From 6637a7517c8148b2397bb3d498eeda24e389b744 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 5 Jun 2024 17:11:23 -0400 Subject: [PATCH 1/5] Swap out fishpond for eds --- components/dependencies.R | 2 +- renv.lock | 50 +++++++++------------------------------ 2 files changed, 12 insertions(+), 40 deletions(-) diff --git a/components/dependencies.R b/components/dependencies.R index 9332a8a4..fe381a4e 100644 --- a/components/dependencies.R +++ b/components/dependencies.R @@ -7,7 +7,7 @@ library(markdown) library(magick) # Recommended by tximport -library(fishpond) +library(eds) # Required for DESeq2::lfcShrink() library(apeglm) diff --git a/renv.lock b/renv.lock index a0f0fa36..4bc475c2 100644 --- a/renv.lock +++ b/renv.lock @@ -2378,6 +2378,17 @@ ], "Hash": "20783ecb7e7cea3f351e8b21153e3eb8" }, + "eds": { + "Package": "eds", + "Version": "1.6.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "Matrix", + "Rcpp" + ], + "Hash": "ab19d02b3418e44d6f32ffb8060427d2" + }, "ellipsis": { "Package": "ellipsis", "Version": "0.3.2", @@ -2631,31 +2642,6 @@ ], "Hash": "192053c276525c8495ccfd523aa8f2d1" }, - "fishpond": { - "Package": "fishpond", - "Version": "2.10.0", - "Source": "Bioconductor", - "Repository": "Bioconductor 3.19", - "Requirements": [ - "GenomicRanges", - "IRanges", - "Matrix", - "S4Vectors", - "SingleCellExperiment", - "SummarizedExperiment", - "abind", - "graphics", - "gtools", - "jsonlite", - "matrixStats", - "methods", - "qvalue", - "stats", - "svMisc", - "utils" - ], - "Hash": "9091a296b5cdb86da7c4c35f958c67f6" - }, "flexmix": { "Package": "flexmix", "Version": "2.3-19", @@ -5008,20 +4994,6 @@ ], "Hash": "184d7799bca4ba8c3be72ea396f4b9a3" }, - "svMisc": { - "Package": "svMisc", - "Version": "1.2.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "stats", - "tools", - "utils" - ], - "Hash": "b13f5680860f67c32ccb006ad38f24f4" - }, "sys": { "Package": "sys", "Version": "3.4.2", From 42abac0eb0eba522edf352b8bda6355978f17748 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 5 Jun 2024 18:12:15 -0400 Subject: [PATCH 2/5] RSamtools broken package fix --- .github/workflows/build-docker.yml | 2 +- Dockerfile | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-docker.yml b/.github/workflows/build-docker.yml index 958ee38c..7c818e4a 100644 --- a/.github/workflows/build-docker.yml +++ b/.github/workflows/build-docker.yml @@ -1,4 +1,4 @@ -name: Build Docker Image and Push to Dockerhub +name: Build Docker Image # Every time something is merged to master or a tag is pushed, we build and push # the Docker image diff --git a/Dockerfile b/Dockerfile index bbac26c3..35efb5d5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -68,6 +68,8 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \ COPY requirements.txt requirements.txt RUN pip install -r requirements.txt + + # Use renv for R packages WORKDIR /usr/local/renv ENV RENV_CONFIG_CACHE_ENABLED=FALSE From 7016a59b192978ff412945ff7016540f69399c42 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 5 Jun 2024 18:13:07 -0400 Subject: [PATCH 3/5] No, this is the fix... --- Dockerfile | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 35efb5d5..f54c7f73 100644 --- a/Dockerfile +++ b/Dockerfile @@ -73,8 +73,12 @@ RUN pip install -r requirements.txt # Use renv for R packages WORKDIR /usr/local/renv ENV RENV_CONFIG_CACHE_ENABLED=FALSE -COPY renv.lock renv.lock RUN R -e "install.packages('renv')" + +# Temporary fix for broken(?) RSamtools package +RUN R -e "install.packages('BiocManager'); BiocManager::install('RSamtools')" + +COPY renv.lock renv.lock RUN R -e "renv::restore()" \ rm -rf ~/.cache/R/renv && \ rm -rf /tmp/downloaded_packages && \ From a248c2a53409c1c8b322bebc4528067086430e30 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 5 Jun 2024 18:20:03 -0400 Subject: [PATCH 4/5] capitalization --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f54c7f73..0158de79 100644 --- a/Dockerfile +++ b/Dockerfile @@ -76,7 +76,7 @@ ENV RENV_CONFIG_CACHE_ENABLED=FALSE RUN R -e "install.packages('renv')" # Temporary fix for broken(?) RSamtools package -RUN R -e "install.packages('BiocManager'); BiocManager::install('RSamtools')" +RUN R -e "install.packages('BiocManager'); BiocManager::install('Rsamtools')" COPY renv.lock renv.lock RUN R -e "renv::restore()" \ From 888397a898a7c20f2fdf7f01ef3e0b55373a5fa6 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Wed, 5 Jun 2024 18:20:54 -0400 Subject: [PATCH 5/5] use Rscript --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0158de79..c6162de4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -73,13 +73,13 @@ RUN pip install -r requirements.txt # Use renv for R packages WORKDIR /usr/local/renv ENV RENV_CONFIG_CACHE_ENABLED=FALSE -RUN R -e "install.packages('renv')" +RUN Rscript -e "install.packages('renv')" # Temporary fix for broken(?) RSamtools package -RUN R -e "install.packages('BiocManager'); BiocManager::install('Rsamtools')" +RUN Rscript -e "install.packages('BiocManager'); BiocManager::install('Rsamtools')" COPY renv.lock renv.lock -RUN R -e "renv::restore()" \ +RUN Rscript -e "renv::restore()" \ rm -rf ~/.cache/R/renv && \ rm -rf /tmp/downloaded_packages && \ rm -rf /tmp/Rtmp*