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R CMD BUILD
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* checking for file AnVILVRS/DESCRIPTION ... OK
* preparing AnVILVRS:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building AnVILVRS.Rmd using rmarkdown
Requirement already satisfied: pip in /home/pkgbuild/.virtualenvs/vrs_env/lib/python3.11/site-packages (24.0)
Collecting pip
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Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: setuptools
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Installing collected packages: numpy
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Attempting uninstall: setuptools
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[notice] A new release of pip is available: 23.0.1 -> 25.3
[notice] To update, run: /home/pkgbuild/.virtualenvs/vrs_env/bin/python -m pip install --upgrade pip
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Collecting protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<7.0.0,>=3.19.5
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Building wheels for collected packages: firecloud
Building wheel for firecloud (setup.py): started
Building wheel for firecloud (setup.py): finished with status 'done'
Created wheel for firecloud: filename=firecloud-0.16.38-py3-none-any.whl size=58654 sha256=c19935a0cb7b12eb28b82b987e91817615652812d00a40283600cffb200a6db0
Stored in directory: /home/pkgbuild/.cache/pip/wheels/cf/d9/98/9687b3177b6fdbce617f49ade385d29b001a75f69e405967da
Successfully built firecloud
Installing collected packages: nose, urllib3, tomlkit, six, pyparsing, pycparser, pyasn1, protobuf, platformdirs, mccabe, isort, idna, google-crc32c, dill, charset_normalizer, certifi, astroid, rsa, requests, pylint, pydot, pyasn1-modules, proto-plus, googleapis-common-protos, google-resumable-media, cffi, cryptography, google-auth, google-api-core, google-cloud-core, google-cloud-storage, firecloud
Successfully installed astroid-4.0.3 certifi-2026.1.4 cffi-2.0.0 charset_normalizer-3.4.4 cryptography-46.0.3 dill-0.4.1 firecloud-0.16.38 google-api-core-2.29.0 google-auth-2.48.0 google-cloud-core-2.5.0 google-cloud-storage-3.8.0 google-crc32c-1.8.0 google-resumable-media-2.8.0 googleapis-common-protos-1.72.0 idna-3.11 isort-7.0.0 mccabe-0.7.0 nose-1.3.7 platformdirs-4.5.1 proto-plus-1.27.0 protobuf-6.33.4 pyasn1-0.6.2 pyasn1-modules-0.4.2 pycparser-3.0 pydot-4.0.1 pylint-4.0.4 pyparsing-3.3.2 requests-2.32.5 rsa-4.9.1 six-1.17.0 tomlkit-0.14.0 urllib3-2.6.3
WARNING: There was an error checking the latest version of pip.
Requirement already satisfied: setuptools in /home/pkgbuild/.virtualenvs/vrs_env/lib/python3.11/site-packages (57.5.0)
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Installing collected packages: setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 57.5.0
Uninstalling setuptools-57.5.0:
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Attempting uninstall: pip
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WARNING: There was an error checking the latest version of pip.
Collecting vrs-anvil-toolkit
Downloading vrs_anvil_toolkit-0.3.3-py3-none-any.whl.metadata (14 kB)
Collecting python-dotenv (from vrs-anvil-toolkit)
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Collecting google (from vrs-anvil-toolkit)
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Collecting pandas (from vrs-anvil-toolkit)
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Collecting vrsix==0.1.1 (from vrs-anvil-toolkit)
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Collecting asyncclick (from vrsix==0.1.1->vrs-anvil-toolkit)
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Installing build dependencies: started
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Building wheels for collected packages: psycopg2
Building wheel for psycopg2 (pyproject.toml): started
Building wheel for psycopg2 (pyproject.toml): finished with status 'done'
Created wheel for psycopg2: filename=psycopg2-2.9.11-cp311-cp311-linux_x86_64.whl size=522717 sha256=f19a04a476114acacd7c1f2e90bc681cd70418c8643d166bd7de144401dfbb40
Stored in directory: /home/pkgbuild/.cache/pip/wheels/15/a7/0e/37c6d130333cbaac2e6bb15e4ff41ef3a195af78a70907ca0d
Successfully built psycopg2
Installing collected packages: pure-eval, ptyprocess, parsley, zipp, wcwidth, typing-extensions, traitlets, tqdm, tabulate, sqlparse, soupsieve, pyyaml, python-dotenv, python-dateutil, pysam, pygments, psycopg2-binary, psycopg2, psutil, pexpect, parso, jmespath, humanfriendly, executing, diskcache, dill, decorator, configparser, click, canonicaljson, boltons, attrs, asyncclick, asttokens, annotated-types, vrsix, typing-inspection, stack_data, pydantic-core, prompt_toolkit, pandas, matplotlib-inline, jedi, importlib-metadata, face, coloredlogs, botocore, bioutils, beautifulsoup4, yoyo-migrations, s3transfer, pydantic, ipython, google, glom, ga4gh.vrs, boto3, biocommons.seqrepo, hgvs, ga4gh.cat_vrs, ga4gh.va-spec, vrs-anvil-toolkit
Attempting uninstall: dill
Found existing installation: dill 0.4.1
Uninstalling dill-0.4.1:
Successfully uninstalled dill-0.4.1
Successfully installed annotated-types-0.7.0 asttokens-3.0.1 asyncclick-8.3.0.7 attrs-25.4.0 beautifulsoup4-4.14.3 biocommons.seqrepo-0.6.11 bioutils-0.6.1 boltons-25.0.0 boto3-1.42.35 botocore-1.42.35 canonicaljson-2.0.0 click-8.3.1 coloredlogs-15.0.1 configparser-7.2.0 decorator-5.2.1 dill-0.3.9 diskcache-5.6.3 executing-2.2.1 face-24.0.0 ga4gh.cat_vrs-0.7.2 ga4gh.va-spec-0.4.3 ga4gh.vrs-2.2.0 glom-25.12.0 google-3.0.0 hgvs-1.5.4 humanfriendly-10.0 importlib-metadata-8.7.1 ipython-8.38.0 jedi-0.19.2 jmespath-1.1.0 matplotlib-inline-0.2.1 pandas-3.0.0 parsley-1.3 parso-0.8.5 pexpect-4.9.0 prompt_toolkit-3.0.52 psutil-7.2.1 psycopg2-2.9.11 psycopg2-binary-2.9.11 ptyprocess-0.7.0 pure-eval-0.2.3 pydantic-2.12.5 pydantic-core-2.41.5 pygments-2.19.2 pysam-0.23.0 python-dateutil-2.9.0.post0 python-dotenv-1.2.1 pyyaml-6.0.3 s3transfer-0.16.0 soupsieve-2.8.3 sqlparse-0.5.5 stack_data-0.6.3 tabulate-0.9.0 tqdm-4.67.1 traitlets-5.14.3 typing-extensions-4.15.0 typing-inspection-0.4.2 vrs-anvil-toolkit-0.3.3 vrsix-0.1.1 wcwidth-0.5.0 yoyo-migrations-9.0.0 zipp-3.23.0
Collecting plugin_system
Downloading plugin-system-0.0.1.tar.gz (2.1 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: ga4gh.vrs[extras] in /home/pkgbuild/.virtualenvs/vrs_env/lib/python3.11/site-packages (2.2.0)
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Requirement already satisfied: parsley in /home/pkgbuild/.virtualenvs/vrs_env/lib/python3.11/site-packages (from hgvs<1.5.5,>=1.4->ga4gh.vrs[extras]) (1.3)
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Building wheels for collected packages: plugin_system
Building wheel for plugin_system (pyproject.toml): started
Building wheel for plugin_system (pyproject.toml): finished with status 'done'
Created wheel for plugin_system: filename=plugin_system-0.0.1-py3-none-any.whl size=2425 sha256=ac450597423e0312f355ba8e5ffd81b85364b44eb892cf3b70ede779fc186f60
Stored in directory: /home/pkgbuild/.cache/pip/wheels/d7/e8/15/e342ff0094b04c0b74b8969959986ab0c1556b14bb98f65472
Successfully built plugin_system
Installing collected packages: plugin_system
Successfully installed plugin_system-0.0.1
/home/biocbuild/bbs-3.23-bioc/R/site-library/reticulate/python/rpytools/loader.py:120: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
return _find_and_load(name, import_)
Quitting from AnVILVRS.Rmd:133-146 [download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'platform' in selecting a method for function 'avcopy': The runtime environment must be within an AnVIL workspace. To diagnose,
check the workspace environment variables and ensure that you have an
associated 'GOOGLE_PROJECT' or 'WORKSPACE_ID' environment variable
for Google Cloud and Azure workspaces, respectively.
---
Backtrace:
1. AnVILVRS::get_pop_descriptor()
2. AnVILGCP::avcopy(source = uri, destination = destfile, ...)
3. AnVILGCP::avcopy(source = uri, destination = destfile, ...)
4. AnVILBase::avcopy(..., platform = cloud_platform())
5. AnVILBase::cloud_platform()
6. base::stop(errmsg)
7. base::.handleSimpleError(...)
8. base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'AnVILVRS.Rmd' failed with diagnostics:
error in evaluating the argument 'platform' in selecting a method for function 'avcopy': The runtime environment must be within an AnVIL workspace. To diagnose,
check the workspace environment variables and ensure that you have an
associated 'GOOGLE_PROJECT' or 'WORKSPACE_ID' environment variable
for Google Cloud and Azure workspaces, respectively.
--- failed re-building AnVILVRS.Rmd
SUMMARY: processing the following file failed:
AnVILVRS.Rmd
Error: Vignette re-building failed.
Execution halted