Merge pull request #52 from fishR-Core-Team/dev

Prepping update to v0.2.5 (for CRAN)

.github/ISSUE_TEMPLATE/release-prep-template.md

@@ -8,7 +8,7 @@ assignees: ''
 
 ---
 
-Below are the steps used to prepare `FSAdata` for submission to CRAN. The steps should generally be followed in order (i.e., don't move to the next step without success at the current step). It is common to have to repeat some previous steps if an error/warning occurs at a subsequent step (in my experience, this most often happens after checking on the development version of R when using R-winbuilder).
+Below are the steps used to prepare `RFishBC` for submission to CRAN. The steps should generally be followed in order (i.e., don't move to the next step without success at the current step). It is common to have to repeat some previous steps if an error/warning occurs at a subsequent step (in my experience, this most often happens after checking on the development version of R when using R-winbuilder).
 
 It is worth noting that this whole process can take 2-3 hours (or more depending on internet speed) with significant "waiting time" for checks and builds.
 

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RFishBC
-Version: 0.2.4.9000
-Date: 2022-2-18
+Version: 0.2.5
+Date: 2023-8-25
 Title: Back-Calculation of Fish Length
 Authors@R: person("Derek","Ogle",
     email="[email protected]",
@@ -11,8 +11,8 @@ Description: Helps fisheries scientists collect measurements from calcified
     standard procedures and models. This is intended to replace much of the
     functionality provided by the now out-dated 'fishBC' software
     (<https://fisheries.org/bookstore/all-titles/software/70317/>).
-URL: https://derekogle.com/RFishBC/
-BugReports: https://github.com/droglenc/RFishBC/issues
+URL: https://fishr-core-team.github.io/RFishBC/
+BugReports: https://github.com/fishR-Core-Team/RFishBC/issues
 License: GPL-3
 LazyData: true
 Depends: R (>= 3.2.0)
@@ -34,4 +34,4 @@ Suggests:
     pkgdown,
     testthat
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3

R/RFishBC-internals.R

@@ -13,7 +13,7 @@
 .onAttach <- function(lib,pkg,...) {                               # nocov start
   vers <- read.dcf(system.file("DESCRIPTION",package=pkg,lib.loc=lib),
                    fields="Version")
-  msg <- paste0("## RFishBC v",vers,". See vignettes at derekogle.com/RFishBC/.\n")
+  msg <- paste0("## RFishBC v",vers,". See vignettes at fishr-core-team.github.io/RFishBC/.\n")
   packageStartupMessage(msg)
 }                                                                  # nocov end
 

R/RFishBC-package.r

@@ -1,7 +1,10 @@
 #' RFishBC.
 #'
-#' The RFishBC package helps fisheries scientists collect growth data from calcified structures and back-calculate estimated lengths at previous ages. The package is intended to replace much of the functionality provided by the now out-date fishBC software. See the package webpage at [https://derekogle.com/RFishBC].
+#' The RFishBC package helps fisheries scientists collect growth data from calcified structures and back-calculate estimated lengths at previous ages. The package is intended to replace much of the functionality provided by the now out-date fishBC software. See the package webpage at [https://fishr-core-team.github.io/RFishBC/].
 #' 
 #' @name RFishBC
-#' @docType package
+#' 
+#' @keywords internal
+"_PACKAGE"
+
 NULL

R/addFindNotes.R

@@ -7,7 +7,7 @@
 #'
 #' @return None, but the \code{note} object in the R Data file(s) given in \code{nms} will be modified.
 #' 
-#' @details A detailed description of its use is in the "Other Features" vignette on the \href{https://derekogle.com/RFishBC/index.html}{RFishBC website}.
+#' @details A detailed description of its use is in the "Other Features" vignette on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #' 
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #' 
@@ -40,7 +40,7 @@ addNote <- function(nms,note) {
 #'
 #' @return A data.frame that contains the \code{id}, \code{reading}, and \code{notes} from the chosen R Data files.
 #' 
-#' @details A detailed description of its use is in the "Other Features" vignette on the \href{https://derekogle.com/RFishBC/index.html}{RFishBC website}.
+#' @details A detailed description of its use is in the "Other Features" vignette on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #' 
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #' 

R/bcFuns.R

@@ -35,7 +35,7 @@
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @section IFAR Supplement: \url{https://derekogle.com/IFAR/supplements/backcalculation/}
+#' @section IFAR Supplement: \url{https://derekogle.com/IFAR/supplements/backcalculation.html}
 #'
 #' @references
 #' Vigliola, L. and M.G. Meekan. 2009. The back-calculation of fish growth from otoliths. pp. 174-211. in B.S. Green et al. (editors). Tropical Fish Otoliths: Information for Assessment, Management and Ecology. Review: Methods and Technologies in Fish Biology and Fisheries 11. Springer. [Was (is?) available from https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths.]

