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arnejohannesholmin merged 4 commits into from
Sep 2, 2025
Merged

Develop #205

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e8ef0f0
Temporary removing Reca as suggests due to failure to compile on macO…
Sep 1, 2025
9963298
Merge pull request #204 from StoXProject/PreHelpHtml
arnejohannesholmin Sep 1, 2025
bcfe057
Updated the check-full.yaml to be consistent with RstoxData, RstoxBas…
Sep 2, 2025
d84882b
Merge pull request #206 from StoXProject/PreHelpHtml
arnejohannesholmin Sep 2, 2025
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130 changes: 85 additions & 45 deletions .github/workflows/check-full.yaml
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Expand Up @@ -2,13 +2,13 @@ on:
push:
branches:
- master
- develop
- testing
- develop
pull_request:
branches:
- master
- develop
- testing
- develop

name: R-CMD-check

Expand Down Expand Up @@ -38,7 +38,7 @@ jobs:
# ubuntu-latest is 24 as of 2024-10-31. Should we use it?
- {os: ubuntu-22.04, r: 'release', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
- {os: ubuntu-22.04, r: 'oldrel', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
- {os: ubuntu-22.04, r: 'oldrel-1', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"}
# - {os: ubuntu-22.04, r: 'oldrel-2', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} # Skipping the oldrel-2, as we need equal requirements across platforms

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
Expand All @@ -53,7 +53,7 @@ jobs:

- uses: actions/checkout@v4

- name: Do autorelease increment, tagging, and environment setup
- name: Prepare for deployment at push
if: github.event_name == 'push'
run: |
curl "https://raw.githubusercontent.com/StoXProject/unstableRepo/main/scripts/checktag-actions.sh" --output unstableRepo_checktag.sh
Expand Down Expand Up @@ -91,44 +91,19 @@ jobs:




#############################################################################
#### 2. R package installation (with system and R package dependencies): ####
#############################################################################

#- name: Query dependencies
# run: |
# install.packages('remotes')
# saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
# writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
# shell: Rscript {0}

#- name: Cache R packages
# if: runner.os != 'Windows'
# uses: actions/cache@v4
# with:
# path: ${{ env.R_LIBS_USER }}
# key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
# restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

# We don't use the code below using remotes::system_requirements anymore, since we do not have control over that function and should rather hard code the dependencies, which also lists the dependencies explicitely:
#- name: Install system dependencies
# if: runner.os == 'Linux'
# run: |
# while read -r cmd
# do
# eval sudo $cmd
# done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "22.04"))')

- name: Install MacOS system dependencies
## 2a. System dependencies:
- name: Install system dependencies on macOS
if: runner.os == 'macOS'
run: |
# gfortran may not exist in a period after a new R minor release:
gfortranFile='/usr/local/bin/gfortran'
if [ -f "$gfortranFile" ] ; then
rm "$gfortranFile"
fi
rm -f '/usr/local/bin/gfortran'
rm -f '/usr/local/bin/2to3'
rm -f '/usr/local/bin/2to3-3.11'
rm -f '/usr/local/bin/idle3'
Expand All @@ -139,7 +114,8 @@ jobs:
rm -f '/usr/local/bin/python3.11'
rm -f '/usr/local/bin/python3-config'
rm -f '/usr/local/bin/python3.11-config'
export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=false # This prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source".
rm -f '/usr/local/bin/gfortran'
export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK= # This (the value should actually be empty...) prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source".
brew install gdal
shell: bash

Expand All @@ -154,34 +130,100 @@ jobs:
shell: bash


## 2c. R packages needed for this yaml script (not related to the Rstox package itself):
## 2b. R packages needed for this yaml script (not related to the Rstox package itself):
- name: Install CRANdependencies
run: |
install.packages(c("rcmdcheck", "git2r", "sessioninfo", "knitr", "remotes", "drat"))
install.packages(c("rcmdcheck", "git2r", "sessioninfo", "knitr", "drat"))
shell: Rscript {0}


