Pkg.jl: Possible version resolution bug

Created on 1 Jan 2020  ·  19Comments  ·  Source: JuliaLang/Pkg.jl

Over at https://github.com/JuliaRegistries/General/pull/7342 I'm seeing something that looks like a version-resolution bug.

Here are my environment files: https://gist.github.com/timholy/38dff6cfe0aa176bdc2d47bed0201e75
I'm on a fork & branch of General.

The oddity is that add [email protected] goes with v0.11.1 of Colors despite these lines. (Try toggling between v0.19.2 and v0.18.0.)

picture timholy

Most helpful comment

The resolve step has a very small API "surface":

https://github.com/JuliaLang/Pkg.jl/blob/0048fe1af04e2effcbce8ce2a0ed29d11b0e5950/src/Operations.jl#L339-L342

So serializing the graph should be enough to repro and looking at the output (the versions) from resolve should say if there is a bug (if a version is returned that is input as being incompatible). I personally doubt this is actually the case and that there is something wrong with the inputs to the resolver.

picture KristofferC on 4 Jan 2020
👍2

All 19 comments

Hmmm. I'm not able to reproduce this.

Here are the commands that I ran in bash:

rm -rf ~/.julia
git clone https://github.com/timholy/General timholy--General
cd timholy--General
git checkout teh/juliaimages
julia -e 'import Pkg; Pkg.Registry.add(Pkg.RegistrySpec(path = pwd()))'
julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.18.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.19.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.18.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.19.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
julia -e 'import InteractiveUtils; InteractiveUtils.versioninfo(; verbose = true)'

And here is the output: (click to expand)

