From 719d91840f8af9da5016c79ad7af21dc8fc19a41 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 11:45:02 +0100 Subject: [PATCH 01/33] Reconfigure script to push changes to testStatus on pull request --- .github/workflows/dsBase_test_suite.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 2a8fa619..02f00394 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -156,8 +156,11 @@ jobs: git config --global user.email "github-actions[bot]@users.noreply.github.com" git config --global user.name "github-actions[bot]" cd testStatus + + # Reconfigure remote to use GitHub token for authentication + git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ env.REPO_OWNER }}/testStatus.git git checkout master - git pull + git pull origin master mkdir -p logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ mkdir -p docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ @@ -178,8 +181,8 @@ jobs: cp -r docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest git add . - git commit -m "Auto test for ${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }} @ ${{ env.WORKFLOW_ID }}" - git push + git commit -m "Auto test for ${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }} @ ${{ env.WORKFLOW_ID }}" || echo "No changes to commit" + git push origin master env: PROJECT_NAME: ${{ env.PROJECT_NAME }} From 3f622e2e23a9ea789d7f4f79b714f135c070ebf1 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 12:05:17 +0100 Subject: [PATCH 02/33] Remove installation of dependencies via auto detection --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 02f00394..7930841e 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -79,7 +79,7 @@ jobs: cran::kableExtra cran::rmarkdown cran::downlit - needs: check + dependencies: NA - name: Check man files up-to-date run: | From 7fac2581bbdd31fc198865a543336950b0be4667 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 12:14:44 +0100 Subject: [PATCH 03/33] Relocate the dependencies: NA keyword --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 7930841e..5bc1d5a0 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -62,6 +62,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: + dependencies: NA # skip auto detection extra-packages: | any::rcmdcheck cran::devtools @@ -79,7 +80,6 @@ jobs: cran::kableExtra cran::rmarkdown cran::downlit - dependencies: NA - name: Check man files up-to-date run: | From 7d5be42ce04d9521546402984d4e5e466488a741 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 12:26:56 +0100 Subject: [PATCH 04/33] Minor change to dependencies value --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 5bc1d5a0..138a1bc0 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -62,7 +62,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: NA # skip auto detection + dependencies: false # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From 9827d980686838178d34480a8bf67378986bb114 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 13:06:13 +0100 Subject: [PATCH 05/33] Update unrecognised R expression false >>> 'FALSE' --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 138a1bc0..2e39c2e2 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -62,7 +62,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: false # skip auto detection + dependencies: 'FALSE' # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From 2ba2a13d9fc9e7ecf64dffbd5b6fa4547d0af105 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 13:11:56 +0100 Subject: [PATCH 06/33] Add missing dependencies for checking package, fs and usethis --- .github/workflows/dsBase_test_suite.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 2e39c2e2..8346c484 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -80,6 +80,8 @@ jobs: cran::kableExtra cran::rmarkdown cran::downlit + cran::fs + cran::usethis - name: Check man files up-to-date run: | From 41adaf84332374ef5773123cd2beb9b3a910ee55 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 13:30:13 +0100 Subject: [PATCH 07/33] Add new packages for checks: cli and rlang --- .github/workflows/dsBase_test_suite.