Merge pull request #139 from mitre/upd-cran

Make updates for CRAN testing
carriedaymont · Sep 19, 2023 · cd1883f · cd1883f
2 parents aea2631 + 6e13895
commit cd1883f
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Showing 30 changed files with 99 additions and 26 deletions.
diff --git a/R/adjustcarryforward.R b/R/adjustcarryforward.R
@@ -1084,9 +1084,10 @@ acf_answers <- function(subjid,
 #' @rawNamespace import(dplyr, except = c(last, first, summarize, src, between))
 #' @import data.table
 #' @examples
+#' \donttest{
 #' # Run on a small subset of given data
 #' df <- as.data.frame(syngrowth)
-#' df <- df[df$subjid %in% unique(df[, "subjid"])[1:5], ]
+#' df <- df[df$subjid %in% unique(df[, "subjid"])[1:2], ]
 #' clean_df <- cbind(df,
 #'                   "gcr_result" = cleangrowth(df$subjid,
 #'                                              df$param,
@@ -1101,6 +1102,7 @@ acf_answers <- function(subjid,
 #'                                 sex = clean_df$sex,
 #'                                 measurement = clean_df$measurement,
 #'                                 orig.exclude = clean_df$gcr_result)
+#' }
 adjustcarryforward <- function(subjid,
                                param,
                                agedays,

diff --git a/R/cdc.R b/R/cdc.R
@@ -109,6 +109,7 @@ set_cols_first <- function(DT, cols, intersection = TRUE)
 #' @importFrom stats approx pnorm qnorm
 #' @rawNamespace import(R.utils, except = c(extract))
 #' @examples
+#' \donttest{
 #' # Run on a small subset of given data
 #' df <- as.data.frame(syngrowth)
 #' df <- df[df$subjid %in% unique(df[, "subjid"])[1:5], ]
@@ -133,6 +134,7 @@ set_cols_first <- function(DT, cols, intersection = TRUE)
 #' # Disabling conversion of all-integer age in months to (age + 0.5)
 #' dfc <- simple_bmi(df_wide)
 #' df_bmiz <- ext_bmiz(dfc, adjust.integer.age=FALSE)
+#' }
 ext_bmiz <- function (data,
                       age = "agem",
                       wt = "wt",

diff --git a/R/growth.R b/R/growth.R
@@ -1161,12 +1161,14 @@ cleangrowth <- function(subjid,
 #' @import data.table
 #' @importFrom utils read.csv read.table
 #' @examples
+#' \donttest{
 #' # Return calculating function with all defaults
 #' afunc <- read_anthro()
 #'
 #' # Return calculating function while specifying a path and using only CDC data
 #' afunc <- read_anthro(path = system.file("extdata", package = "growthcleanr"),
 #'                      cdc.only = TRUE)
+#' }
 read_anthro <- function(path = "", cdc.only = FALSE, prelim_infants = FALSE) {
   # avoid "no visible bindings" warning
   src <- param <- sex <- age <- ret <- m <- NULL

diff --git a/R/utils.R b/R/utils.R
@@ -178,7 +178,7 @@ recode_sex <- function(input_data,
 #' @examples
 #' # Run on a small subset of given data
 #' df <- as.data.frame(syngrowth)
-#' df <- df[df$subjid %in% unique(df[, "subjid"])[1:5], ]
+#' df <- df[df$subjid %in% unique(df[, "subjid"])[1:2], ]
 #' df <- cbind(df,
 #'             "gcr_result" = cleangrowth(df$subjid,
 #'                                        df$param,
@@ -332,7 +332,7 @@ longwide <-
 #' # Simple usage
 #' # Run on a small subset of given data
 #' df <- as.data.frame(syngrowth)
-#' df <- df[df$subjid %in% unique(df[, "subjid"])[1:5], ]
+#' df <- df[df$subjid %in% unique(df[, "subjid"])[1:2], ]
 #' df <- cbind(df,
 #'             "gcr_result" = cleangrowth(df$subjid,
 #'                                        df$param,

