Unable to update packages from terminal

Tooling Juno
1

I’ve got a strange issue since I’ve updated to the latest version of Juno.

Whenever I try to update packages from the terminal REPL I get the following warning and nothing gets updated:

(@v1.4) pkg> up
   Updating registry at `~/.julia/registries/General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Some registries failed to update:
│     — /Users/matteo/.julia/registries/General — failed to fetch from repo
└ @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Types.jl:1122
   Updating `~/.julia/environments/v1.4/Project.toml`
 [no changes]
   Updating `~/.julia/environments/v1.4/Manifest.toml`
 [no changes]

However, if I repeat this operation a few seconds later from the REPL in Juno/Atom, it works just fine:

Press Enter to start Julia. 
Starting Julia...
[ Info: Precompiling Atom [c52e3926-4ff0-5f6e-af25-54175e0327b1]
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.4.1 (2020-04-14)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(@v1.4) pkg> up
   Updating registry at `~/.julia/registries/General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
  Installed DiffEqSensitivity ─ v6.17.0
   Updating `~/.julia/environments/v1.4/Project.toml`
 [no changes]
   Updating `~/.julia/environments/v1.4/Manifest.toml`
  [41bf760c] ↑ DiffEqSensitivity v6.16.0 ⇒ v6.17.0

This ha been going on for a few days now.

Any thoughts? I’m at a loss here…

For info:

Status `~/.julia/environments/v1.4/Project.toml`
  [c52e3926] Atom v0.12.11
  [6e4b80f9] BenchmarkTools v0.5.0
  [336ed68f] CSV v0.6.1
  [3a865a2d] CuArrays v2.2.0
  [a93c6f00] DataFrames v0.20.2
  [aae7a2af] DiffEqFlux v1.10.3
  [0c46a032] DifferentialEquations v6.14.0
  [587475ba] Flux v0.10.4
  [c91e804a] Gadfly v1.2.1
  [7073ff75] IJulia v1.21.2
  [e5e0dc1b] Juno v0.8.2
  [b964fa9f] LaTeXStrings v1.1.0
  [ee78f7c6] Makie v0.10.0
  [8faf48c0] NeuralNetDiffEq v1.4.0
  [5fb14364] OhMyREPL v0.5.5
  [1dea7af3] OrdinaryDiffEq v5.38.2
  [8314cec4] PGFPlotsX v1.2.6
  [65888b18] ParameterizedFunctions v5.3.0
  [91a5bcdd] Plots v1.3.2
  [1a8c2f83] Query v0.12.2
  [90137ffa] StaticArrays v0.12.3
  [c3572dad] Sundials v4.2.2
  [b8865327] UnicodePlots v1.2.0
  [112f6efa] VegaLite v2.1.3
  [44d3d7a6] Weave v0.10.2
  [e88e6eb3] Zygote v0.4.20
2

That’s curious. Have you tried to update the local registry repository manually from the command line with git?

1 Like
3

I’m not quite sure how to do that (i.e. which folder, and from which repo)

By the way, it works absolutely fine with VS Code as well…

4

It’s written in the output of your ]up command: ~/.julia/registries/General

1 Like
5

It seems to be working ok - no updates, but I’d just updated a few minutes ago from VS code, so it might be ok. At least there are no warnings/error. I might retry later…

~/.julia/registries/General master
❯ git pull
Auto packing the repository in background for optimum performance.
See "git help gc" for manual housekeeping.
Already up to date.
6

Yes, this is likely the case, merges to the upstream repo happen every about 12 minutes.

I honestly can’t easily think to a reason why ]up would fail when run directly in the terminal but not in an IDE. Are you sure you’re using the same Julia application in all cases?

7

Yep, it worked:

~/.julia/registries/General master
❯ git pull
remote: Enumerating objects: 8, done.
remote: Counting objects: 100% (8/8), done.
remote: Total 35 (delta 8), reused 8 (delta 8), pack-reused 27
Unpacking objects: 100% (35/35), done.
From https://github.com/JuliaRegistries/General
   7ffc7ce08e..71a74c034a  master     -> origin/master
Updating 7ffc7ce08e..71a74c034a
Fast-forward
 G/GenomeGraphs/Compat.toml      |  5 +++++
 G/GenomeGraphs/Deps.toml        |  4 ++++
 G/GenomeGraphs/Package.toml     |  3 +++
 G/GenomeGraphs/Versions.toml    |  2 ++
 G/GeoMakie/Compat.toml          |  7 ++++++-
 G/GeoMakie/Versions.toml        |  3 +++
 M/MortalityTables/Versions.toml |  3 +++
 P/Pseudoseq/Compat.toml         | 10 ++++++++++
 P/Pseudoseq/Deps.toml           |  7 +++++++
 P/Pseudoseq/Package.toml        |  3 +++
 P/Pseudoseq/Versions.toml       |  5 +++++
 R/ReadDatastores/Compat.toml    |  6 ++++++
 R/ReadDatastores/Deps.toml      |  3 +++
 R/ReadDatastores/Package.toml   |  3 +++
 R/ReadDatastores/Versions.toml  | 11 +++++++++++
 Registry.toml                   |  4 ++++
 T/TwoBit/Compat.toml            |  4 ++++
 T/TwoBit/Deps.toml              |  3 +++
 T/TwoBit/Package.toml           |  3 +++
 T/TwoBit/Versions.toml          |  2 ++
 20 files changed, 90 insertions(+), 1 deletion(-)
 create mode 100644 G/GenomeGraphs/Compat.toml
 create mode 100644 G/GenomeGraphs/Deps.toml
 create mode 100644 G/GenomeGraphs/Package.toml
 create mode 100644 G/GenomeGraphs/Versions.toml
 create mode 100644 P/Pseudoseq/Compat.toml
 create mode 100644 P/Pseudoseq/Deps.toml
 create mode 100644 P/Pseudoseq/Package.toml
 create mode 100644 P/Pseudoseq/Versions.toml
 create mode 100644 R/ReadDatastores/Compat.toml
 create mode 100644 R/ReadDatastores/Deps.toml
 create mode 100644 R/ReadDatastores/Package.toml
 create mode 100644 R/ReadDatastores/Versions.toml
 create mode 100644 T/TwoBit/Compat.toml
 create mode 100644 T/TwoBit/Deps.toml
 create mode 100644 T/TwoBit/Package.toml
 create mode 100644 T/TwoBit/Versions.toml

Thanks for your help anyway. It is indeed very strange. I’ve recently cleared my HD so there is only one Julia app in my laptop, at the moment…

1 Like
8

…and after updating the registry via git, now the terminal REPL works again for updating packages. The warning disappeared

A mystery… thanks for the suggestion @giordano

1 Like