Alert: 5 dependencies skipped during auto compilation due to previous errors!

I am getting the following alert when I update the packages:
“140 dependencies successfully precompiled in 319 seconds (279 already precompiled, 5 skipped during auto due to previous errors)”
I have done what the Pkg package follows, at the end of the update.
Helps me to solve this problem.

julia> import Pkg

julia> Pkg.precompile()
Precompiling project...
  ✗ libpng_jll
  ✗ InteractBase
  ✗ GR_jll
  ✗ Interact
  0 dependencies successfully precompiled in 22 seconds (421 already precompiled)

ERROR: The following 1 direct dependency failed to precompile:

Interact [c601a237-2ae4-5e1e-952c-7a85b0c7eef1]

WARNING: Method definition istextmime(Base.Multimedia.MIME{Symbol("application/vnd.webio.node+json")}) in module WebIO at C:\Users\Hermesr\.julia\packages\WebIO\Fy9h1\src\WebIO.jl:32 overwritten in module WebIO on the same line (check for duplicate calls to `include`).
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition istextmime(Base.Multimedia.MIME{Symbol("application/vnd.webio.application+html")}) in module WebIO at C:\Users\Hermesr\.julia\packages\WebIO\Fy9h1\src\WebIO.jl:35 overwritten in module WebIO on the same line (check for duplicate calls to `include`).
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition show(IO, Base.Multimedia.MIME{Symbol("application/vnd.webio.node+json")}, Union{Observables.Observable{T} where T, Widgets.AbstractWidget{T, S} where S where T}) in module WebIO at C:\Users\Hermesr\.julia\packages\WebIO\Fy9h1\src\render.jl:330 overwritten in module WebIO on the same line (check for duplicate calls to `include`).
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition show(IO, Base.Multimedia.MIME{Symbol("text/html")}, Observables.Observable{T} where T) in module WebIO at C:\Users\Hermesr\.julia\packages\WebIO\Fy9h1\src\render.jl:326 overwritten in module WebIO on the same line (check for duplicate calls to `include`).
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition node##kw(Any, typeof(Widgets.node), Any...) in module WebIO at C:\Users\Hermesr\.julia\packages\WebIO\Fy9h1\src\node.jl:53 overwritten in module WebIO on the same line (check for duplicate calls to `include`).
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition node(Any...) in module WebIO at C:\Users\Hermesr\.julia\packages\WebIO\Fy9h1\src\node.jl:53 overwritten in module WebIO on the same line (check for duplicate calls to `include`).
  ** incremental compilation may be fatally broken for this module **

┌ Warning: Replacing module `WebIO`
└ @ Base loading.jl:937
┌ Warning: Module WebIO with build ID 86343002665997 is missing from the cache.
│ This may mean WebIO [0f1e0344-ec1d-5b48-a673-e5cf874b6c29] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1008
┌ Warning: Module WebIO with build ID 86343002665997 is missing from the cache.
│ This may mean WebIO [0f1e0344-ec1d-5b48-a673-e5cf874b6c29] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1008
WARNING: both JSExpr and WebIO export "@js_str"; uses of it in module InteractBase must be qualified
ERROR: LoadError: LoadError: LoadError: LoadError: UndefVarError: @js_str not defined
Stacktrace:
  [1] top-level scope
    @ :0
  [2] #macroexpand#50
    @ .\expr.jl:112 [inlined]
  [3] macroexpand
    @ .\expr.jl:111 [inlined]
  [4] docm(source::LineNumberNode, mod::Module, meta::Any, ex::Any, define::Bool) (repeats 2 times)
    @ Base.Docs .\docs\Docs.jl:537
  [5] var"@doc"(__source__::LineNumberNode, __module__::Module, x::Vararg{Any, N} where N)
    @ Core .\boot.jl:508
  [6] include(mod::Module, _path::String)
    @ Base .\Base.jl:386
  [7] include(x::String)
    @ InteractBase C:\Users\Hermesr\.julia\packages\InteractBase\Zfu5P\src\InteractBase.jl:1
  [8] top-level scope
    @ C:\Users\Hermesr\.julia\packages\InteractBase\Zfu5P\src\InteractBase.jl:99
  [9] include
    @ .\Base.jl:386 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
    @ Base .\loading.jl:1213
 [11] top-level scope
    @ none:1
 [12] eval
    @ .\boot.jl:360 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude .\client.jl:446
 [14] top-level scope
    @ none:1
in expression starting at C:\Users\Hermesr\.julia\packages\InteractBase\Zfu5P\src\input.jl:19
in expression starting at C:\Users\Hermesr\.julia\packages\InteractBase\Zfu5P\src\input.jl:5
in expression starting at C:\Users\Hermesr\.julia\packages\InteractBase\Zfu5P\src\input.jl:5
in expression starting at C:\Users\Hermesr\.julia\packages\InteractBase\Zfu5P\src\InteractBase.jl:1
ERROR: LoadError: Failed to precompile InteractBase [d3863d7c-f0c8-5437-a7b4-3ae773c01009] to C:\Users\Hermesr\.julia\compiled\v1.6\InteractBase\jl_4B70.tmp.
Stacktrace:
  [1] error(s::String)
    @ Base .\error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream})
    @ Base .\loading.jl:1360
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base .\loading.jl:1306
  [4] _require(pkg::Base.PkgId)
    @ Base .\loading.jl:1021
  [5] require(uuidkey::Base.PkgId)
    @ Base .\loading.jl:914
  [6] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:901
  [7] include
    @ .\Base.jl:386 [inlined]
  [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base .\loading.jl:1213
  [9] top-level scope
    @ none:1
 [10] eval
    @ .\boot.jl:360 [inlined]
 [11] eval(x::Expr)
    @ Base.MainInclude .\client.jl:446
 [12] top-level scope
    @ none:1
in expression starting at C:\Users\Hermesr\.julia\packages\Interact\SbgIk\src\Interact.jl:1
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\Types.jl:55
 [2] precompile(ctx::Pkg.Types.Context; internal_call::Bool, strict::Bool, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\API.jl:1244
 [3] precompile
   @ C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\API.jl:920 [inlined]
 [4] #precompile#196
   @ C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\API.jl:918 [inlined]
 [5] precompile()
   @ Pkg.API C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\API.jl:918
 [6] top-level scope
   @ REPL[3]:1

