install.sh: CERTIFICATE_VERIFY_FAILED
On some unreported macOS, the scripts/install.sh script fails to setup the tagging backend due to an SSL error on downloading Poetry:
$ curl -sSL "https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/dev/scripts/install.sh?ref_type=heads&inline=false" | /bin/bash -s -- --with-backend --experimental
The --experimental flag is deprecated and is now default
Checking for new Julia versions
'1.10' is already installed.
Configured the default Julia version to be '1.10'.
WARNING: the default tagging backend is not supported by macOS
Retrieving Poetry metadata
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1348, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1282, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1328, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1277, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1037, in _send_output
self.send(msg)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 975, in send
self.connect()
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1454, in connect
self.sock = self._context.wrap_socket(self.sock,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1075, in _create
self.do_handshake()
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1346, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 959, in <module>
File "<stdin>", line 937, in main
File "<stdin>", line 538, in run
File "<stdin>", line 800, in get_version
File "<stdin>", line 861, in _get
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 519, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1391, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1351, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:992)>
Extending the PATH environment variable in /Users/tihanajovanic/.bash_profile
~/.local/share/larvatagger ~
PlanarLarvae.jl installation found; skipping
LarvaTagger.jl installation found; skipping
Resolving package versions...
No Changes to `~/.local/share/larvatagger/LarvaTagger.jl/Project.toml`
No Changes to `~/.local/share/larvatagger/LarvaTagger.jl/Manifest.toml`
x TaggingBackends-main/
x TaggingBackends-main/.gitignore
x TaggingBackends-main/.gitlab-ci.yml
x TaggingBackends-main/Artifacts.toml
x TaggingBackends-main/LICENSE
x TaggingBackends-main/Manifest.toml
x TaggingBackends-main/Project.toml
x TaggingBackends-main/README.md
x TaggingBackends-main/pyproject.toml
x TaggingBackends-main/scripts/
x TaggingBackends-main/scripts/confusion.py
x TaggingBackends-main/scripts/tagging-backend
x TaggingBackends-main/src/
x TaggingBackends-main/src/LarvaDatasets.jl
x TaggingBackends-main/src/TaggingBackends.jl
x TaggingBackends-main/src/examplebackend/
x TaggingBackends-main/src/examplebackend/__init__.py
x TaggingBackends-main/src/examplebackend/data/
x TaggingBackends-main/src/examplebackend/data/make_dataset.py
x TaggingBackends-main/src/examplebackend/features/
x TaggingBackends-main/src/examplebackend/features/build_features.py
x TaggingBackends-main/src/examplebackend/models/
x TaggingBackends-main/src/examplebackend/models/__init__.py
x TaggingBackends-main/src/examplebackend/models/mymodel.py
x TaggingBackends-main/src/examplebackend/models/predict_model.py
x TaggingBackends-main/src/examplebackend/models/train_model.py
x TaggingBackends-main/src/taggingbackends/
x TaggingBackends-main/src/taggingbackends/__init__.py
x TaggingBackends-main/src/taggingbackends/data/
x TaggingBackends-main/src/taggingbackends/data/__init__.py
x TaggingBackends-main/src/taggingbackends/data/chore.py
x TaggingBackends-main/src/taggingbackends/data/convert.py
x TaggingBackends-main/src/taggingbackends/data/dataset.py
x TaggingBackends-main/src/taggingbackends/data/fimtrack.py
x TaggingBackends-main/src/taggingbackends/data/labels.py
x TaggingBackends-main/src/taggingbackends/data/trxmat.py
x TaggingBackends-main/src/taggingbackends/explorer.py
x TaggingBackends-main/src/taggingbackends/features/
x TaggingBackends-main/src/taggingbackends/features/__init__.py
x TaggingBackends-main/src/taggingbackends/features/skeleton.py
x TaggingBackends-main/src/taggingbackends/info.py
x TaggingBackends-main/src/taggingbackends/main.py
x TaggingBackends-main/test/
x TaggingBackends-main/test/Makefile
x TaggingBackends-main/test/__init__.py
x TaggingBackends-main/test/dummylabels.sh
x TaggingBackends-main/test/examplebackend.sh
x TaggingBackends-main/test/makedata.jl
x TaggingBackends-main/test/makedata.py
x TaggingBackends-main/test/runtests.jl
x TaggingBackends-main/test/test_taggingbackends.py
/bin/bash: line 373: poetry: command not found
Resolving package versions...
Installed OpenSSL_jll ───────────── v1.1.20+0
Installed OffsetArrays ──────────── v1.12.9
Installed Preferences ───────────── v1.4.0
Installed Conda ─────────────────── v1.8.0
Installed JSON3 ─────────────────── v1.12.0
Installed Tables ────────────────── v1.10.1
Installed PyCall ────────────────── v1.95.1
Installed DataAPI ───────────────── v1.15.0
Installed Parsers ───────────────── v2.5.10
Installed JLLWrappers ───────────── v1.4.1
Installed StaticArraysCore ──────── v1.4.0
Installed OrderedCollections ────── v1.6.0
Installed NearestNeighbors ──────── v0.4.13
Installed StaticArrays ──────────── v1.5.25
Installed PrecompileTools ───────── v1.1.1
Installed SnoopPrecompile ───────── v1.0.3
Installed VersionParsing ────────── v1.3.0
Installed Memoization ───────────── v0.2.0
Installed LogExpFunctions ───────── v0.3.23
Installed DataStructures ────────── v0.18.13
Installed MAT ───────────────────── v0.10.4
Installed HDF5 ──────────────────── v0.16.14
Installed MacroTools ────────────── v0.5.10
Installed BufferedStreams ───────── v1.1.0
Installed CircularArrays ────────── v1.3.2
Installed Compat ────────────────── v4.6.1
Installed StatsAPI ──────────────── v1.6.0
Installed Distances ─────────────── v0.10.8
Installed Crayons ───────────────── v4.1.1
Installed HDF5_jll ──────────────── v1.12.2+2
Installed CodecZlib ─────────────── v0.7.1
Installed SortingAlgorithms ─────── v1.1.0
Installed Adapt ─────────────────── v3.6.2
Installed IterTools ─────────────── v1.4.0
Installed ReferenceFrameRotations ─ v3.0.0
Installed Meshes ────────────────── v0.28.1
Downloaded artifact: OpenSSL
Downloaded artifact: HDF5
Updating `~/.local/share/larvatagger/TaggingBackends/Project.toml`
[c2615984] ~ PlanarLarvae v0.16.0 `https://gitlab.pasteur.fr/nyx/PlanarLarvae.jl#main` ⇒ v0.16.0 `../PlanarLarvae`
Updating `~/.local/share/larvatagger/TaggingBackends/Manifest.toml`
[c2615984] ~ PlanarLarvae v0.16.0 `https://gitlab.pasteur.fr/nyx/PlanarLarvae.jl#main` ⇒ v0.16.0 `../PlanarLarvae`
[e66e0078] ↑ CompilerSupportLibraries_jll v1.1.0+0 ⇒ v1.1.1+0
[8e850b90] ↑ libblastrampoline_jll v5.8.0+1 ⇒ v5.11.0+0
Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/e32a90da027ca45d84678b826fffd3110bb3fc90/build.log`
Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/62f417f6ad727987c755549e9cd88c46578da562/build.log`
Building HDF5 ──→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/3dab31542b3da9f25a6a1d11159d4af8fdce7d67/build.log`
/bin/bash: line 373: poetry: command not found
x MaggotUBA-adapter-torch2/
x MaggotUBA-adapter-torch2/.gitignore
x MaggotUBA-adapter-torch2/Artifacts.toml
x MaggotUBA-adapter-torch2/LICENSE
x MaggotUBA-adapter-torch2/Project.toml
x MaggotUBA-adapter-torch2/README.md
x MaggotUBA-adapter-torch2/pretrained_models/
x MaggotUBA-adapter-torch2/pretrained_models/20230129/
x MaggotUBA-adapter-torch2/pretrained_models/20230129/autoencoder_config.json
x MaggotUBA-adapter-torch2/pretrained_models/20230129/best_validated_encoder.pt
x MaggotUBA-adapter-torch2/pretrained_models/former-default
x MaggotUBA-adapter-torch2/pyproject.toml
x MaggotUBA-adapter-torch2/requirements.txt
x MaggotUBA-adapter-torch2/scripts/
x MaggotUBA-adapter-torch2/scripts/make_models.jl
x MaggotUBA-adapter-torch2/scripts/reinstall.sh
x MaggotUBA-adapter-torch2/scripts/revert_label_mapping.jl
x MaggotUBA-adapter-torch2/src/
x MaggotUBA-adapter-torch2/src/maggotuba/
x MaggotUBA-adapter-torch2/src/maggotuba/__init__.py
x MaggotUBA-adapter-torch2/src/maggotuba/data/
x MaggotUBA-adapter-torch2/src/maggotuba/data/make_dataset.py
x MaggotUBA-adapter-torch2/src/maggotuba/features/
x MaggotUBA-adapter-torch2/src/maggotuba/features/__init__.py
x MaggotUBA-adapter-torch2/src/maggotuba/features/preprocess.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/
x MaggotUBA-adapter-torch2/src/maggotuba/models/__init__.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/embed_model.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/finetune_model.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/modules.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/predict_model.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/train_model.py
x MaggotUBA-adapter-torch2/src/maggotuba/models/trainers.py
x MaggotUBA-adapter-torch2/test/
x MaggotUBA-adapter-torch2/test/train_no_pretrain.sh
x MaggotUBA-adapter-torch2/test/train_subset3.sh
/bin/bash: line 373: poetry: command not found
/bin/bash: line 373: poetry: command not found
Failure artifact: 20230524-6behaviors-25
Downloaded artifact: 20230524-6behaviors-25
Failure artifact: 20230524-hunch-25
Downloaded artifact: 20230524-hunch-25
Failure artifact: 20230524-roll-25
Downloaded artifact: 20230524-roll-25
Failure artifact: 20230311
Downloaded artifact: 20230311
Failure artifact: 20230311-0
Downloaded artifact: 20230311-0brew install certifi did not fix the issue.