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,9 +1,9 @@
-# CRAN submission growthcleanr 2.2.0
+# CRAN submission growthcleanr 2.2.0 (1)
 
 ## R CMD check results
 There were no ERRORs or WARNINGs.
 
-There was one note:
+There was one NOTE:
 
 ❯ checking installed package size ... NOTE
     installed size is  5.9Mb
@@ -15,8 +15,57 @@ extdata has been compressed as much as possible -- data in that folder is necess
 ## Downstream dependencies
 There are currently no downstream dependencies for this package.
 
+## CRAN test
+
+We have addressed each of the notes in the test as noted below:
+
+* Maintainer: ‘Carrie Daymont <[email protected]>’
+
+Size of tarball: 5529529 bytes
+
+The package has been compressed as much as possible, as noted above -- data included is necessary to run the package.
+
+* NOTE
+Examples with CPU (user + system) or elapsed time > 5s
+                    user system elapsed
+ext_bmiz           6.911  0.120   0.925
+simple_bmi         6.740  0.167   0.783
+adjustcarryforward 6.494  0.140   1.179
+longwide           5.072  0.135   0.834
+Examples with CPU time > 2.5 times elapsed time
+                    user system elapsed ratio
+simple_bmi         6.740  0.167   0.783 8.821
+read_anthro        2.323  0.060   0.276 8.634
+ext_bmiz           6.911  0.120   0.925 7.601
+longwide           5.072  0.135   0.834 6.243
+adjustcarryforward 6.494  0.140   1.179 5.627
+
+Examples have been reduced in length or set to donttest.
+
+*   Running ‘testthat.R’ [230s/74s]
+Running R code in ‘testthat.R’ had CPU time 3.1 times elapsed time
+
+Tests have been set to not run on CRAN.
+
 # Previous Submissions
 
+# CRAN submission growthcleanr 2.2.0
+
+## R CMD check results
+There were no ERRORs or WARNINGs.
+
+There was one note:
+
+❯ checking installed package size ... NOTE
+    installed size is  5.9Mb
+    sub-directories of 1Mb or more:
+      extdata   5.0Mb
+
+extdata has been compressed as much as possible -- data in that folder is necessary to run the package.
+
+## Downstream dependencies
+There are currently no downstream dependencies for this package.
+
 # CRAN submission growthcleanr 2.1.1
 
 ## R CMD check results

diff --git a/docs/articles/adult-algorithm.html b/docs/articles/adult-algorithm.html
diff --git a/docs/articles/configuration.html b/docs/articles/configuration.html
diff --git a/docs/articles/developer-guidelines.html b/docs/articles/developer-guidelines.html
diff --git a/docs/articles/installation.html b/docs/articles/installation.html
diff --git a/docs/articles/large-data-sets.html b/docs/articles/large-data-sets.html
diff --git a/docs/articles/next-steps.html b/docs/articles/next-steps.html
diff --git a/docs/articles/output.html b/docs/articles/output.html
diff --git a/docs/articles/prelim-infants-algorithm.html b/docs/articles/prelim-infants-algorithm.html
diff --git a/docs/articles/quickstart.html b/docs/articles/quickstart.html
diff --git a/docs/articles/usage.html b/docs/articles/usage.html
diff --git a/docs/articles/utilities.html b/docs/articles/utilities.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -13,5 +13,5 @@ articles:
   quickstart: quickstart.html
   usage: usage.html
   utilities: utilities.html
-last_built: 2023-09-13T23:26Z
+last_built: 2023-09-15T16:20Z
 
diff --git a/docs/reference/adjustcarryforward.html b/docs/reference/adjustcarryforward.html
diff --git a/docs/reference/ext_bmiz.html b/docs/reference/ext_bmiz.html
diff --git a/docs/reference/longwide.html b/docs/reference/longwide.html