R/combineData.R

@@ -9,7 +9,7 @@
 #'
 #' @return A data.frame that contains the radii data created with \code{\link{digitizeRadii}} for all files given in \code{nms}.
 #' 
-#' @details A detailed description of its use is in \href{https://derekogle.com/RFishBC/articles/MeasureRadii/collectRadiiData.html}{this vignette} on the \href{https://derekogle.com/RFishBC/index.html}{RFishBC website}. The list of R data file names may be efficiently created with \code{\link{listFiles}} as described in that vignette. The R data file names may also be selected from a dialog box if using Windows.
+#' @details A detailed description of its use is in \href{https://fishr-core-team.github.io/RFishBC/articles/collectRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}. The list of R data file names may be efficiently created with \code{\link{listFiles}} as described in that vignette. The R data file names may also be selected from a dialog box if using Windows.
 #' 
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #' 

R/digitizeRadii.R

@@ -58,7 +58,7 @@
 #'   \item{\code{note}: }{A string that contains a note about the reading (e.g., a note that the image was poor, some annulus were suspect, or the image should be re-read.)}
 #' }.
 #' 
-#' @details This function requires interaction from the user. A detailed description of its use is in the vignettes on the \href{https://derekogle.com/RFishBC/index.html}{RFishBC website}.
+#' @details This function requires interaction from the user. A detailed description of its use is in the vignettes on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #' 
 #' @seealso \code{\link{showDigitizedImage}} and \code{\link{RFBCoptions}}.
 #'

R/listFiles.R

@@ -10,7 +10,7 @@
 #' 
 #' @seealso \code{\link{digitizeRadii}} and \code{\link{combineData}}; and \code{\link{list.files}} in base R.
 #'
-#' @details An example of using this function is in \href{https://derekogle.com/RFishBC/articles/MeasureRadii/collectRadiiData.html}{this vignette} and \href{https://derekogle.com/RFishBC/articles/MeasureRadii/seeRadiiData.html}{this vignette} on the \href{https://derekogle.com/RFishBC/index.html}{RFishBC website}.
+#' @details An example of using this function is in \href{https://fishr-core-team.github.io/RFishBC/articles/MeasureRadii/collectRadiiData.html}{this vignette} and \href{https://fishr-core-team.github.io/RFishBC/articles/MeasureRadii/seeRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #'
 #' @return Character vector.
 #' 

R/showDigitizedImage.R

@@ -22,7 +22,7 @@
 #'
 #' @return A list that contains the size of the window in \code{windowSize} and the pixel width to heigh ration in \code{pixW2H}. In addition, an image is plotted with, at least, the selected points.
 #' 
-#' @details This function requires interaction from the user. A detailed description of its use is in \href{https://derekogle.com/RFishBC/articles/MeasureRadii/seeRadiiData.html}{this vignette} on the \href{https://derekogle.com/RFishBC/index.html}{RFishBC website}.
+#' @details This function requires interaction from the user. A detailed description of its use is in \href{https://fishr-core-team.github.io/RFishBC/articles/MeasureRadii/seeRadiiData.html}{this vignette} on the \href{https://fishr-core-team.github.io/RFishBC/index.html}{RFishBC website}.
 #'
 #' @seealso \code{\link{digitizeRadii}} and \code{\link{RFBCoptions}}.
 #' 

cran-comments/cran-comments-v0_2_5.md

@@ -0,0 +1,9 @@
+* This updates the existing RFishBC package on CRAN with minor fixes and correction for package alias per e-mail from Kurt Hornik on 19-Aug-23.
+
+## Notes
+* If there is a note about "fishBC" being misspelled in the description, then note that this is not a misspelling.
+
+## Testing Environments
+* My Windows machine.
+* Win Builder -- old-release, release, and development.
+* GitHub Action (R-CMD-check.yaml)