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 8346c484..da902469 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -82,6 +82,8 @@ jobs: cran::downlit cran::fs cran::usethis + cran::cli + cran::rlang - name: Check man files up-to-date run: | From db997e96d9ff8f39e172bf4ff344205557ef5275 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 13:35:25 +0100 Subject: [PATCH 08/33] Add ellipsis and glue --- .github/workflows/dsBase_test_suite.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index da902469..509355fa 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -84,6 +84,8 @@ jobs: cran::usethis cran::cli cran::rlang + cran::ellipsis + cran::glue - name: Check man files up-to-date run: | From 7c99ea21f81df06ef154f508e6f8bfe82d3e1141 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 13:39:50 +0100 Subject: [PATCH 09/33] Add lifecycle --- .github/workflows/dsBase_test_suite.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 509355fa..5656a5f3 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -86,6 +86,7 @@ jobs: cran::rlang cran::ellipsis cran::glue + cran::lifecycle - name: Check man files up-to-date run: | From cf7f02b2f4ac113744fbcd87a7223862e97f1631 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 13:47:20 +0100 Subject: [PATCH 10/33] Add memoise and vctrs --- .github/workflows/dsBase_test_suite.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 5656a5f3..77dd5c52 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -87,6 +87,8 @@ jobs: cran::ellipsis cran::glue cran::lifecycle + cran::memoise + cran::vctrs - name: Check man files up-to-date run: | From 3df6f483f3d964854d4806732638922a9c190e6c Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 14:04:49 +0100 Subject: [PATCH 11/33] Add cachem --- .github/workflows/dsBase_test_suite.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 77dd5c52..59408c63 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -89,6 +89,7 @@ jobs: cran::lifecycle cran::memoise cran::vctrs + cran::cachem - name: Check man files up-to-date run: | From ae31b659f3aaf84276691a985bc2002aa26c0b01 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 14:14:43 +0100 Subject: [PATCH 12/33] Add fastmap --- .github/workflows/dsBase_test_suite.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 59408c63..5ed94282 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -90,6 +90,7 @@ jobs: cran::memoise cran::vctrs cran::cachem + cran::fastmap - name: Check man files up-to-date run: | From 56ea43886be0d304f08f2ec8cf69bb8e2a6e34c3 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 14:33:39 +0100 Subject: [PATCH 13/33] Add missing dependencies, extracted with pak --- .github/workflows/dsBase_test_suite.yaml | 117 +++++++++++++++++++++++ 1 file changed, 117 insertions(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 5ed94282..6ebbc1db 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -91,6 +91,123 @@ jobs: cran::vctrs cran::cachem cran::fastmap + cran::miniUI + cran::admisc + cran::askpass + cran::backports + cran::bit + cran::bit64 + cran::boot + cran::broom + cran::cellranger + cran::childsds + cran::cli + cran::clipr + cran::colorspace + cran::crayon + cran::curl + cran::data.table + cran::deldir + cran::DescTools + cran::dplyr + cran::e1071 + cran::Exact + cran::expm + cran::farver + cran::forcats + cran::foreach + cran::fs + cran::gamlss + cran::gamlss.data + cran::gamlss.dist + cran::generics + cran::ggplot2 + cran::gld + cran::glmnet + cran::glue + cran::gtable + cran::haven + cran::hms + cran::httr + cran::class + cran::codetools + cran::lattice + cran::MASS + cran::mgcv + cran::nlme + cran::nnet + cran::rpart + cran::survival + cran::interp + cran::isoband + cran::iterators + cran::jomo + cran::jsonlite + cran::labeling + cran::lifecycle + cran::lme4 + cran::lmom + cran::interp + cran::isoband + cran::iterators + cran::jomo + cran::jsonlite + cran::labeling + cran::lifecycle + cran::lme4 + cran::lmom + cran::local::. + cran::lubridate + cran::magrittr + cran::Matrix + cran::mice + cran::mime + cran::minqa + cran::mitml + cran::mvtnorm + cran::nloptr + cran::numDeriv + cran::openssl + cran::ordinal + cran::pan + cran::pillar + cran::pkgconfig + cran::plyr + cran::polycor + cran::proxy + cran::purrr + cran::purrrlyr + cran::R6 + cran::RANN + cran::rbibutils + cran::RColorBrewer + cran::Rcpp + cran::Rdpack + cran::readr + cran::readxl + cran::reformulas + cran::rematch + cran::reshape2 + cran::rlang + cran::rootSolve + cran::rstudioapi + cran::scales + cran::shape + cran::stringi + cran::stringr + cran::sys + cran::tibble + cran::tidyr + cran::tidyselect + cran::timechange + cran::tzdb + cran::ucminf + cran::utf8 + cran::vctrs + cran::VGAM + cran::viridisLite + cran::vroom + cran::withr - name: Check man files up-to-date run: | From ee005940e37b1084f28184c5c8bf93b6d4710314 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 15:02:13 +0100 Subject: [PATCH 14/33] Remove dependency local::. --- .github/workflows/dsBase_test_suite.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 6ebbc1db..e91d7c60 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -156,7 +156,6 @@ jobs: cran::lifecycle cran::lme4 cran::lmom - cran::local::. cran::lubridate cran::magrittr cran::Matrix From eed38f45ae89d35539c75673c358e71de82a6d10 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 15:09:08 +0100 Subject: [PATCH 15/33] Add shiny as a dependency and remove duplicates --- .github/workflows/dsBase_test_suite.yaml | 22 +--------------------- 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index e91d7c60..3ab09ce1 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -80,15 +80,9 @@ jobs: cran::kableExtra cran::rmarkdown cran::downlit - cran::fs cran::usethis - cran::cli - cran::rlang cran::ellipsis - cran::glue - cran::lifecycle cran::memoise - cran::vctrs cran::cachem cran::fastmap cran::miniUI @@ -109,7 +103,6 @@ jobs: cran::data.table cran::deldir cran::DescTools - cran::dplyr cran::e1071 cran::Exact cran::expm @@ -147,17 +140,7 @@ jobs: cran::lifecycle cran::lme4 cran::lmom - cran::interp - cran::isoband - cran::iterators - cran::jomo - cran::jsonlite - cran::labeling - cran::lifecycle - cran::lme4 - cran::lmom cran::lubridate - cran::magrittr cran::Matrix cran::mice cran::mime @@ -174,7 +157,6 @@ jobs: cran::plyr cran::polycor cran::proxy - cran::purrr cran::purrrlyr cran::R6 cran::RANN @@ -182,7 +164,6 @@ jobs: cran::RColorBrewer cran::Rcpp cran::Rdpack - cran::readr cran::readxl cran::reformulas cran::rematch @@ -192,11 +173,10 @@ jobs: cran::rstudioapi cran::scales cran::shape + cran::shiny cran::stringi - cran::stringr cran::sys cran::tibble - cran::tidyr cran::tidyselect cran::timechange cran::tzdb From 5b850d08f3f23763d5e24955fb38b5e894090294 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 15:20:05 +0100 Subject: [PATCH 16/33] Add dependencies of key packages --- .github/workflows/dsBase_test_suite.yaml | 240 +++++++++++++++++++++++ 1 file changed, 240 insertions(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 3ab09ce1..10d67c7e 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -86,42 +86,120 @@ jobs: cran::cachem cran::fastmap cran::miniUI + cran::abind cran::admisc + cran::AER + cran::Amelia + cran::archive cran::askpass + cran::AUC cran::backports + cran::base + cran::bbmle + cran::bench + cran::betareg + cran::biglm + cran::binGroup cran::bit cran::bit64 + cran::blob cran::boot + cran::brio cran::broom + cran::broom.mixed + cran::btergm + cran::callr + cran::car + cran::carData + cran::caret + cran::carrier + cran::cba cran::cellranger cran::childsds + cran::chron + cran::class cran::cli cran::clipr + cran::cluster + cran::cmprsk + cran::coda + cran::codetools cran::colorspace + cran::covr + cran::cpp11 cran::crayon cran::curl cran::data.table + cran::datasets + cran::DBI + cran::dbplyr + cran::debugme cran::deldir + cran::Deriv + cran::desc cran::DescTools + cran::dfoptim + cran::DiagrammeR + cran::dichromat + cran::digest + cran::disposables + cran::distributions3 + cran::doMC + cran::doParallel + cran::dplyr + cran::drc cran::e1071 + cran::emmeans + cran::epiR + cran::ergm + cran::evaluate cran::Exact + cran::ExactData cran::expm cran::farver + cran::ff + cran::fixest cran::forcats cran::foreach + cran::formattable cran::fs + cran::furrr + cran::future + cran::gam cran::gamlss cran::gamlss.data cran::gamlss.dist + cran::gamm4 + cran::gbRd + cran::gee + cran::geepack cran::generics cran::ggplot2 + cran::ggplot2movies cran::gld + cran::glmmTMB cran::glmnet + cran::glmnetUtils cran::glue + cran::gmm + cran::graph + cran::graphics + cran::grDevices + cran::grid + cran::gridExtra + cran::gt cran::gtable cran::haven + cran::here + cran::hexbin + cran::Hmisc cran::hms + cran::HSAUR3 + cran::htmltools + cran::htmlwidgets + cran::httpuv cran::httr + cran::inline cran::class cran::codetools cran::lattice @@ -132,61 +210,223 @@ jobs: cran::rpart cran::survival cran::interp + cran::irlba cran::isoband cran::iterators + cran::itertools + cran::joineRML cran::jomo + cran::jose + cran::jpeg cran::jsonlite + cran::Kendall + cran::kernlab + cran::KernSmooth + cran::knitr + cran::ks cran::labeling + cran::Lahman + cran::lars + cran::later + cran::lattice + cran::lavaan + cran::leaps + cran::lfe cran::lifecycle + cran::lintr + cran::literanger + cran::lm.beta cran::lme4 + cran::lmodel2 cran::lmom + cran::lmtest + cran::lobstr + cran::lsmeans cran::lubridate + cran::magick + cran::magrittr + cran::mapproj + cran::maps + cran::margins + cran::markdown + cran::MASS cran::Matrix + cran::mclust + cran::mediation + cran::MEMSS + cran::merDeriv + cran::metafor + cran::methods + cran::mfx + cran::mgcv cran::mice + cran::miceadds + cran::microbenchmark cran::mime cran::minqa + cran::mirai cran::mitml + cran::mitools + cran::mlbench + cran::mlmRev + cran::mlogit + cran::mockery + cran::modeldata + cran::modeltests + cran::muhaz + cran::multcomp + cran::munsell cran::mvtnorm + cran::nanotime + cran::network + cran::nlme cran::nloptr + cran::nnet cran::numDeriv + cran::nycflights13 cran::openssl + cran::optimx cran::ordinal + cran::palmerpenguins cran::pan + cran::parallel + cran::parallelly + cran::patchwork + cran::pbkrtest cran::pillar cran::pkgconfig + cran::pkgdown + cran::pkgKitten + cran::pkgload + cran::plm cran::plyr + cran::png + cran::poLCA + cran::polyclip cran::polycor + cran::prettyunits + cran::processx + cran::profvis + cran::progress cran::proxy + cran::ps + cran::psych + cran::purrr cran::purrrlyr + cran::QCA + cran::qrng + cran::quantreg + cran::R + cran::R.rsp + cran::R.utils cran::R6 + cran::ragg + cran::randomForest + cran::ranger cran::RANN + cran::rbenchmark cran::rbibutils + cran::rcartocolor cran::RColorBrewer cran::Rcpp + cran::RcppEigen + cran::RDCOMClient cran::Rdpack + cran::readr cran::readxl cran::reformulas cran::rematch + cran::repurrrsive cran::reshape2 cran::rlang + cran::rmarkdown + cran::Rmpfr + cran::RMySQL + cran::robust + cran::robustbase cran::rootSolve + cran::roxygen2 + cran::rpart + cran::RPostgreSQL + cran::rprojroot + cran::rr2 + cran::rsample + cran::RSQLite + cran::rstan cran::rstudioapi + cran::RUnit + cran::Ryacas + cran::sandwich cran::scales + cran::scatterplot3d + cran::scico + cran::semEff + cran::sf + cran::sfsmisc cran::shape cran::shiny + cran::shinyjs + cran::slam + cran::sodium + cran::sp + cran::SparseM + cran::spatialreg + cran::spdep + cran::speedglm + cran::spelling + cran::splines + cran::statmod + cran::stats + cran::stats4 cran::stringi + cran::stringr + cran::survey + cran::survival + cran::svglite cran::sys + cran::systemfit + cran::tcltk + cran::testthat cran::tibble + cran::tidyr cran::tidyselect + cran::tidyverse cran::timechange + cran::timeDate + cran::tinytest + cran::tis + cran::tools + cran::tseries cran::tzdb cran::ucminf + cran::units + cran::unix + cran::usethis cran::utf8 + cran::utils + cran::vars + cran::vcd cran::vctrs + cran::vdiffr cran::VGAM + cran::VGAMdata + cran::VGAMextra + cran::viridis cran::viridisLite cran::vroom + cran::waldo + cran::webutils + cran::wesanderson + cran::whoami + cran::winch cran::withr + cran::xfun + cran::xml2 + cran::xtable + cran::xts + cran::yaml + cran::zeallot + cran::zoo - name: Check man files up-to-date run: | From 0ed63c4e9a2d0b00631cd321b59de25dbe2ea21a Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 15:27:47 +0100 Subject: [PATCH 17/33] Update reference to dependencies --- .github/workflows/dsBase_test_suite.