## 2d. Rstox packages and dependencies (the complicated if condition is needed since the reference to branch name is not consistent across event names). There is the issue that R sorts packge versions alphabetically, while StoX uses semantic versioning. Consequently a pre-release such as 1.2.3-9001 will be considered as newer than the official release 1.2.3 by R. We have solved this by separating the pre-releases and official releases into different repos "unstableRepo" and "testingRepo" for pre-releases and "repo" of official releases). This potentially breaks with remotes::install_deps() as it silently appends the Additional_repositories from the DESCRIPTION file to the repos, but since this would only be a problem if a pre-release is ranked as newer than the official release it will not be a problem when installing dependencies from the "repo" since the Additional_repositories points to that same repo:
## 2c. Rstox packages and dependencies (the complicated if condition is needed since the reference to branch name is not consistent across event names). There is the issue that R sorts packge versions alphabetically, while StoX uses semantic versioning. Consequently a pre-release such as 1.2.3-9001 will be considered as newer than the official release 1.2.3 by R. We have solved this by separating the pre-releases and official releases into different repos "unstableRepo" and "testingRepo" for pre-releases and "repo" of official releases). This potentially breaks with remotes::install_deps() as it silently appends the Additional_repositories from the DESCRIPTION file to the repos, but since this would only be a problem if a pre-release is ranked as newer than the official release it will not be a problem when installing dependencies from the "repo" since the Additional_repositories points to that same repo:
- name: Install R package dependencies from the unstableRepo
if: (github.event_name == 'push' && github.ref_name == 'develop') || (github.event_name == 'pull_request' && github.base_ref == 'develop')
run: |
remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/unstableRepo/", "https://cloud.r-project.org/"))
# We hard code the list of top level dependencies, since the behavior of remotes::install_deps() that we used before is very unclear (e.g. how is the Additional_repositories included in the list of repos?):
topLevelDeps <- c(
# Imports:
"data.table",
"ggplot2",
"gridExtra",
"methods",
"RColorBrewer",
"rnaturalearth",
"rnaturalearthdata",
"RstoxData",
"RstoxBase",
"sf",
# Suggests:
"knitr",
"rmarkdown",
"tinytest"
)
install.packages(
topLevelDeps,
dependencies = TRUE,
repos = c("https://stoxproject.github.io/unstableRepo/", "https://cloud.r-project.org/")
)
shell: Rscript {0}

- name: Install R package dependencies from the testingRepo
if: (github.event_name == 'push' && github.ref_name == 'testing') || (github.event_name == 'pull_request' && github.base_ref == 'testing')
run: |
remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/testingRepo/", "https://cloud.r-project.org/"))
# We hard code the list of top level dependencies, since the behavior of remotes::install_deps() that we used before is very unclear (e.g. how is the Additional_repositories included in the list of repos?):
topLevelDeps <- c(
# Imports:
"data.table",
"ggplot2",
"gridExtra",
"methods",
"RColorBrewer",
"rnaturalearth",
"rnaturalearthdata",
"RstoxData",
"RstoxBase",
"sf",
# Suggests:
"knitr",
"rmarkdown",
"tinytest"
)
install.packages(
topLevelDeps,
dependencies = TRUE,
repos = c("https://stoxproject.github.io/unstableRepo/", "https://cloud.r-project.org/")
)
shell: Rscript {0}

- name: Install R package dependencies from the official repo
if: (github.event_name == 'push' && github.ref_name == 'master') || (github.event_name == 'pull_request' && github.base_ref == 'master')
run: |
remotes::install_deps(dependencies = TRUE, repos = c("https://stoxproject.github.io/repo/", "https://cloud.r-project.org/"))
# We hard code the list of top level dependencies, since the behavior of remotes::install_deps() that we used before is very unclear (e.g. how is the Additional_repositories included in the list of repos?):
topLevelDeps <- c(
# Imports:
"data.table",
"ggplot2",
"gridExtra",
"methods",
"RColorBrewer",
"rnaturalearth",
"rnaturalearthdata",
"RstoxData",
"RstoxBase",
"sf",
# Suggests:
"knitr",
"rmarkdown",
"tinytest"
)
install.packages(
topLevelDeps,
dependencies = TRUE,
repos = c("https://stoxproject.github.io/unstableRepo/", "https://cloud.r-project.org/")
)
shell: Rscript {0}


## 2e. Session info:
## 2d. Session info:
- name: Session info
run: |
options(width = 100)
Expand Down Expand Up @@ -225,13 +267,12 @@ jobs:




#######################################################
#### 4. Build the package source and binary files: ####
#######################################################

- name: Build package source archive from branches develop, testing and master
if: runner.os == 'Linux' && matrix.config.r == '4.3' && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop')
- name: Build package source archive from branches develop, testing and master (on Linux for some reason)
if: runner.os == 'Linux' && matrix.config.r == 'release' && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop')
run: |
pkgbuild::build(".", dest_path = ".", binary = FALSE)
system(paste0("PKG_FREL=", Sys.getenv("PKG_FILE"), " >> ", Sys.getenv("GITHUB_ENV")))
Expand All @@ -250,7 +291,6 @@ jobs:




######################################
#### 5. Deploy to the drat repos: ####
######################################
Expand Down Expand Up @@ -291,7 +331,7 @@ jobs:
###############################

