From 4777aee93338d3aa150ea158b4d346f227e33fbb Mon Sep 17 00:00:00 2001 From: pchelle Date: Mon, 29 Jul 2024 11:25:05 -0400 Subject: [PATCH 01/12] Fixes #1258 install dependencies from Github --- .github/workflows/install_dependencies.R | 20 +++++--------------- 1 file changed, 5 insertions(+), 15 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 73f716b3..5ccbfd25 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,15 +1,5 @@ -install.packages(c('dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') -download.file('https://github.com/Open-Systems-Pharmacology/rSharp/releases/download/v1.0.0/rSharp-v1.0.0-Windows-r_4.4.0.zip', destfile = "rsharp.zip", mode = "wb") -unzip("rsharp.zip") -rSharp_archive <- list.files( pattern = "rSharp.*\\.zip") -install.packages(rSharp_archive, repos = NULL, type = "binary") -unlink(c("rsharp.zip", rSharp_archive)) -download.file('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-rutils/artifacts/ospsuite.utils.zip?pr=false', destfile = 'ospsuite.utils.zip', mode='wb') -install.packages('ospsuite.utils.zip', repos = NULL, type = 'binary') -unlink('ospsuite.utils.zip') -download.file('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/tlf-library/artifacts/tlf.zip?pr=false', destfile = 'tlf.zip', mode='wb') -install.packages('tlf.zip', repos = NULL, type = 'binary') -unlink('tlf.zip') -download.file('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-r-rsharp/artifacts/ospsuite.zip?pr=false', destfile = 'ospsuite.zip', mode='wb') -install.packages('ospsuite.zip', repos = NULL, type = 'binary') -unlink('ospsuite.zip') +install.packages(c('remotes','dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') +remotes::install_github("Open-Systems-Pharmacology/OSPSuite.RUtils", ref ='develop') +remotes::install_github("Open-Systems-Pharmacology/rSharp", ref ='develop') +remotes::install_github("Open-Systems-Pharmacology/TLF-Library", ref ='develop') +remotes::install_github("Open-Systems-Pharmacology/OSPSuite-R", ref ='develop') From 144302fcc6feda6d7aa957afd44934643ea10b78 Mon Sep 17 00:00:00 2001 From: pchelle Date: Tue, 30 Jul 2024 10:58:57 -0400 Subject: [PATCH 02/12] Trigger appveyor build --- appveyor.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/appveyor.yml b/appveyor.yml index 49789950..40856533 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -74,7 +74,7 @@ skip_commits: - .github/workflows/*.yml - .github/workflows/*.sh - .github/workflows/Dockerfile - - .github/workflows/*.R +# - .github/workflows/*.R - '_pkgdown.yml' skip_branch_with_pr: true From 38e68a5bc6b12a5e484e77303ebde7549b8bfe16 Mon Sep 17 00:00:00 2001 From: pchelle Date: Tue, 30 Jul 2024 11:28:52 -0400 Subject: [PATCH 03/12] Add github pat in environment --- appveyor.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/appveyor.yml b/appveyor.yml index 40856533..e17057e0 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -22,6 +22,7 @@ environment: R_ARCH: x64 R_VERSION: "4.3.1" R_CHECK_ARGS: --no-build-vignettes --no-manual --as-cran + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} version: "$(app_version).{build}" From 08007afcc75bd912fd4e5b75258bc1b979f1d987 Mon Sep 17 00:00:00 2001 From: pchelle Date: Tue, 30 Jul 2024 11:41:09 -0400 Subject: [PATCH 04/12] Revert "Add github pat in environment" This reverts commit 38e68a5bc6b12a5e484e77303ebde7549b8bfe16. --- appveyor.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/appveyor.yml b/appveyor.yml index e17057e0..40856533 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -22,7 +22,6 @@ environment: R_ARCH: x64 R_VERSION: "4.3.1" R_CHECK_ARGS: --no-build-vignettes --no-manual --as-cran - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} version: "$(app_version).