DMBP:TEMP dilum$ rm -rf ~/.julia
DMBP:TEMP dilum$ git clone https://github.com/timholy/General timholy--General
Cloning into 'timholy--General'...
remote: Enumerating objects: 67, done.
remote: Counting objects: 100% (67/67), done.
remote: Compressing objects: 100% (66/66), done.
remote: Total 256317 (delta 7), reused 34 (delta 1), pack-reused 256250
Receiving objects: 100% (256317/256317), 43.71 MiB | 10.23 MiB/s, done.
Resolving deltas: 100% (133069/133069), done.
Updating files: 100% (10674/10674), done.
DMBP:TEMP dilum$ cd timholy--General
DMBP:timholy--General dilum$ git checkout teh/juliaimages
Updating files: 100% (11432/11432), done.
Branch 'teh/juliaimages' set up to track remote branch 'teh/juliaimages' from 'origin'.
Switched to a new branch 'teh/juliaimages'
DMBP:timholy--General dilum$ julia -e 'import Pkg; Pkg.Registry.add(Pkg.RegistrySpec(path = pwd()))'
   Copying registry from `~/Downloads/TEMP/timholy--General`
     Added registry `General` to `~/.julia/registries/General`
DMBP:timholy--General dilum$ julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.18.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/timholy/General`
 Resolving package versions...
 Installed Missings ────────────────── v0.4.3
 Installed Images ──────────────────── v0.18.0
 Installed ImageMorphology ─────────── v0.2.5
 Installed RangeArrays ─────────────── v0.3.2
 Installed SimpleTraits ────────────── v0.9.1
 Installed ImageShow ───────────────── v0.2.2
 Installed ColorTypes ──────────────── v0.8.1
 Installed DataStructures ──────────── v0.17.6
 Installed IntelOpenMP_jll ─────────── v2018.0.3+0
 Installed Graphics ────────────────── v0.4.0
 Installed NaNMath ─────────────────── v0.3.3
 Installed IntervalSets ────────────── v0.3.2
 Installed ImageMetadata ───────────── v0.7.2
 Installed AbstractFFTs ────────────── v0.5.0
 Installed FileIO ──────────────────── v1.2.1
 Installed MacroTools ──────────────── v0.5.3
 Installed CustomUnitRanges ────────── v0.2.0
 Installed DataAPI ─────────────────── v1.1.0
 Installed Ratios ──────────────────── v0.3.1
 Installed Distances ───────────────── v0.8.2
 Installed OffsetArrays ────────────── v0.11.4
 Installed ColorVectorSpace ────────── v0.7.1
 Installed ImageCore ───────────────── v0.8.10
 Installed MappedArrays ────────────── v0.2.2
 Installed MKL_jll ─────────────────── v2019.0.117+0
 Installed FixedPointNumbers ───────── v0.6.1
 Installed ImageFiltering ──────────── v0.6.9
 Installed ImageTransformations ────── v0.8.1
 Installed ComputationalResources ──── v0.3.0
 Installed Rotations ───────────────── v0.13.0
 Installed WoodburyMatrices ────────── v0.4.1
 Installed SortingAlgorithms ───────── v0.3.1
 Installed FFTW_jll ────────────────── v3.3.9+3
 Installed FFTViews ────────────────── v0.3.0
 Installed Compat ──────────────────── v2.2.0
 Installed StatsBase ───────────────── v0.32.0
 Installed Colors ──────────────────── v0.9.6
 Installed StaticArrays ────────────── v0.12.1
 Installed PaddedViews ─────────────── v0.4.2
 Installed SpecialFunctions ────────── v0.9.0
 Installed Reexport ────────────────── v0.2.0
 Installed CatIndices ──────────────── v0.2.0
 Installed TiledIteration ──────────── v0.2.3
 Installed Requires ────────────────── v1.0.0
 Installed OrderedCollections ──────── v1.1.0
 Installed IdentityRanges ──────────── v0.3.0
 Installed AxisArrays ──────────────── v0.3.3
 Installed ImageAxes ───────────────── v0.6.2
 Installed Interpolations ──────────── v0.12.5
 Installed AxisAlgorithms ──────────── v1.0.0
 Installed IterTools ───────────────── v1.3.0
 Installed OpenSpecFun_jll ─────────── v0.5.3+1
 Installed CoordinateTransformations ─ v0.5.0
 Installed IndirectArrays ──────────── v0.5.1
 Installed FFTW ────────────────────── v1.2.0
 Installed ImageDistances ──────────── v0.2.7
  Updating `~/.julia/environments/v1.4/Project.toml`
  [916415d5] + Images v0.18.0
  Updating `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] + AbstractFFTs v0.5.0
  [13072b0f] + AxisAlgorithms v1.0.0
