From 9dbb334d71f596a85b49c365010a655afe6402e0 Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Wed, 25 Jan 2023 15:29:06 +0000 Subject: [PATCH 1/4] Rm old branches --- .github/workflows/memcheck.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml index 7330c98ed..1fda94b79 100644 --- a/.github/workflows/memcheck.yml +++ b/.github/workflows/memcheck.yml @@ -87,11 +87,7 @@ jobs: - name: Install dependencies run: | - remotes::install_github("ms609/TreeTools") # for v1.4.5.9007 remotes::install_deps(dependencies = TRUE) - if ("${{ matrix.config.test }}" == 'tests') { - remotes::install_github('r-lib/brio#20') # brio mem leak - } remotes::install_cran("devtools") shell: Rscript {0} From a445ab47b44f6b7aa50a04ce1f542cee036af07a Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Wed, 25 Jan 2023 15:45:26 +0000 Subject: [PATCH 2/4] ms609/actions/memcheck@main --- .Rbuildignore | 1 - .github/workflows/memcheck.yml | 53 +++------------------------------- memcheck/all.R | 4 --- memcheck/examples.R | 5 ---- memcheck/tests.R | 5 ---- memcheck/vignettes.R | 5 ---- 6 files changed, 4 insertions(+), 69 deletions(-) delete mode 100644 memcheck/all.R delete mode 100644 memcheck/examples.R delete mode 100644 memcheck/tests.R delete mode 100644 memcheck/vignettes.R diff --git a/.Rbuildignore b/.Rbuildignore index a4706c3ac..e2fca8142 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,7 +1,6 @@ ^Meta$ ^doc$ ^data-raw$ -^memcheck$ ^CRAN-RELEASE$ ^src\- CONTRIBUTING diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml index 1fda94b79..7eabcdaba 100644 --- a/.github/workflows/memcheck.yml +++ b/.github/workflows/memcheck.yml @@ -36,7 +36,7 @@ jobs: mem-check: runs-on: ubuntu-20.04 - name: valgrind ${{ matrix.config.test }}, ubuntu, R release + name: valgrind ${{ matrix.config.test }} strategy: fail-fast: false @@ -45,7 +45,7 @@ jobs: - {test: 'tests'} - {test: 'examples'} - {test: 'vignettes'} - + env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true _R_CHECK_FORCE_SUGGESTS_: false @@ -53,51 +53,6 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v2 + - uses: ms609/actions/memcheck@main with: - r-version: release - - - uses: r-lib/actions/setup-pandoc@master - - - name: Install valgrind - run: sudo apt-get install valgrind texlive-latex-base - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - uses: actions/cache@v2 - 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- - - - name: Install system dependencies - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("devtools") - shell: Rscript {0} - - - name: Install TreeDist - run: | - cd .. - R CMD build --no-manual --no-resave-data TreeDist - R CMD INSTALL TreeDist*.tar.gz - cd TreeDist - - - name: valgrind - memcheck ${{ matrix.config.test }} - run: | - R -d "valgrind --tool=memcheck --leak-check=full --error-exitcode=1" --vanilla < memcheck/${{ matrix.config.test }}.R + test: ${{ matrix.config.test}} diff --git a/memcheck/all.R b/memcheck/all.R deleted file mode 100644 index 622f618f5..000000000 --- a/memcheck/all.R +++ /dev/null @@ -1,4 +0,0 @@ -devtools::load_all() -devtools::run_examples() -devtools::build_vignettes() -devtools::test() \ No newline at end of file diff --git a/memcheck/examples.R b/memcheck/examples.R deleted file mode 100644 index 1b3c6eb76..000000000 --- a/memcheck/examples.R +++ /dev/null @@ -1,5 +0,0 @@ -# Code to be run with -# R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < tests/thisfile.R -# First build and install the package. -library("TreeDist") -devtools::run_examples() diff --git a/memcheck/tests.R b/memcheck/tests.R deleted file mode 100644 index 4456a9d46..000000000 --- a/memcheck/tests.R +++ /dev/null @@ -1,5 +0,0 @@ -# Code to be run with -# R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < tests/thisfile.R -# First build and install the package. -library("TreeDist") -devtools::test() diff --git a/memcheck/vignettes.R b/memcheck/vignettes.R deleted file mode 100644 index 74430cd1c..000000000 --- a/memcheck/vignettes.R +++ /dev/null @@ -1,5 +0,0 @@ -# Code to be run with -# R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < tests/thisfile.R -# First build and install the package. -library("TreeDist") -devtools::build_vignettes() From 4199ea5cdcdcdda687182eaf92df30e3efe0961d Mon Sep 17 00:00:00 2001 From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com> Date: Wed, 25 Jan 2023 16:09:44 +0000 Subject: [PATCH 3/4] extra-repositories --- .github/workflows/memcheck.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml index 7eabcdaba..2837c2095 100644 --- a/.github/workflows/memcheck.yml +++ b/.github/workflows/memcheck.yml @@ -55,4 +55,5 @@ jobs: steps: - uses: ms609/actions/memcheck@main with: + extra-repositories: "https://ms609.github.io/packages/" test: ${{ matrix.config.test}} From 5f0841af3ceb1085dd6c2e0dadc8a882886654a1 Mon Sep 17 00:00:00 2001 From: RevBayes analysis <1695515+ms609@users.noreply.github.com> Date: Fri, 22 Aug 2025 10:17:02 +0100 Subject: [PATCH 4/4] Restore missing memcheck files --- memcheck/all.R | 4 ++++ memcheck/tests.R | 5 +++++ memcheck/vignettes.R | 5 +++++ 3 files changed, 14 insertions(+) create mode 100644 memcheck/all.R create mode 100644 memcheck/tests.R create mode 100644 memcheck/vignettes.R diff --git a/memcheck/all.R b/memcheck/all.R new file mode 100644 index 000000000..75506a416 --- /dev/null +++ b/memcheck/all.R @@ -0,0 +1,4 @@ +devtools::load_all() +devtools::run_examples() +devtools::build_vignettes() +devtools::test() diff --git a/memcheck/tests.R b/memcheck/tests.R new file mode 100644 index 000000000..4456a9d46 --- /dev/null +++ b/memcheck/tests.R @@ -0,0 +1,5 @@ +# Code to be run with +# R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < tests/thisfile.R +# First build and install the package. +library("TreeDist") +devtools::test() diff --git a/memcheck/vignettes.R b/memcheck/vignettes.R new file mode 100644 index 000000000..74430cd1c --- /dev/null +++ b/memcheck/vignettes.R @@ -0,0 +1,5 @@ +# Code to be run with +# R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < tests/thisfile.R +# First build and install the package. +library("TreeDist") +devtools::build_vignettes()