fix for CRAN errors

Blue-Matter · Sep 24, 2024 · dc25a48 · dc25a48
1 parent 4eb806e
commit dc25a48
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Showing 7 changed files with 15 additions and 10 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -26,3 +26,4 @@ netlify.toml
 ^man-roxygen
 ^test_objects
 DEVELOPMENT.R
+^CRAN-SUBMISSION$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -22,6 +22,7 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'devel'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,7 @@ Description: The 'openMSE' package is designed for building operating models,
     'openMSE', users have access to the full functionality contained within
     these packages. Learn more about 'openMSE' at <https://openmse.com/>.
 License: GPL-3
-URL: https://openmse.com/, https://github.com/Blue-Matter/openMSE, https://blue-matter.github.io/openMSE/
+URL: https://openmse.com/, https://github.com/Blue-Matter/openMSE, https://openMSE.openMSE.com
 BugReports: https://github.com/Blue-Matter/openMSE/issues
 Encoding: UTF-8
 LazyData: true

diff --git a/NAMESPACE b/NAMESPACE
@@ -28,7 +28,6 @@ S3method(get_ts,MMSE)
 S3method(get_ts,MSE)
 S3method(get_ts,list)
 S3method(get_ts,multiHist)
-S3method(hist,recruits)
 export(cm2inch)
 export(demo)
 export(divide_10)

diff --git a/R/get_data_frames.R b/R/get_data_frames.R
@@ -846,13 +846,12 @@ get_F <- function(x, model='Model 1', ...) {
   get_ts(x, variable='Apical Fishing Mortality', model=model, ...)
 }
 
-#' @export
-hist.recruits <- function(x) {
+hist_recruits <- function(x) {
   as.vector(apply(x@AtAge$Number[,1,,], 1:2, sum))
 }
 
 
-mse.recruits <- function(x) {
+mse_recruits <- function(x) {
   dd <- dim(x@N)
   if (length(dd)==3) {
     if (length(x@Misc$extended)<1)
@@ -864,8 +863,7 @@ mse.recruits <- function(x) {
 
 }
 
-mmse.recruits <- function(x) {
-
+mmse_recruits <- function(x) {
   apply(x@N[,,1,,,, drop=FALSE], c(1,2,4,5), sum)
 }
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,9 @@
+## Note to CRAN Maintainers
+
+Re-submission:
+* replaced the old URL in DESCRIPTION
+* fixed mismatch for methods registered for non-generic
+
 
 ## Test environments
 * local - Windows 4.4.1

diff --git a/data-raw/TS_Variables.csv b/data-raw/TS_Variables.csv
@@ -12,9 +12,9 @@ Landings,MMSE,Catch
 Removals,Hist,Removals
 Removals,MSE,Removals
 Removals,MMSE,Removals
-Recruits,Hist,hist.recruits()
-Recruits,MSE,mse.recruits()
-Recruits,MMSE,mmse.recruits()
+Recruits,Hist,hist_recruits()
+Recruits,MSE,mse_recruits()
+Recruits,MMSE,mmse_recruits()
 Spawning Biomass,MMSE,SSB
 Biomass,MMSE,B
 Apical Fishing Mortality,Hist,Find