EvaYiwenWang/PLSDAbatch_workflow

Unable to build vignette when install?

Closed this issue · 2 comments

dikiprawisuda commented

Dear developer(s), thank you for the package.
I found an error when installing when turning build_vignettes = TRUE. With it being FALSE however, there's no problem.

Please find the error message as the following (after installing mixOmics):
`Downloading GitHub repo EvaYiwenWang/PLSDAbatch@HEAD
Skipping 1 packages not available: mixOmics
√ checking for file 'C:\Users\dikip\AppData\Local\Temp\RtmpuGhFHh\remotesbe82bc482d\EvaYiwenWang-PLSDAbatch-45c4798/DESCRIPTION' ...

  • preparing 'PLSDAbatch': (873ms)
    √ checking DESCRIPTION meta-information ...

  • installing the package to process help pages
    Loading required namespace: PLSDAbatch
    Registered S3 methods overwritten by 'lme4':
    method from
    cooks.distance.influence.merMod car
    influence.merMod car
    dfbeta.influence.merMod car
    dfbetas.influence.merMod car

  • saving partial Rd database (533ms)
    E creating vignettes (4s)
    --- re-building 'case_studies.Rmd' using rmarkdown
    Registered S3 methods overwritten by 'lme4':
    method from
    cooks.distance.influence.merMod car
    influence.merMod car
    dfbeta.influence.merMod car
    dfbetas.influence.merMod car
    Loading required package: MASS
    Loading required package: lattice
    Loading required package: ggplot2

    Loaded mixOmics 6.14.0
    Thank you for using mixOmics!
    Tutorials: http://mixomics.org
    Bookdown vignette: https://mixomicsteam.github.io/Bookdown
    Questions, issues: Follow the prompts at http://mixomics.org/contact-us
    Cite us: citation('mixOmics')

    Quitting from lines 41-48 (case_studies.Rmd)
    Error: processing vignette 'case_studies.Rmd' failed with diagnostics:
    there is no package called 'sva'
    --- failed re-building 'case_studies.Rmd'

    --- re-building 'simulation_study.Rmd' using rmarkdown
    Quitting from lines 60-65 (simulation_study.Rmd)
    Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
    there is no package called 'sva'
    --- failed re-building 'simulation_study.Rmd'

    SUMMARY: processing the following files failed:
    'case_studies.Rmd' 'simulation_study.Rmd'

    Error: Vignette re-building failed.
    Execution halted
    Error: Failed to install 'PLSDAbatch' from GitHub:
    System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
    E> Quitting from lines 60-65 (simulation_study.Rmd)
    E> Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
    E> there is no package called 'sva'
    E> --- failed re-building 'simulation_study.Rmd'
    E>
    E> SUMMARY: processing the following files failed:
    E> 'case_studies.Rmd' 'simulation_study.Rmd'
    E>
    E> Error: Vignette re-building failed.
    E> Execution halted`

Thank you.

EvaYiwenWang commented

Hi dikiprawisuda, thanks for using our package. I think the reason why you cannot build the vignette is that you lack the packages required for the vignette. Could you try 'devtools::install_github("https://github.com/EvaYiwenWang/PLSDAbatch", dependencies = T, build_vignettes = T)'? Let me know if the problem is solved.

dikiprawisuda commented

Hi, yes it worked for me. Thank you!