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 10d67c7e..567e2aab 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -154,7 +154,7 @@ jobs: cran::ergm cran::evaluate cran::Exact - cran::ExactData + any::ExactData cran::expm cran::farver cran::ff @@ -316,7 +316,6 @@ jobs: cran::QCA cran::qrng cran::quantreg - cran::R cran::R.rsp cran::R.utils cran::R6 @@ -330,7 +329,7 @@ jobs: cran::RColorBrewer cran::Rcpp cran::RcppEigen - cran::RDCOMClient + any::RDCOMClient cran::Rdpack cran::readr cran::readxl From cc265247226caa90dba9e347f1bfdc2b1668b70d Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 15:52:42 +0100 Subject: [PATCH 18/33] Remove the ExactData dependency as the drat server in which is hosted doesn't seem to work --- .github/workflows/dsBase_test_suite.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 567e2aab..d08c5220 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -154,7 +154,6 @@ jobs: cran::ergm cran::evaluate cran::Exact - any::ExactData cran::expm cran::farver cran::ff @@ -329,7 +328,7 @@ jobs: cran::RColorBrewer cran::Rcpp cran::RcppEigen - any::RDCOMClient + github::omegahat/RDCOMClient cran::Rdpack cran::readr cran::readxl From 28cbdf2d479e7051037ef800326bde3dbcc6b5eb Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 16:00:51 +0100 Subject: [PATCH 19/33] Remove the RDCOMClient package --- .github/workflows/dsBase_test_suite.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index d08c5220..f9bdf40b 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -328,7 +328,6 @@ jobs: cran::RColorBrewer cran::Rcpp cran::RcppEigen - github::omegahat/RDCOMClient cran::Rdpack cran::readr cran::readxl From 0de287273b4014c4f8e0bdc4b0ecd29c3ae3e7ac Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Tue, 2 Sep 2025 16:33:33 +0100 Subject: [PATCH 20/33] Add Bioconductor dependency, BiocGenerics --- .github/workflows/dsBase_test_suite.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index f9bdf40b..8f44ff87 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -65,6 +65,7 @@ jobs: dependencies: 'FALSE' # skip auto detection extra-packages: | any::rcmdcheck + bioc::BiocGenerics cran::devtools cran::git2r cran::RCurl From 94562e4cb29a9833bf036dcaab65d73358e51f0f Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 09:29:09 +0100 Subject: [PATCH 21/33] Add generics to list of dependencies --- .github/workflows/dsBase_test_suite.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 8f44ff87..0d662929 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -66,6 +66,7 @@ jobs: extra-packages: | any::rcmdcheck bioc::BiocGenerics + cran::generics cran::devtools cran::git2r cran::RCurl From b2af53044c129b4b47c29b30cff18efdac0a4011 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 09:53:33 +0100 Subject: [PATCH 22/33] Add step for local installation of dsBase and revert changes done to the setup-r-dependencies@v2 step --- .github/workflows/dsBase_test_suite.yaml | 392 ++--------------------- 1 file changed, 27 insertions(+), 365 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 0d662929..b9abff42 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -59,373 +59,35 @@ jobs: r-version: release http-user-agent: release use-public-rspm: true - + + - name: Install dsBase + run: | + R CMD INSTALL . + with: + path: dsBase + - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: 'FALSE' # skip auto detection - extra-packages: | - any::rcmdcheck - bioc::BiocGenerics - cran::generics - cran::devtools - cran::git2r - cran::RCurl - cran::readr - cran::magrittr - cran::xml2 - cran::purrr - cran::dplyr - cran::stringr - cran::tidyr - cran::quarto - cran::knitr - cran::kableExtra - cran::rmarkdown - cran::downlit - cran::usethis - cran::ellipsis - cran::memoise - cran::cachem - cran::fastmap - cran::miniUI - cran::abind - cran::admisc - cran::AER - cran::Amelia - cran::archive - cran::askpass - cran::AUC - cran::backports - cran::base - cran::bbmle - cran::bench - cran::betareg - cran::biglm - cran::binGroup - cran::bit - cran::bit64 - cran::blob - cran::boot - cran::brio - cran::broom - cran::broom.mixed - cran::btergm - cran::callr - cran::car - cran::carData - cran::caret - cran::carrier - cran::cba - cran::cellranger - cran::childsds - cran::chron - cran::class - cran::cli - cran::clipr - cran::cluster - cran::cmprsk - cran::coda - cran::codetools - cran::colorspace - cran::covr - cran::cpp11 - cran::crayon - cran::curl - cran::data.table - cran::datasets - cran::DBI - cran::dbplyr - cran::debugme - cran::deldir - cran::Deriv - cran::desc - cran::DescTools - cran::dfoptim - cran::DiagrammeR - cran::dichromat - cran::digest - cran::disposables - cran::distributions3 - cran::doMC - cran::doParallel - cran::dplyr - cran::drc - cran::e1071 - cran::emmeans - cran::epiR - cran::ergm - cran::evaluate - cran::Exact - cran::expm - cran::farver - cran::ff - cran::fixest - cran::forcats - cran::foreach - cran::formattable - cran::fs - cran::furrr - cran::future - cran::gam - cran::gamlss - cran::gamlss.data - cran::gamlss.dist - cran::gamm4 - cran::gbRd - cran::gee - cran::geepack - cran::generics - cran::ggplot2 - cran::ggplot2movies - cran::gld - cran::glmmTMB - cran::glmnet - cran::glmnetUtils - cran::glue - cran::gmm - cran::graph - cran::graphics - cran::grDevices - cran::grid - cran::gridExtra - cran::gt - cran::gtable - cran::haven - cran::here - cran::hexbin - cran::Hmisc - cran::hms - cran::HSAUR3 - cran::htmltools - cran::htmlwidgets - cran::httpuv - cran::httr - cran::inline - cran::class - cran::codetools - cran::lattice - cran::MASS - cran::mgcv - cran::nlme - cran::nnet - cran::rpart - cran::survival - cran::interp - cran::irlba - cran::isoband - cran::iterators - cran::itertools - cran::joineRML - cran::jomo - cran::jose - cran::jpeg - cran::jsonlite - cran::Kendall - cran::kernlab - cran::KernSmooth - cran::knitr - cran::ks - cran::labeling - cran::Lahman - cran::lars - cran::later - cran::lattice - cran::lavaan - cran::leaps - cran::lfe - cran::lifecycle - cran::lintr - cran::literanger - cran::lm.beta - cran::lme4 - cran::lmodel2 - cran::lmom - cran::lmtest - cran::lobstr - cran::lsmeans - cran::lubridate - cran::magick - cran::magrittr - cran::mapproj - cran::maps - cran::margins - cran::markdown - cran::MASS - cran::Matrix - cran::mclust - cran::mediation - cran::MEMSS - cran::merDeriv - cran::metafor - cran::methods - cran::mfx - cran::mgcv - cran::mice - cran::miceadds - cran::microbenchmark - cran::mime - cran::minqa - cran::mirai - cran::mitml - cran::mitools - cran::mlbench - cran::mlmRev - cran::mlogit - cran::mockery - cran::modeldata - cran::modeltests - cran::muhaz - cran::multcomp - cran::munsell - cran::mvtnorm - cran::nanotime - cran::network - cran::nlme - cran::nloptr - cran::nnet - cran::numDeriv - cran::nycflights13 - cran::openssl - cran::optimx - cran::ordinal - cran::palmerpenguins - cran::pan - cran::parallel - cran::parallelly - cran::patchwork - cran::pbkrtest - cran::pillar - cran::pkgconfig - cran::pkgdown - cran::pkgKitten - cran::pkgload - cran::plm - cran::plyr - cran::png - cran::poLCA - cran::polyclip - cran::polycor - cran::prettyunits - cran::processx - cran::profvis - cran::progress - cran::proxy - cran::ps - cran::psych - cran::purrr - cran::purrrlyr - cran::QCA - cran::qrng - cran::quantreg - cran::R.rsp - cran::R.utils - cran::R6 - cran::ragg - cran::randomForest - cran::ranger - cran::RANN - cran::rbenchmark - cran::rbibutils - cran::rcartocolor - cran::RColorBrewer - cran::Rcpp - cran::RcppEigen - cran::Rdpack - cran::readr - cran::readxl - cran::reformulas - cran::rematch - cran::repurrrsive - cran::reshape2 - cran::rlang - cran::rmarkdown - cran::Rmpfr - cran::RMySQL - cran::robust - cran::robustbase - cran::rootSolve - cran::roxygen2 - cran::rpart - cran::RPostgreSQL - cran::rprojroot - cran::rr2 - cran::rsample - cran::RSQLite - cran::rstan - cran::rstudioapi - cran::RUnit - cran::Ryacas - cran::sandwich - cran::scales - cran::scatterplot3d - cran::scico - cran::semEff - cran::sf - cran::sfsmisc - cran::shape - cran::shiny - cran::shinyjs - cran::slam - cran::sodium - cran::sp - cran::SparseM - cran::spatialreg - cran::spdep - cran::speedglm - cran::spelling - cran::splines - cran::statmod - cran::stats - cran::stats4 - cran::stringi - cran::stringr - cran::survey - cran::survival - cran::svglite - cran::sys - cran::systemfit - cran::tcltk - cran::testthat - cran::tibble - cran::tidyr - cran::tidyselect - cran::tidyverse - cran::timechange - cran::timeDate - cran::tinytest - cran::tis - cran::tools - cran::tseries - cran::tzdb - cran::ucminf - cran::units - cran::unix - cran::usethis - cran::utf8 - cran::utils - cran::vars - cran::vcd - cran::vctrs - cran::vdiffr - cran::VGAM - cran::VGAMdata - cran::VGAMextra - cran::viridis - cran::viridisLite - cran::vroom - cran::waldo - cran::webutils - cran::wesanderson - cran::whoami - cran::winch - cran::withr - cran::xfun - cran::xml2 - cran::xtable - cran::xts - cran::yaml - cran::zeallot - cran::zoo + # dependencies: 'FALSE' # skip auto detection + with: + extra-packages: | + any::rcmdcheck + cran::devtools + cran::git2r + cran::RCurl + cran::readr + cran::magrittr + cran::xml2 + cran::purrr + cran::dplyr + cran::stringr + cran::tidyr + cran::quarto + cran::knitr + cran::kableExtra + cran::rmarkdown + cran::downlit + needs: check - name: Check man files up-to-date run: | From ccd1bb68c132859db7e593c9f2c9ebaf8aca0b1b Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 09:59:26 +0100 Subject: [PATCH 23/33] Fix invalid notation in new step --- .github/workflows/dsBase_test_suite.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index b9abff42..aeaeedf0 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -62,9 +62,7 @@ jobs: - name: Install dsBase run: | - R CMD INSTALL . - with: - path: dsBase + R CMD INSTALL dsBase - uses: r-lib/actions/setup-r-dependencies@v2 with: From 47ac437fd79d8e2c098aa739114e8ff0d3e77ef0 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:04:49 +0100 Subject: [PATCH 24/33] Simplify notation --- .github/workflows/dsBase_test_suite.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index aeaeedf0..61212fba 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -61,8 +61,7 @@ jobs: use-public-rspm: true - name: Install dsBase - run: | - R CMD INSTALL dsBase + run: R CMD INSTALL ./dsBase - uses: r-lib/actions/setup-r-dependencies@v2 with: From 41591d6154e11a1a0a97fd26b07910f0e1949e9b Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:08:07 +0100 Subject: [PATCH 25/33] Remove duplicated 'with' section --- .github/workflows/dsBase_test_suite.yaml | 37 ++++++++++++------------ 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 61212fba..8e56dcd4 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -66,25 +66,24 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: # dependencies: 'FALSE' # skip auto detection - with: - extra-packages: | - any::rcmdcheck - cran::devtools - cran::git2r - cran::RCurl - cran::readr - cran::magrittr - cran::xml2 - cran::purrr - cran::dplyr - cran::stringr - cran::tidyr - cran::quarto - cran::knitr - cran::kableExtra - cran::rmarkdown - cran::downlit - needs: check + extra-packages: | + any::rcmdcheck + cran::devtools + cran::git2r + cran::RCurl + cran::readr + cran::magrittr + cran::xml2 + cran::purrr + cran::dplyr + cran::stringr + cran::tidyr + cran::quarto + cran::knitr + cran::kableExtra + cran::rmarkdown + cran::downlit + needs: check - name: Check man files up-to-date run: | From 3493307641545e1685d0cfc9b85074d344b1784a Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:12:24 +0100 Subject: [PATCH 26/33] Add dependencies for dsBase --- .github/workflows/dsBase_test_suite.