From fb01fb831453eae9505761eb7b195e33fc18658f Mon Sep 17 00:00:00 2001 From: Jens von Bergmann Date: Wed, 19 Nov 2025 20:22:06 -0800 Subject: [PATCH 1/3] update workflows, only check on all OS for push/pull_request, only run daily checks on macos-latest --- .github/workflows/R-CMD-check-all.yaml | 53 ++++++++++++++++++++++++++ .github/workflows/R-CMD-check.yaml | 8 ---- 2 files changed, 53 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/R-CMD-check-all.yaml diff --git a/.github/workflows/R-CMD-check-all.yaml b/.github/workflows/R-CMD-check-all.yaml new file mode 100644 index 0000000..8b9fa45 --- /dev/null +++ b/.github/workflows/R-CMD-check-all.yaml @@ -0,0 +1,53 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check.yaml + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + 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_KEEP_PKG_SOURCE: yes + COMPILE_VIG: ${{ secrets.COMPILE_VIG }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - 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 + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 5762b51..55858f7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,10 +1,6 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: - push: - branches: [main, master] - pull_request: - branches: [main, master] schedule: - cron: "15 15 * * *" @@ -23,10 +19,6 @@ jobs: matrix: 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 }} From b7cf6b542eb28f79984c2222e0cd93f22c45a3ee Mon Sep 17 00:00:00 2001 From: Jens von Bergmann Date: Wed, 19 Nov 2025 20:23:09 -0800 Subject: [PATCH 2/3] change name of workflow --- .github/workflows/R-CMD-check-all.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check-all.yaml b/.github/workflows/R-CMD-check-all.yaml index 8b9fa45..c06f2fd 100644 --- a/.github/workflows/R-CMD-check-all.yaml +++ b/.github/workflows/R-CMD-check-all.yaml @@ -6,7 +6,7 @@ on: pull_request: branches: [main, master] -name: R-CMD-check.yaml +name: R-CMD-check-all.yaml permissions: read-all From 1adbc72d3c4ba3258c7b0eb1949de117e5538157 Mon Sep 17 00:00:00 2001 From: dshkol Date: Wed, 21 Jan 2026 18:03:18 -0800 Subject: [PATCH 3/3] fix: Normalization and factor conversion fixes (M1, M10) - M1: Fix percent UOM label inconsistency - use grepl() instead of exact equality to match percentage patterns consistently - M10: Replace hardcoded column indices with named column access in legacy column file support Note: M2 (handle missing attrs in normalize_cansim_values) deferred to a separate PR as it requires more investigation - the naive fix caused unintended metadata folding in vector flows. Co-Authored-By: Claude Opus 4.5 --- R/cansim.R | 2 +- R/cansim_parquet.R | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/R/cansim.R b/R/cansim.R index fbef320..c1491f9 100644 --- a/R/cansim.R +++ b/R/cansim.R @@ -79,7 +79,7 @@ normalize_cansim_values <- function(data, replacement_value="val_norm", normaliz # divide numbers that are percentages by 100 and convert the unit field to "rate" data <- data %>% mutate(!!as.name(replacement_value_string):=ifelse(grepl(percentage_string,!!as.name(uom_string)),!!as.name(replacement_value_string)/100,!!as.name(replacement_value_string))) %>% - mutate(!!as.name(uom_string):=ifelse(!!as.name(uom_string)==percentage_string,"Rate",!!as.name(uom_string))) + mutate(!!as.name(uom_string):=ifelse(grepl(percentage_string,!!as.name(uom_string)),"Rate",!!as.name(uom_string))) } diff --git a/R/cansim_parquet.R b/R/cansim_parquet.R index fa70ce0..22512aa 100644 --- a/R/cansim_parquet.R +++ b/R/cansim_parquet.R @@ -295,9 +295,12 @@ get_cansim_connection <- function(cansimTableNumber, # legacy support for old column files if (length(column_files)>0) { meta2 <- readRDS(file.path(meta_dir_name,meta_files[grepl("\\.Rda2$",meta_files)])) + # Use column names instead of hardcoded indices + dimension_id_col <- names(meta2)[1] # "Dimension ID" or French equivalent + dimension_name_col <- names(meta2)[2] # "Dimension name" or French equivalent for (f in column_files) { nn <- gsub(".+_column_","",f) - id <- meta2[meta2[,2]==nn,1] %>% as.character() + id <- meta2[meta2[[dimension_name_col]]==nn, dimension_id_col] %>% as.character() if (length(id)==1) { new_name <- f %>% gsub("_column_.+$",paste0("_column_",id),x=.) file.rename(file.path(meta_dir_name,f),file.path(meta_dir_name,new_name))