Error during Pkg.test("Circuitscape") #377

harshadkarandikar · 2023-02-03T22:39:07Z

Hi,

I am trying to install Circuitscape on a M1 Mac Studio with Julia 1.8.5. While the installation goes smoothly, Pkg.test("Circuitscape") throws up errors. I tried running a job that runs on another M1 Mac (in case there was just an issue with testing), but it did not work.

Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
WARNING: method definition for multiple_solver at /Users/abcd/.julia/packages/Circuitscape/HNOrX/src/raster/advanced.jl:275 declares type variable S but does not use it.
WARNING: could not import Circuitscape.compute_mklpardiso into Main
pwd = /Users/abcd/.julia/packages/Circuitscape/HNOrX/test
Test Summary: | Pass  Total  Time
Unit tests    |   16     16  7.5s
┌ Warning: 2023-02-03 14:24:03 : CHOLMOD only works with double precision. Converting single precision matrix to double
└ @ Circuitscape ~/.julia/packages/Circuitscape/HNOrX/src/logging.jl:25

signal (10): Bus error: 10
in expression starting at /Users/abcd/.julia/packages/Circuitscape/HNOrX/test/runtests.jl:15
unknown function (ip: 0x120b78b04)
Allocations: 145519460 (Pool: 145435731; Big: 83729); GC: 110
ERROR: Package Circuitscape errored during testing (received signal: 10)
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1813
  [3] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:434
  [4] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:156
  [5] test(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:145
  [6] #test#87
    @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:144 [inlined]
  [7] test
    @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:144 [inlined]
  [8] #test#86
    @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:143 [inlined]
  [9] test(pkg::String)
    @ Pkg.API /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:143
 [10] top-level scope
    @ REPL[5]:1

Circuitscape and Julia version
Circuitscape v5.12.2 (obtained from running using Pkg; Pkg.status() and Julia v1.8.5 (obtained from running versioninfo())

Am I missing anything? Thank you!

The text was updated successfully, but these errors were encountered:

harshadkarandikar · 2023-03-23T14:12:58Z

Hello,

I still haven't been able to resolve this issue. Any ideas on what I could possibly try to get Circuitscape running? Thank you!

nataliemyers12 · 2023-07-03T19:16:05Z

I am also having this error and would love any insight available

ViralBShah · 2023-07-20T04:49:49Z

Try the latest Circuitscape master and see if it helps. It works fine on my M2.

knussear · 2023-08-10T22:44:12Z

I'm also getting a stacktrace error after a fresh install of julia and circuitscape

I'm on Ubuntu 22.04

julia> using Pkg; Pkg.status()
Status ~/.julia/environments/v1.9/Project.toml
[2b7a1792] Circuitscape v5.12.3
[fd094767] Suppressor v0.2.4

Pkg.test("Circuitscape")

in expression starting at /home/knussear/.julia/packages/Circuitscape/33lUW/test/runtests.jl:1
ERROR: Package Circuitscape errored during testing
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /usr/share/julia/stdlib/v1.9/Pkg/src/Types.jl:69
[2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
@ Pkg.Operations /usr/share/julia/stdlib/v1.9/Pkg/src/Operations.jl:2026
[3] test
@ /usr/share/julia/stdlib/v1.9/Pkg/src/Operations.jl:1907 [inlined]
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
@ Pkg.API /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:441
[5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:156
[6] test(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:145
[7] #test#75
@ /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:144 [inlined]
[8] test
@ /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:144 [inlined]
[9] #test#74
@ /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:143 [inlined]
[10] test(pkg::String)
@ Pkg.API /usr/share/julia/stdlib/v1.9/Pkg/src/API.jl:143
[11] top-level scope
@ REPL[4]:1

ViralBShah · 2023-08-11T12:57:43Z

Just tried: All tests pass for me on ubuntu.

(@v1.9) pkg> st
Status ~/.julia/environments/v1.9/Project.toml
[2b7a1792] Circuitscape v5.12.3

ranjanan · 2023-08-11T13:07:38Z

Okay I am able to reproduce this on v1.9 on my M2 Mac. Bizarre, looking into this.

ViralBShah · 2023-08-11T13:16:12Z

Dup of #364

ViralBShah · 2023-08-11T13:41:54Z

I'm now getting it to crash on my M2 as well on Julia 1.9.2 and getting a precompile error on master for ArchGDAL.

ranjanan · 2023-08-11T13:58:16Z

This was breaking at the file writing stage, just like in #379. When I update my packages on Julia 1.9 and confirm that I have ArchGDAL 0.10.1, the tests pass.