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 8e56dcd4..d52591bf 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -61,7 +61,9 @@ jobs: use-public-rspm: true - name: Install dsBase - run: R CMD INSTALL ./dsBase + run: | + Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds"), dependencies = TRUE)' + R CMD INSTALL ./dsBase - uses: r-lib/actions/setup-r-dependencies@v2 with: From 617de4709ab980e80f93f1b150bb981430a8298b Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:19:36 +0100 Subject: [PATCH 27/33] Skip dependencies --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index d52591bf..1db84236 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -67,7 +67,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - # dependencies: 'FALSE' # skip auto detection + dependencies: 'FALSE' # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From e79ece234c3d618b7684a4c949d03c05da2ba1b9 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:24:04 +0100 Subject: [PATCH 28/33] Remove single quotes from dependencies: 'FALSE' --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 1db84236..bbf89f3e 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -67,7 +67,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: 'FALSE' # skip auto detection + dependencies: FALSE # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From facd06828b5e990e12a9b0f22f093c08d268a2c8 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:30:51 +0100 Subject: [PATCH 29/33] Replace FALSE by `FALSE` --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index bbf89f3e..864dd0cd 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -67,7 +67,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: FALSE # skip auto detection + dependencies: `FALSE` # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From d5c4ba2d0c63ad0624bb7c26d0eb4aec7d5d8d67 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:34:48 +0100 Subject: [PATCH 30/33] Add missing single quotes for dependencies value --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 864dd0cd..6401a585 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -67,7 +67,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: `FALSE` # skip auto detection + dependencies: '`FALSE`' # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From 4a0882aa71230e9889f88f110ea31b81a47aaf11 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:47:12 +0100 Subject: [PATCH 31/33] Fix invalid R expression pass to dependencies --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 6401a585..020a1249 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -67,7 +67,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: '`FALSE`' # skip auto detection + dependencies: "FALSE" # skip auto detection extra-packages: | any::rcmdcheck cran::devtools From 457802b4e24229a60d8221c9f2d96cdf55d9fe2d Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 10:57:04 +0100 Subject: [PATCH 32/33] Replace skipping auto detection of dependencies --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 020a1249..42c7e588 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -67,7 +67,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - dependencies: "FALSE" # skip auto detection + dependencies: 'c("Imports")' extra-packages: | any::rcmdcheck cran::devtools From f48889bb230d3c2e9413a425354bd19e54a7fea9 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 3 Sep 2025 11:06:57 +0100 Subject: [PATCH 33/33] Add usethis and devtools --- .github/workflows/dsBase_test_suite.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dsBase_test_suite.yaml b/.github/workflows/dsBase_test_suite.yaml index 42c7e588..44020e83 100644 --- a/.github/workflows/dsBase_test_suite.yaml +++ b/.github/workflows/dsBase_test_suite.yaml @@ -62,7 +62,7 @@ jobs: - name: Install dsBase run: | - Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds"), dependencies = TRUE)' + Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds", "usethis", "devtools"), dependencies = TRUE)' R CMD INSTALL ./dsBase - uses: r-lib/actions/setup-r-dependencies@v2