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processing vignette 'HMMERutils.Rmd' failed with diagnostics:

Vignette re-building failed.

Failed to install 'HMMERutils' from local:

Process completed with exit code 1.

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The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

No files were found with the provided path: check. No artifacts will be uploaded.

Unused dummy argument ‘itry’ at (1) [-Wunused-dummy-argument]

Unused variable ‘t4’ declared at (1) [-Wunused-variable]

Unused variable ‘t5’ declared at (1) [-Wunused-variable]

‘i2’ may be used uninitialized in this function [-Wmaybe-uninitialized]

Unused dummy argument ‘a’ at (1) [-Wunused-dummy-argument]

Unused variable ‘i’ declared at (1) [-Wunused-variable]

Unused dummy argument ‘idigit’ at (1) [-Wunused-dummy-argument]

Unused dummy argument ‘ifmt’ at (1) [-Wunused-dummy-argument]

Unused variable ‘j’ declared at (1) [-Wunused-variable]

Unused variable ‘k1’ declared at (1) [-Wunused-variable]

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

cannot remove prior installation of package 'boot'

restored 'boot'

cannot remove prior installation of package 'cluster'

restored 'cluster'

cannot remove prior installation of package 'codetools'

restored 'codetools'

cannot remove prior installation of package 'foreign'

restored 'foreign'

cannot remove prior installation of package 'lattice'