renv tests

workflows/R-renv-docker/.Rprofile

+source("renv/activate.R")

workflows/R-renv-docker/README.md

@@ -2,4 +2,6 @@
 
 ## Build docker image
 
-docker build --pull --rm -f "workflows/_R-docker/Dockerfile" -t rdocker-test:latest "workflows/_R-docker"
+```bash
+docker build --pull --rm -f "workflows/R-renv-docker/Dockerfile" -t rdocker-test:latest "workflows/R-renv-docker"
+```
\ No newline at end of file

workflows/R-renv-docker/renv-test.R

+
+
+
+
+library("BiocManager")
+library("sleuth")
+
+print("hello")
+x=as.character(sessionInfo())
+
+write.table(as.character(sessionInfo()),file="test")
+

workflows/R-renv-docker/renv-test.cwl

+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+    ShellCommandRequirement: {}
+
+inputs: []
+
+outputs:
+    outfile:
+        type: File
+        outputBinding:
+            glob: "test"
+
+baseCommand: [R]
+
+arguments:
+    - valueFrom: -e 'write.table(as.character(sessionInfo()),file="test")'
+      shellQuote: false
+

workflows/R-renv-docker/renv.lock

+{
+  "R": {
+    "Version": "4.4.1",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Bioconductor": {
+    "Version": "3.19"
+  },
+  "Packages": {
+    "BiocManager": {
+      "Package": "BiocManager",
+      "Version": "1.30.23",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "47e968dfe563c1b22c2e20a067ec21d5"
+    },
+    "R6": {
+      "Package": "R6",
+      "Version": "2.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "fastmap",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "lifecycle",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "b21916dd77a27642b447374a5d30ecf3"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.36",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "fd6824ad91ede64151e93af67df6376b"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "0.24.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "a1066cbc05caee9a4bf6d90f194ff4da"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.7.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
+    },
+    "highr": {
+      "Package": "highr",
+      "Version": "0.11",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "xfun"
+      ],
+      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
+    },
+    "htmltools": {
+      "Package": "htmltools",
+      "Version": "0.5.8.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "digest",
+        "fastmap",
+        "grDevices",
+        "rlang",
+        "utils"
+      ],
+      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
+    },
+    "jquerylib": {
+      "Package": "jquerylib",
+      "Version": "0.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "htmltools"
+      ],
+      "Hash": "5aab57a3bd297eee1c1d862735972182"
+    },
+    "jsonlite": {
+      "Package": "jsonlite",
+      "Version": "1.8.8",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods"
+      ],
+      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
+    },
+    "knitr": {
+      "Package": "knitr",
+      "Version": "1.48",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "evaluate",
+        "highr",
+        "methods",
+        "tools",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "acf380f300c721da9fde7df115a5f86f"
+    },
+    "lifecycle": {
+      "Package": "lifecycle",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "rlang"
+      ],
+      "Hash": "b8552d117e1b808b09a832f589b79035"
+    },
+    "memoise": {
+      "Package": "memoise",
+      "Version": "2.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "cachem",
+        "rlang"
+      ],
+      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+    },
+    "mime": {
+      "Package": "mime",
+      "Version": "0.12",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "tools"
+      ],
+      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+    },
+    "rappdirs": {
+      "Package": "rappdirs",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "1.0.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "397b7b2a265bc5a7a06852524dabae20"
+    },
+    "rlang": {
+      "Package": "rlang",
+      "Version": "1.1.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+    },
+    "rmarkdown": {
+      "Package": "rmarkdown",
+      "Version": "2.27",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bslib",
+        "evaluate",
+        "fontawesome",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "knitr",
+        "methods",
+        "tinytex",
+        "tools",
+        "utils",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
+    },
+    "sass": {
+      "Package": "sass",
+      "Version": "0.4.9",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+    },
+    "tinytex": {
+      "Package": "tinytex",
+      "Version": "0.52",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "xfun"
+      ],
+      "Hash": "cfbad971a71f0e27cec22e544a08bc3b"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.46",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "grDevices",
+        "stats",
+        "tools"
+      ],
+      "Hash": "00ce32f398db0415dde61abfef11300c"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.10",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
+    }
+  }
+}

workflows/R-renv-docker/renv.rmd

@@ -16,10 +16,15 @@ renv::dependencies()
 renv::snapshot()
 
 ```
+
 ```{r}
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 BiocManager::install(version = "3.19")
+
+
+BiocManager::install("sleuth")
+
 ```
 
 

workflows/R-renv-docker/renv/.gitignore

+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

workflows/R-renv-docker/renv/settings.json

+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}

workflows/R-renv-docker/test

+"x"
+"1" "list(platform = \"x86_64-apple-darwin20\", arch = \"x86_64\", os = \"darwin20\", system = \"x86_64, darwin20\", status = \"\", major = \"4\", minor = \"4.1\", year = \"2024\", month = \"06\", day = \"14\", `svn rev` = \"86737\", language = \"R\", version.string = \"R version 4.4.1 (2024-06-14)\", nickname = \"Race for Your Life\")"
+"2" "x86_64-apple-darwin20"
+"3" "C"
+"4" "Europe/Berlin"
+"5" "internal"
+"6" "macOS Sonoma 14.5"
+"7" "c(\"Mersenne-Twister\", \"Inversion\", \"Rejection\")"
+"8" "c(\"stats\", \"graphics\", \"grDevices\", \"utils\", \"datasets\", \"methods\", \"base\")"
+"9" "list(compiler = list(Package = \"compiler\", Version = \"4.4.1\", Priority = \"base\", Title = \"The R Compiler Package\", Author = \"Luke Tierney <luke-tierney@uiowa.edu>\", Maintainer = \"R Core Team <do-use-Contact-address@r-project.org>\", Contact = \"R-help mailing list <r-help@r-project.org>\", Description = \"Byte code compiler for R.\", License = \"Part of R 4.4.1\", Built = \"R 4.4.1; ; 2024-06-15 17:30:44 UTC; unix\"))"
+"10" "default"
+"11" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib"
+"12" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib"
+"13" "3.12.0"