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Add runHMMER function for HMMER analysis #36

Add runHMMER function for HMMER analysis

Add runHMMER function for HMMER analysis #36

Triggered via pull request March 30, 2026 22:12
Status Failure
Total duration 1h 0m 40s
Artifacts 4

R-CMD-check.yaml

on: pull_request
Matrix: R-CMD-check
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13 errors and 17 warnings
ubuntu-latest (oldrel-1)
Process completed with exit code 1.
macos-latest (release)
Process completed with exit code 1.
macos-latest (release)
R CMD check found ERRORs
macos-latest (release)
Running examples in ‘amRdata-Ex.R’ failed
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, 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/
macos-latest (release)
Files not of a type allowed in a ‘data’ directory:
macos-latest (release)
Undocumented arguments in Rd file 'CDHIT2duckdb.Rd'
macos-latest (release)
Variables with usage in Rd file 'class_abbr.Rd' but not in code:
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:a9d8d0552d90a43b7d484b6eae63cc7728e13b3c09da435f4720abac9ba0a60c
Linux-X64-rrelease-3-results
43.8 MB
sha256:3cfa46ab69aa5a9b04fe32ec6b7e4cbb42de5718c2bdce9bd7730f54d60ecd51
Windows-X64-rrelease-1-results
43.8 MB
sha256:0bbb8826f40325876a545d1276068b5589e8768fe1750cf2f0540155ca3a3169
macOS-ARM64-rrelease-0-results
43.8 MB
sha256:cb66b74798b58d7b3ae8c25186f7621506dbe06dfbe35f24e8ba66f4ed3c0942