diff --git a/.github/workflows/run-pollock-tests-by-fleet.yml b/.github/workflows/run-pollock-tests-by-fleet.yml index bf108b5..eaf75fe 100644 --- a/.github/workflows/run-pollock-tests-by-fleet.yml +++ b/.github/workflows/run-pollock-tests-by-fleet.yml @@ -20,7 +20,7 @@ jobs: - name: Run pollock tests run: | # Names of required packages - packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "remotes", "lubridate") + packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "devtools", "lubridate") # Install packages not yet installed installed_packages <- packages %in% rownames(installed.packages()) @@ -28,13 +28,11 @@ jobs: install.packages(packages[!installed_packages], repos = "http://cran.us.r-project.org") } - install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org")) - + # install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org")) + devtools::install_github("NOAA-FIMS/FIMS") + # Load packages invisible(lapply(packages, library, character.only = TRUE)) source(file.path(getwd(), "content", "run_pollock_tests_by_fleet.R")) - shell: Rscript {0} - - - name: Upload artifact - uses: actions/upload-pages-artifact@v3 + shell: Rscript {0} \ No newline at end of file diff --git a/.github/workflows/run-pollock-tests-by-process.yml b/.github/workflows/run-pollock-tests-by-process.yml index 89f735b..ab9d1cd 100644 --- a/.github/workflows/run-pollock-tests-by-process.yml +++ b/.github/workflows/run-pollock-tests-by-process.yml @@ -20,7 +20,7 @@ jobs: - name: Run pollock tests run: | # Names of required packages - packages <- c("TMB") + packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "devtools", "lubridate") # Install packages not yet installed installed_packages <- packages %in% rownames(installed.packages()) @@ -28,13 +28,11 @@ jobs: install.packages(packages[!installed_packages], repos = "http://cran.us.r-project.org") } - install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org")) - + # install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org")) + devtools::install_github("NOAA-FIMS/FIMS") + # Load packages invisible(lapply(packages, library, character.only = TRUE)) source(file.path(getwd(), "content", "run_pollock_tests.R")) - shell: Rscript {0} - - - name: Upload artifact - uses: actions/upload-pages-artifact@v3 + shell: Rscript {0} \ No newline at end of file diff --git a/content/run_pollock_tests.R b/content/run_pollock_tests.R index e82f952..ca18e2f 100644 --- a/content/run_pollock_tests.R +++ b/content/run_pollock_tests.R @@ -63,4 +63,4 @@ opt2 <- with(obj2, nlminb(par,fn,gr)) all.equal(obj1$report(opt1$par), obj2$report(opt2$par)) sum(obj1$par)-sum(obj2$par) -cbind(sort(opt1$par)- sort(opt2$par)) +print(cbind(sort(opt1$par)- sort(opt2$par)))