  [39de3d68] + AxisArrays v0.3.3
  [aafaddc9] + CatIndices v0.2.0
  [3da002f7] + ColorTypes v0.8.1
  [c3611d14] + ColorVectorSpace v0.7.1
  [5ae59095] + Colors v0.9.6
  [34da2185] + Compat v2.2.0
  [ed09eef8] + ComputationalResources v0.3.0
  [150eb455] + CoordinateTransformations v0.5.0
  [dc8bdbbb] + CustomUnitRanges v0.2.0
  [9a962f9c] + DataAPI v1.1.0
  [864edb3b] + DataStructures v0.17.6
  [b4f34e82] + Distances v0.8.2
  [4f61f5a4] + FFTViews v0.3.0
  [7a1cc6ca] + FFTW v1.2.0
  [f5851436] + FFTW_jll v3.3.9+3
  [5789e2e9] + FileIO v1.2.1
  [53c48c17] + FixedPointNumbers v0.6.1
  [a2bd30eb] + Graphics v0.4.0
  [bbac6d45] + IdentityRanges v0.3.0
  [2803e5a7] + ImageAxes v0.6.2
  [a09fc81d] + ImageCore v0.8.10
  [51556ac3] + ImageDistances v0.2.7
  [6a3955dd] + ImageFiltering v0.6.9
  [bc367c6b] + ImageMetadata v0.7.2
  [787d08f9] + ImageMorphology v0.2.5
  [4e3cecfd] + ImageShow v0.2.2
  [02fcd773] + ImageTransformations v0.8.1
  [916415d5] + Images v0.18.0
  [9b13fd28] + IndirectArrays v0.5.1
  [1d5cc7b8] + IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] + Interpolations v0.12.5
  [8197267c] + IntervalSets v0.3.2
  [c8e1da08] + IterTools v1.3.0
  [856f044c] + MKL_jll v2019.0.117+0
  [1914dd2f] + MacroTools v0.5.3
  [dbb5928d] + MappedArrays v0.2.2
  [e1d29d7a] + Missings v0.4.3
  [77ba4419] + NaNMath v0.3.3
  [6fe1bfb0] + OffsetArrays v0.11.4
  [efe28fd5] + OpenSpecFun_jll v0.5.3+1
  [bac558e1] + OrderedCollections v1.1.0
  [5432bcbf] + PaddedViews v0.4.2
  [b3c3ace0] + RangeArrays v0.3.2
  [c84ed2f1] + Ratios v0.3.1
  [189a3867] + Reexport v0.2.0
  [ae029012] + Requires v1.0.0
  [6038ab10] + Rotations v0.13.0
  [699a6c99] + SimpleTraits v0.9.1
  [a2af1166] + SortingAlgorithms v0.3.1
  [276daf66] + SpecialFunctions v0.9.0
  [90137ffa] + StaticArrays v0.12.1
  [2913bbd2] + StatsBase v0.32.0
  [06e1c1a7] + TiledIteration v0.2.3
  [efce3f68] + WoodburyMatrices v0.4.1
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [8bb1440f] + DelimitedFiles
  [8ba89e20] + Distributed
  [b77e0a4c] + InteractiveUtils
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [44cfe95a] + Pkg
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA
  [9e88b42a] + Serialization
  [1a1011a3] + SharedArrays
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays
  [10745b16] + Statistics
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  Building FFTW → `~/.julia/packages/FFTW/qqcBj/deps/build.log`
  Updating `/private/var/folders/48/n09p39y53bx6dnbnf244s2jc0000gp/T/jl_TVDkxN/Project.toml`
 [no changes]
  Updating `/private/var/folders/48/n09p39y53bx6dnbnf244s2jc0000gp/T/jl_TVDkxN/Manifest.toml`
 [no changes]
Status `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.3.3
  [aafaddc9] CatIndices v0.2.0
  [3da002f7] ColorTypes v0.8.1
  [c3611d14] ColorVectorSpace v0.7.1
  [5ae59095] Colors v0.9.6
  [34da2185] Compat v2.2.0
  [ed09eef8] ComputationalResources v0.3.0
  [150eb455] CoordinateTransformations v0.5.0
  [dc8bdbbb] CustomUnitRanges v0.2.0
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.6
  [b4f34e82] Distances v0.8.2
  [4f61f5a4] FFTViews v0.3.0
  [7a1cc6ca] FFTW v1.2.0
  [f5851436] FFTW_jll v3.3.9+3
  [5789e2e9] FileIO v1.2.1
  [53c48c17] FixedPointNumbers v0.6.1
  [a2bd30eb] Graphics v0.4.0
  [bbac6d45] IdentityRanges v0.3.0
  [2803e5a7] ImageAxes v0.6.2
  [a09fc81d] ImageCore v0.8.10
  [51556ac3] ImageDistances v0.2.7
  [6a3955dd] ImageFiltering v0.6.9
  [bc367c6b] ImageMetadata v0.7.2
  [787d08f9] ImageMorphology v0.2.5
  [4e3cecfd] ImageShow v0.2.2
  [02fcd773] ImageTransformations v0.8.1
  [916415d5] Images v0.18.0
  [9b13fd28] IndirectArrays v0.5.1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] Interpolations v0.12.5
  [8197267c] IntervalSets v0.3.2
  [c8e1da08] IterTools v1.3.0
  [856f044c] MKL_jll v2019.0.117+0
  [1914dd2f] MacroTools v0.5.3
  [dbb5928d] MappedArrays v0.2.2
  [e1d29d7a] Missings v0.4.3
  [77ba4419] NaNMath v0.3.3
  [6fe1bfb0] OffsetArrays v0.11.4
  [efe28fd5] OpenSpecFun_jll v0.5.3+1
  [bac558e1] OrderedCollections v1.1.0
