Check gradual deprecation #193

R/environment.R

@@ -782,7 +782,7 @@ bru_log_active <- function(activation = NULL) {
 #' }
 #'
 init.tutorial <- function() {
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     "2.5.0",
     I("init.tutorial()"),
     I(

R/fmesher_crs.R

@@ -5,11 +5,9 @@
 #' @export
 
 fm_has_PROJ6 <- function() {
-  # TODO: deprecate_warn
-  lifecycle::deprecate_stop("2.7.1",
+  lifecycle::deprecate_stop("2.8.0",
     "fm_has_PROJ6()",
     details = c(
-      i = "Since inlabru 2.7.1, fm_has_PROJ6() always returns TRUE",
       i = "rgdal/PROJ4 is no longer supported."
     )
   )
@@ -20,28 +18,17 @@ fm_has_PROJ6 <- function() {
 #' features even though PROJ6 is available
 
 fm_not_for_PROJ6 <- function(fun = NULL) {
-  lifecycle::deprecate_warn("2.7.1",
+  lifecycle::deprecate_stop("2.8.0",
     "fm_not_for_PROJ6()",
     details = c(x = "rgdal/PROJ4 is no longer supported.")
   )
-  fun <- fm_caller_name(1, fun)
-  msg <- paste0(
-    "Call stack:\n",
-    paste0(fm_call_stack(end = 1), collapse = "\n")
-  )
-  stop(paste0(
-    "'",
-    fun,
-    "()' should not be used with PROJ6 and rgdal v3\n",
-    msg
-  ))
 }
 
 #' @describeIn inlabru-deprecated `fm_not_for_PROJ4` is called to give an error when
 #' calling methods that are only available for PROJ6
 
 fm_not_for_PROJ4 <- function(fun = NULL) {
-  lifecycle::deprecate_stop("2.7.1",
+  lifecycle::deprecate_stop("2.8.0",
     "fm_not_for_PROJ4()",
     details = c(x = "rgdal/PROJ4 is no longer supported.")
   )
@@ -51,7 +38,7 @@ fm_not_for_PROJ4 <- function(fun = NULL) {
 #' to using old PROJ4 methods when a PROJ6 method hasn't been implemented
 
 fm_fallback_PROJ6 <- function(fun = NULL) {
-  lifecycle::deprecate_stop("2.7.1",
+  lifecycle::deprecate_stop("2.8.0",
     "fm_not_for_PROJ4()",
     details = c(x = "rgdal/PROJ4 requested by PROJ4 is no longer supported.")
   )
@@ -64,11 +51,10 @@ fm_fallback_PROJ6 <- function(fun = NULL) {
 #' is required but not available
 
 fm_requires_PROJ6 <- function(fun = NULL) {
-  lifecycle::deprecate_stop("2.7.1",
+  lifecycle::deprecate_stop("2.8.0",
     "fm_requires_PROJ6()",
-    details = c(x = "Now always returns TRUE. rgdal/PROJ4 is no longer supported.")
+    details = c(x = "rgdal/PROJ4 is no longer supported.")
   )
-  TRUE
 }
 
 
@@ -100,7 +86,7 @@ fm_as_sp_crs <- function(x, ...) {
 #' @export
 
 fm_sp_get_crs <- function(x) {
-  lifecycle::deprecate_warn("2.7.1", "fm_sp_get_crs()", "fm_CRS()")
+  lifecycle::deprecate_warn("2.8.0", "fm_sp_get_crs()", "fm_CRS()")
   fm_CRS(x)
 }
 
@@ -1311,7 +1297,7 @@ fm_list_as_CRS <- function(x, ...) {
 #' print(fm_proj4string(crs1))
 #' print(fm_proj4string(crs2))
 fm_CRSargs <- function(x, ...) {
-  lifecycle::deprecate_warn("2.7.0.9012", "fm_CRSargs()", "fm_proj4string()")
+  lifecycle::deprecate_warn("2.8.0", "fm_CRSargs()", "fm_proj4string()")
 
   fm_proj4string(x)
 }
@@ -1386,7 +1372,7 @@ fm_proj4string <- function(crs) {
 
 fm_crs_get_wkt <- function(crs) {
   lifecycle::deprecate_warn(
-    "2.7.0.9012",
+    "2.8.0",
     "fm_crs_get_wkt()",
     "fm_wkt()"
   )
@@ -1997,7 +1983,7 @@ fm_transform.inla.mesh.segment <- function(x, crs = fm_crs(x), ..., passthrough
 #' @seealso [fm_transform()]
 #' @export
 fm_spTransform <- function(x, ...) {
-  lifecycle::deprecate_soft("2.7.1", "fm_spTransform()", "fm_transform()")
+  lifecycle::deprecate_soft("2.8.0", "fm_spTransform()", "fm_transform()")
   UseMethod("fm_spTransform")
 }
 

