Occasional Pkg git error on precompiling JuliaC #2648
Description
I see this coming back every now and then. Possibly a Pkg bug with git dependencies; our PackageCompiler fork.
Details
15:53:41 ✨ Pixi task (build in default): julia --project --check-bounds=yes build/build.jl
15:53:42 Precompiling packages...
15:54:05 23670.0 ms ✓ JuliaC
15:54:05 1 dependency successfully precompiled in 24 seconds. 38 already precompiled.
15:54:18 Activating project at `/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/core`
15:54:18 Activating project at `/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim`
15:54:19 Running: setenv(`/u/svc-teamcity-ansible/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/bin/julia -C generic -J/u/svc-teamcity-ansible/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/lib/julia/sys.so --check-bounds=yes -g1 --project=core -e 'using Pkg; Pkg.instantiate(); Pkg.precompile()'`,["GDAL_DRIVER_PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/lib/gdalplugins", "DENO_DOM_VERSION=0.1.41-alpha", "PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin:/opt/apps/gcc/12.2.0_gcc12.2.0/bin:/opt/apps/pixi:/usr/share/Modules/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin", "TEAMCITY_VERSION=2025.07.3 (build 197398)", "JRE_HOME=/lib/jvm/jre-openjdk", "TEAMCITY_PROCESS_PARENT_FLOW_ID=", "BUILD_VCS_NUMBER_Ribasim_Ribasim=67916157c29a0449c68f2ce2a6aca31ef3dbedeb", "LD_LIBRARY_PATH=/opt/apps/gcc/12.2.0_gcc12.2.0/lib:/opt/apps/gcc/12.2.0_gcc12.2.0/lib64", "QUARTO_ESBUILD=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin/esbuild", "GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=", "MANPATH=:", "BUILD_URL=https://dpcbuild.deltares.nl/build/6387287", "MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/opt/apps/modules", "PIXI_ENVIRONMENT_PLATFORMS=linux-64,win-64,osx-arm64,linux-aarch64", "PIXI_IN_SHELL=1", "BUILD_NUMBER=1914", "TMP=/opt/teamcityagent/temp/buildTmp", "BUILD_VCS_NUMBER=67916157c29a0449c68f2ce2a6aca31ef3dbedeb", "PROJ_NETWORK=ON", "TEAMCITY_BUILDCONF_NAME=Build Ribasim", "PROJ_DATA=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/proj", "TEAMCITY_BUILD_PROPERTIES_FILE=/opt/teamcityagent/temp/buildTmp/teamcity.build.parameters", "OPENBLAS_DEFAULT_NUM_THREADS=1", "QUARTO_PANDOC=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin/pandoc", "CPLUS_INCLUDE_PATH=/opt/apps/gcc/12.2.0_gcc12.2.0/include", "USER=svc-teamcity-ansible", "TEAMCITY_GIT_PATH=/usr/bin/git", "TYPST_PACKAGE_PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/typst/packages", "JAVA_HOME=/lib/jvm/jre-openjdk", "C_INCLUDE_PATH=/opt/apps/gcc/12.2.0_gcc12.2.0/include", "BASH_FUNC_module%%=() { unset _mlshdbg;\n if [ \"\${MODULES_SILENT_SHELL_DEBUG:-0}\" = '1' ]; then\n case \"\$-\" in \n *v*x*)\n set +vx;\n _mlshdbg='vx'\n ;;\n *v*)\n set +v;\n _mlshdbg='v'\n ;;\n *x*)\n set +x;\n _mlshdbg='x'\n ;;\n *)\n _mlshdbg=''\n ;;\n esac;\n fi;\n unset _mlre _mlIFS;\n if [ -n \"\${IFS+x}\" ]; then\n _mlIFS=\$IFS;\n fi;\n IFS=' ';\n for _mlv in \${MODULES_RUN_QUARANTINE:-};\n do\n if [ \"\${_mlv}\" = \"\${_mlv##*[!A-Za-z0-9_]}\" -a \"\${_mlv}\" = \"\${_mlv#[0-9]}\" ]; then\n if [ -n \"`eval 'echo \${'\$_mlv'+x}'`\" ]; then\n _mlre=\"\${_mlre:-}\${_mlv}_modquar='`eval 'echo \${'\$_mlv'}'`' \";\n fi;\n _mlrv=\"MODULES_RUNENV_\${_mlv}\";\n _mlre=\"\${_mlre:-}\${_mlv}='`eval 'echo \${'\$_mlrv':-}'`' \";\n fi;\n done;\n if [ -n \"\${_mlre:-}\" ]; then\n eval `eval \${_mlre} /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash '\"\$@\"'`;\n else\n eval `/usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl bash \"\$@\"`;\n fi;\n _mlstatus=\$?;\n if [ -n \"\${_mlIFS+x}\" ]; then\n IFS=\$_mlIFS;\n else\n unset IFS;\n fi;\n unset _mlre _mlv _mlrv _mlIFS;\n if [ -n \"\${_mlshdbg:-}\" ]; then\n set -\$_mlshdbg;\n fi;\n unset _mlshdbg;\n return \$_mlstatus\n}", "TEAMCITY_CAPTURE_ENV=\"/usr/lib/jvm/java-21-openjdk-21.0.8.0.9-1.el8.x86_64/bin/java\" -jar \"/opt/teamcityagent/plugins/environment-fetcher/lib/environment-fetcher-bin-2025.07-197398-jar-with-dependencies.jar\"", "SHELL=/bin/bash", "QT_PLUGIN_PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/plugins:", "TMPDIR=/opt/teamcityagent/temp/buildTmp", "MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl", "PATH_modshare=/usr/sbin:1:/usr/bin:1:/opt/apps/gcc/12.2.0_gcc12.2.0/bin:1:/opt/apps/pixi:1:/usr/local/sbin:1:/usr/share/Modules/bin:1:/usr/local/bin:1", "TEAMCITY_GIT_VERSION=2.43.7.0", "QGIS_PREFIX_PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default", "JDK_HOME=/lib/jvm/jre-openjdk", "PIXI_PROJECT_ROOT=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim", "INIT_CWD=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim", "JULIA_CONDAPKG_BACKEND=Null", "SIGRID_CI_TOKEN=*******", "BASH_FUNC_switchml%%=() { typeset swfound=1;\n if [ \"\${MODULES_USE_COMPAT_VERSION:-0}\" = '1' ]; then\n typeset swname='main';\n if [ -e /usr/share/Modules/libexec/modulecmd.tcl ]; then\n typeset swfound=0;\n unset MODULES_USE_COMPAT_VERSION;\n fi;\n else\n typeset swname='compatibility';\n if [ -e /usr/share/Modules/libexec/modulecmd-compat ]; then\n typeset swfound=0;\n MODULES_USE_COMPAT_VERSION=1;\n export MODULES_USE_COMPAT_VERSION;\n fi;\n fi;\n if [ \$swfound -eq 0 ]; then\n echo \"Switching to Modules \$swname version\";\n source /usr/share/Modules/init/bash;\n else\n echo \"Cannot switch to Modules \$swname version, command not found\";\n return 1;\n fi\n}", "TYPST_FONT_PATHS=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/fonts", "HOME=/u/svc-teamcity-ansible", "TEMP=/opt/teamcityagent/temp/buildTmp", "SIGRID_CI_ACCOUNT=*******", "BASH_FUNC_ml%%=() { module ml \"\$@\"\n}", "MODULEPATH_modshare=/opt/apps/modules:1:/usr/share/Modules/modulefiles:2:/etc/modulefiles:2:/usr/share/modulefiles:2", "CPLUS_INCLUDE_PATH_modshare=/opt/apps/gcc/12.2.0_gcc12.2.0/include:1", "PIXI_PROJECT_MANIFEST=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/pixi.toml", "INVOCATION_ID=f5de48824b6e4deba74c4fa72bb47f62", "?=0", "QUARTO_DENO_DOM=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/lib/deno_dom.so", "TEAMCITY_PROCESS_FLOW_ID=2214200501252673", "LANG=en_US.UTF-8", "GSETTINGS_SCHEMA_DIR=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/glib-2.0/schemas", "CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin/x86_64-conda-linux-gnu-cc", "JDK_21_0=/lib/jvm/jre-openjdk", "LOADEDMODULES=pixi/default:gcc/12.2.0_gcc12.2.0", "LOGNAME=svc-teamcity-ansible", "PIXI_PROMPT=(Ribasim) ", "OLDPWD=/opt/teamcityagent/bin", "PIXI_ENVIRONMENT_NAME=default", "SHLVL=3", "_LMFILES_=/opt/apps/modules/pixi/default:/opt/apps/modules/gcc/12.2.0_gcc12.2.0", "_=/opt/apps/pixi/pixi", "CONDA_DEFAULT_ENV=Ribasim", "QUARTO_CONDA_PREFIX=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default", "LOADEDMODULES_modshare=gcc/12.2.0_gcc12.2.0:1:pixi/default:1", "QUARTO_TYPST=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin/typst", "PIXI_PROJECT_NAME=Ribasim", "JULIA_NUM_THREADS=8", "GDAL_DATA=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/gdal", "MODULESHOME=/usr/share/Modules", "PWD=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim", "QUARTO_DART_SASS=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin/sass", "_LMFILES__modshare=/opt/apps/modules/gcc/12.2.0_gcc12.2.0:1:/opt/apps/modules/pixi/default:1", "LD_LIBRARY_PATH_modshare=/opt/apps/gcc/12.2.0_gcc12.2.0/lib:1:/opt/apps/gcc/12.2.0_gcc12.2.0/lib64:1", "CPL_ZIP_ENCODING=UTF-8", "PDAL_DRIVER_PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/lib", "DENO_INSTALL_ROOT=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default", "PYTHONPATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/qgis/python/plugins:/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/qgis/python:", "DENO_DOM_PLUGIN=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/lib/deno_dom.so", "MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD", "XML_CATALOG_FILES=file:///opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/etc/xml/catalog file:///etc/xml/catalog", "QUARTO_SHARE_PATH=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/share/quarto", "PIXI_EXE=/opt/apps/pixi/pixi", "PKG_CONFIG_PATH_modshare=/opt/apps/gcc/12.2.0_gcc12.2.0/lib/pkgconfig:1", "CONDA_PREFIX=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default", "C_INCLUDE_PATH_modshare=/opt/apps/gcc/12.2.0_gcc12.2.0/include:1", "JOURNAL_STREAM=9:32709", "PKG_CONFIG_PATH=/opt/apps/gcc/12.2.0_gcc12.2.0/lib/pkgconfig", "QUARTO_DENO=/opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/bin/deno", "UID=1028537", "TEAMCITY_PROJECT_NAME=Ribasim_Linux", "JULIA_CPU_TARGET=generic;sandybridge,-xsaveopt,clone_all;haswell,-rdrnd,base(1)", "PIXI_PROJECT_VERSION=2025.5.0", "JDK_21_0_x64=/lib/jvm/jre-openjdk", "OPENBLAS_MAIN_FREE=1"])
15:54:23 ERROR: ArgumentError: collection must be non-empty
15:54:23 Stacktrace:
15:54:23 [1] first
15:54:23 @ ./abstractarray.jl:473 [inlined]
15:54:23 [2] install_git(io::IOContext{IO}, uuid::Base.UUID, name::String, hash::Base.SHA1, urls::Set{String}, version_path::String)
15:54:23 @ Pkg.Operations ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:796
15:54:23 [3] download_source(ctx::Pkg.Types.Context, pkgs::Base.ValueIterator{Dict{Base.UUID, Pkg.Types.PackageEntry}}; readonly::Bool)
15:54:23 @ Pkg.Operations ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1174
15:54:23 [4] download_source
15:54:23 @ ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1056 [inlined]
15:54:23 [5] download_source
15:54:23 @ ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:1054 [inlined]
15:54:23 [6] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, workspace::Bool, julia_version_strict::Bool, kwargs::@Kwargs{})
15:54:23 @ Pkg.API ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/API.jl:1279
15:54:23 [7] instantiate
15:54:23 @ ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/API.jl:1176 [inlined]
15:54:23 [8] instantiate(; kwargs::@Kwargs{})
15:54:23 @ Pkg.API ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/Pkg/src/API.jl:1175
15:54:23 [9] top-level scope
15:54:23 @ none:1
15:54:23 [10] eval(m::Module, e::Any)
15:54:23 @ Core ./boot.jl:489
15:54:23 [11] exec_options(opts::Base.JLOptions)
15:54:23 @ Base ./client.jl:283
15:54:23 [12] _start()
15:54:23 @ Base ./client.jl:550
15:54:25 ERROR: Error encountered during instantiate/precompile of app project.
15:54:25 Stacktrace:
15:54:25 [1] error(s::String)
15:54:25 @ Base ./error.jl:44
15:54:25 [2] compile_products(recipe::ImageRecipe)
15:54:25 @ JuliaC /opt/teamcityagent/work/ecd2b8f9b25b1609/.julia/packages/JuliaC/vTRbe/src/compiling.jl:86
15:54:25 [3] main(::Vector{String})
15:54:25 @ Main /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/build/build.jl:35
15:54:25 [4] _start()
15:54:25 @ Base ./client.jl:556
Restarting usually works. I think I only saw this on Linux.