- name: Create release on GitHub and upload files for testing branch
if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'testing'
if: ( (runner.os == 'Windows') || (runner.os == 'macOS') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'testing'
uses: ncipollo/release-action@v1
with:
allowUpdates: true
Expand All @@ -302,7 +342,7 @@ jobs:
token: ${{ secrets.GITHUB_TOKEN }}

- name: Create release on GitHub and upload files for master branch
if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.3') ) && github.event_name == 'push' && github.ref_name == 'master'
if: ( (runner.os == 'Windows') || (runner.os == 'macOS') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'master'
uses: ncipollo/release-action@v1
with:
allowUpdates: true
Expand Down
17 changes: 7 additions & 10 deletions DESCRIPTION
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@@ -1,6 +1,6 @@
Package: RstoxFDA
Version: 1.6.0
Date: 2025-03-18
Version: 1.7.0-9001
Date: 2025-09-01
Title: Fisheries Dependent Analysis with RstoX
Authors@R: c(
person(given = "Edvin",
Expand All @@ -10,14 +10,15 @@ Authors@R: c(
person(given = "Arne Johannes",
family = "Holmin",
role = "aut"))
Depends: R (>= 4.3)
Depends: R (>= 4.4)
Description: Fisheries dependent analysis, including running the Estimated Catch at Age
model through the Reca package developed by the Norwegian Computing Center.
URL: https://github.com/StoXProject/RstoxFDA
BugReports: https://github.com/StoXProject/RstoxFDA/issues
License: LGPL-3
LazyData: true
Encoding: UTF-8
VignetteBuilder: knitr
Imports:
data.table (>= 1.12.6),
ggplot2 (>= 3.2.1),
Expand All @@ -26,17 +27,13 @@ Imports:
RColorBrewer (>= 1.1-2),
rnaturalearth (>= 1.0.1),
rnaturalearthdata (>= 1.0.0),
RstoxBase (>= 2.1.1),
RstoxData (>= 2.1.1),
sf (>= 1.0.0),
stats (>= 3.5.0),
utils (>= 3.5.0)
RstoxBase (>= 2.2.0-9002),
RstoxData (>= 2.2.0-9002),
sf (>= 1.0.0)
Suggests:
knitr,
Reca,
rmarkdown,
tinytest
Additional_repositories:
https://stoxproject.github.io/repo
VignetteBuilder: knitr
RoxygenNote: 7.3.2
5 changes: 5 additions & 0 deletions NEWS.md
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@@ -1,3 +1,8 @@
# RstoxFDA v1.7.0-9001
* Temporary removing Reca as suggests due to failure to compile on macOS and Windows.
* Pre-generated help HTLM pages using the latest RstoxBuild.


