Closed mptrsen closed 6 months ago
Following the instructions here, the compilation fails with the complete error here. The main cause is this:
$ mamba create -p conda/patchwork -c bioconda -c conda-forge diamond julia $ mamba activate conda/patchwork/ $ git clone https://github.com/fethalen/patchwork $ cd patchwork/ $ mkdir local $ julia src/compile.jl . src/precompiled.jl local [... list of dependencies ...] ERROR: The following 1 direct dependency failed to precompile: PackageCompiler [9b87118b-4619-50d2-8e1e-99f35a4d4d9d] Error: Missing source file for PackageCompiler [9b87118b-4619-50d2-8e1e-99f35a4d4d9d Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types ~/projects/patchwork_test/conda/patchwork/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67 [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{String}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Pkg.API ~/projects/patchwork_test/conda/patchwork/share/julia/stdlib/v1.8/Pkg/src/API.jl:1432 [3] precompile @ ~/projects/patchwork_test/conda/patchwork/share/julia/stdlib/v1.8/Pkg/src/API.jl:1063 [inlined] [4] #precompile#225 @ ~/projects/patchwork_test/conda/patchwork/share/julia/stdlib/v1.8/Pkg/src/API.jl:1062 [inlined] [5] precompile (repeats 2 times) @ ~/projects/patchwork_test/conda/patchwork/share/julia/stdlib/v1.8/Pkg/src/API.jl:1062 [inlined] [6] top-level scope @ none:1 ERROR: LoadError: failed process: Process(setenv(`/home/malte/projects/patchwork_test/conda/patchwork/bin/julia --color=yes --startup-file=no --sysimage=/tmp/jl_FxcNAf/sys.ji -e 'using Pkg; Pkg.precompile()'`,["CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu", "DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus", "CONDA_BACKUP_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/malte/projects/patchwork_test/conda/busco/include", "CONDA_JL_HOME_BACKUP=", "XDG_CONFIG_DIRS=/etc/xdg/xdg-xubuntu:/etc/xdg:/etc/xdg", "CONDA_BACKUP_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/malte/projects/patchwork_test/conda/busco/include", "LC_NUMERIC=de_DE.UTF-8", "LC_MEASUREMENT=de_DE.UTF-8", "JULIA_PROJECT=@patchwork", "CONDA_PROMPT_MODIFIER=(/home/malte/projects/patchwork_test/conda/patchwork) " … "CONDA_BACKUP_SIZE=/home/malte/projects/patchwork_test/conda/busco/bin/x86_64-conda-linux-gnu-size", "GDM_LANG=en_US", "LC_PAPER=de_DE.UTF-8", "_=/home/malte/projects/patchwork_test/conda/patchwork/bin/julia", "CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/malte/projects/patchwork_test/conda/busco/include", "CONDA_BACKUP_RANLIB=/home/malte/projects/patchwork_test/conda/busco/bin/x86_64-conda-linux-gnu-ranlib", "CONDA_BACKUP_STRIP=/home/malte/projects/patchwork_test/conda/busco/bin/x86_64-conda-linux-gnu-strip", "LC_IDENTIFICATION=de_DE.UTF-8", "JULIA_LOAD_PATH=/home/malte/projects/patchwork_test/patchwork:@stdlib", "LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:"]), ProcessExited(1)) [1] [stack trace]
The updated compilation procedure should solve the issues you were having. If not, consider reopening this issue.
Following the instructions here, the compilation fails with the complete error here. The main cause is this: