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c57c6e6db63dba844339d60d8aebed9dbf130f11 Mon Sep 17 00:00:00 2001 From: "Lea@Mac" Date: Wed, 3 Jul 2024 15:18:16 +0200 Subject: [PATCH 3/6] now also update of ggplot2 --- program/renv.lock | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/program/renv.lock b/program/renv.lock index 5d2595cc..433001cb 100644 --- a/program/renv.lock +++ b/program/renv.lock @@ -4,23 +4,23 @@ "Repositories": [ { "Name": "BioCsoft", - "URL": "https://bioconductor.org/packages/3.15/bioc" + "URL": "https://bioconductor.org/packages/3.16/bioc" }, { "Name": "BioCann", - "URL": "https://bioconductor.org/packages/3.15/data/annotation" + "URL": "https://bioconductor.org/packages/3.16/data/annotation" }, { "Name": "BioCexp", - "URL": "https://bioconductor.org/packages/3.15/data/experiment" + "URL": "https://bioconductor.org/packages/3.16/data/experiment" }, { "Name": "BioCworkflows", - "URL": "https://bioconductor.org/packages/3.15/workflows" + "URL": "https://bioconductor.org/packages/3.16/workflows" }, { "Name": "BioCbooks", - "URL": "https://bioconductor.org/packages/3.15/books" + "URL": "https://bioconductor.org/packages/3.16/books" }, { "Name": "CRAN", From a0b2793753df35abeb2c0c4ae17d92f268ee7b68 Mon Sep 17 00:00:00 2001 From: Lea Seep <74967328+LeaSeep@users.noreply.github.com> Date: Wed, 3 Jul 2024 15:52:06 +0200 Subject: [PATCH 4/6] Update startOmicShiny.sh --- startOmicShiny.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/startOmicShiny.sh b/startOmicShiny.sh index 37995de1..6a577c69 100755 --- a/startOmicShiny.sh +++ b/startOmicShiny.sh @@ -3,8 +3,9 @@ cd program git pull #git checkout pca_worflow_integrated git checkout develop +git pull Rscript -e "library(renv)" -Rscript -e "renv::init(bioconductor = TRUE)" +#Rscript -e "renv::init(bioconductor = TRUE)" pwd #RScript -e "renv::init(bioconductor = TRUE)" echo ReInit From 53354c579db22680014274e46f642f39dcf74505 Mon Sep 17 00:00:00 2001 From: "Lea@Mac" Date: Wed, 3 Jul 2024 16:48:41 +0200 Subject: [PATCH 5/6] update renv and hope for succeess --- program/renv.lock | 2108 +++++++++++++++++++++++++++----------------- renv.lock | 2118 ++++++++++++++++++++++++++++----------------- 2 files changed, 2611 insertions(+), 1615 deletions(-) diff --git a/program/renv.lock b/program/renv.lock index 433001cb..b68660c1 100644 --- a/program/renv.lock +++ b/program/renv.lock @@ -36,157 +36,159 @@ "Package": "AnnotationDbi", "Version": "1.60.2", "Source": "Bioconductor", - "git_url": "https://git.bioconductor.org/packages/AnnotationDbi", - "git_branch": "RELEASE_3_16", - "git_last_commit": "eebebb2", - "git_last_commit_date": "2023-03-09", - "Hash": "14966d2e5ffaa621945cc2b9a115f377", "Requirements": [ "Biobase", "BiocGenerics", "DBI", "IRanges", "KEGGREST", + "R", "RSQLite", - "S4Vectors" - ] + "S4Vectors", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "14966d2e5ffaa621945cc2b9a115f377" }, "BH": { "Package": "BH", "Version": 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"Version": "2.3.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "d98c94dacb7e0efcf83b0a133a705504", - "Requirements": [] + "Hash": "d98c94dacb7e0efcf83b0a133a705504" }, "zlibbioc": { "Package": "zlibbioc", "Version": "1.44.0", "Source": "Bioconductor", - "git_url": "https://git.bioconductor.org/packages/zlibbioc", - "git_branch": "RELEASE_3_16", - "git_last_commit": "d39f0b0", - "git_last_commit_date": "2022-11-01", - "Hash": "6f578730acbdfc7ce2ca49df29bb5352", - "Requirements": [] + "Hash": "6f578730acbdfc7ce2ca49df29bb5352" } } } From 81e94c95b21813dddce91d8d870486f19ce4d3ce Mon Sep 17 00:00:00 2001 From: "Lea@Mac" Date: Wed, 3 Jul 2024 17:23:33 +0200 Subject: [PATCH 6/6] update system dependencies required for package 'textshaping' --- .github/workflows/start_check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/start_check.yaml b/.github/workflows/start_check.yaml index 3dcbe2b8..6c5a577e 100644 --- a/.github/workflows/start_check.yaml +++ b/.github/workflows/start_check.yaml @@ -27,7 +27,7 @@ jobs: - name: Install system dependencies run: | sudo apt-get update - sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libsqlite3-dev libglu1-mesa-dev default-jdk libmagick++-dev + sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libsqlite3-dev libglu1-mesa-dev default-jdk libmagick++-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev sudo apt install curl - name: Install and activate renv