Advance deprecation status (#1478)

NEWS.md

@@ -93,6 +93,10 @@
 
 ## Minor improvements and bug fixes
 
+* Deprecation status of functions deprecated in previous versions (at least
+  2 years old) have been advanced. In particular, `src_sql()` is now defunct,
+  as is the use of `partial_eval()` with character `data`.
+
 * Database errors now show the generated SQL, which hopefully will make it
   faster to track down problems (#1401).
 

R/backend-teradata.R

@@ -221,7 +221,7 @@ utils::globalVariables(c("ATAN2", "SUBSTR", "DECIMAL", "WEEKNUMBER_OF_YEAR", "SU
 #' @export
 #' @rdname win_over
 win_rank_tdata <- function(f) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.4.0",
     what = "win_rank_tdata()",
     with = "win_rank()"

R/db-sql.R

@@ -823,9 +823,9 @@ sql_query_append <- function(con,
                              ...,
                              returning_cols = NULL) {
   if (is_tbl_lazy(from)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       when = "2.3.2",
-      what = "sql_query_append(from = 'must be a table identifier or an SQL query, not a lazy table.')",
+      what = "sql_query_append(from = 'must be a table identifier or an SQL query, not a lazy table.')"
     )
 
     insert_cols <- colnames(from)

R/src-sql.R

@@ -12,13 +12,11 @@
 #' @param con the connection object
 #' @param ... fields used by object
 src_sql <- function(subclass, con, ...) {
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     when = "1.4.0",
     what = "src_sql()",
     always = TRUE
   )
-  subclass <- paste0("src_", subclass)
-  structure(list(con = con, ...), class = c(subclass, "src_sql", "src"))
 }
 
 

R/tidyeval.R

@@ -51,19 +51,16 @@
 #' f <- function(x) x + 1
 #' partial_eval(quote(year > f(1980)), lf)
 #' partial_eval(quote(year > local(f(1980))), lf)
-partial_eval <- function(call, data, env = caller_env(), vars = NULL, error_call) {
-  if (!is_null(vars)) {
-    lifecycle::deprecate_warn("2.1.2", "partial_eval(vars)", always = TRUE)
-    data <- lazy_frame(!!!rep_named(vars, list(logical())))
+partial_eval <- function(call,
+                         data,
+                         env = caller_env(),
+                         vars = deprecated(),
+                         error_call) {
+  if (lifecycle::is_present(vars)) {
+    lifecycle::deprecate_stop("2.1.2", "partial_eval(vars)")
   }
-
   if (is.character(data)) {
-    lifecycle::deprecate_warn(
-      "2.1.2",
-      "partial_eval(data = 'must be a lazy frame')",
-      always = TRUE
-    )
-    data <- lazy_frame(!!!rep_named(data, list(logical())))
+    lifecycle::deprecate_stop("2.1.2", "partial_eval(data = 'must be a lazy frame')", )
   }
 
   if (is_sql_literal(call)) {

R/verb-group_by.R

@@ -24,17 +24,11 @@
 #'   group_by(g) %>%
 #'   mutate(x2 = x / sum(x, na.rm = TRUE)) %>%
 #'   show_query()
-group_by.tbl_lazy <- function(.data, ..., .add = FALSE, add = NULL, .drop = TRUE) {
+group_by.tbl_lazy <- function(.data, ..., .add = FALSE, add = deprecated(), .drop = TRUE) {
   dots <- partial_eval_dots(.data, ..., .named = FALSE)
 
-  if (!missing(add)) {
-    lifecycle::deprecate_warn(
-      "1.0.0",
-      "dplyr::group_by(add = )",
-      "group_by(.add = )",
-      always = TRUE
-    )
-    .add <- add
+  if (lifecycle::is_present(add)) {
+    lifecycle::deprecate_stop("1.0.0", "dplyr::group_by(add)", "group_by(.add)")
   }
 
   check_unsupported_arg(.drop, TRUE)

R/verb-joins.R

@@ -584,7 +584,7 @@ join_prepare_by <- function(by,
                             user_env = caller_env(3)) {
   if (identical(by, character()) && is.null(sql_on)) {
     if (type != "cross") {
-      lifecycle::deprecate_soft(
+      lifecycle::deprecate_warn(
         when = "1.1.0",
         what = I("Using `by = character()` to perform a cross join"),
         with = "cross_join()",

revdep/README.md

@@ -16,17 +16,16 @@
 |SQLDataFrame       |?       |      |        |     |
 |synaptome.db       |?       |      |        |     |
 