  [5432bcbf] PaddedViews v0.4.2
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.3.1
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.0.0
  [6038ab10] Rotations v0.13.0
  [699a6c99] SimpleTraits v0.9.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.9.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.32.0
  [06e1c1a7] TiledIteration v0.2.3
  [efce3f68] WoodburyMatrices v0.4.1
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
DMBP:timholy--General dilum$ julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.19.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/timholy/General`
 Resolving package versions...
 Installed Images ─ v0.19.0
  Updating `~/.julia/environments/v1.4/Project.toml`
  [916415d5] ↑ Images v0.18.0 ⇒ v0.19.0
  Updating `~/.julia/environments/v1.4/Manifest.toml`
  [916415d5] ↑ Images v0.18.0 ⇒ v0.19.0
Status `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.3.3
  [aafaddc9] CatIndices v0.2.0
  [3da002f7] ColorTypes v0.8.1
  [c3611d14] ColorVectorSpace v0.7.1
  [5ae59095] Colors v0.9.6
  [34da2185] Compat v2.2.0
  [ed09eef8] ComputationalResources v0.3.0
  [150eb455] CoordinateTransformations v0.5.0
  [dc8bdbbb] CustomUnitRanges v0.2.0
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.6
  [b4f34e82] Distances v0.8.2
  [4f61f5a4] FFTViews v0.3.0
  [7a1cc6ca] FFTW v1.2.0
  [f5851436] FFTW_jll v3.3.9+3
  [5789e2e9] FileIO v1.2.1
  [53c48c17] FixedPointNumbers v0.6.1
  [a2bd30eb] Graphics v0.4.0
  [bbac6d45] IdentityRanges v0.3.0
  [2803e5a7] ImageAxes v0.6.2
  [a09fc81d] ImageCore v0.8.10
  [51556ac3] ImageDistances v0.2.7
  [6a3955dd] ImageFiltering v0.6.9
  [bc367c6b] ImageMetadata v0.7.2
  [787d08f9] ImageMorphology v0.2.5
  [4e3cecfd] ImageShow v0.2.2
  [02fcd773] ImageTransformations v0.8.1
  [916415d5] Images v0.19.0
  [9b13fd28] IndirectArrays v0.5.1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] Interpolations v0.12.5
  [8197267c] IntervalSets v0.3.2
  [c8e1da08] IterTools v1.3.0
  [856f044c] MKL_jll v2019.0.117+0
  [1914dd2f] MacroTools v0.5.3
  [dbb5928d] MappedArrays v0.2.2
  [e1d29d7a] Missings v0.4.3
  [77ba4419] NaNMath v0.3.3
  [6fe1bfb0] OffsetArrays v0.11.4
  [efe28fd5] OpenSpecFun_jll v0.5.3+1
  [bac558e1] OrderedCollections v1.1.0
  [5432bcbf] PaddedViews v0.4.2
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.3.1
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.0.0
  [6038ab10] Rotations v0.13.0
  [699a6c99] SimpleTraits v0.9.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.9.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.32.0
  [06e1c1a7] TiledIteration v0.2.3
  [efce3f68] WoodburyMatrices v0.4.1
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
DMBP:timholy--General dilum$ julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.18.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/timholy/General`
 Resolving package versions...
  Updating `~/.julia/environments/v1.4/Project.toml`
  [916415d5] ↓ Images v0.19.0 ⇒ v0.18.0
  Updating `~/.julia/environments/v1.4/Manifest.toml`
  [916415d5] ↓ Images v0.19.0 ⇒ v0.18.0
Status `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.3.3
  [aafaddc9] CatIndices v0.2.0
  [3da002f7] ColorTypes v0.8.1
  [c3611d14] ColorVectorSpace v0.7.1
  [5ae59095] Colors v0.9.6
  [34da2185] Compat v2.2.0
  [ed09eef8] ComputationalResources v0.3.0
  [150eb455] CoordinateTransformations v0.5.0
  [dc8bdbbb] CustomUnitRanges v0.2.0
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.6
  [b4f34e82] Distances v0.8.2
  [4f61f5a4] FFTViews v0.3.0
  [7a1cc6ca] FFTW v1.2.0
  [f5851436] FFTW_jll v3.3.9+3
  [5789e2e9] FileIO v1.2.1
  [53c48c17] FixedPointNumbers v0.6.1
  [a2bd30eb] Graphics v0.4.0
  [bbac6d45] IdentityRanges v0.3.0
  [2803e5a7] ImageAxes v0.6.2
  [a09fc81d] ImageCore v0.8.10
  [51556ac3] ImageDistances v0.2.7
  [6a3955dd] ImageFiltering v0.6.9
  [bc367c6b] ImageMetadata v0.7.2
  [787d08f9] ImageMorphology v0.2.5
  [4e3cecfd] ImageShow v0.2.2
  [02fcd773] ImageTransformations v0.8.1
  [916415d5] Images v0.18.0
