removed conflicts package startup messages

jtlandis · Oct 28, 2024 · b6287e3 · b6287e3
1 parent 2c7a7ed
commit b6287e3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: plyxp
 Title: Data masks for SummarizedExperiment enabling dplyr-like manipulation
-Version: 0.99.23
+Version: 0.99.24
 Authors@R: c(
     person("Justin", "Landis", email = "[email protected]", role = c("aut", "cre"),
     comment = c(ORCID = "0000-0001-5501-4934")),

diff --git a/NEWS b/NEWS
@@ -1,9 +1,14 @@
 
+## plyxp 0.99.24
+
+* Since `plyxp` does not have a conflict with `tidySummarizedExperiment` anymore,
+  we have removed package startup messages warning of potential conflicts.
+
 ## plyxp 0.99.21
 
 * Fixed documentation of `?plyxp::mutate` and other dplyr functions reexported
   by `plyxp`.
-* `PlySummarizedExperiment` should be able to hold any `SummarizedExperiment` 
+* `PlySummarizedExperiment` should be able to hold any `SummarizedExperiment`
   object
 
 ## plyxp 0.99.20

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,101 +1,101 @@
-conflict_info <- c(
-    "Note that these packages are exclusive and present different APIs ",
-    "for working with {.cls SummarizedExperiment} objects. As such conflicts ",
-    "and unexpected behaviors may arise!"
-)
+# conflict_info <- c(
+#     "Note that these packages are exclusive and present different APIs ",
+#     "for working with {.cls SummarizedExperiment} objects. As such conflicts ",
+#     "and unexpected behaviors may arise!"
+# )
+
+# rule <- function (pad = "-", gap = 2L) {
+#   paste0(rep(pad, getOption("width") - gap), collapse = "")
+# }
+
+# tidySE_opt <- list(quote(tidySummarizedExperiment), "tidySummarizedExperiment")
+
+# attaching_tidySE <- function(expr) {
+#   if (is_call(expr, name = "library")) {
+#     call <- match.call(library, call = expr)
+#     out <- tidySE_opt |>
+#       vapply(identical, y = call$package, logical(1)) |>
+#       any()
+#     return(out)
+#   }
+#   FALSE
+
+# }
 
-rule <- function (pad = "-", gap = 2L) {
-  paste0(rep(pad, getOption("width") - gap), collapse = "")
-}
 
-tidySE_opt <- list(quote(tidySummarizedExperiment), "tidySummarizedExperiment")
 
-attaching_tidySE <- function(expr) {
-  if (is_call(expr, name = "library")) {
-    call <- match.call(library, call = expr)
-    out <- tidySE_opt |>
-      vapply(identical, y = call$package, logical(1)) |>
-      any()
-    return(out)
-  } 
-  FALSE
-
-}
+# you_have_loaded <- function(pkg1, pkg2, .class = NULL) {
+#   if (!is.null(.class)) {
+#     local_options(cli.message_class = .class)
+#   }
+#   withRestarts({
+#     cli::cli_rule()
+#     cli::cli_alert_warning(
+#       "you have loaded {.pkg {pkg1}} after {.pkg {pkg2}}\n"
+#     )
+#     cli::cli_text("")
+#     cli::cli_text(conflict_info)
+#     cli::cli_text("")
+#   },
+#   muffleMessage = function() NULL)
 
+# }
 
+# # a package can either be loaded, or completely attached. R only informs
+# # of conflicts when the package is loaded, and when attached these can be
+# # overwritten silently
 
-you_have_loaded <- function(pkg1, pkg2, .class = NULL) {
-  if (!is.null(.class)) {
-    local_options(cli.message_class = .class)
-  }
-  withRestarts({
-    cli::cli_rule()
-    cli::cli_alert_warning(
-      "you have loaded {.pkg {pkg1}} after {.pkg {pkg2}}\n"
-    )
-    cli::cli_text("")
-    cli::cli_text(conflict_info)
-    cli::cli_text("")
-  },
-  muffleMessage = function() NULL)
-
-}
+# .onAttach <- function(libname, pkgname) {
+#   # check if `tidySummarizedExperiment` is already loaded
+#   conflict <- grep("tidySummarizedExperiment", search(), value = TRUE)
+#   if (length(conflict)) {
+#     you_have_loaded("plyxp","tidySummarizedExperiment",
+#                     .class = c("packageStartupMessage", "message"))
+#   }
+#   # set hook for if `tidySummarizedExperiment` gets attached latter
+#   setHook(
+#     packageEvent(pkgname = "tidySummarizedExperiment",
+#                  event = "attach"),
+#     function(...) {
+#       you_have_loaded("tidySummarizedExperiment","plyxp",
+#                       .class = c("packageStartupMessage", "message"))
+#     }
 
