its length
seq_qual_extractor = make_seq_qual_extractor(bc_start, bc_len)
else
bc_range = bc_start:bc_start+(bc_len-1)
seq_qual_extractor = make_seq_qual_extractor(bc_range)
end
So it is the result of either one of the following functions:
function make_seq_qual_extractor(bc_range::UnitRange{Int})
function seq_qual_extractor(record::fq.Record)::Tuple{String,Vector{UInt8}}
subseq = fq.sequence(String, record, bc_range)
quals = fq.quality(record, :illumina18, bc_range)
return (subseq, quals)
end
end
function make_seq_qual_extractor(bc_start::Int, bc_len::Int)
@assert bc_start < 0 "*bc_start* should be negative."
function seq_qual_extractor(record::fq.Record)::Tuple{String,Vector{UInt8}}
seq = fq.sequence(String, record)
seq_len = length(seq)
real_start = seq_len + bc_start + 1
bc_range = real_start:real_start+(bc_len-1)
quals = fq.quality(record, :illumina18, bc_range)
return (seq[bc_range], quals)
end
end
It turns out that on this machine, I use a locally-compiled Julia, and that the failure to compile was due to the use of cpu_target="x86_64"
$ cat deps/build.jl
import Pkg
println("Building qaf_demux")
Pkg.add("REPL")
Pkg.add("PackageCompiler")
#push!(LOAD_PATH, abspath(joinpath(@__DIR__, "../src/")))
using PackageCompiler
# setting cpu_target does not work with a self-built Julia: https://github.com/NHDaly/ApplicationBuilder.jl/issues/62#issuecomment-503721859
# Compile:
build_executable(joinpath(@__DIR__, "../bin/qaf_demux_to_compile.jl"), "qaf_demux", snoopfile=joinpath(@__DIR__, "../bin/snoop.jl"))
# Does not compile:
# build_executable(joinpath(@__DIR__, "../bin/qaf_demux_to_compile.jl"), "qaf_demux", snoopfile=joinpath(@__DIR__, "../bin/snoop.jl"), cpu_target="x86_64")
How come this generates the kind of compile error above ?!