-## New problems (9)
+## New problems (8)
 
-|package             |version |error  |warning |note |
-|:-------------------|:-------|:------|:-------|:----|
-|[Andromeda](problems.md#andromeda)|0.6.5   |__+3__ |        |     |
-|[CDMConnector](problems.md#cdmconnector)|1.3.0   |__+2__ |        |1    |
-|[childesr](problems.md#childesr)|0.2.3   |__+1__ |        |1    |
-|[CohortSurvival](problems.md#cohortsurvival)|0.3.0   |__+2__ |        |     |
-|[diseasystore](problems.md#diseasystore)|0.1.1   |__+1__ |        |     |
-|[DrugUtilisation](problems.md#drugutilisation)|0.5.0   |__+2__ |        |     |
-|[IncidencePrevalence](problems.md#incidenceprevalence)|0.7.1   |__+2__ |        |     |
-|[PatientProfiles](problems.md#patientprofiles)|0.6.1   |__+2__ |        |     |
-|[SCDB](problems.md#scdb)|0.3     |__+3__ |        |     |
+|package             |version |error    |warning |note |
+|:-------------------|:-------|:--------|:-------|:----|
+|[Andromeda](problems.md#andromeda)|0.6.5   |__+3__   |-1      |     |
+|[CDMConnector](problems.md#cdmconnector)|1.3.0   |__+2__   |        |1    |
+|[CohortSurvival](problems.md#cohortsurvival)|0.3.0   |__+2__   |        |     |
+|[diseasystore](problems.md#diseasystore)|0.1.1   |__+1__   |        |     |
+|[DrugUtilisation](problems.md#drugutilisation)|0.5.2   |__+2__   |        |     |
+|[IncidencePrevalence](problems.md#incidenceprevalence)|0.7.1   |__+2__   |        |     |
+|[PatientProfiles](problems.md#patientprofiles)|0.6.2   |1 __+1__ |        |     |
+|[SCDB](problems.md#scdb)|0.3     |__+3__   |        |     |
 

revdep/cran.md

@@ -1,8 +1,8 @@
 ## revdepcheck results
 
-We checked 111 reverse dependencies (100 from CRAN + 11 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 112 reverse dependencies (101 from CRAN + 11 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 9 new problems
+ * We saw 8 new problems
  * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
@@ -19,9 +19,6 @@ Issues with CRAN packages are summarised below.
   checking tests ... ERROR
   checking re-building of vignette outputs ... ERROR
 
-* childesr
-  checking re-building of vignette outputs ... ERROR
-
 * CohortSurvival
   checking tests ... ERROR
   checking re-building of vignette outputs ... ERROR
@@ -38,7 +35,6 @@ Issues with CRAN packages are summarised below.
   checking re-building of vignette outputs ... ERROR
 
 * PatientProfiles
-  checking tests ... ERROR
   checking re-building of vignette outputs ... ERROR
 
 * SCDB

revdep/failures.md

@@ -110,7 +110,7 @@ Run `revdepcheck::cloud_details(, "CompoundDb")` for more info
 * Version: NA
 * GitHub: NA
 * Source code: https://github.com/cran/CuratedAtlasQueryR
-* Number of recursive dependencies: 197
+* Number of recursive dependencies: 196
 
 Run `revdepcheck::cloud_details(, "CuratedAtlasQueryR")` for more info
 
@@ -215,7 +215,7 @@ Run `revdepcheck::cloud_details(, "grasp2db")` for more info
 * Version: NA
 * GitHub: NA
 * Source code: https://github.com/cran/msPurity
-* Number of recursive dependencies: 185
+* Number of recursive dependencies: 183
 
 Run `revdepcheck::cloud_details(, "msPurity")` for more info
 
@@ -320,7 +320,7 @@ Run `revdepcheck::cloud_details(, "Organism.dplyr")` for more info
 * Version: NA
 * GitHub: NA
 * Source code: https://github.com/cran/SQLDataFrame
-* Number of recursive dependencies: 95
+* Number of recursive dependencies: 93
 
 Run `revdepcheck::cloud_details(, "SQLDataFrame")` for more info
 
@@ -355,7 +355,7 @@ Run `revdepcheck::cloud_details(, "SQLDataFrame")` for more info
 * Version: NA
 * GitHub: NA
 * Source code: https://github.com/cran/synaptome.db
-* Number of recursive dependencies: 151
+* Number of recursive dependencies: 149
 
 Run `revdepcheck::cloud_details(, "synaptome.db")` for more info