--- re-building ‘INCOMMON.Rmd’ using rmarkdown

processing vignette 'a1_pcawg_priors.Rmd' failed with diagnostics:

processing vignette 'a2_classify_mutations.Rmd' failed with diagnostics:

Vignette re-building failed.

Build process failed

Process completed with exit code 1.

--- re-building ‘INCOMMON.Rmd’ using rmarkdown

processing vignette 'a1_pcawg_priors.Rmd' failed with diagnostics:

processing vignette 'a2_classify_mutations.Rmd' failed with diagnostics:

Vignette re-building failed.

Build process failed

Process completed with exit code 1.

--- re-building ‘INCOMMON.Rmd’ using rmarkdown

processing vignette 'a1_pcawg_priors.Rmd' failed with diagnostics:

processing vignette 'a2_classify_mutations.Rmd' failed with diagnostics:

Vignette re-building failed.

Build process failed

Process completed with exit code 1.

--- re-building ‘a1_classify_mutations.Rmd’ using rmarkdown

processing vignette 'a1_pcawg_priors.Rmd' failed with diagnostics:

processing vignette 'a2_classify_mutations.Rmd' failed with diagnostics:

Vignette re-building failed.

Build process failed

Process completed with exit code 1.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "1. Inference of copy number and mutation multiplicity", and the latter is "2. Inference of copy number and mutation multiplicity". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "2. Survival analysis", and the latter is "2. Survival analysis of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "3. Analysis of metastatic patterns", and the latter is "3. Analysis of metastatic propensity and tropism of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

No files were found with the provided path: /home/runner/work/INCOMMON/INCOMMON/check. No artifacts will be uploaded.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@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 vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "1. Inference of copy number and mutation multiplicity", and the latter is "2. Inference of copy number and mutation multiplicity". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "2. Survival analysis", and the latter is "2. Survival analysis of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "3. Analysis of metastatic patterns", and the latter is "3. Analysis of metastatic propensity and tropism of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

No files were found with the provided path: /home/runner/work/INCOMMON/INCOMMON/check. No artifacts will be uploaded.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@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 vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "1. Inference of copy number and mutation multiplicity", and the latter is "2. Inference of copy number and mutation multiplicity". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "2. Survival analysis", and the latter is "2. Survival analysis of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "3. Analysis of metastatic patterns", and the latter is "3. Analysis of metastatic propensity and tropism of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

No files were found with the provided path: /home/runner/work/INCOMMON/INCOMMON/check. No artifacts will be uploaded.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@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 vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "1. Inference of copy number and mutation multiplicity", and the latter is "2. Inference of copy number and mutation multiplicity". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "2. Survival analysis", and the latter is "2. Survival analysis of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "3. Analysis of metastatic patterns", and the latter is "3. Analysis of metastatic propensity and tropism of the MSK-MetTropism Cohort". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.

No files were found with the provided path: /Users/runner/work/INCOMMON/INCOMMON/check. No artifacts will be uploaded.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.