  [9b13fd28] IndirectArrays v0.5.1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] Interpolations v0.12.5
  [8197267c] IntervalSets v0.3.2
  [c8e1da08] IterTools v1.3.0
  [856f044c] MKL_jll v2019.0.117+0
  [1914dd2f] MacroTools v0.5.3
  [dbb5928d] MappedArrays v0.2.2
  [e1d29d7a] Missings v0.4.3
  [77ba4419] NaNMath v0.3.3
  [6fe1bfb0] OffsetArrays v0.11.4
  [efe28fd5] OpenSpecFun_jll v0.5.3+1
  [bac558e1] OrderedCollections v1.1.0
  [5432bcbf] PaddedViews v0.4.2
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.3.1
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.0.0
  [6038ab10] Rotations v0.13.0
  [699a6c99] SimpleTraits v0.9.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.9.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.32.0
  [06e1c1a7] TiledIteration v0.2.3
  [efce3f68] WoodburyMatrices v0.4.1
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
DMBP:timholy--General dilum$ julia -e 'import Pkg; Pkg.add(Pkg.PackageSpec(name = "Images", version = "0.19.0")); Pkg.status(; mode = Pkg.PKGMODE_MANIFEST)'
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/timholy/General`
 Resolving package versions...
  Updating `~/.julia/environments/v1.4/Project.toml`
  [916415d5] ↑ Images v0.18.0 ⇒ v0.19.0
  Updating `~/.julia/environments/v1.4/Manifest.toml`
  [916415d5] ↑ Images v0.18.0 ⇒ v0.19.0
Status `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.3.3
  [aafaddc9] CatIndices v0.2.0
  [3da002f7] ColorTypes v0.8.1
  [c3611d14] ColorVectorSpace v0.7.1
  [5ae59095] Colors v0.9.6
  [34da2185] Compat v2.2.0
  [ed09eef8] ComputationalResources v0.3.0
  [150eb455] CoordinateTransformations v0.5.0
  [dc8bdbbb] CustomUnitRanges v0.2.0
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.6
  [b4f34e82] Distances v0.8.2
  [4f61f5a4] FFTViews v0.3.0
  [7a1cc6ca] FFTW v1.2.0
  [f5851436] FFTW_jll v3.3.9+3
  [5789e2e9] FileIO v1.2.1
  [53c48c17] FixedPointNumbers v0.6.1
  [a2bd30eb] Graphics v0.4.0
  [bbac6d45] IdentityRanges v0.3.0
  [2803e5a7] ImageAxes v0.6.2
  [a09fc81d] ImageCore v0.8.10
  [51556ac3] ImageDistances v0.2.7
  [6a3955dd] ImageFiltering v0.6.9
  [bc367c6b] ImageMetadata v0.7.2
  [787d08f9] ImageMorphology v0.2.5
  [4e3cecfd] ImageShow v0.2.2
  [02fcd773] ImageTransformations v0.8.1
  [916415d5] Images v0.19.0
  [9b13fd28] IndirectArrays v0.5.1
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [a98d9a8b] Interpolations v0.12.5
  [8197267c] IntervalSets v0.3.2
  [c8e1da08] IterTools v1.3.0
  [856f044c] MKL_jll v2019.0.117+0
  [1914dd2f] MacroTools v0.5.3
  [dbb5928d] MappedArrays v0.2.2
  [e1d29d7a] Missings v0.4.3
  [77ba4419] NaNMath v0.3.3
  [6fe1bfb0] OffsetArrays v0.11.4
  [efe28fd5] OpenSpecFun_jll v0.5.3+1
  [bac558e1] OrderedCollections v1.1.0
  [5432bcbf] PaddedViews v0.4.2
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.3.1
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.0.0
  [6038ab10] Rotations v0.13.0
  [699a6c99] SimpleTraits v0.9.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.9.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.32.0
  [06e1c1a7] TiledIteration v0.2.3
  [efce3f68] WoodburyMatrices v0.4.1
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
DMBP:timholy--General dilum$ julia -e 'import InteractiveUtils; InteractiveUtils.versioninfo(; verbose = true)'
Julia Version 1.4.0-DEV.660
Commit 27eb582279 (2019-12-23 19:29 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.2.0)
  uname: Darwin 19.2.0 Darwin Kernel Version 19.2.0: Sat Nov  9 03:47:04 PST 2019; root:xnu-6153.61.1~20/RELEASE_X86_64 x86_64 i386
  CPU: Intel(R) Core(TM) i5-4278U CPU @ 2.60GHz:
              speed         user         nice          sys         idle          irq
       #1  2600 MHz      63039 s          0 s      32941 s     210924 s          0 s
       #2  2600 MHz      21248 s          0 s      12215 s     273431 s          0 s
       #3  2600 MHz      64178 s          0 s      27960 s     214756 s          0 s
       #4  2600 MHz      20236 s          0 s      11373 s     275285 s          0 s

  Memory: 8.0 GB (768.03125 MB free)
  Uptime: 82209.0 sec
  Load Avg:  6.22705078125  5.921875  5.318359375
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.1 (ORCJIT, haswell)
Environment:
  GEM_HOME = /Users/dilum/.rvm/gems/ruby-2.4.1
  TERM = xterm-256color
  MY_RUBY_HOME = /Users/dilum/.rvm/rubies/ruby-2.4.1
  PATH = /Users/dilum/.cargo/bin:/Users/dilum/.rvm/gems/ruby-2.4.1/bin:/Users/dilum/.rvm/gems/ruby-2.4.1@global/bin:/Users/dilum/.rvm/rubies/ruby-2.4.1/bin:/Users/dilum/.rvm/bin:/Users/dilum/.cargo/bin:/Users/dilum/bin:/Applications/Racket-v7.3/bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/go/bin:/usr/local/MacGPG2/bin:/opt/X11/bin
  XPC_FLAGS = 0x0
  HOME = /Users/dilum
  GEM_PATH = /Users/dilum/.rvm/gems/ruby-2.4.1:/Users/dilum/.rvm/gems/ruby-2.4.1@global

DilumAluthge picture DilumAluthge on 1 Jan 2020

Are you able to reproduce this on Julia master?

DilumAluthge picture DilumAluthge on 1 Jan 2020

Yes, but only with the given Project.toml and Manifest.toml files.

timholy picture timholy on 2 Jan 2020

What happens if you run import Pkg; Pkg.resolve()?

DilumAluthge picture DilumAluthge on 2 Jan 2020

If I download your Project.toml and Manifest.toml file and then run julia --project -e 'import Pkg; Pkg.resolve()', I get the following error:

ERROR: Unsatisfiable requirements detected for package Images [916415d5]:
 Images [916415d5] log:
 ├─possible versions are: [0.17.3, 0.18.0, 0.19.0-0.19.3] or uninstalled
 ├─restricted to versions 0.18.0 by an explicit requirement, leaving only versions 0.18.0
 └─restricted by compatibility requirements with Colors [5ae59095] to versions: 0.19.3 or uninstalled — no versions left
   └─Colors [5ae59095] log:
     ├─possible versions are: [0.9.0, 0.9.2-0.9.6, 0.10.0-0.10.1, 0.11.0-0.11.1] or uninstalled
     └─restricted to versions 0.11.1 by an explicit requirement, leaving only versions 0.11.1
DilumAluthge picture DilumAluthge on 2 Jan 2020

Try add [email protected] or something; if you play with versions enough this should resolve.

timholy picture timholy on 2 Jan 2020

Well that's the problem.

  • If I do resolve, I get the error shown above.
  • If instead I do instantiate, it instantiates and gives me Colors v0.11.1. This is the only time I'm able to get Colors v0.11.1
  • If instead I do either add [email protected] or add [email protected], then it immediately downgrades Colors v0.11.1 ⇒ v0.9.6.
DilumAluthge picture DilumAluthge on 2 Jan 2020

Weird. It doesn't downgrade for me on 0.18.0. It does downgrade on 0.19.2, as expected.

timholy picture timholy on 2 Jan 2020

So I'm still not able to reproduce your original report, which is that when you toggle between add [email protected] and add [email protected], it gives you Colors v0.11.1when you are on Images 0.18.0.

