I don’t understand this error reported by Documenter.jl - in particular, why is Documenter prefixing my PATH with the strange artifact? why:
floswald@PTL11077 ~/.j/d/P/docs (main)> /Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin/git remote show origin
dyld[93378]: Library not loaded: @rpath/libpcre2-8.0.dylib
Referenced from: <4C4C4432-5555-3144-A1A5-EBD11D7E8E32> /Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin/_git
Reason: tried: '/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin/../lib/libpcre2-8.0.dylib' (no such file), '/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/workspace/destdir/lib/libpcre2-8.0.dylib' (no such file), '/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin/../lib/libpcre2-8.0.dylib' (no such file), '/libpcre2-8.0.dylib' (no such file)
fish: Job 1, '/Users/floswald/.julia/artifact…' terminated by signal SIGABRT (Abort)
when this works perfectly well?
floswald@PTL11077 ~/.j/d/P/docs (main) [SIGABRT]> git remote show origin
* remote origin
Fetch URL: git@github.com:floswald/PIIScanner.jl.git
Push URL: git@github.com:floswald/PIIScanner.jl.git
HEAD branch: main
Remote branch:
main tracked
Local branch configured for 'git pull':
main merges with remote main
Local ref configured for 'git push':
main pushes to main (up to date)
floswald@PTL11077 ~/.j/d/P/docs (main)>
here is the full output of make.jl
floswald@PTL11077 ~/.j/d/P/docs (main)> JULIA_DEBUG=Documenter julia --project make.jl
┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master".
│ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error.
│ Unless this is due to a configuration error, the relevant variable should be set explicitly.
└ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/utilities/utilities.jl:680
┌ Debug: Command: setenv(`/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin/git remote show origin`,["PATH=/Users/floswald/.julia/artifacts/154306f0b5fcd9c59ee1d37c70553c8b8ab75ba4/bin:/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin:/Users/floswald/.julia/artifacts/3fa3ae5a55c864014d9c801405cb178ff567c9ea/bin:/Applications/google-cloud-sdk/bin:/opt/homebrew/Cellar/pyenv-virtualenv/1.2.4/shims:/Users/floswald/.pyenv/shims:/Users/floswald/.julia/bin:/Users/floswald/.local/share/gem/ruby/3.4.0/bin:/Applications/StataNow/StataMP.app/Contents/MacOS:/Users/floswald/.duckdb/cli/latest:/Applications/Stata/StataMP.app/Contents/MacOS:/opt/homebrew/opt/ruby/bin:/Users/floswald/.pixi/bin:/Applications/quarto/bin:/opt/homebrew/bin:/Users/floswald/.juliaup/bin:/usr/bin:/usr/local/bin:/Library/TeX/texbin:/bin:/usr/sbin:/System/Cryptexes/App/usr/bin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Users/floswald/.orbstack/bin", "EDITOR=vi", "R_LIBS_USER=/Users/floswald/Library/R/arm64/4.5/library", "LETTER_TEMPLATES=/Users/floswald/Dropbox/supervision/templates", "EJ_DB=/Users/floswald/Dropbox/EJ", "R_PDFVIEWER=/usr/bin/open", "JPE_TOOLS_JL=/Users/floswald/git/JPEtools", "SLACK_FILES=xoxb-437685214404-1790526147312-1WvTgLis5nxrWaIOlacvfst6", "R_GMAIL_EJ=/Users/floswald/git/EJData/gmail-clients/EJ/ej.json", "PYENV_VIRTUALENV_INIT=1", "R_INCLUDE_DIR=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/include", "R_TEXI2DVICMD=/opt/R/arm64/bin/texi2dvi", "JPE_DUCKDB=/Users/floswald/Dropbox/JPE/database/jpe.duckdb", "R_HOME=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources", "PYENV_ROOT=/Users/floswald/.pyenv", "SIGNATURE=/Users/floswald/signature.png", "OPENAI=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", "R_BZIPCMD=/usr/bin/bzip2", "GIT_TERMINAL_PROMPT=0", "SED=/usr/bin/sed", "JPE_GOOGLE_KEY=/Users/floswald/Dropbox/JPE/keys/analog-stage-459414-f2-be89612d0b81.json", "JPE_DBOX_APP_REFRESH=G7EqV3_EV7kAAAAAAAAAAaNuuaadk9x21-fH_gzI5KfCdWJemCRy95G7gc9uhi3g", "OPENBLAS_DEFAULT_NUM_THREADS=1", "GIT_TEMPLATE_DIR=/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/share/git-core/templates", "USER=floswald", "JL_DB_EJ=/Users/floswald/Dropbox/EJ", "JLL_DYLD_FALLBACK_LIBRARY_PATH=/Users/floswald/.julia/juliaup/julia-1.12.4+0.aarch64.apple.darwin14/lib/julia:/Users/floswald/.julia/artifacts/d017b9246247518792dcb16dae9af38dfb0c5eb6/lib:/Users/floswald/.julia/artifacts/b820a0a437e8501d06a17439abd84feaa5b6cca3/lib:/Users/floswald/.julia/juliaup/julia-1.12.4+0.aarch64.apple.darwin14/bin/../lib/julia:/Users/floswald/.julia/juliaup/julia-1.12.4+0.aarch64.apple.darwin14/bin/../lib", "JPE_DBOX=/Users/floswald/Dropbox/JPE", "DROPBOXSDK_ACCESS_TOKEN=/Users/floswald/.julia/config/dropbox/RES_token.JSON", "SHELL=/opt/homebrew/bin/fish", "NUVOLOS=3424-hfbGnwcSSUqaGUqcGr8Y2JYDeiL_rYQxRkO0zv92-gI", "TAR=/usr/bin/tar", "R_PLATFORM=aarch64-apple-darwin20", "JPE_DV=22f0a051-eef5-4460-a3f6-1ee9d642e76b", "TMPDIR=/var/folders/5q/yhcyv3z55wvg6lhgc3h22kk00000gq/T/", "R_LANDUSE=/Users/floswald/Downloads/package-submission/ReplicationPackage-submit", "DROPBOX_SECRETS=/Users/floswald/.julia/config/dropbox/RES_secrets.JSON", "DE_DB=sl.Bqeo5iiQ_CwWO_TdHUe1o8Hny7pSd7XVu_ZTfBe2SYPHkGM_Jwj8zmYOZp9_vGIOlr33pIXzYKD95144jFzN-77ZjJSNsyWfn_3maQIWq-GV5rLh5zm1fZx8whcTqWxwKZ9uV7e4RLnLEP0", "JPE_GMAIL_TOKEN=/Users/floswald/Dropbox/JPE/keys/gmail_tokens.json", "GIT_SSH_COMMAND=ssh -o \"BatchMode yes\"", "JPE_DBOX_APPS=/Users/floswald/Dropbox/Apps/JPE-packages", "R_QPDF=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/bin/qpdf", "R_STRIP_SHARED_LIB=strip -x", "JULIA_DEBUG=Documenter", "TERM=xterm-256color", "HOME=/Users/floswald", "JPE_PACKAGES=/Users/floswald/Dropbox/Apps/JPE-packages", "R_STRIP_STATIC_LIB=strip -S", "XPC_FLAGS=0x0", "STATA_LICENSE_PATH=/Users/floswald/Dropbox/licenses/stata.lic", "XPC_SERVICE_NAME=0", "R_GZIPCMD=/usr/bin/gzip", "GIT_EXEC_PATH=/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/libexec/git-core", "DYLD_FALLBACK_LIBRARY_PATH=/Users/floswald/.julia/juliaup/julia-1.12.4+0.aarch64.apple.darwin14/lib/julia:/Users/floswald/.julia/artifacts/d017b9246247518792dcb16dae9af38dfb0c5eb6/lib:/Users/floswald/.julia/artifacts/b820a0a437e8501d06a17439abd84feaa5b6cca3/lib", "__CF_USER_TEXT_ENCODING=0x1F7:0x0:0x2", "R_GMAIL_ECTJ=/Users/floswald/git/EJData/gmail-clients/ECTJ/ectj.json", "CSL=/Users/floswald/git/styles", "LC_CTYPE=UTF-8", "MAKE=make", "__CFBundleIdentifier=com.apple.Terminal", "R_SESSION_TMPDIR=/var/folders/5q/yhcyv3z55wvg6lhgc3h22kk00000gq/T//RtmpMNoOZB", "RES_PROD=true", "JPE_GMAIL_CLIENT=/Users/floswald/Dropbox/JPE/keys/jpe-gmail-client.json", "OSTYPE=darwin24", "R_PAPERSIZE=a4", "PYENV_SHELL=fish", "SHLVL=1", "LOGNAME=floswald", "SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