Package manager error "but no such entry exists in the manifest"

Tooling Package Management
1

On Julia version 1.9.2 on a Linux system (cluster with a module system) the package manager gets confused even with deleting Manifest.toml.

MWE

]activate --temp
add SpecialFunctions

results in persistent error (even on ]status)

   Resolving package versions...
ERROR: `LogExpFunctions=2ab3a3ac-af41-5b50-aa03-7779005ae688` depends on `ChainRulesCore=d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4`, but no such entry exists in the manifest.

The Manifest.toml after the MWE is

# This file is machine-generated - editing it directly is not advised

julia_version = "1.9.2"
manifest_format = "2.0"
project_hash = "32c0278da543896ba4c65b647e6101cb19099f73"

[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.1"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"

[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "1.0.5+0"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[deps.DocStringExtensions]]
deps = ["LibGit2"]
git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.9.3"

[[deps.Downloads]]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[deps.InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.IrrationalConstants]]
git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
version = "0.2.2"

[[deps.JLLWrappers]]
deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.5.0"

[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.3"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "7.84.0+0"

[[deps.LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"

[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.10.2+0"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"

[[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[deps.LogExpFunctions]]
git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.26"

    [deps.LogExpFunctions.deps]
    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
    ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
    DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
    InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
    IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6"
    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[deps.Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.2+0"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2022.10.11"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
version = "0.3.21+4"

[[deps.OpenLibm_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
version = "0.8.1+0"

[[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.5+0"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.9.2"

[[deps.Preferences]]
deps = ["TOML"]
git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.4.0"

[[deps.Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[[deps.REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[deps.Random]]
deps = ["SHA", "Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[deps.Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[deps.SpecialFunctions]]
deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "2.3.1"

    [deps.SpecialFunctions.extensions]
    SpecialFunctionsChainRulesCoreExt = "ChainRulesCore"

    [deps.SpecialFunctions.weakdeps]
    ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.3"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+0"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.8.0+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"
2

It works fine here (linux, julia-1.9.2 too),
maybe there are some packages in the outer (1.9) environment ?

What is the output of

(jl_OuiFay) pkg> activate
  Activating project at `~/.julia/environments/v1.9`

(@v1.9) pkg> status   # check twice that the prompt is (@v1.9)
Status `~/.julia/environments/v1.9/Project.toml`
  [1e6cf692] TestEnv v1.100.1

# I currently have only TestEnv there

on your system ? There might be in the outer environment (@v1.9)
an old version of some of the SpecialFunctions dependencies that is triggering the issue.

3

Thanks for testing on your setup. How can I check the “outer environment?”

My load path of the MWE is:

julia> LOAD_PATH
3-element Vector{String}:
 "@"
 "@v#.#"
 "@stdlib"

The 1.9 environment is

(jl_lTK75Y) pkg> activate 
(v1.9) pkg> st
Status `/Net/Groups/BGI/scratch/twutz/julia_cluster_depots/environments/v1.9/Project.toml`
⌃ [295af30f] Revise v3.5.2
4

That’s what I requested, good.

> (jl_TdA24y) pkg> ?activate
  activate

  Activate the environment at the given path,
  or the home project environment if no path is specified.

By the way, the output of status -m is a more compact and readable
way of showing the Manifest.toml content, next time you have to.

5

It works here with Revise added first and then SpecialFunctions

(@v1.9) pkg> activate --temp
(jl_EYziBY) pkg> add Revise
   Resolving package versions...
    Updating `/tmp/jl_EYziBY/Project.toml`
  [295af30f] + Revise v3.5.3
...
(jl_EYziBY) pkg> add SpecialFunctions
   Resolving package versions...
    Updating `/tmp/jl_EYziBY/Project.toml`
  [276daf66] + SpecialFunctions v2.3.1
...

But the version of Revise is v3.5.3 instead of 3.5.2.
Could you please give the output of status -m in your mwe while I check with your Revise version ?

6

Nope, that not Revise (no surprise)

(jl_50415E) pkg> add Revise@3.5.2
   Installed Revise ─ v3.5.2
(jl_50415E) pkg> add SpecialFunctions
  [276daf66] + SpecialFunctions v2.3.1
#  works fine here too

By the way, we have the same standard LOAD_PATH:

julia> LOAD_PATH
3-element Vector{String}:
 "@"
 "@v#.#"
 "@stdlib"

So it looks like something became corrupt on your system.
You might want to try to remove and add the registry again
(from Pkg cannot find registered packages - #2 by fredrikekre)

# Remove
rm(joinpath(DEPOT_PATH[1], "registries", "General"); force=true, recursive=true)
# Add
import Pkg
Pkg.Registry.add("General")

But that probably won’t be sufficient.
Otherwise, you can try this ?

7

Remove Revise from global environment, so that its empty - error persists.

In addition followed https://discourse.julialang.org/t/pkg-cannot-find-registered-packages/54008/2 - error persists.

In addition deleted in ~/.julia compiled, packages (did not found artifacts, clones) and removed the global Manifest.toml - error in MWE persists.

8

Deleted in my Depot path (type DEPOT_PATH at the julia prompt): compiled, packages, artifacts and clones.

This resolved the problem with the MWE.

1 Like
9

Thanks for the confirmation about DEPOT_PATH.

Do not hesitate to add Revise back in the home environment (@v1.9),
it is well maintained and usually put there by most people, as other development tools.