Merge pull request #276 from AlexsLemonade/jashapiro/unslim-a-bit

Add rtracklayer and updates

Author: jashapiro

.github/workflows/build-docker.yaml

@@ -39,6 +39,7 @@ jobs:
           tags: |
             type=semver,pattern={{raw}}
             type=edge,branch=main
+            type=ref,event=pr
 
       - name: Build full image
         uses: docker/build-push-action@v5

docker/make-requirements.sh

@@ -14,7 +14,7 @@ pip-compile --no-annotate --strip-extras --output-file=requirements_anndata.txt
 pip-compile --no-annotate --strip-extras --output-file=requirements_scvi.txt requirements_scvi.in
 
 # slim lockfile
-Rscript scripts/make-lockfile.R -f renv_slim.lock -p batchelor
+Rscript scripts/make-lockfile.R -f renv_slim.lock -p batchelor,rtracklayer
 
 # reports lockfile
 Rscript scripts/make-lockfile.R -f renv_reports.lock -p ComplexHeatmap,ggforce,kableExtra,rmarkdown

docker/renv_reports.lock

@@ -68,13 +68,13 @@
     },
     "BiocManager": {
       "Package": "BiocManager",
-      "Version": "1.30.22",
+      "Version": "1.30.23",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "utils"
       ],
-      "Hash": "d57e43105a1aa9cb54fdb4629725acb1"
+      "Hash": "47e968dfe563c1b22c2e20a067ec21d5"
     },
     "BiocNeighbors": {
       "Package": "BiocNeighbors",
@@ -652,7 +652,7 @@
     },
     "SparseArray": {
       "Package": "SparseArray",
-      "Version": "1.4.0",
+      "Version": "1.4.1",
       "Source": "Bioconductor",
       "Repository": "Bioconductor 3.19",
       "Requirements": [
@@ -666,9 +666,10 @@
         "XVector",
         "matrixStats",
         "methods",
-        "stats"
+        "stats",
+        "utils"
       ],
-      "Hash": "84697af365cd2a6367fa5d2c1086298c"
+      "Hash": "c309b75cfb1f52407e40ebbd151af932"
     },
     "SummarizedExperiment": {
       "Package": "SummarizedExperiment",
@@ -852,14 +853,13 @@
     },
     "broom": {
       "Package": "broom",
-      "Version": "1.0.5",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "R",
         "backports",
         "dplyr",
-        "ellipsis",
         "generics",
         "glue",
         "lifecycle",
@@ -869,7 +869,7 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c"
+      "Hash": "a4652c36d1f8abfc3ddf4774f768c934"
     },
     "bslib": {
       "Package": "bslib",
@@ -895,14 +895,14 @@
     },
     "cachem": {
       "Package": "cachem",
-      "Version": "1.0.8",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "fastmap",
         "rlang"
       ],
-      "Hash": "c35768291560ce302c0a6589f92e837d"
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
     },
     "callr": {
       "Package": "callr",
@@ -1155,7 +1155,7 @@
     },
     "dqrng": {
       "Package": "dqrng",
-      "Version": "0.3.2",
+      "Version": "0.4.0",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1164,7 +1164,7 @@
         "Rcpp",
         "sitmo"
       ],
-      "Hash": "824df2aeba88d701df5e79018b35b815"
+      "Hash": "b31198e6268008976689b196bf9d883f"
     },
     "dtplyr": {
       "Package": "dtplyr",
@@ -1202,17 +1202,6 @@
       ],
       "Hash": "20783ecb7e7cea3f351e8b21153e3eb8"
     },
-    "ellipsis": {
-      "Package": "ellipsis",
-      "Version": "0.3.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "rlang"
-      ],
-      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
-    },
     "evaluate": {
       "Package": "evaluate",
       "Version": "0.23",
@@ -1238,17 +1227,17 @@
     },
     "farver": {
       "Package": "farver",
-      "Version": "2.1.1",
+      "Version": "2.1.2",
       "Source": "Repository",
       "Repository": "RSPM",
-      "Hash": "8106d78941f34855c440ddb946b8f7a5"
+      "Hash": "680887028577f3fa2a81e410ed0d6e42"
     },
     "fastmap": {
       "Package": "fastmap",
-      "Version": "1.1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "RSPM",
-      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
     },
     "fishpond": {
       "Package": "fishpond",
@@ -2077,13 +2066,13 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.1.2",
+      "Version": "2.2.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "ea2475b073243d9d338aa8f086ce973e"
+      "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e"
     },
     "optparse": {
       "Package": "optparse",
@@ -2251,14 +2240,14 @@
     },
     "ragg": {
       "Package": "ragg",
-      "Version": "1.3.0",
+      "Version": "1.3.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "systemfonts",
         "textshaping"
       ],
-      "Hash": "082e1a198e3329d571f4448ef0ede4bc"
+      "Hash": "e3087db406e079a8a2fd87f413918ed3"
     },
     "rappdirs": {
       "Package": "rappdirs",
@@ -2406,7 +2395,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.26",
+      "Version": "2.27",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -2425,7 +2414,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
+      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
     },
     "rstudioapi": {
       "Package": "rstudioapi",
@@ -2664,7 +2653,7 @@
     },
     "stringi": {
       "Package": "stringi",
-      "Version": "1.8.3",
+      "Version": "1.8.4",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -2673,7 +2662,7 @@
         "tools",
         "utils"
       ],
-      "Hash": "058aebddea264f4c99401515182e656a"
+      "Hash": "39e1144fd75428983dc3f63aa53dfa91"
     },
     "stringr": {
       "Package": "stringr",
@@ -2727,14 +2716,15 @@
     },
     "systemfonts": {
       "Package": "systemfonts",
-      "Version": "1.0.6",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "R",
-        "cpp11"
+        "cpp11",
+        "lifecycle"
       ],
-      "Hash": "6d538cff441f0f1f36db2209ac7495ac"
+      "Hash": "213b6b8ed5afbf934843e6c3b090d418"
     },
     "textshaping": {
       "Package": "textshaping",
@@ -2859,13 +2849,13 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.50",
+      "Version": "0.51",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "be7a76845222ad20adb761f462eed3ea"
+      "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
     },
     "tweenr": {
       "Package": "tweenr",
@@ -3032,15 +3022,15 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.43",
+      "Version": "0.44",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
+      "Hash": "317a0538d32f4a009658bcedb7923f4b"
     },
     "xml2": {
       "Package": "xml2",