Notify downstream maintainers of changes in upstream packages

The biocRevDepEmail function collects all the emails of the reverse dependencies and sends a notification that upstream package(s) have been deprecated or removed. It uses a template found in inst/resources with the templatePath() function.

biocRevDepEmail(
  packages,
  which = c("strong", "most", "all"),
  PS = character(1L),
  version = BiocManager::version(),
  dry.run = TRUE,
  cc = NULL,
  emailTemplate = templatePath("revdepnote"),
  core.name = NULL,
  core.email = NULL,
  core.id = NULL,
  textOnly = FALSE,
  verbose = FALSE,
  credFile = "~/.blastula_creds",
  ...,
  pkg
)

Arguments

packages: character() A vector of CRAN and/or Bioconductor packages for whose reverse dependencies are to be checked and notified.
which: a character vector listing the types of dependencies, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"). Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector.
PS: character(1) Postscript, an additional note to the recipient of the email (i.e., the package maintainer)
version: character() A vector indicating which version of Bioconductor the package is failing in (either 'release' or 'devel'; defaults to both)
dry.run: logical(1) Display the email without sending to the recipient. It only works for HTML email reports and ignored when textOnly=TRUE
cc: character() A vector of email addresses for sending the message as a carbon copy.
emailTemplate: character(1) The path to the email template Rmd file as obtained by templatePath(). A custom template can be provided as file path.
core.name: character(1) The full name of the core team member
core.email: character(1) The Roswell Park email of the core team member
core.id: character(1) The internal identifier for the Roswell employee. This ID usually matches ^[A-Z]{2}[0-9]{5} for more recent identifiers.
textOnly: logical(1) Whether to return the text of the email only. This avoids the use of the 'blastula' package and adds the text to the system clipboard if the clipr package is installed (default: FALSE)
verbose: logical(1) Whether to output full email information from 'smtp_send' (when dry.run is FALSE and 'blastula' is installed)
credFile: character(1) An optional file generated by the blastula::create_smtp_creds_file function containing email authentication information (default: "~/.blastula_creds"). See ?biocBuildEmail details.
pkg: character(1) DEPRECATED. The name of a single package whose reverse dependencies are to be checked and notified.
...: Additional inputs to internal functions (not used).

Examples


biocRevDepEmail(
    "FindMyFriends", version = "3.13", dry.run = TRUE, textOnly = TRUE
)
#> Provide your full name: 
#> What is your core-team email? 
#> What is your employee ID (e.g., AB12345, leave blank if N/A)? 
#> Saved data to: /home/runner/.cache/R/BiocPkgTools
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com
#> Message not sent: Set 'dry.run=FALSE'
#> [1] "thomasp85@gmail.com\nPackage(s) Deprecation Notification\n\n\n\nHi Maintainers,\n\nUnfortunately, due to the deprecation of the  package(s), your packages\nhave been affected. Please remove the facilities of the deprecated\npackages from your packages. This includes the removal of imported functions\nand the package from your `DESCRIPTION` file.\n\nHere is the full list of affected Bioconductor packages:\n\n[PanVizGenerator](https://bioconductor.org/checkResults/3.13/bioc-LATEST/PanVizGenerator)\n\nWe apologize for the inconvenience and if you have any questions please\ndirect them to the mailing list at bioc-devel@bioconductor.org.\n\n\n\nBest regards,\n\nNA\n\n"