Hello folks,
I am trying to release a new version of a registered package that depends on PyPlot, namely SeisPlot.jl. During the CI job that tries to automerge the new release they check if the packaged can be added. From the 3 times it was tried during the CI job, the third time failed complaining that matplotlib was not available, despite having succeeded two other times.
I’d appreciate any tips on how to proceed, thanks in advance.
Here is a snippet of the CI log:
[...]
┌ Info: Compat (with upper bound) for all dependencies
│ meets_this_guideline = true
└ message = ""
┌ Info: If it is a patch release on a post-1.0 package, then it does not narrow the `[compat]` range for `julia`.
│ meets_this_guideline = true
└ message = ""
┌ Info: xvfb:
└ xvfb = "/usr/bin/xvfb-run"
[ Info: Attempting to `Pkg.add` the package
Copying registry from `~/work/General/General`
Copied registry `General` to `/tmp/jl_QQdwIq/registries/General`
[ Info: Attempting to `Pkg.add` package...
Updating registry at `/tmp/jl_QQdwIq/registries/General`
┌ Error: Some registries failed to update:
│ — `/tmp/jl_QQdwIq/registries/General` — registry dirty
└ @ Pkg.Registry /opt/hostedtoolcache/julia/1.9.2/x64/share/julia/stdlib/v1.9/Pkg/src/Registry/Registry.jl:510
Resolving package versions...
Installed Conda ─────────────── v1.9.1
Installed OpenSSL_jll ───────── v1.1.21+0
Installed FFTW ──────────────── v1.7.1
Installed Preferences ───────── v1.4.0
Installed JSON ──────────────── v0.21.4
Installed IOCapture ─────────── v0.2.3
Installed ColorTypes ────────── v0.11.4
Installed Parsers ───────────── v2.7.1
Installed FixedPointNumbers ─── v0.8.4
Installed libsass_jll ───────── v3.6.4+0
Installed PyCall ────────────── v1.96.1
Installed DocumenterTools ───── v0.1.17
Installed Documenter ────────── v0.27.25
Installed JLLWrappers ───────── v1.4.1
Installed PrecompileTools ───── v1.1.2
Installed MKL_jll ───────────── v2023.1.0+0
Installed VersionParsing ────── v1.3.0
Installed AbstractTrees ─────── v0.4.4
Installed AbstractFFTs ──────── v1.4.0
Installed PyPlot ────────────── v2.11.1
Installed LaTeXStrings ──────── v1.3.0
Installed Gumbo ─────────────── v0.8.2
Installed OpenSSH_jll ───────── v8.9.0+1
Installed Gumbo_jll ─────────── v0.10.2+0
Installed Reexport ──────────── v1.2.2
Installed Colors ────────────── v0.12.10
Installed FFTW_jll ──────────── v3.3.10+0
Installed Sass ──────────────── v0.2.0
Installed MacroTools ────────── v0.5.10
Installed IntelOpenMP_jll ───── v2023.1.0+0
Installed DocStringExtensions ─ v0.9.3
Installed ANSIColoredPrinters ─ v0.0.1
Installed SeisPlot ──────────── v0.1.1
Installed SeisMain ──────────── v0.1.1
Updating `/tmp/jl_QQdwIq/environments/v1.9/Project.toml`
[00783350] + SeisPlot v0.1.1
Updating `/tmp/jl_QQdwIq/environments/v1.9/Manifest.toml`
[a4c015fc] + ANSIColoredPrinters v0.0.1
[621f4979] + AbstractFFTs v1.4.0
[1520ce14] + AbstractTrees v0.4.4
[3da002f7] + ColorTypes v0.11.4
[5ae59095] + Colors v0.12.10
[8f4d0f93] + Conda v1.9.1
[ffbed154] + DocStringExtensions v0.9.3
[e30172f5] + Documenter v0.27.25
[35a29f4d] + DocumenterTools v0.1.17
[7a1cc6ca] + FFTW v1.7.1
[53c48c17] + FixedPointNumbers v0.8.4
[708ec375] + Gumbo v0.8.2
[b5f81e59] + IOCapture v0.2.3
[692b3bcd] + JLLWrappers v1.4.1
[682c06a0] + JSON v0.21.4
[b964fa9f] + LaTeXStrings v1.3.0
[1914dd2f] + MacroTools v0.5.10
[69de0a69] + Parsers v2.7.1
[aea7be01] + PrecompileTools v1.1.2
[21216c6a] + Preferences v1.4.0
[438e738f] + PyCall v1.96.1
[d330b81b] + PyPlot v2.11.1
[189a3867] + Reexport v1.2.2
[322a6be2] + Sass v0.2.0
[5696fd22] + SeisMain v0.1.1
[00783350] + SeisPlot v0.1.1
[81def892] + VersionParsing v1.3.0
[f5851436] + FFTW_jll v3.3.10+0
[528830af] + Gumbo_jll v0.10.2+0
[1d5cc7b8] + IntelOpenMP_jll v2023.1.0+0
[856f044c] + MKL_jll v2023.1.0+0
⌅ [9bd350c2] + OpenSSH_jll v8.9.0+1
⌅ [458c3c95] + OpenSSL_jll v1.1.21+0
[47bcb7c8] + libsass_jll v3.6.4+0
[0dad84c5] + ArgTools v1.1.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL v0.6.3
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.9.2
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics v1.9.0
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll v1.0.5+0
[deac9b47] + LibCURL_jll v7.84.0+0
[29816b5a] + LibSSH2_jll v1.10.2+0
[c8ffd9c3] + MbedTLS_jll v2.28.2+0
[14a3606d] + MozillaCACerts_jll v2022.10.11
[4536629a] + OpenBLAS_jll v0.3.21+4
[bea87d4a] + SuiteSparse_jll v5.10.1+6
[83775a58] + Zlib_jll v1.2.13+0
[8e850b90] + libblastrampoline_jll v5.8.0+0
[8e850ede] + nghttp2_jll v1.48.0+0
[3f19e933] + p7zip_jll v17.4.0+0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Building Conda ───→ `/tmp/jl_QQdwIq/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8c86e48c0db1564a1d49548d3515ced5d604c408/build.log`
Building PyCall ──→ `/tmp/jl_QQdwIq/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/43d304ac6f0354755f1d60730ece8c499980f7ba/build.log`
Building SeisPlot → `/tmp/jl_QQdwIq/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/4f40cb00468c28b30d07c0fb872f765395a9fdb0/build.log`
[ Info: Successfully `Pkg.add`ed package
[ Info: Successfully `Pkg.add`ed the package
┌ Info: Version can be `Pkg.add`ed
│ meets_this_guideline = true
└ message = ""
[ Info: Attempting to clone...
┌ Info: Code can be downloaded.
│ meets_this_guideline = true
└ message = ""
┌ Info: License check passed; results
│ osi_results =
│ 1-element Vector{String}:
│ "MIT license in LICENSE"
└ non_osi_results = String[]
┌ Info: Version has OSI-approved license
│ meets_this_guideline = true
└ message = "Found OSI-approved license(s): MIT license in LICENSE. Found no other licenses."
┌ Info: `src` files and directories names are OK
│ meets_this_guideline = true
└ message = ""
┌ Info: xvfb:
└ xvfb = "/usr/bin/xvfb-run"
[ Info: Attempting to `import` the package
Copying registry from `~/work/General/General`
Copied registry `General` to `/tmp/jl_XSQ4UR/registries/General`
[ Info: Attempting to `Pkg.add` package...
Updating registry at `/tmp/jl_XSQ4UR/registries/General`
┌ Error: Some registries failed to update:
│ — `/tmp/jl_XSQ4UR/registries/General` — registry dirty
└ @ Pkg.Registry /opt/hostedtoolcache/julia/1.9.2/x64/share/julia/stdlib/v1.9/Pkg/src/Registry/Registry.jl:510
Resolving package versions...
Installed Preferences ───────── v1.4.0
Installed OpenSSL_jll ───────── v1.1.21+0
Installed JSON ──────────────── v0.21.4
Installed FFTW ──────────────── v1.7.1
Installed Conda ─────────────── v1.9.1
Installed ColorTypes ────────── v0.11.4
Installed IOCapture ─────────── v0.2.3
Installed libsass_jll ───────── v3.6.4+0
Installed Parsers ───────────── v2.7.1
Installed DocumenterTools ───── v0.1.17
Installed Documenter ────────── v0.27.25
Installed PyCall ────────────── v1.96.1
Installed FixedPointNumbers ─── v0.8.4
Installed AbstractFFTs ──────── v1.4.0
Installed PrecompileTools ───── v1.1.2
Installed VersionParsing ────── v1.3.0
Installed JLLWrappers ───────── v1.4.1
Installed PyPlot ────────────── v2.11.1
Installed MKL_jll ───────────── v2023.1.0+0
Installed LaTeXStrings ──────── v1.3.0
Installed AbstractTrees ─────── v0.4.4
Installed Gumbo ─────────────── v0.8.2
Installed OpenSSH_jll ───────── v8.9.0+1
Installed Gumbo_jll ─────────── v0.10.2+0
Installed Reexport ──────────── v1.2.2
Installed IntelOpenMP_jll ───── v2023.1.0+0
