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AMR
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unit test fix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-08-28 20:10:05 +02:00
parent c44ddf272f
commit 21b4552f5a
3 changed files with 10 additions and 12 deletions
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18
.github/workflows/check.yaml vendored
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@ -112,13 +112,13 @@ jobs:
shell: Rscript {0} shell: Rscript {0}
- name: Remove vignettes on R without knitr support - name: Remove vignettes on R without knitr support
if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3'
# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite
run: | run: |
rm -rf AMR/vignettes rm -rf vignettes
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')" Rscript -e "writeLines(readLines('DESCRIPTION')[!grepl('VignetteBuilder', readLines('DESCRIPTION'))], 'DESCRIPTION2')"
rm AMR/DESCRIPTION rm DESCRIPTION
mv AMR/DESCRIPTION2 AMR/DESCRIPTION mv DESCRIPTION2 DESCRIPTION
shell: bash shell: bash
- name: Run R CMD check - name: Run R CMD check
@ -135,7 +135,6 @@ jobs:
R_RUN_TINYTEST: true R_RUN_TINYTEST: true
run: | run: |
cd .. cd ..
ls -lh
R CMD build AMR R CMD build AMR
R CMD check --no-manual --run-donttest --run-dontrun AMR_*.tar.gz R CMD check --no-manual --run-donttest --run-dontrun AMR_*.tar.gz
shell: bash shell: bash
@ -143,8 +142,7 @@ jobs:
- name: Show unit tests output - name: Show unit tests output
if: always() if: always()
run: | run: |
ls -lh cd ../AMR.Rcheck
cd AMR
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash shell: bash
@ -153,4 +151,4 @@ jobs:
uses: actions/upload-artifact@v2 uses: actions/upload-artifact@v2
with: with:
name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }} name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
path: AMR.Rcheck path: ../AMR.Rcheck

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.1.9040 Version: 1.8.1.9041
Date: 2022-08-28 Date: 2022-08-28
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.1.9040 # AMR 1.8.1.9041
### New ### New
* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations. * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.