R/fmesher_evaluator.R

@@ -57,10 +57,12 @@ fm_evaluate <- function(...) {
 #' @export
 #' @rdname fm_evaluate
 fm_evaluate.inla.mesh <- function(mesh, field, ...) {
-  lifecycle::deprecate_stop(
-    "2.8.0",
-    "fm_evaluate(field = ' must not be missing or NULL.')",
-    "fm_evaluator()")
+  if (missing(field) || is.null(field)) {
+    lifecycle::deprecate_stop(
+      "2.8.0",
+      "fm_evaluate(field = ' must not be missing or NULL.')",
+      "fm_evaluator()")
+  }
 
   proj <- fm_evaluator(mesh, ...)
   fm_evaluate(proj, field = field)
@@ -70,7 +72,12 @@ fm_evaluate.inla.mesh <- function(mesh, field, ...) {
 #' @export
 #' @rdname fm_evaluate
 fm_evaluate.inla.mesh.1d <- function(mesh, field, ...) {
-  stopifnot(!missing(field) && !is.null(field))
+  if (missing(field) || is.null(field)) {
+    lifecycle::deprecate_stop(
+      "2.8.0",
+      "fm_evaluate(field = ' must not be missing or NULL.')",
+      "fm_evaluator()")
+  }
 
   proj <- fm_evaluator(mesh, ...)
   fm_evaluate(proj, field)

R/mappers.R

@@ -106,7 +106,7 @@ ibm_values <- function(mapper, inla_f = FALSE, ...) {
 #' the allowed type of input format.
 #' @export
 ibm_amatrix <- function(mapper, input, state = NULL, inla_f = FALSE, ...) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.7.0",
     "ibm_amatrix()",
     "ibm_jacobian()"
@@ -749,7 +749,7 @@ ibm_jacobian.bru_mapper_inla_mesh_2d <- function(mapper, input, ...) {
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_inla_mesh_2d <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 
@@ -807,7 +807,7 @@ ibm_jacobian.bru_mapper_inla_mesh_1d <- function(mapper, input, ...) {
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_inla_mesh_1d <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 
@@ -850,7 +850,7 @@ ibm_jacobian.bru_mapper_index <- function(mapper, input, state, ...) {
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_index <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 
@@ -1098,7 +1098,7 @@ ibm_jacobian.bru_mapper_linear <- function(mapper, input, ...) {
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_linear <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 
@@ -1274,7 +1274,7 @@ ibm_jacobian.bru_mapper_factor <- function(mapper, input, ...) {
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_factor <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 
@@ -1323,28 +1323,28 @@ ibm_eval.bru_mapper_const <- function(mapper, input, state = NULL, ...) {
 #' @export
 #' @describeIn inlabru-deprecated Creates a [bru_mapper_const()] mapper.
 bru_mapper_offset <- function(...) {
-  lifecycle::deprecate_soft("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
+  lifecycle::deprecate_warn("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
   bru_mapper_define(bru_mapper_const(), new_class = "bru_mapper_offset")
 }
 
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [bru_mapper_const] methods
 ibm_n.bru_mapper_offset <- function(...) {
-  lifecycle::deprecate_soft("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
+  lifecycle::deprecate_warn("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
   NextMethod()
 }
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [bru_mapper_const] methods
 ibm_values.bru_mapper_offset <- function(...) {
-  lifecycle::deprecate_soft("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
+  lifecycle::deprecate_warn("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
   NextMethod()
 }
 
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [bru_mapper_const] methods
 ibm_amatrix.bru_mapper_offset <- function(...) {
-  lifecycle::deprecate_soft("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_warn("2.6.0", "bru_mapper_offset()", "bru_mapper_const()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   NextMethod()
 }
 
@@ -2283,7 +2283,7 @@ ibm_jacobian.bru_mapper_multi <- function(mapper,
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_multi <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 
@@ -2676,7 +2676,7 @@ ibm_jacobian.bru_mapper_collect <- function(mapper, input, state = NULL,
 #' @export
 #' @describeIn inlabru-deprecated Replaced by [ibm_jacobian()]
 ibm_amatrix.bru_mapper_collect <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
+  lifecycle::deprecate_stop("2.6.0", "ibm_amatrix()", "ibm_jacobian()")
   ibm_jacobian(...)
 }
 

R/mesh.R

@@ -101,12 +101,12 @@ vertices.inla.mesh <- function(...) {
 #' }
 #'
 pixels <- function(mesh, nx = 150, ny = 150, mask = TRUE) {
-  #  lifecycle::deprecate_soft(
-  #    "2.8.0",
-  #    "pixels()",
-  #   "fm_pixels(format = 'sp')",
-  #   details = "The fm_pixels() function can generate sf, terra, and sp output."
-  # )
+  lifecycle::deprecate_soft(
+    "2.8.0",
+    "pixels()",
+    "fm_pixels(format = 'sp')",
+    details = "The fm_pixels() function can generate sf, terra, and sp output."
+  )
   fm_pixels(mesh, nx = nx, ny = ny, mask = mask, format = "sp")
 }
 

R/utils.R

@@ -314,7 +314,7 @@ eval_spatial <- function(data, where, layer = NULL, selector = NULL) {
 
 #' @describeIn inlabru-deprecated Replaced by the generic [eval_spatial()]
 eval_SpatialDF <- function(...) {
-  lifecycle::deprecate_warn("2.6.0", "eval_spatial()")
+  lifecycle::deprecate_stop("2.6.0", "eval_spatial()")
   eval_spatial(...)
 }