# RstoxFDA v1.6
* Fixed issue with plotting with other column variables than 'Area' in PlotFisheriesOverviewSpatial (#147)
* Fixed ordering of age groups in ReportAnalyticalCatchAtAge (#134)
Expand Down
14 changes: 7 additions & 7 deletions R/StoxAnalysisFunctions.R
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Expand Up @@ -214,7 +214,7 @@ warnMissingLandings <- function(StoxBiotic, StoxLanding, effects){
#' \code{\link[RstoxFDA]{CarNeighbours}}, mandatory if 'carEffect' is given.
#' Identifies which values of the carEffect are to be considered as neighbours.
#' @param CellEffect
#' Configures the cell effect. Defaults to `r RstoxFDA:::stoxFunctionAttributes$PrepareRecaEstimate$functionParameterDefaults$CellEffect`. If 'All', an interaction term will be added with all covariates that in the cell (whether they are fixed or random effects).
#' Configures the cell effect. Defaults to `r RstoxFDA::stoxFunctionAttributes$PrepareRecaEstimate$functionParameterDefaults$CellEffect`. If 'All', an interaction term will be added with all covariates that in the cell (whether they are fixed or random effects).
#' Any CAR-effect is always included in the cell effect.
#' @param UseAgingError
#' If TRUE, aging, error parameters will be incorporated in the models.
Expand All @@ -240,7 +240,7 @@ warnMissingLandings <- function(StoxBiotic, StoxLanding, effects){
#' optional, resolution for length measurements in cm.
#' If not provided modal value from data is used.
#' @param HatchDay
#' defaults to Defaults to `r RstoxFDA:::stoxFunctionAttributes$PrepareRecaEstimate$functionParameterDefaults$HatchDay`.
#' defaults to Defaults to `r RstoxFDA::stoxFunctionAttributes$PrepareRecaEstimate$functionParameterDefaults$HatchDay`.
#' encoding the day of the year when fish is consider to transition from one age to the next. 1 represents Jan 1st.
#' @return \code{\link[RstoxFDA]{RecaData}} Data prepared for running Reca.
#' @seealso
Expand Down Expand Up @@ -564,10 +564,10 @@ RunRecaEstimate <- function(RecaData, Nsamples=integer(), Burnin=integer(), Thin
#' @param RecaData \code{\link[RstoxFDA]{RecaData}} as returned from \code{\link[RstoxFDA]{PrepareRecaEstimate}}
#' @param Nsamples number of MCMC samples that will be made available for \code{\link[Reca]{eca.predict}}. See documentation for \code{\link[Reca]{eca.estimate}},
#' @param Burnin number of MCMC samples run and discarded by \code{\link[Reca]{eca.estimate}} before any samples are saved. See documentation for \code{\link[Reca]{eca.estimate}}.
#' @param Lgamodel The length age relationship to use for length-age fits (options: "log-linear", "non-linear": Schnute-Richards model). See documentation for \code{\link[Reca]{eca.estimate}}. Defaults to `r RstoxFDA:::stoxFunctionAttributes$ParameterizeRecaModels$functionParameterDefaults$Lgamodel`
#' @param Lgamodel The length age relationship to use for length-age fits (options: "log-linear", "non-linear": Schnute-Richards model). See documentation for \code{\link[Reca]{eca.estimate}}. Defaults to `r RstoxFDA::stoxFunctionAttributes$ParameterizeRecaModels$functionParameterDefaults$Lgamodel`
#' @param ResultDirectory a directory where Reca may store temp-files \code{\link[Reca]{eca.estimate}} and \code{\link[Reca]{eca.predict}}. See details.
#' @param Thin controls how many iterations are run between each samples saved. Defaults to `r RstoxFDA:::stoxFunctionAttributes$ParameterizeRecaModels$functionParameterDefaults$Thin`. This may be set to account for autocorrelation introduced by Metropolis-Hastings simulation. see documentation for \code{\link[Reca]{eca.estimate}}
#' @param Delta.age see documentation for \code{\link[Reca]{eca.estimate}}. Defaults to `r RstoxFDA:::stoxFunctionAttributes$ParameterizeRecaModels$functionParameterDefaults$Delta.age`.
#' @param Thin controls how many iterations are run between each samples saved. Defaults to `r RstoxFDA::stoxFunctionAttributes$ParameterizeRecaModels$functionParameterDefaults$Thin`. This may be set to account for autocorrelation introduced by Metropolis-Hastings simulation. see documentation for \code{\link[Reca]{eca.estimate}}
#' @param Delta.age see documentation for \code{\link[Reca]{eca.estimate}}. Defaults to `r RstoxFDA::stoxFunctionAttributes$ParameterizeRecaModels$functionParameterDefaults$Delta.age`.
#' @param Seed see documentation for \code{\link[Reca]{eca.estimate}}. Defaults to random seed.
#' @param UseCachedData if TRUE Parameterization is not run, but any previous runs for exactly the same arguments are returned.
#' @return \code{\link[RstoxFDA]{RecaParameterData}} results from Reca Model Parameterization.
Expand Down Expand Up @@ -738,10 +738,10 @@ getLandingsFromStoxLandings <- function(RecaParameterData, StoxLandingData, Temp
#' @param StoxLandingData Landings data (\code{\link[RstoxData]{StoxLandingData}}).
#' @param GroupingVariables character vector identifying columns in 'StoxLandingData' that results should be provided for.
#' @param TemporalResolution
#' Code for temporal resolution in landings: "Month" or "Quarter". Defaults to `r RstoxFDA:::stoxFunctionAttributes$RunRecaModels$functionParameterDefaults$TemporalResolution`.
#' Code for temporal resolution in landings: "Month" or "Quarter". Defaults to `r RstoxFDA::stoxFunctionAttributes$RunRecaModels$functionParameterDefaults$TemporalResolution`.
#' Regulates temporal resolution for calculating fractional ages of fish.
#' Not to be confused with any temporal covariate.
#' @param Caa.burnin see documentation for \code{\link[Reca]{eca.predict}}. Defaults to `r RstoxFDA:::stoxFunctionAttributes$RunRecaModels$functionParameterDefaults$Caa.burnin`.
#' @param Caa.burnin see documentation for \code{\link[Reca]{eca.predict}}. Defaults to `r RstoxFDA::stoxFunctionAttributes$RunRecaModels$functionParameterDefaults$Caa.burnin`.
#' @param CollapseLength indicates whether length groups should be collapsed in result. Defaults to TRUE. See details.
#' @return \code{\link[RstoxFDA]{RecaCatchAtAge}}
#' @seealso \code{\link[RstoxFDA]{ParameterizeRecaModels}} for model parameterisation,
Expand Down
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