.RmYe6CDDgX/Listeners", "GUROBI_HOME=/Users/floswald/", "JPE_DBOX_APP=l5g60uc0i2yn2iw", "AUTOJUMP_SOURCED=1", "PAGER=/usr/bin/less", "SLACK_HOOK=https://hooks.slack.com/services/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", "R_RD4PDF=times,inconsolata,hyper", "R_DROPBOX=~/Dropbox/research", "TERM_PROGRAM_VERSION=455.1", "IPUMS_API_KEY=59cba10d8a5da536fc06b59d9ac7d661f42b412d8c7df88a21002e33", "R_LIBS_SITE=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/site-library", "PWD=/Users/floswald/.julia/dev/PIIScanner.jl/docs", "DISPLAY=/private/tmp/com.apple.launchd.kgleEUFoek/org.xquartz:0", "JPE_DBOX_APP_SECRET=0b2zxcxogohm5ag", "TERM_PROGRAM=Apple_Terminal", "PYTHONPATH=/opt/homebrew/opt/python@3.10/", "R_ZIPCMD=/usr/bin/zip", "AUTOJUMP_ERROR_PATH=/Users/floswald/Library/autojump/errors.log", "TFL_KEY=b9a56830cac3473fb6d2ac63b2991f24", "DROPBOX_JPE=/Users/floswald/Dropbox/JPE", "JPE_DB=/Users/floswald/JPE", "TERM_SESSION_ID=8251582C-2882-45BA-8056-C0A2CC860ACF", "R_UNZIPCMD=/usr/bin/unzip", "R_BROWSER=/usr/bin/open", "R_DB_EJ=~/Dropbox/EJ", "ZENODO_READ=lxqSLNPJI8aKHSZ84o046IQnuUEl6ad1KSo9KS4aoy4vgxxcEkbCjWvwh8JY", "R_PRINTCMD=lpr", "R_SHARE_DIR=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/share", "TIM_GDRIVE=/Users/floswald/Google Drive/My Drive/TIM", "R_DOC_DIR=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/doc", "GIT_SSL_CAINFO=/Users/floswald/.julia/juliaup/julia-1.12.4+0.aarch64.apple.darwin14/share/julia/cert.pem", "JPE_DB_BACKUPS=/Users/floswald/Dropbox/JPE/database", "OPENBLAS_MAIN_FREE=1", "LN_S=ln -s"]; dir="/Users/floswald/.julia/dev/PIIScanner.jl/docs")
│ exception =
│ failed process: Process(setenv(`/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin/git remote show origin`,["PATH=/Users/floswald/.julia/artifacts/154306f0b5fcd9c59ee1d37c70553c8b8ab75ba4/bin:/Users/floswald/.julia/artifacts/9a049d4b53ce75a92a831b451896c8c029234177/bin:/Users/floswald/.julia/artifacts/3fa3ae5a55c864014d9c801405cb178ff567c9ea/bin:/Applications/google-cloud-sdk/bin:/opt/homebrew/Cellar/pyenv-virtualenv/1.2.4/shims:/Users/floswald/.pyenv/shims:/Users/floswald/.julia/bin:/Users/floswald/.local/share/gem/ruby/3.4.0/bin:/Applications/StataNow/StataMP.app/Contents/MacOS:/Users/floswald/.duckdb/cli/latest:/Applications/Stata/StataMP.app/Contents/MacOS:/opt/homebrew/opt/ruby/bin:/Users/floswald/.pixi/bin:/Applications/quarto/bin:/opt/homebrew/bin:/Users/floswald/.juliaup/bin:/usr/bin:/usr/local/bin:/Library/TeX/texbin:/bin:/usr/sbin:/System/Cryptexes/App/usr/bin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Users/floswald/.orbstack/bin", "EDITOR=vi", "R_LIBS_USER=/Users/floswald/Library/R/arm64/4.5/library", "LETTER_TEMPLATES=/Users/floswald/Dropbox/supervision/templates", "EJ_DB=/Users/floswald/Dropbox/EJ", "R_PDFVIEWER=/usr/bin/open", "JPE_TOOLS_JL=/Users/floswald/git/JPEtools", "SLACK_FILES=xoxb-437685214404-1790526147312-1WvTgLis5nxrWaIOlacvfst6", "R_GMAIL_EJ=/Users/floswald/git/EJData/gmail-clients/EJ/ej.json", "PYENV_VIRTUALENV_INIT=1" … "R_DB_EJ=~/Dropbox/EJ", "ZENODO_READ=lxqSLNPJI8aKHSZ84o046IQnuUEl6ad1KSo9KS4aoy4vgxxcEkbCjWvwh8JY", "R_PRINTCMD=lpr", "R_SHARE_DIR=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/share", "TIM_GDRIVE=/Users/floswald/Google Drive/My Drive/TIM", "R_DOC_DIR=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/doc", "GIT_SSL_CAINFO=/Users/floswald/.julia/juliaup/julia-1.12.4+0.aarch64.apple.darwin14/share/julia/cert.pem", "JPE_DB_BACKUPS=/Users/floswald/Dropbox/JPE/database", "OPENBLAS_MAIN_FREE=1", "LN_S=ln -s"]; dir="/Users/floswald/.julia/dev/PIIScanner.jl/docs"), ProcessExited(128)) [128]
