Removing \donttest{} from examples and adding explanation of NOTE in …

…cran-comments.md instead

DESCRIPTION

@@ -2,7 +2,7 @@ Package: DSSAT
 Type: Package
 Title: A Comprehensive R Interface for the DSSAT Cropping Systems Model
 Version: 0.0.7
-Date: 2023-03-22
+Date: 2023-03-27
 Author: Phillip D. Alderman [aut, cre]
 Maintainer: Phillip D. Alderman <[email protected]>
 Description: The purpose of this package is to provide a comprehensive

R/read_casupro_eco.R

@@ -14,8 +14,6 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' sample_eco <- c('CA0001  (CP 80-1743; CP 88-1762)',
 #' '!-------------------',
 #' '  KCAN_ECO      0.80    Superseeds KCAN from .SPE file',
@@ -30,7 +28,7 @@
 #' '  SENDAY        0.05    Maximum fraction of existing leaf weight which can be senesced on')
 #'
 #' read_casupro_eco(sample_eco)
-#' }
+#'
 
 read_casupro_eco <- function(raw_lines){
 

R/read_dssat.R

@@ -29,12 +29,10 @@
 #'
 #' @examples
 #'
-#' \donttest{
 #' # Extract file path for sample output file path
 #' sample_output <- system.file('extdata','SAMPLE.OUT',package='DSSAT')
 #'
 #' read_dssat(sample_output)
-#' }
 #'
 
 read_dssat <- function(file_name,col_types=NULL,col_names=NULL,na_strings=NULL,

R/read_output.R

@@ -15,14 +15,11 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' # Extract file path for sample output file path
 #' sample_output <- system.file('extdata','SAMPLE.OUT',package='DSSAT')
 #'
 #' out <- read_output(sample_output)
 #'
-#' }
 
 read_output <- function(file_name, col_types = NULL, col_names = NULL,
                         left_justified = NULL, read_only = NULL,

R/read_soil_profile.R

@@ -14,8 +14,6 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' sample_sol <- c(
 #' "*IB00000001  IBSNAT      SIC     210 DEFAULT - DEEP SILTY CLAY",
 #' "@SITE        COUNTRY          LAT     LONG SCS FAMILY",
@@ -36,7 +34,6 @@
 #'
 #' read_soil_profile(sample_sol)
 #'
-#' }
 
 read_soil_profile <- function(raw_lines,left_justified=NULL,
                               col_types=NULL,col_names=NULL){

R/read_sol.R

@@ -15,14 +15,11 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' # Extract file path for sample soil file
 #' sample_sol <- system.file('extdata','SAMPLE.SOL',package='DSSAT')
 #'
 #' sol <- read_sol(sample_sol)
 #'
-#' }
 
 read_sol <- function(file_name,id_soil=NULL,left_justified=NULL,col_types=NULL,col_names=NULL){
 

R/write_casupro_eco.R

@@ -11,8 +11,6 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' sample_eco <- c('CA0001  (CP 80-1743; CP 88-1762)',
 #' '!-------------------',
 #' '  KCAN_ECO      0.80    Superseeds KCAN from .SPE file',
@@ -30,7 +28,6 @@
 #'
 #' write_casupro_eco(eco)
 #'
-#' }
 
 write_casupro_eco <- function(eco){
 

R/write_filet.R

@@ -16,8 +16,6 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' # Extract FileT path for sample file
 #' sample_filet <- system.file('extdata','SAMPLE.CRT',package='DSSAT')
 #'
@@ -29,8 +27,6 @@
 #' # Write out sample FileA
 #' write_filet(filet,sample_filet2)
 #'
-#' }
-#'
 
 write_filet <- function(filet,file_name,drop_duplicate_rows=TRUE){
 

R/write_sol.R

@@ -23,8 +23,6 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#'
 #' # Extract file path for sample soil file
 #' sample_sol <- system.file('extdata','SAMPLE.SOL',package='DSSAT')
 #'
@@ -37,8 +35,6 @@
 #' # Write example soil file
 #' write_sol(sol,sample_sol2)
 #'
-#' }
-#'
 
 write_sol <- function(sol,file_name,title=NULL,append=TRUE,force_std_fmt=TRUE){
 

cran-comments.md

@@ -1,11 +1,10 @@
 ## Test environments
 
 * local Ubuntu 22.04.2 LTS, R 4.2.3, GCC
-* R-hub Ubuntu Linux 20.04.1 LTS, R-release, GCC (ubuntu-gcc-release)
-* R-hub Debian Linux, R-devel, GCC (debian-gcc-devel)
+* win-builder (devel and release)
 * R-hub Fedora Linux, R-devel, clang, gfortran (fedora-clang-devel)
+* R-hub Debian Linux, R-devel, clang (debian-clang-devel)
 * R-hub Windows Server 2022, R-release, 64 bit (windows-x86_64-release)
-* win-builder (devel and release)
 
 ## R CMD check results
 
@@ -15,19 +14,30 @@ There were no ERRORs or WARNINGs. There were 2 NOTEs:
 
 ```
     * checking for detritus in the temp directory ... NOTE
+```
+
+Inspecting the logs revealed this message:
+
+```
     Found the following files/directories:
-      'lastMiKTeXException'
+    * DONE
+    'lastMiKTeXException'
 ```
-    As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this is likely due to a bug/crash in MiKTeX and can likely be ignored.
 
-* ONLY on R-hub Fedora Linux, R-devel, clang, gfortran:
+As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this is likely due to a bug/crash in MiKTeX and can likely be ignored.
+
+* ONLY on R-hub Debian Linux, R-devel, clang:
 
 ```
-    * checking HTML version of manual ... NOTE
-    Skipping checking HTML validation: no command 'tidy' found
+* checking examples ... [31s/75s] NOTE
+Examples with CPU (user + system) or elapsed time > 5s
+            user system elapsed
+write_sol  3.074  0.012   7.317
+read_dssat 2.047  0.025   5.449
+read_sol   2.022  0.003   5.048
 ```
 
-    This NOTE is due to the `tidy` utility being unavailable on the R-hub Fedora server. I think this can be safely ignored given that HTML checks are passing on all other platforms.
+I do not think this is a problem. Although I am not sure why these examples are running slowly in this environment, elapsed time for each example is less than 3 seconds for the other test environments.
 
 ## Downstream dependencies