ViralBShah · 2023-08-11T15:19:10Z

Should we update the dependency for ArchGDAL.jl to 0.10.1?

ranjanan · 2023-08-11T15:35:44Z

I am running tests with ArchGDAL 0.10.0 and Julia 1.8 and 1.9 and they all work fine. The folks in the thread seem to be on 5.12 and not 5.13.

import Pkg
Pkg.update()

should fix things for them.

ranjanan · 2023-08-11T15:36:14Z

My previous version that crashed had ArchGDAL 0.9.8

ranjanan · 2023-08-11T15:36:42Z

@harshadkarandikar could you try this out?

ViralBShah · 2023-08-11T15:41:24Z

On Julia 1.9, I am unable to get Circuitscape 5.12.3 pick up ArchGDAL 0.10.1. It insists on 0.9.4. On Julia master, I get the latest versions.

(@v1.9) pkg> st
Status `~/.julia/environments/v1.9/Project.toml`
⌅ [c9ce4bd3] ArchGDAL v0.9.4
  [2b7a1792] Circuitscape v5.12.3
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated`

(@v1.9) pkg> st --outdated -m
Status `~/.julia/environments/v1.9/Manifest.toml`
⌅ [c9ce4bd3] ArchGDAL v0.9.4 (<v0.10.1): Circuitscape
⌅ [c3611d14] ColorVectorSpace v0.9.10 (<v0.10.0): ImageCore
⌃ [add2ef01] GDAL v1.4.0 (<v1.6.0)
⌅ [a09fc81d] ImageCore v0.9.4 (<v0.10.1): ArchGDAL
⌅ [a7073274] GDAL_jll v300.500.200+0 (<v301.600.200+0): ArchGDAL, GDAL
⌅ [0234f1f7] HDF5_jll v1.12.2+2 (<v1.14.1+0): GDAL_jll, NetCDF_jll
⌅ [89763e89] Libtiff_jll v4.4.0+0 (<v4.5.1+1): GDAL_jll, LittleCMS_jll, OpenJpeg_jll, PROJ_jll, libgeotiff_jll
⌃ [7243133f] NetCDF_jll v400.902.206+0 (<v400.902.208+0)
⌅ [458c3c95] OpenSSL_jll v1.1.22+0 (<v3.0.10+0): HDF5_jll, LibPQ_jll
⌅ [58948b4f] PROJ_jll v900.100.0+0 (<v900.200.100+0): GDAL_jll, libgeotiff_jll
⌃ [06c338fa] libgeotiff_jll v100.700.100+0 (<v100.700.101+0)

evetion · 2023-08-11T15:58:31Z

This is a bug in ArchGDAL before v0.9.4 on aarch64 and Julia 1.8.2+. It was fixed in yeesian/ArchGDAL.jl#352. Let me know if you can reproduce it on current versions of ArchGDAL.

ranjanan · 2023-08-11T16:07:58Z

Thank you @evetion. This means we will bump our Julia version compat to 1.9.

ViralBShah · 2023-08-11T16:20:46Z

Folks, try Circuitscape 5.13 tomorrow.

ranjanan · 2023-08-11T16:22:44Z

JuliaRegistries/General#89450

ViralBShah mentioned this issue Aug 11, 2023

pkg test failed #364

Closed

ViralBShah closed this as completed Aug 11, 2023

ViralBShah reopened this Aug 11, 2023

ViralBShah closed this as completed Aug 11, 2023

ViralBShah reopened this Aug 11, 2023

This was referenced Aug 11, 2023

Add LTS to CI #383

Closed

Update Julia version compat to 1.9 #384

Merged

ViralBShah closed this as completed Aug 11, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Error during Pkg.test("Circuitscape") #377

Error during Pkg.test("Circuitscape") #377

harshadkarandikar commented Feb 3, 2023

harshadkarandikar commented Mar 23, 2023

nataliemyers12 commented Jul 3, 2023

ViralBShah commented Jul 20, 2023

knussear commented Aug 10, 2023

ViralBShah commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023

ViralBShah commented Aug 11, 2023 •

edited

Loading

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023 •

edited

Loading

evetion commented Aug 11, 2023 •

edited

Loading

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023

ranjanan commented Aug 11, 2023

Error during Pkg.test("Circuitscape") #377

Error during Pkg.test("Circuitscape") #377

Comments

harshadkarandikar commented Feb 3, 2023

harshadkarandikar commented Mar 23, 2023

nataliemyers12 commented Jul 3, 2023

ViralBShah commented Jul 20, 2023

knussear commented Aug 10, 2023

ViralBShah commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023

ViralBShah commented Aug 11, 2023 • edited Loading

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023 • edited Loading

evetion commented Aug 11, 2023 • edited Loading

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023

ranjanan commented Aug 11, 2023

ViralBShah commented Aug 11, 2023 •

edited

Loading

ViralBShah commented Aug 11, 2023 •

edited

Loading

evetion commented Aug 11, 2023 •

edited

Loading