Suppress the prompt from the remotes package

[Jiefei-Wang]

When installing a GitHub package, the remotes package will prompt the user whether to update the package dependencies, which is duplicated as BiocManager will also ask the user the same question. It is better to handle the update only in BiocManager.

> BiocManager::install("Bioconductor/AnVIL", ask = T)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16.3), R 4.1.2 (2021-11-01)
Installing github package(s) 'Bioconductor/AnVIL'
Downloading GitHub repo Bioconductor/AnVIL@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                             
2: CRAN packages only              
3: None                            
4: crayon   (1.4.1 -> 1.4.2) [CRAN]
5: cli      (3.0.1 -> 3.1.0) [CRAN]
6: tibble   (3.1.5 -> 3.1.6) [CRAN]
7: glue     (1.4.2 -> 1.5.1) [CRAN]
8: generics (0.1.0 -> 0.1.1) [CRAN]
9: cpp11    (0.4.0 -> 0.4.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
√  checking for file 'C:\Users\lenovo\AppData\Local\Temp\RtmpumCSnq\remotes191c1a58751a\Bioconductor-AnVIL-0c56086/DESCRIPTION' ... 
-  preparing 'AnVIL': (6.3s)
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'AnVIL_1.7.2.tar.gz'
   
* installing *source* package 'AnVIL' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AnVIL'
    finding HTML links ... done
    Response                                html  
    Service                                 html  
    Services                                html  
    av                                      html  
    avnotebooks                             html  
    avworkflow                              html  
    avworkspace                             html  
    drs                                     html  
    gcloud                                  html  
    gsutil                                  html  
    install                                 html  
    localize                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AnVIL)
Old packages: 'AnnotationDbi', 'AnnotationHub', 'AzureGraph', 'backports', 'BH', 'Biobase',
  'BiocFileCache', 'BiocGenerics', 'BiocIO', 'BiocStyle', 'biomaRt', 'Biostrings', 'brio',
  'BSgenome', 'cli', 'cpp11', 'crayon', 'credentials', 'crosstalk', 'DelayedArray',
  'devtools', 'digest', 'DNAcopy', 'DT', 'edgeR', 'ExperimentHub', 'fgsea', 'fs',
  'generics', 'GenomeInfoDb', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges',
  'GEOquery', 'gert', 'glue', 'graph', 'httpuv', 'igraph', 'illuminaio',
  'interactiveDisplayBase', 'IRanges', 'ISAnalytics', 'jose', 'KEGGREST', 'KSgeneral',
  'limma', 'Matrix', 'MatrixGenerics', 'memoise', 'pbdZMQ', 'pkgbuild', 'pkgload',
  'preprocessCore', 'RcppArmadillo', 'RCy3', 'readr', 'remotes', 'rex', 'Rhtslib', 'Rmpi',
  'RNAseqData.HNRNPC.bam.chr14', 'Rsamtools', 'RSQLite', 'rtracklayer', 'S4Vectors',
  'sesame', 'sesameData', 'sessioninfo', 'SharedObject', 'ShortRead', 'snow', 'SRAdb',
  'stringi', 'SummarizedExperiment', 'testthat', 'tibble', 'tinytex', 'Travel', 'tzdb',
  'usethis', 'uuid', 'VariantAnnotation', 'vroom', 'withr', 'xfun', 'xml2', 'XVector',
  'zlibbioc'
Update all/some/none? [a/s/n]: 
n

[LiNk-NY]

I am also encountering this with ask = FALSE.

> BiocManager::install("LiNk-NY/terraTCGAdata", dependencies = TRUE, update = TRUE, ask = FALSE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://packagemanager.rstudio.com/all/__linux__/focal/latest

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing github package(s) 'LiNk-NY/terraTCGAdata'
Downloading GitHub repo LiNk-NY/terraTCGAdata@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                  
 2: CRAN packages only                   
 3: None                                 
 4: stringi (1.7.5    -> 1.7.6   ) [CRAN]
 5: glue    (1.5.0    -> 1.6.0   ) [CRAN]
 6: fansi   (0.5.0    -> 1.0.0   ) [CRAN]
 7: openssl (1.4.5    -> 1.4.6   ) [CRAN]
 8: xml2    (1.3.2    -> 1.3.3   ) [CRAN]
 9: cpp11   (0.4.1    -> 0.4.2   ) [CRAN]
10: withr   (2.4.2    -> 2.4.3   ) [CRAN]
11: vroom   (1.5.6    -> 1.5.7   ) [CRAN]
12: readr   (2.1.0    -> 2.1.1   ) [CRAN]
13: BH      (1.75.0-0 -> 1.78.0-0) [CRAN]
14: memoise (2.0.0    -> 2.0.1   ) [CRAN]
15: digest  (0.6.28   -> 0.6.29  ) [CRAN]
16: DBI     (1.1.1    -> 1.1.2   ) [CRAN]
17: AnVIL   (1.6.0    -> 1.6.2   ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: