Julia Markdown not "Weaving"

How-to
1

Hello!

I am new to using Pumas and am working on basic structural model identification. I am currently using a Julia Markdown file and want to view it as an HTML/PDF. Although, when I try to use Weave.jl, I get the following error:

julia> Pkg.add("Weave")
    Updating registry at `C:\Users\preru\.julia\registries\General`
ERROR: GitError(Code:ENOTFOUND, Class:Config, config value 'safe.directory' was not found)
Stacktrace:
  [1] macro expansion
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\LibGit2\src\error.jl:111 [inlined]
  [2] LibGit2.GitRepo(path::String)
    @ LibGit2 C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\LibGit2\src\repository.jl:11
  [3] (::Pkg.Registry.var"#73#78"{Base.TTY, Dates.Day, Dict{String, Any}, String, Vector{Pkg.Registry.RegistryInstance}})()
    @ Pkg.Registry C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:449
  [4] mkpidlock(f::Pkg.Registry.var"#73#78"{Base.TTY, Dates.Day, Dict{String, Any}, String, Vector{Pkg.Registry.RegistryInstance}}, at::String, pid::Int32; kwopts::Base.Pairs{Symbol, Int64, Tuple{Symbol}, NamedTuple{(:stale_age,), Tuple{Int64}}})
    @ FileWatching.Pidfile C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\FileWatching\src\pidfile.jl:82
  [5] #mkpidlock#6
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\FileWatching\src\pidfile.jl:77 [inlined]
  [6] mkpidlock
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\FileWatching\src\pidfile.jl:77 [inlined]
  [7] update(regs::Vector{Pkg.Registry.RegistrySpec}; io::Base.TTY, force::Bool, depots::Vector{String}, update_cooldown::Dates.Day)
    @ Pkg.Registry C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:379
  [8] update
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:372 [inlined]
  [9] update_registries(ctx::Pkg.Types.Context; force::Bool, kwargs::Base.Pairs{Symbol, Dates.Day, Tuple{Symbol}, NamedTuple{(:update_cooldown,), Tuple{Dates.Day}}})
    @ Pkg.Operations C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Operations.jl:1266
 [10] update_registries
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Operations.jl:1263 [inlined]
 [11] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform,
 kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:259
 [12] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:156
 [13] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:145
 [14] #add#25
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:144 [inlined]
 [15] add
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:144 [inlined]
 [16] #add#24
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:143 [inlined]
 [17] add(pkg::String)
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:143
 [18] top-level scope
    @ REPL[1]:1

Please provide guidance on how to resolve this.

Thanks,
Prerna

2

Hello Prerna,

Would you be able to run the following commands

using Pkg
Pkg.Registry.rm("General")
Pkg.Registry.add("General")
Pkg.add("Weave")

and let us know if you see any errors? Please be aware, though, that in the next release of Pumas, Quarto will be supported and provide similar (better?) functionality than Weave.

3

Thanks for your response! Look forward to the Quarto integration.
This is the error I get now:

Pkg.add("Weave")
   Resolving package versions...
  License Type:      Time Limited
  Status:            Active
  Trial:             false
  Activated offline: false
  Times Activated:   1
  Max Activations:   2
ERROR: SystemError: opening file "C:\\Users\\preru\\.julia\\environments\\Pumas_v2.5.1\\Project.toml": Permission denied
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base .\error.jl:176
  [2] #systemerror#82
    @ .\error.jl:175 [inlined]
  [3] systemerror
    @ .\error.jl:175 [inlined]
  [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Bool, append::Nothing)
    @ Base .\iostream.jl:293
  [5] open
    @ .\iostream.jl:275 [inlined]
  [6] open(fname::String, mode::String; lock::Bool)
    @ Base .\iostream.jl:356
  [7] open(fname::String, mode::String)
    @ Base .\iostream.jl:355
  [8] open(::Base.var"#414#415"{String, Tuple{}}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base .\io.jl:393
  [9] open
    @ .\io.jl:392 [inlined]
 [10] write
    @ .\io.jl:459 [inlined]
 [11] write_project
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\project.jl:210 [inlined]
 [12] write_project
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\project.jl:199 [inlined]
 [13] write_project(env::Pkg.Types.EnvCache)
    @ Pkg.Types C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\project.jl:197
 [14] write_env(env::Pkg.Types.EnvCache; update_undo::Bool, skip_writing_project::Bool)
    @ Pkg.Types C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Types.jl:1086
 [15] write_env
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Types.jl:1083 [inlined]
 [16] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Operations.jl:1393
 [17] add
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\Operations.jl:1373 [inlined]
 [18] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:275
 [19] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:156
 [20] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:145
 [21] #add#25
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:144 [inlined]
 [22] add
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:144 [inlined]
 [23] #add#24
    @ C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:143 [inlined]
 [24] add(pkg::String)
    @ Pkg.API C:\Pumas-v2.5.1\Julia-1.9.3\share\julia\stdlib\v1.9\Pkg\src\API.jl:143
 [25] top-level scope
    @ REPL[5]:1
4

It looks like there is a permission issue on your computer. A similar issue has been reported by other people at your institution so I suspect that this has something to do with restrictions that your IT department has put on your desktop. Hence, please ask them if they can adjust the permissions such that Pumas/Julia has write access within the .julia folder. If that is not possible then it won’t be possible to install any packages.

5

@andreasnoack I am facing a similar problem of installing Weave on my Macbook M2.

julia> Pkg.add("Weave")
   Resolving package versions...
  License Type:      Time Limited
  Status:            Active
  Trial:             false
  Activated offline: false
  Times Activated:   1
  Max Activations:   2
ERROR: SystemError: opening file "/Users/abhimanyu/.julia/environments/Pumas_v2.5/Project.toml": Permission denied
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base /Applications/Pumas-2.5.1.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
  [2] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Bool, append::Nothing)
    @ Base /Applications/Pumas-2.5.1.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
  [3] open(fname::String, mode::String; lock::Bool)
    @ Base /Applications/Pumas-2.5.1.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
  [4] open(fname::String, mode::String)
    @ Base /Applications/Pumas-2.5.1.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
  [5] open(::Base.var"#414#415"{String, Tuple{}}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base /Applications/Pumas-2.5.1.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
  [6] write_env(env::Pkg.Types.EnvCache; update_undo::Bool, skip_writing_project::Bool)
    @ Pkg.Types /Applications/Pumas-2.5.1.app/Contents/Resources/julia/lib/julia/sys.pumas.dylib:-1
  [7] write_env
    @ /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/Types.jl:1083 [inlined]
  [8] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/Operations.jl:1393
  [9] add
    @ /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/Operations.jl:1373 [inlined]
 [10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:275
 [11] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:156
 [12] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:145
 [13] #add#25
    @ /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:144 [inlined]
 [14] add
    @ /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:144 [inlined]
 [15] #add#24
    @ /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:143 [inlined]
 [16] add(pkg::String)
    @ Pkg.API /Applications/Pumas-2.5.1.app/Contents/Resources/julia/share/julia/stdlib/v1.9/Pkg/src/API.jl:143
 [17] top-level scope
    @ REPL[5]:1
6

Please notice that Weave has not been supported for some time. In the next release (2.6.0), which will be released very soon, there will be support for Quarto which has a similar functionality.