{build}" From ad87b950759afc99ae8b09e2d2c79fea79ed94b0 Mon Sep 17 00:00:00 2001 From: pchelle Date: Tue, 30 Jul 2024 11:55:27 -0400 Subject: [PATCH 05/12] Check if unsetting the PAT works in using install github --- .github/workflows/install_dependencies.R | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 5ccbfd25..548d2023 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,5 +1,6 @@ install.packages(c('remotes','dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') -remotes::install_github("Open-Systems-Pharmacology/OSPSuite.RUtils", ref ='develop') -remotes::install_github("Open-Systems-Pharmacology/rSharp", ref ='develop') -remotes::install_github("Open-Systems-Pharmacology/TLF-Library", ref ='develop') -remotes::install_github("Open-Systems-Pharmacology/OSPSuite-R", ref ='develop') +Sys.unsetenv("GITHUB_PAT") +remotes::install_github("Open-Systems-Pharmacology/OSPSuite.RUtils", ref ='develop', upgrade = 'never') +remotes::install_github("Open-Systems-Pharmacology/rSharp", ref ='develop', upgrade = 'never') +remotes::install_github("Open-Systems-Pharmacology/TLF-Library", ref ='develop', upgrade = 'never') +remotes::install_github("Open-Systems-Pharmacology/OSPSuite-R", ref ='develop', upgrade = 'never') From 54b5b5899158d4793e5969fb906107f14f155e95 Mon Sep 17 00:00:00 2001 From: pchelle Date: Thu, 1 Aug 2024 05:26:08 -0400 Subject: [PATCH 06/12] Revert "Check if unsetting the PAT works in using install github" This reverts commit ad87b950759afc99ae8b09e2d2c79fea79ed94b0. --- .github/workflows/install_dependencies.R | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 548d2023..5ccbfd25 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,6 +1,5 @@ install.packages(c('remotes','dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') -Sys.unsetenv("GITHUB_PAT") -remotes::install_github("Open-Systems-Pharmacology/OSPSuite.RUtils", ref ='develop', upgrade = 'never') -remotes::install_github("Open-Systems-Pharmacology/rSharp", ref ='develop', upgrade = 'never') -remotes::install_github("Open-Systems-Pharmacology/TLF-Library", ref ='develop', upgrade = 'never') -remotes::install_github("Open-Systems-Pharmacology/OSPSuite-R", ref ='develop', upgrade = 'never') +remotes::install_github("Open-Systems-Pharmacology/OSPSuite.RUtils", ref ='develop') +remotes::install_github("Open-Systems-Pharmacology/rSharp", ref ='develop') +remotes::install_github("Open-Systems-Pharmacology/TLF-Library", ref ='develop') +remotes::install_github("Open-Systems-Pharmacology/OSPSuite-R", ref ='develop') From c4e06f8079aa0f4acd071592bf1d9806ce179e61 Mon Sep 17 00:00:00 2001 From: pchelle Date: Thu, 1 Aug 2024 08:56:13 -0400 Subject: [PATCH 07/12] Use pak instead of remotes --- .github/workflows/install_dependencies.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 5ccbfd25..4ec04e37 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,5 +1,5 @@ -install.packages(c('remotes','dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') -remotes::install_github("Open-Systems-Pharmacology/OSPSuite.RUtils", ref ='develop') -remotes::install_github("Open-Systems-Pharmacology/rSharp", ref ='develop') -remotes::install_github("Open-Systems-Pharmacology/TLF-Library", ref ='develop') -remotes::install_github("Open-Systems-Pharmacology/OSPSuite-R", ref ='develop') +install.packages(c('remotes','pak','dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') +pak::pak("Open-Systems-Pharmacology/OSPSuite.RUtils") +pak::pak("Open-Systems-Pharmacology/rSharp") +pak::pak("Open-Systems-Pharmacology/TLF-Library") +pak::pak("Open-Systems-Pharmacology/OSPSuite-R") From 3740d9b569d63ff29a3eeef4d2cd0f9b54a0c46c Mon Sep 17 00:00:00 2001 From: pchelle Date: Tue, 6 Aug 2024 07:24:24 -0400 Subject: [PATCH 08/12] Use release archives --- .github/workflows/install_dependencies.R | 26 +++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 4ec04e37..7806c831 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,5 +1,21 @@ -install.packages(c('remotes','pak','dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') -pak::pak("Open-Systems-Pharmacology/OSPSuite.RUtils") -pak::pak("Open-Systems-Pharmacology/rSharp") -pak::pak("Open-Systems-Pharmacology/TLF-Library") -pak::pak("Open-Systems-Pharmacology/OSPSuite-R") +install.packages(c('dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') +download.file('https://github.com/Open-Systems-Pharmacology/rSharp/releases/download/v1.0.0/rSharp-v1.0.0-Windows-r_4.4.0.zip', destfile = "rsharp.zip", mode = "wb") +download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/releases/download/v1.5.30/ospsuite.utils_1.5.30.zip', destfile = "ospsuite-utils.zip", mode = "wb") +download.file('https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/download/v1.5.158/tlf_1.5.158.zip', destfile = "tlf.zip", mode = "wb") +download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases/download/v12.1.0/ospsuite_12.1.0.zip', destfile = "ospsuite.zip", mode = "wb") +unzip("rsharp.zip") +unzip("ospsuite-utils.zip") +unzip("tlf.zip") +unzip("ospsuite.zip") +rSharp_archive <- list.files( pattern = "rSharp.*\\.zip") +ospsuiteUtils_archive <- list.files( pattern = "ospsuite-utils.*\\.zip") +tlf_archive <- list.files( pattern = "tlf.*\\.zip") +ospsuite_archive <- list.files( pattern = "ospsuite.*\\.zip") +install.packages(rSharp_archive, repos = NULL, type = "binary") +install.packages(ospsuiteUtils_archive, repos = NULL, type = "binary") +install.packages(tlf_archive, repos = NULL, type = "binary") +install.packages(ospsuite_archive, repos = NULL, type = "binary") +unlink("rsharp.zip") +unlink("ospsuite-utils.zip") +unlink("tlf.zip") +unlink("ospsuite.zip") From d209dbc36c7c530e9f29b8f85c6689df2d741ac0 Mon Sep 17 00:00:00 2001 From: pchelle Date: Fri, 9 Aug 2024 04:31:54 -0400 Subject: [PATCH 09/12] zip archives are directly packages --- .github/workflows/install_dependencies.R | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 7806c831..6a87f8f8 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -4,17 +4,11 @@ download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/rele download.file('https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/download/v1.5.158/tlf_1.5.158.zip', destfile = "tlf.zip", mode = "wb") download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases/download/v12.1.0/ospsuite_12.1.0.zip', destfile = "ospsuite.zip", mode = "wb") unzip("rsharp.zip") -unzip("ospsuite-utils.zip") -unzip("tlf.zip") -unzip("ospsuite.zip") rSharp_archive <- list.files( pattern = "rSharp.*\\.zip") -ospsuiteUtils_archive <- list.files( pattern = "ospsuite-utils.*\\.zip") -tlf_archive <- list.files( pattern = "tlf.*\\.zip") -ospsuite_archive <- list.files( pattern = "ospsuite.*\\.zip") install.packages(rSharp_archive, repos = NULL, type = "binary") -install.packages(ospsuiteUtils_archive, repos = NULL, type = "binary") -install.packages(tlf_archive, repos = NULL, type = "binary") -install.packages(ospsuite_archive, repos = NULL, type = "binary") +install.packages("ospsuite-utils.zip", repos = NULL, type = "binary") +install.packages("tlf.zip", repos = NULL, type = "binary") +install.packages("ospsuite.zip", repos = NULL, type = "binary") unlink("rsharp.zip") unlink("ospsuite-utils.zip") unlink("tlf.zip") From 8aa67c465866b8b772498b41d71f7a4588529615 Mon Sep 17 00:00:00 2001 From: pchelle Date: Fri, 9 Aug 2024 04:53:08 -0400 Subject: [PATCH 10/12] Download and package name should match for installation --- .github/workflows/install_dependencies.