julia>

Try to update Interact/InteractBase? It seems like it is broken (maybe two of its dependencies started exporting a macro they did not export before, and the semantic versioning was not sufficient to avoid the breakage).

How to run the Interact / Interact Base update?

(@v1.6) pkg> add CairoMakie
    Updating registry at `C:\Users\Hermesr\.julia\registries\General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Resolving package versions...
   Installed CairoMakie ─ v0.5.10
    Updating `C:\Users\Hermesr\.julia\environments\v1.6\Project.toml`
  [13f3f980] + CairoMakie v0.5.10
    Updating `C:\Users\Hermesr\.julia\environments\v1.6\Manifest.toml`
  [159f3aea] + Cairo v1.0.5
  [13f3f980] + CairoMakie v0.5.10
  [3b182d85] + Graphite2_jll v1.3.14+0
  [2e76f6c2] + HarfBuzz_jll v2.8.1+0
  [36c8627f] + Pango_jll v1.42.4+10
Precompiling project...
  ✗ HarfBuzz_jll
  ✗ Pango_jll
  ✗ Cairo
  ✗ CairoMakie
  0 dependencies successfully precompiled in 35 seconds (421 already precompiled, 5 skipped during auto due to previous errors)
  4 dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages

I think Henrique meant pkg> up Interact, InteractBase – or perhaps even just pkg> up if your compat entries are up to date.
Errors like the one you show after add CairoMakie I see all the time. Restarting the REPL often resolves those.

 up Interact
    Updating registry at `C:\Users\Hermesr\.julia\registries\General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Some registries failed to update:
│     — C:\Users\Hermesr\.julia\registries\General — failed to fetch from repo
└ @ Pkg.Types C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\Types.jl:1229
  No Changes to `C:\Users\Hermesr\.julia\environments\v1.6\Project.toml`
    Updating `C:\Users\Hermesr\.julia\environments\v1.6\Manifest.toml`
  [82e4d734] ↑ ImageIO v0.4.1 ⇒ v0.5.5
  [eebad327] + PkgVersion v0.1.1
  [276daf66] ↑ SpecialFunctions v1.1.0 ⇒ v1.5.1
  [731e570b] + TiffImages v0.3.2
Precompiling project...
  ✗ CairoMakie
  62 dependencies successfully precompiled in 222 seconds (362 already precompiled, 8 skipped during auto due to previous errors)
  1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package

(@v1.6) pkg> up InteractBase
    Updating registry at `C:\Users\Hermesr\.julia\registries\General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Some registries failed to update:
│     — C:\Users\Hermesr\.julia\registries\General — failed to fetch from repo
└ @ Pkg.Types C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\Pkg\src\Types.jl:1229
ERROR: The following package names could not be resolved:
 * InteractBase (d3863d7c-f0c8-5437-a7b4-3ae773c01009 in manifest but not in project)

The second error says that InteractBase is not a direct dependency (it’s presumably in the Manifest b/c Interact depends on it). So InteractBase's version is something you don’t have to worry about.
The first error is hard to diagnose. My rule of thumb with registry problems is: just remove the registry with registry rm General. It will be reinstalled automatically when needed.
There are various reports on discourse about registry updating problems on windows machines. One thing that may or may not help is to set ENV["JULIA_PKG_SERVER"] = "" after removing the registry.

See also

julia> ENV["JULIA_PKG_SERVER"] = ""
""

(@v1.6) pkg> up
  Installing known registries into `C:\Users\Hermesr\.julia`
     Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: failed to clone from https://github.com/JuliaRegistries/General.git, error: GitError(Code:ERROR, Class:Net, malformed URL 'fproxy2.ecp.elco.co.il:8080')
~~~\
julia> ENV["JULIA_PKG_SERVER"] = ""
""

(@v1.6) pkg> registry add General
     Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: failed to clone from https://github.com/JuliaRegistries/General.git, error: GitError(Code:ERROR, Class:Net, malformed URL 'fproxy2.ecp.elco.co.il:8080')

(@v1.6) pkg>

Previously this worked for me. And managed to update the registries!

Z:\>set http_proxy=fproxy2.ecp.elco.co.il:8080

Z:\>set https_proxy=fproxy2.ecp.elco.co.il:8080

Z:\>set JULIA_NO_VERIFY_HOSTS=**

Z:\>C:\Users\Hermesr\AppData\Local\Programs\Julia-1.6.1\bin\julia.exe
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.1 (2021-04-23)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(@v1.6) pkg> register add General
ERROR: Could not determine command

(@v1.6) pkg> registry add General
     Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: failed to clone from https://github.com/JuliaRegistries/General.git, error: GitError(Code:ERROR, Class:Net, malformed URL 'fproxy2.ecp.elco.co.il:8080')