Installed MacroTools ────────── v0.5.10
Installed FFTW_jll ──────────── v3.3.10+0
Installed Sass ──────────────── v0.2.0
Installed SeisMain ──────────── v0.1.1
Installed ANSIColoredPrinters ─ v0.0.1
Installed Colors ────────────── v0.12.10
Installed DocStringExtensions ─ v0.9.3
Installed SeisPlot ──────────── v0.1.1
Updating `/tmp/jl_XSQ4UR/environments/v1.9/Project.toml`
[00783350] + SeisPlot v0.1.1
Updating `/tmp/jl_XSQ4UR/environments/v1.9/Manifest.toml`
[a4c015fc] + ANSIColoredPrinters v0.0.1
[621f4979] + AbstractFFTs v1.4.0
[1520ce14] + AbstractTrees v0.4.4
[3da002f7] + ColorTypes v0.11.4
[5ae59095] + Colors v0.12.10
[8f4d0f93] + Conda v1.9.1
[ffbed154] + DocStringExtensions v0.9.3
[e30172f5] + Documenter v0.27.25
[35a29f4d] + DocumenterTools v0.1.17
[7a1cc6ca] + FFTW v1.7.1
[53c48c17] + FixedPointNumbers v0.8.4
[708ec375] + Gumbo v0.8.2
[b5f81e59] + IOCapture v0.2.3
[692b3bcd] + JLLWrappers v1.4.1
[682c06a0] + JSON v0.21.4
[b964fa9f] + LaTeXStrings v1.3.0
[1914dd2f] + MacroTools v0.5.10
[69de0a69] + Parsers v2.7.1
[aea7be01] + PrecompileTools v1.1.2
[21216c6a] + Preferences v1.4.0
[438e738f] + PyCall v1.96.1
[d330b81b] + PyPlot v2.11.1
[189a3867] + Reexport v1.2.2
[322a6be2] + Sass v0.2.0
[5696fd22] + SeisMain v0.1.1
[00783350] + SeisPlot v0.1.1
[81def892] + VersionParsing v1.3.0
[f5851436] + FFTW_jll v3.3.10+0
[528830af] + Gumbo_jll v0.10.2+0
[1d5cc7b8] + IntelOpenMP_jll v2023.1.0+0
[856f044c] + MKL_jll v2023.1.0+0
⌅ [9bd350c2] + OpenSSH_jll v8.9.0+1
⌅ [458c3c95] + OpenSSL_jll v1.1.21+0
[47bcb7c8] + libsass_jll v3.6.4+0
[0dad84c5] + ArgTools v1.1.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL v0.6.3
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.9.2
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics v1.9.0
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll v1.0.5+0
[deac9b47] + LibCURL_jll v7.84.0+0
[29816b5a] + LibSSH2_jll v1.10.2+0
[c8ffd9c3] + MbedTLS_jll v2.28.2+0
[14a3606d] + MozillaCACerts_jll v2022.10.11
[4536629a] + OpenBLAS_jll v0.3.21+4
[bea87d4a] + SuiteSparse_jll v5.10.1+6
[83775a58] + Zlib_jll v1.2.13+0
[8e850b90] + libblastrampoline_jll v5.8.0+0
[8e850ede] + nghttp2_jll v1.48.0+0
[3f19e933] + p7zip_jll v17.4.0+0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Building Conda ───→ `/tmp/jl_XSQ4UR/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8c86e48c0db1564a1d49548d3515ced5d604c408/build.log`
Building PyCall ──→ `/tmp/jl_XSQ4UR/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/43d304ac6f0354755f1d60730ece8c499980f7ba/build.log`
Building SeisPlot → `/tmp/jl_XSQ4UR/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/4f40cb00468c28b30d07c0fb872f765395a9fdb0/build.log`
[ Info: Successfully `Pkg.add`ed package
[ Info: Attempting to `import` package
Precompiling project...
✓ Statistics
✓ DocStringExtensions
✓ VersionParsing
✓ AbstractFFTs
✓ LaTeXStrings
✓ CompilerSupportLibraries_jll
✓ ANSIColoredPrinters
✓ Reexport
✓ MbedTLS_jll
✓ MacroTools
✓ Zlib_jll
✓ SuiteSparse_jll
✓ IOCapture
✓ Preferences
✓ AbstractTrees
✓ LibSSH2_jll
✓ PrecompileTools
✓ JLLWrappers
✓ OpenSSL_jll
✓ IntelOpenMP_jll
✓ FFTW_jll
✓ Gumbo_jll
✓ FixedPointNumbers
✓ libsass_jll
✓ MKL_jll
✓ OpenSSH_jll
✓ Gumbo
✓ Sass
✓ ColorTypes
✓ Colors
✓ FFTW
✓ Parsers
✓ JSON
✓ Conda
✓ Documenter
✓ DocumenterTools
✓ SeisMain
✓ PyCall
✓ PyPlot
✗ SeisPlot
39 dependencies successfully precompiled in 101 seconds
ERROR: The following 1 direct dependency failed to precompile:
SeisPlot [00783350-183d-11e9-0ed7-9f3f45823183]
Failed to precompile SeisPlot [00783350-183d-11e9-0ed7-9f3f45823183] to "/tmp/jl_XSQ4UR/compiled/v1.9/SeisPlot/jl_JR9fJR".
[ Info: Installing matplotlib via the Conda matplotlib package...
[ Info: Running `conda install -y matplotlib` in root environment
ResolvePackageNotFound:
- conda==23.1.0
ERROR: LoadError: InitError: failed process: Process(setenv(`/tmp/jl_XSQ4UR/conda/3/x86_64/bin/conda install -y matplotlib`,["PYTHONIOENCODING=UTF-8", "PATH=/opt/hostedtoolcache/julia/1.9.2/x64/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin", "JULIA_IMAGE_THREADS=1", "***", "CONDA_PREFIX=/tmp/jl_XSQ4UR/conda/3/x86_64", "DISPLAY=:99", "JULIA_LOAD_PATH=/tmp/jl_XSQ4UR/environments/v1.9/Project.toml:/opt/hostedtoolcache/julia/1.9.2/x64/share/julia/stdlib/v1.9", "OPENBLAS_DEFAULT_NUM_THREADS=1", "JULIA_REGISTRYCI_AUTOMERGE=true", "OPENBLAS_NUM_THREADS=1", "XAUTHORITY=/tmp/xvfb-run.RQrCkQ/Xauthority", "HOME=/home/runner", "JULIA_PKG_PRECOMPILE_AUTO=0", "CONDARC=/tmp/jl_XSQ4UR/conda/3/x86_64/condarc-julia.yml", "JULIA_DEPOT_PATH=/tmp/jl_XSQ4UR", "OPENBLAS_MAIN_FREE=1", "R_HOME=*", "JULIA_NUM_THREADS=1"]), ProcessExited(1)) [1]
Stacktrace:
[1] pipeline_error
@ ./process.jl:565 [inlined]
[2] run(::Cmd; wait::Bool)
@ Base ./process.jl:480
[3] run
@ ./process.jl:477 [inlined]
[4] runconda(args::Cmd, env::String)
@ Conda /tmp/jl_XSQ4UR/packages/Conda/2lg2O/src/Conda.jl:128
[5] add(pkg::String, env::String; channel::String, satisfied_skip_solve::Bool, args::Cmd)
@ Conda /tmp/jl_XSQ4UR/packages/Conda/2lg2O/src/Conda.jl:256
[6] add (repeats 2 times)
@ /tmp/jl_XSQ4UR/packages/Conda/2lg2O/src/Conda.jl:239 [inlined]
[7] pyimport_conda
@ /tmp/jl_XSQ4UR/packages/PyCall/ilqDX/src/PyCall.jl:721
[8] pyimport_conda
@ /tmp/jl_XSQ4UR/packages/PyCall/ilqDX/src/PyCall.jl:715 [inlined]
[9] __init__()
@ PyPlot /tmp/jl_XSQ4UR/packages/PyPlot/H01LC/src/init.jl:173
[10] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1115
[11] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
@ Base ./loading.jl:1061
[12] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
@ Base ./loading.jl:1506
[13] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1783
[14] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1660
[15] macro expansion
@ ./loading.jl:1648 [inlined]
[16] macro expansion
@ ./lock.jl:267 [inlined]
[17] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1611
[18] include
@ ./Base.jl:457 [inlined]
[19] 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, UInt128}}, source::Nothing)
@ Base ./loading.jl:2049
[20] top-level scope
@ stdin:3
during initialization of module PyPlot
in expression starting at /tmp/jl_XSQ4UR/packages/SeisPlot/qUYYX/src/SeisPlot.jl:1
in expression starting at stdin:3
caused by: PyError (PyImport_ImportModule
The Python package matplotlib could not be imported by pyimport. Usually this means
that you did not install matplotlib in the Python version being used by PyCall.
PyCall is currently configured to use the Julia-specific Python distribution
installed by the Conda.jl package. To install the matplotlib module, you can
use `pyimport_conda("matplotlib", PKG)`, where PKG is the Anaconda
package that contains the module matplotlib, or alternatively you can use the
Conda package directly (via `using Conda` followed by `Conda.add` etcetera).
Alternatively, if you want to use a different Python distribution on your
system, such as a system-wide Python (as opposed to the Julia-specific Python),
you can re-configure PyCall with that Python. As explained in the PyCall
documentation, set ENV["PYTHON"] to the path/name of the python executable
you want to use, run Pkg.build("PyCall"), and re-launch Julia.
) <class 'ModuleNotFoundError'>
ModuleNotFoundError("No module named 'matplotlib'")
[...]