chore: pin actions SHA

[walkowif]

No description provided.

[github-actions]

✅ All contributors have signed the CLA
_{Posted by the CLA Assistant Lite bot.}

[walkowif]

I have read the CLA Document and I hereby sign the CLA

[github-actions]

❌ BiocCheck FAILED.

─ BiocCheckVersion: 1.34.3
─ BiocVersion: 3.16
─ Package: BiocManager
─ PackageVersion: 1.30.27
─ sourceDir: /home/runner/work/bioc-check-action/bioc-check-action/BiocManager
─ installDir: /tmp/Rtmp41LkdD/file26903b4c6221
─ BiocCheckDir: /home/runner/work/bioc-check-action/bioc-check-action/BiocManager.BiocCheck
─ platform: unix
─ isTarBall: FALSE

Click here to show log

─ BiocCheckVersion: 1.34.3
─ BiocVersion: 3.16
─ Package: BiocManager
─ PackageVersion: 1.30.27
─ sourceDir: /home/runner/work/bioc-check-action/bioc-check-action/BiocManager
─ installDir: /tmp/Rtmp41LkdD/file26903b4c6221
─ BiocCheckDir: /home/runner/work/bioc-check-action/bioc-check-action/BiocManager.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking version number validity...
* Checking R version dependency...
* Checking package size...
      Skipped... only checked on source tarball
* Checking individual file sizes...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import stats in DESCRIPTION as well as NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking package installation calls in R code...
    * NOTE: install, biocLite, install.packages, or update.packages
      found in R files
* Checking for library/require of BiocManager...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
    * ERROR: Remove install() calls (found 2 times)
    * NOTE: Avoid '<<-' if possible (found 2 times)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 100 functions greater than 50 lines.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 12 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 76 lines
      (2%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
    * ERROR: Package must be removed from CRAN.

─ BiocCheck results ──
2 ERRORS | 2 WARNINGS | 8 NOTES

See the BiocManager.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

Summary

2 ERRORS
2 WARNINGS
8 NOTES

[github-actions]

❌ BiocCheck FAILED.

This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...

Click here to show log

This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking version number validity...
* Checking R Version dependency...
* Checking package size...
        Skipped... only checked on source tarball
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import stats in DESCRIPTION as well as NAMESPACE.
* Checking .Rbuildignore...
* Checking vignette directory...
    * WARNING: Evaluate more vignette chunks.
        # of code chunks: 32
        # of eval=FALSE: 12
        # of nonexecutable code chunks by syntax: 13
        # total unevaluated 25 (78%)
    * WARNING: BiocInstaller code found in vignette(s)
      Found in file(s):
        BiocManager.Rmd (line 418)
* Checking package installation calls in R code...
    * NOTE: install, biocLite, install.packages, or update.packages
      found in R files
        install.packages() in R/inet.R (line 87, column 13)
        update.packages() in R/inet.R (line 129, column 13)
* Checking for library/require of BiocManager...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        version.R (line 200, column 32)
        version.R (line 255, column 41)
        version.R (line 291, column 19)
        version.R (line 308, column 30)
        version.R (line 396, column 41)
* Checking parsed R code in R directory, examples, vignettes...
    * ERROR: Remove install() calls (found 1 times)
        install.packages() in R/inet.R (line 87, column 13)
    * NOTE: Avoid '<<-' if possible (found 2 times)
        <<- in R/version.R (line 145, column 24)
        <<- in R/version.R (line 230, column 25)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
        suppressWarnings() in R/repositories.R (line 322, column 9)
        suppressWarnings() in R/utilities.R (line 42, column 5)
* Checking function lengths................
    * NOTE: Recommended function length <= 50 lines.
      There are 4 functions > 50 lines.
      The longest 5 functions are:
        install() (R/install.R, line 380): 71 lines
        .version_validity() (R/version.R, line 274): 63 lines
        .version_map_get_online() (R/version.R, line 136): 56 lines
        .package_filter_unwriteable() (R/install.R, line 11): 55 lines
        valid() (R/valid.R, line 112): 44 lines
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      install.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      33% of man pages use one of these cases.
      Found in the following files:
        install.Rd
        repositories.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        install.Rd
        repositories.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 12 lines (0%) are > 80 characters
      long.
    First 6 lines:
      R/inet.R:81     if (identical(as.integer(getOption("timeout")), 60L)) {...
      R/valid.R:198     cat("more details: BiocManager::valid()$too_new, Bioc...
      man/BiocManager-package.Rd:20 \item \code{BiocManager::version()}: Repo...
      man/BiocManager-package.Rd:40 \item \code{"repos"}, \code{"BiocManager....
      man/BiocManager-package.Rd:84 \strong{Maintainer}: Marcel Ramos \email{...
      man/BiocManager-package.Rd:88   \item Martin Morgan \email{martin.morga...
    * NOTE: Consider multiples of 4 spaces for line indents, 83
      lines(3%) are not.
    First 6 lines:
      R/valid.R:14              lib.loc=NULL, priority="NA", type=getOption("...
      R/valid.R:15              filters=NULL, ..., checkBuilt, site_repository)
      R/valid.R:41              lib.loc=NULL, priority="NA")
      R/valid.R:114              lib.loc=NULL, priority="NA", type=getOption(...
      R/valid.R:115              filters=NULL, ..., checkBuilt = FALSE,
      R/valid.R:116              site_repository = character())
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
    * ERROR: Package must be removed from CRAN.
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      bioc-devel mailing list (requires admin credentials).  Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.


Summary:
ERROR count: 3
WARNING count: 4
NOTE count: 11
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "No biocViews terms found."             
[2] "Remove install() calls (found 1 times)"
[3] "Package must be removed from CRAN."    

$warning
[1] "Description field in the DESCRIPTION file is too concise"
[2] "Import stats in DESCRIPTION as well as NAMESPACE."       
[3] "Evaluate more vignette chunks."                          
[4] " BiocInstaller code found in vignette(s)"                

$note
 [1] "install, biocLite, install.packages, or update.packages found in R files"                                                                                                          
 [2] " Avoid 1:...; use seq_len() or seq_along()"                                                                                                                                        
 [3] "Avoid '<<-' if possible (found 2 times)"                                                                                                                                           
 [4] "Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)"                                                                                                                  
 [5] "Recommended function length <= 50 lines."                                                                                                                                          
 [6] "Consider adding runnable examples to the following man pages which document exported objects:"                                                                                     
 [7] "Usage of dontrun{} / donttest{} found in man page examples."                                                                                                                       
 [8] "Use donttest{} instead of dontrun{}."                                                                                                                                              
 [9] "Consider shorter lines; 12 lines (0%) are > 80 characters long."                                                                                                                   
[10] "Consider multiples of 4 spaces for line indents, 83 lines(3%) are not."                                                                                                            
[11] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials).  Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"

Summary

ERROR count: 3
WARNING count: 4
NOTE count: 11