│
│ Stacktrace:
│ [1] pipeline_error
│ @ ./process.jl:597 [inlined]
│ [2] read(cmd::Base.CmdRedirect)
│ @ Base ./process.jl:481
│ [3] read
│ @ ./process.jl:490 [inlined]
│ [4] git_remote_head_branch(varname::String, root::String; remotename::String, fallback::String)
│ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/utilities/utilities.jl:678
│ [5] git_remote_head_branch
│ @ ~/.julia/packages/Documenter/xvqbW/src/utilities/utilities.jl:659 [inlined]
│ [6] Documenter.HTMLWriter.HTML()
│ @ Documenter.HTMLWriter ~/.julia/packages/Documenter/xvqbW/src/html/HTMLWriter.jl:507
│ [7] top-level scope
│ @ ~/.julia/dev/PIIScanner.jl/docs/make.jl:3
│ [8] include(mod::Module, _path::String)
│ @ Base ./Base.jl:306
│ [9] exec_options(opts::Base.JLOptions)
│ @ Base ./client.jl:317
│ [10] _start()
│ @ Base ./client.jl:550
│ stderr = "dyld[90809]: Library not loaded: @rpath/libcrypto.3.dylib\n Referenced from: <4C4C44BD-5555-3144-A1F5-00E5742482C4> /Users/floswald/.julia/artifacts/3fa3ae5a55c864014d9c801405cb178ff567c9ea/bin/ssh\n Reason: tried: '/Users/floswald/.julia/artifacts/3fa3ae5a55c864014d9c801405cb178ff567c9ea/bin/../lib/libcrypto.3.dylib' (no such file), '/Users/floswald/.julia/artifacts/3fa3ae5a55c864014d9c801405cb178ff567c9ea/bin/../lib/libcrypto.3.dylib' (no such file), '/usr/local/lib/libcrypto.3.dylib' (no such file), '/usr/lib/libcrypto.3.dylib' (no such file, not in dyld cache)\nfatal: Could not read from remote repository.\n\nPlease make sure you have the correct access rights\nand the repository exists.\n"
└ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/utilities/utilities.jl:685
┌ Debug: interpret_repo_and_remotes
│ remotes_checked = Documenter.RemoteRepository[]
│ repo_normalized = Documenter.Remotes.GitHub("floswald", "PIIScanner.jl")
│ makedocs_root_remoteref = nothing
│ makedocs_root_repo = "/Users/floswald/.julia/dev/PIIScanner.jl"
│ makedocs_root_remote = Documenter.Remotes.GitHub("floswald", "PIIScanner.jl")
└ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/documents.jl:604
┌ Debug: Remotes: using automatically determined remote
│ makedocs_root_remoteref = nothing
│ makedocs_root_repo = "/Users/floswald/.julia/dev/PIIScanner.jl"
│ makedocs_root_remote = Documenter.Remotes.GitHub("floswald", "PIIScanner.jl")
│ repo_normalized = Documenter.Remotes.GitHub("floswald", "PIIScanner.jl")
└ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/documents.jl:669
┌ Debug: Document: remotes
│ remote = Documenter.Remotes.GitHub("floswald", "PIIScanner.jl")
│ remotes =
│ 1-element Vector{Documenter.RemoteRepository}:
│ Documenter.RemoteRepository("/Users/floswald/.julia/dev/PIIScanner.jl", Documenter.Remotes.GitHub("floswald", "PIIScanner.jl"), "df74c7b917e5c142eabff44a1d4a2696782f6b96")
└ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/documents.jl:462
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
┌ Debug: Running doctests.