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Add runHMMER function for HMMER analysis #37

Add runHMMER function for HMMER analysis

Add runHMMER function for HMMER analysis #37

Triggered via pull request March 31, 2026 22:26
Status Failure
Total duration 1h 1m 21s
Artifacts 3

R-CMD-check.yaml

on: pull_request
Matrix: R-CMD-check
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11 errors and 14 warnings
ubuntu-latest (oldrel-1)
Process completed with exit code 1.
macos-latest (release)
Process completed with exit code 1.
windows-latest (release)
Process completed with exit code 1.
windows-latest (release)
R CMD check found ERRORs
windows-latest (release)
Running examples in 'amRdata-Ex.R' failed
ubuntu-latest (release)
Process completed with exit code 1.
ubuntu-latest (release)
R CMD check found ERRORs
ubuntu-latest (release)
Running examples in ‘amRdata-Ex.R’ failed
ubuntu-latest (devel)
Process completed with exit code 1.
ubuntu-latest (devel)
R CMD check found ERRORs
ubuntu-latest (devel)
Running examples in ‘amRdata-Ex.R’ failed
ubuntu-latest (oldrel-1)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
macos-latest (release)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
windows-latest (release)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/upload-artifact@v4, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
windows-latest (release)
Files not of a type allowed in a 'data' directory:
windows-latest (release)
Undocumented arguments in Rd file 'CDHIT2duckdb.Rd'
windows-latest (release)
Variables with usage in Rd file 'class_abbr.Rd' but not in code:
ubuntu-latest (release)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/upload-artifact@v4, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
ubuntu-latest (release)
Files not of a type allowed in a ‘data’ directory:
ubuntu-latest (release)
Undocumented arguments in Rd file 'CDHIT2duckdb.Rd'
ubuntu-latest (release)
Variables with usage in Rd file 'class_abbr.Rd' but not in code:
ubuntu-latest (devel)
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, actions/checkout@v4, actions/upload-artifact@v4, r-lib/actions/setup-pandoc@v2, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
ubuntu-latest (devel)
Files not of a type allowed in a ‘data’ directory:
ubuntu-latest (devel)
Undocumented arguments in Rd file 'CDHIT2duckdb.Rd'
ubuntu-latest (devel)
Variables with usage in Rd file 'class_abbr.Rd' but not in code:

Artifacts

Produced during runtime
Name Size Digest
Linux-X64-rdevel-2-results
43.8 MB
sha256:a9ced1ca96ef4727cb6a3473965136f84d436448a759a3cecb3f93d68a71a5d1
Linux-X64-rrelease-3-results
43.8 MB
sha256:f197b9a6ed301688429fe61d94946de8ff2dc0698a313b1e4d7b09bee3648832
Windows-X64-rrelease-1-results
43.8 MB
sha256:caaa163239f56cc5b9a601000113314c44e4a2281e4dd71ac8361680cae64a35