From d859b20edf418c20831c81c3d7d4290d97a8e3a2 Mon Sep 17 00:00:00 2001 From: Nikolas Burkoff Date: Thu, 30 Jun 2022 14:14:38 +0100 Subject: [PATCH 1/6] news and description --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 28698bb..ba48874 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: staged.dependencies Type: Package Title: Install R packages from Particular Git Branches -Version: 0.2.6 +Version: 0.2.7 Authors@R: c( person("Adrian", "Waddell", email = "adrian.waddell@roche.com", role = c("aut", "cre")), person("Maximilian", "Mordig", email = "maximilian_oliver.mordig@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 2336ab5..588397b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# staged.dependencies 0.2.7 + +* Fixed a bug whereby the cache file for packages with compiled code was not reset after installation thereby `dependency_table` +failed on a 2nd run. + # staged.dependencies 0.2.6 * Fixed bug whereby `renv` did not recognize internal dependencies already installed. From 49fc3b1601c49b14d152a50d854267df28a5f43f Mon Sep 17 00:00:00 2001 From: Nikolas Burkoff Date: Thu, 30 Jun 2022 14:28:25 +0100 Subject: [PATCH 2/6] add git clean when resetting repo --- R/git_tools.R | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/R/git_tools.R b/R/git_tools.R index 2dc1d2f..d15d5fb 100644 --- a/R/git_tools.R +++ b/R/git_tools.R @@ -289,7 +289,11 @@ install_repo_add_sha <- function(repo_dir, # once we have installed or failed to install the package we reset the repo # so that further operations on the repo do not fail by the above # "the git directory contains changes" check - on.exit(git2r::reset(git2r::commits(repo_dir)[[1]], reset_type = "hard")) + on.exit({ + git2r::reset(git2r::commits(repo_dir)[[1]], reset_type = "hard") + # git clean + try(unlink(rlang::flatten_chr(git2r::status()$untracked))) + }) desc <- utils::modifyList(desc, metadata) write_dcf(source_desc, desc) From fbfa208700dcee3d3467630369ae778be1ec95aa Mon Sep 17 00:00:00 2001 From: Nikolas Burkoff Date: Thu, 30 Jun 2022 14:52:41 +0100 Subject: [PATCH 3/6] fix --- R/git_tools.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/git_tools.R b/R/git_tools.R index d15d5fb..150ea10 100644 --- a/R/git_tools.R +++ b/R/git_tools.R @@ -292,7 +292,7 @@ install_repo_add_sha <- function(repo_dir, on.exit({ git2r::reset(git2r::commits(repo_dir)[[1]], reset_type = "hard") # git clean - try(unlink(rlang::flatten_chr(git2r::status()$untracked))) + try(unlink(rlang::flatten_chr(git2r::status(repo_dir)$untracked), recursive = TRUE)) }) desc <- utils::modifyList(desc, metadata) From b3f9a808494765794c6cc49bab8322dc0b9f2e50 Mon Sep 17 00:00:00 2001 From: Nikolas Burkoff Date: Thu, 30 Jun 2022 15:16:40 +0100 Subject: [PATCH 4/6] fix --- R/git_tools.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/git_tools.R b/R/git_tools.R index 150ea10..0413128 100644 --- a/R/git_tools.R +++ b/R/git_tools.R @@ -292,7 +292,7 @@ install_repo_add_sha <- function(repo_dir, on.exit({ git2r::reset(git2r::commits(repo_dir)[[1]], reset_type = "hard") # git clean - try(unlink(rlang::flatten_chr(git2r::status(repo_dir)$untracked), recursive = TRUE)) + try(unlink(file.path(repo_dir, rlang::flatten_chr(git2r::status(repo_dir)$untracked)), recursive = TRUE)) }) desc <- utils::modifyList(desc, metadata) From 044e0bd927873c32c8bdea19d624efb50224e18f Mon Sep 17 00:00:00 2001 From: Nikolas Burkoff Date: Thu, 30 Jun 2022 15:35:52 +0100 Subject: [PATCH 5/6] Update NEWS.md --- NEWS.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 588397b..df1ca81 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,6 @@ # staged.dependencies 0.2.7 -* Fixed a bug whereby the cache file for packages with compiled code was not reset after installation thereby `dependency_table` -failed on a 2nd run. +* Fixed a bug whereby the cache file for packages with compiled code was not reset after installation thereby `dependency_table` failed on a 2nd run. # staged.dependencies 0.2.6 From 05255b8d5d8500363fb35b9d2428f9d3cba64d43 Mon Sep 17 00:00:00 2001 From: Dinakar <26552821+dinakar29@users.noreply.github.com> Date: Thu, 30 Jun 2022 09:58:38 -0500 Subject: [PATCH 6/6] Update R and BioC versions for E2E tests (#162) --- .github/workflows/check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index e0ffbd8..c76ee65 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -59,7 +59,7 @@ jobs: fail-fast: false matrix: config: - - {image: ghcr.io/insightsengineering/rstudio_4.1.2_bioc_3.14, tag: latest} + - {image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15, tag: latest} steps: - name: Install package run: >