DilumAluthge picture DilumAluthge on 2 Jan 2020

Just to double-check we are working with the same stuff: I'm using the HolyLabRegistry latest master branch.

I.e. I added it with: import Pkg; Pkg.Registry.add(Pkg.RegistrySpec(url = "https://github.com/HolyLab/HolyLabRegistry"))

DilumAluthge picture DilumAluthge on 2 Jan 2020
👍1

Also, I added your fork/branch of General before I added HolyLabRegistry. I'm not sure if registry behavior is order-dependent.

DilumAluthge picture DilumAluthge on 2 Jan 2020

What happens if you do rm Images followed by either add [email protected] or add [email protected]?

DilumAluthge picture DilumAluthge on 2 Jan 2020

An additional question: What happens if you delete the Manifest, and then instantiate, and then try toggling between add [email protected] or add [email protected]?

DilumAluthge picture DilumAluthge on 2 Jan 2020

If I download your Project.toml and Manifest.toml file and then run julia --project -e 'import Pkg; Pkg.resolve()', I get the following error:

I tried freshly again and didn't get that error. But I likely have many Colors versions installed already in my packages directory.

Just to double-check we are working with the same stuff: I'm using the HolyLabRegistry latest master branch.

Sorry, I thought I had deleted all the HolyLabRegistry packages. Thanks for figuring out that you needed to add that.

What happens if you do rm Images followed by either add [email protected] or add [email protected]?

I get Colors 0.11.1 with add [email protected]

What happens if you delete the Manifest, and then instantiate, and then try toggling between add [email protected] or add [email protected]?

Doesn't help.

Just to be certain I didn't have some modification of Pkg causing trouble (I sometimes make tweaks via Revise but I'm not always sure where pathof(Pkg) really gets symlinked to), I deleted my $JULIADIR/usr directory, all versions of Pkg-* in $JULIADIR/stdlib/, and rebuilt on the latest nightly.

That didn't help. But what did fix it was to start completely fresh: JULIA_DEPOT_PATH=/tmp/pkgs julia and then copy all the requisite settings. So there's something about the state of my .julia directory that's different from a fresh one.

timholy picture timholy on 2 Jan 2020
👍1

That didn't help. But what did fix it was to start completely fresh: JULIA_DEPOT_PATH=/tmp/pkgs julia and then copy all the requisite settings. So there's something about the state of my .julia directory that's different from a fresh one.

That is fascinating. So the issue is something in your ~/.julia directory?

Is there any confidential info in your ~/.julia directory? If not, you could share it and we could see if anyone else can reproduce.

(But that will be tricky if you have lab-private code in your ~/.julia directory.)

DilumAluthge picture DilumAluthge on 3 Jan 2020

Yeah, there's a ton of not-yet-ready-for-exposure stuff in there.

Any tips on how I'd go about debugging this? Even though I've poked at Pkg several times, I've never taken the plunge deeply enough to have a good sense for its overall organization.

timholy picture timholy on 3 Jan 2020

If you haven’t done so already, I’d make a .tar.gz of your ~/.julia folder and store it somewhere (e.g. Google Drive) so that at least you can reproduce the error yourself at a later date.

As far as where to start debugging, it does seem to me that this is probably a resolver bug. @00vareladavid is probably the most knowledgeable on the resolver and perhaps he can tell us where to start?

DilumAluthge picture DilumAluthge on 4 Jan 2020

The resolve step has a very small API "surface":

https://github.com/JuliaLang/Pkg.jl/blob/0048fe1af04e2effcbce8ce2a0ed29d11b0e5950/src/Operations.jl#L339-L342

So serializing the graph should be enough to repro and looking at the output (the versions) from resolve should say if there is a bug (if a version is returned that is input as being incompatible). I personally doubt this is actually the case and that there is something wrong with the inputs to the resolver.

KristofferC picture KristofferC on 4 Jan 2020
👍2

Even with https://gist.github.com/timholy/38dff6cfe0aa176bdc2d47bed0201e75 I can no longer reproduce this. Sorry I didn't ever figure out what was causing this, but hopefully it's a weird corner case.

timholy picture timholy on 15 Jan 2020
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