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 6a87f8f8..54b9a64b 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,12 +1,12 @@ install.packages(c('dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') download.file('https://github.com/Open-Systems-Pharmacology/rSharp/releases/download/v1.0.0/rSharp-v1.0.0-Windows-r_4.4.0.zip', destfile = "rsharp.zip", mode = "wb") -download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/releases/download/v1.5.30/ospsuite.utils_1.5.30.zip', destfile = "ospsuite-utils.zip", mode = "wb") +download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/releases/download/v1.5.30/ospsuite.utils_1.5.30.zip', destfile = "ospsuite.utils.zip", mode = "wb") download.file('https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/download/v1.5.158/tlf_1.5.158.zip', destfile = "tlf.zip", mode = "wb") download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases/download/v12.1.0/ospsuite_12.1.0.zip', destfile = "ospsuite.zip", mode = "wb") unzip("rsharp.zip") rSharp_archive <- list.files( pattern = "rSharp.*\\.zip") install.packages(rSharp_archive, repos = NULL, type = "binary") -install.packages("ospsuite-utils.zip", repos = NULL, type = "binary") +install.packages("ospsuite.utils.zip", repos = NULL, type = "binary") install.packages("tlf.zip", repos = NULL, type = "binary") install.packages("ospsuite.zip", repos = NULL, type = "binary") unlink("rsharp.zip") From b1b7373ad92ef389e0b7bb2b9e2d7c208fa99619 Mon Sep 17 00:00:00 2001 From: pchelle Date: Mon, 12 Aug 2024 04:32:15 -0400 Subject: [PATCH 11/12] Use develop version for utils --- .github/workflows/install_dependencies.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 54b9a64b..869a2a45 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,6 +1,6 @@ install.packages(c('dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') download.file('https://github.com/Open-Systems-Pharmacology/rSharp/releases/download/v1.0.0/rSharp-v1.0.0-Windows-r_4.4.0.zip', destfile = "rsharp.zip", mode = "wb") -download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/releases/download/v1.5.30/ospsuite.utils_1.5.30.zip', destfile = "ospsuite.utils.zip", mode = "wb") +download.file('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-rutils/artifacts/ospsuite.utils.zip?pr=false', destfile = 'ospsuite.utils.zip', mode='wb') download.file('https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/download/v1.5.158/tlf_1.5.158.zip', destfile = "tlf.zip", mode = "wb") download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases/download/v12.1.0/ospsuite_12.1.0.zip', destfile = "ospsuite.zip", mode = "wb") unzip("rsharp.zip") From efe96198093345c8e1f8f57af9fa194c8a9b9cc3 Mon Sep 17 00:00:00 2001 From: pchelle Date: Mon, 12 Aug 2024 05:17:54 -0400 Subject: [PATCH 12/12] Use develop version of tlf --- .github/workflows/install_dependencies.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/install_dependencies.R b/.github/workflows/install_dependencies.R index 869a2a45..3527b60e 100644 --- a/.github/workflows/install_dependencies.R +++ b/.github/workflows/install_dependencies.R @@ -1,7 +1,7 @@ install.packages(c('dplyr','purrr','covr','readr','tidyr','webshot','spelling','readxl','data.table','gridtext','ggtext','tidyselect','testthat','rmarkdown','pkgdown','openxlsx'), repos = 'http://cran.us.r-project.org', type='win.binary') download.file('https://github.com/Open-Systems-Pharmacology/rSharp/releases/download/v1.0.0/rSharp-v1.0.0-Windows-r_4.4.0.zip', destfile = "rsharp.zip", mode = "wb") download.file('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-rutils/artifacts/ospsuite.utils.zip?pr=false', destfile = 'ospsuite.utils.zip', mode='wb') -download.file('https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/download/v1.5.158/tlf_1.5.158.zip', destfile = "tlf.zip", mode = "wb") +download.file('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/tlf-library/artifacts/tlf.zip?pr=false', destfile = 'tlf.zip', mode='wb') download.file('https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases/download/v12.1.0/ospsuite_12.1.0.zip', destfile = "ospsuite.zip", mode = "wb") unzip("rsharp.zip") rSharp_archive <- list.files( pattern = "rSharp.*\\.zip")