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merge Dev_merge to fit manual for ecosim.R and Rpath_Support.R
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* using log directory ‘/home/rklasky/R/packages/Rpath/..Rcheck’ | ||
* using R version 4.3.1 (2023-06-16) | ||
* using platform: x86_64-pc-linux-gnu (64-bit) | ||
* R was compiled by | ||
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 | ||
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 | ||
* running under: Linux Mint 20 | ||
* using session charset: UTF-8 | ||
* checking for file ‘./DESCRIPTION’ ... ERROR | ||
Required fields missing or empty: | ||
‘Author’ ‘Maintainer’ | ||
* DONE | ||
Status: 1 ERROR |
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^.*\.Rproj$ | ||
^\.Rproj\.user$ | ||
^\.github$ | ||
^_pkgdown\.yml$ | ||
^docs$ | ||
^pkgdown$ | ||
^data-raw$ | ||
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^.*\.Rproj$ | ||
^\.Rproj\.user$ | ||
^\.github$ | ||
^_pkgdown\.yml$ | ||
^docs$ | ||
^pkgdown$ | ||
^data-raw$ | ||
^doc$ | ||
^Meta$ |
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_R_CHECK_DONTTEST_EXAMPLES_=FALSE |
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on: | ||
push: | ||
paths: | ||
- '.github/workflows/tests.yml' | ||
- 'R/*' | ||
- 'tests/testthat/*' | ||
- 'README.md' | ||
- 'DESCRIPTION' | ||
pull_request: | ||
paths: | ||
- '.github/workflows/tests.yml' | ||
- 'R/*' | ||
- 'tests/testthat/*' | ||
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name: Unit-Tests | ||
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jobs: | ||
# build: | ||
# runs-on: ubuntu-latest | ||
# steps: | ||
# - uses: actions/checkout@v2 | ||
# - uses: r-lib/actions/setup-r@v2 | ||
# - uses: r-lib/actions/setup-pandoc@v2 | ||
# - name: Install dependencies | ||
# run: Rscript -e "install.packages(c('testthat', 'tidyverse', 'here'))" | ||
# - name: Run tests | ||
# run: Rscript -e "source('tests/testthat.R')" | ||
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Unit-Tests: | ||
runs-on: ${{matrix.config.os}} | ||
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name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
#os: [macos-latest, ubuntu-latest, windows-latest] | ||
#os: [ubuntu-latest] | ||
config: | ||
- {os: macos-latest, r: 'release'} | ||
- {os: windows-latest, r: 'release'} | ||
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | ||
- {os: ubuntu-latest, r: 'release'} | ||
- {os: ubuntu-latest, r: 'oldrel-1'} | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
# R_REMOTES_NO_ERRORS_FROM_WARNINGS: false | ||
R_KEEP_PKG_SOURCE: yes | ||
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steps: | ||
- uses: actions/checkout@v4 | ||
# with: | ||
# fetch-depth: 0 | ||
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- uses: r-lib/actions/setup-pandoc@v2 | ||
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- uses: r-lib/actions/setup-r@v2 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
http-user-agent: ${{ matrix.config.http-user-agent }} | ||
use-public-rspm: true | ||
# r-version: '4.3.1' | ||
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- uses: r-lib/actions/setup-r-dependencies@v2 | ||
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- name: Install command line packages | ||
if: runner.os == 'Linux' | ||
run: | | ||
sudo apt update | ||
sudo apt-get install libcurl4-openssl-dev libgit2-dev | ||
- name: Install dependencies | ||
#run: Rscript -e "install.packages(c('remotes','testthat', 'tidyverse', 'here'))" | ||
run: | | ||
install.packages(c('usethis','remotes','testthat','tidyverse','here','rmarkdown','qpdf','distillery','ggpubr','rlist')) | ||
remotes::install_github("NOAA-EDAB/Rpath") | ||
shell: Rscript {0} | ||
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- name: Run tests | ||
#run: Rscript -e "source('tests/testthat.R')" | ||
run: | | ||
source(here::here("data-raw/REcosystem.R")) | ||
source(here::here("tests/testthat.R")) | ||
shell: Rscript {0} | ||
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# - name: commit data files | ||
# run: | | ||
# git config user.name github-actions | ||
# git config user.email github-actions@github.com | ||
# file.copy('here::here("tests/testthat/Rplots.pdf")",to=here::here("inst/extdata/Rplots.pdf")) | ||
# git add inst/extdata/Rplots.pdf | ||
# git commit -m "automated commit from testthat yml" | ||
# git push |
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.Rproj.user | ||
.Rhistory | ||
.RData | ||
*.png | ||
.Renviron | ||
*.jpg | ||
*.tif | ||
*.tar | ||
*.so | ||
outputs | ||
code | ||
*.xlsx | ||
*.docx | ||
Ecopath_dev | ||
Rpath.Rcheck* | ||
src/*.o | ||
src/*.dll | ||
NAMESPACE | ||
tests/testthat/data/output/* | ||
tests/testthat/data/bkup/* | ||
tests/testthat/data/input/REcosystem_Current_*.dat | ||
tests/testthat/data/input/REcosystem_Current_*.rds | ||
tests/testthat/data/input/REcosystem_Current_*.csv | ||
tests/testthat/old/* | ||
tests/testthat/bkup/* | ||
tests/testthat/old dat files/* | ||
docs | ||
doc | ||
Meta | ||
Rpath.Rproj |
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# Generated by using Rcpp::compileAttributes() -> do not edit by hand | ||
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 | ||
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rk4_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear) { | ||
.Call('_Rpath_rk4_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear) | ||
} | ||
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Adams_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv) { | ||
.Call('_Rpath_Adams_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv) | ||
} | ||
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deriv_vector <- function(params, state, forcing, fishing, stanzas, inyear, m, tt) { | ||
.Call('_Rpath_deriv_vector', PACKAGE = 'Rpath', params, state, forcing, fishing, stanzas, inyear, m, tt) | ||
} | ||
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SplitSetPred <- function(stanzas, state) { | ||
.Call('_Rpath_SplitSetPred', PACKAGE = 'Rpath', stanzas, state) | ||
} | ||
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SplitUpdate <- function(stanzas, state, forcing, deriv, yr, mon) { | ||
.Call('_Rpath_SplitUpdate', PACKAGE = 'Rpath', stanzas, state, forcing, deriv, yr, mon) | ||
} | ||
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# Generated by using Rcpp::compileAttributes() -> do not edit by hand | ||
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 | ||
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rk4_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear) { | ||
.Call('_Rpath_rk4_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear) | ||
} | ||
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Adams_run <- function(params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv) { | ||
.Call('_Rpath_Adams_run', PACKAGE = 'Rpath', params, instate, forcing, fishing, stanzas, StartYear, EndYear, InitDeriv) | ||
} | ||
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deriv_vector <- function(params, state, forcing, fishing, stanzas, inyear, m, tt) { | ||
.Call('_Rpath_deriv_vector', PACKAGE = 'Rpath', params, state, forcing, fishing, stanzas, inyear, m, tt) | ||
} | ||
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SplitSetPred <- function(stanzas, state) { | ||
.Call('_Rpath_SplitSetPred', PACKAGE = 'Rpath', stanzas, state) | ||
} | ||
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SplitUpdate <- function(stanzas, state, forcing, deriv, yr, mon) { | ||
.Call('_Rpath_SplitUpdate', PACKAGE = 'Rpath', stanzas, state, forcing, deriv, yr, mon) | ||
} | ||
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