-# a package can either be loaded, or completely attached. R only informs
-# of conflicts when the package is loaded, and when attached these can be
-# overwritten silently
+#   )
+#   # hook for when tidySummarizedExperiment:: is used after plyxp is attached
+#   setHook(
+#     packageEvent(pkgname = "tidySummarizedExperiment",
+#                  event = "onLoad"),
+#     function(...) {
+#       calls <- sys.calls()
+#       called_via_library <- vapply(calls, attaching_tidySE, logical(1))
+#       if (!any(called_via_library)) {
+#         # if this callback was not executed via library(tidySummarizedExperiment)
+#         # then warn that plyxp dplyr methods have likely been overwritten!
+#         # otherwise, let the .onAttach method warn the user
+#         cli::cli_inform(
+#           .frequency = "regularly",
+#           .frequency_id = "tidySummarizedExperiment_loaded_after_plyxp_attach",
+#           class = "plyxp_loaded_conflict",
+#           message = c(
+#             "!" = paste0(
+#               "You have likely loaded {.pkg tidySummarizedExperiment} after ",
+#               "{.pkg plyxp} via {.code tidySummarizedExperiment::...}"
+#             ),
+#             "*" = paste(conflict_info, collapse = ""),
+#             "!" = "This has likely caused {.pkg dplyr} methods from {.pkg plyxp} to be over-written!",
+#             "i" = "If this wasn't your intention, consider restarting your R session"))
+#       }
 
-.onAttach <- function(libname, pkgname) {
-  # check if `tidySummarizedExperiment` is already loaded
-  conflict <- grep("tidySummarizedExperiment", search(), value = TRUE)
-  if (length(conflict)) {
-    you_have_loaded("plyxp","tidySummarizedExperiment",
-                    .class = c("packageStartupMessage", "message"))
-  }
-  # set hook for if `tidySummarizedExperiment` gets attached latter
-  setHook(
-    packageEvent(pkgname = "tidySummarizedExperiment",
-                 event = "attach"),
-    function(...) {
-      you_have_loaded("tidySummarizedExperiment","plyxp",
-                      .class = c("packageStartupMessage", "message"))
-    }
-
-  )
-  # hook for when tidySummarizedExperiment:: is used after plyxp is attached
-  setHook(
-    packageEvent(pkgname = "tidySummarizedExperiment",
-                 event = "onLoad"),
-    function(...) {
-      calls <- sys.calls()
-      called_via_library <- vapply(calls, attaching_tidySE, logical(1))
-      if (!any(called_via_library)) {
-        # if this callback was not executed via library(tidySummarizedExperiment)
-        # then warn that plyxp dplyr methods have likely been overwritten!
-        # otherwise, let the .onAttach method warn the user
-        cli::cli_inform(
-          .frequency = "regularly", 
-          .frequency_id = "tidySummarizedExperiment_loaded_after_plyxp_attach",
-          class = "plyxp_loaded_conflict",
-          message = c(
-            "!" = paste0(
-              "You have likely loaded {.pkg tidySummarizedExperiment} after ",
-              "{.pkg plyxp} via {.code tidySummarizedExperiment::...}"
-            ),
-            "*" = paste(conflict_info, collapse = ""),
-            "!" = "This has likely caused {.pkg dplyr} methods from {.pkg plyxp} to be over-written!",
-            "i" = "If this wasn't your intention, consider restarting your R session"))
-      }
-
-    }
-  )
-}
+#     }
+#   )
+# }
 
-.onDetach <- function(libpath) {
-  # remove verbose message when `plyxp` is removed from attach list
-  setHook(packageEvent("tidySummarizedExperiment", "attach"), NULL, "replace")
-  setHook(packageEvent("tidySummarizedExperiment", "onLoad"), NULL, "replace")
-}
+# .onDetach <- function(libpath) {
+#   # remove verbose message when `plyxp` is removed from attach list
+#   setHook(packageEvent("tidySummarizedExperiment", "attach"), NULL, "replace")
+#   setHook(packageEvent("tidySummarizedExperiment", "onLoad"), NULL, "replace")
+# }
 
 # check_dplyr_s3_method <- function(method) {
 #   tbl <- getNamespace("dplyr")[[".__S3MethodsTable__."]]