From 689deada3a43097e0d2d60ca62701cf15babbc57 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 23 May 2024 08:14:54 -0400 Subject: [PATCH 1/3] add rtracklayer to slim image --- docker/make-requirements.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/make-requirements.sh b/docker/make-requirements.sh index 7406729..06e7728 100755 --- a/docker/make-requirements.sh +++ b/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 From 75ecab00ccb7bdfe5303579eedb4bc00fa865349 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 23 May 2024 08:15:41 -0400 Subject: [PATCH 2/3] renv updates --- docker/renv_reports.lock | 78 +++++----- docker/renv_seurat.lock | 94 ++++++------ docker/renv_slim.lock | 253 +++++++++++++++++++++++++++------ docker/renv_zellkonverter.lock | 82 +++++------ renv.lock | 114 +++++++-------- 5 files changed, 373 insertions(+), 248 deletions(-) diff --git a/docker/renv_reports.lock b/docker/renv_reports.lock index d07e9b8..37890e0 100644 --- a/docker/renv_reports.lock +++ b/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", @@ -3032,7 +3022,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -3040,7 +3030,7 @@ "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "317a0538d32f4a009658bcedb7923f4b" }, "xml2": { "Package": "xml2", diff --git a/docker/renv_seurat.lock b/docker/renv_seurat.lock index 621f56f..07b9cde 100644 --- a/docker/renv_seurat.lock +++ b/docker/renv_seurat.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", @@ -502,7 +502,7 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.8.2.1", + "Version": "0.12.8.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -512,7 +512,7 @@ "stats", "utils" ], - "Hash": "d5448fb24fb114c4da1275a37a571f37" + "Hash": "1eb4a0603478b5557b77d75534251371" }, "RcppEigen": { "Package": "RcppEigen", @@ -639,7 +639,7 @@ }, "Seurat": { "Package": "Seurat", - "Version": "5.0.3", + "Version": "5.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -702,11 +702,11 @@ "utils", "uwot" ], - "Hash": "f5325a968489ef65254a51d74dc0c520" + "Hash": "aa2040fec3d03e3e598e0b406a84a104" }, "SeuratObject": { "Package": "SeuratObject", - "Version": "5.0.1", + "Version": "5.0.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -729,7 +729,7 @@ "tools", "utils" ], - "Hash": "424c2b9e50b053c86fc38f17e09917da" + "Hash": "e9b70412b7e04571b46101f5dcbaacad" }, "SingleCellExperiment": { "Package": "SingleCellExperiment", @@ -750,7 +750,7 @@ }, "SparseArray": { "Package": "SparseArray", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -764,9 +764,10 @@ "XVector", "matrixStats", "methods", - "stats" + "stats", + "utils" ], - "Hash": "84697af365cd2a6367fa5d2c1086298c" + "Hash": "c309b75cfb1f52407e40ebbd151af932" }, "SummarizedExperiment": { "Package": "SummarizedExperiment", @@ -957,14 +958,13 @@ }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -974,7 +974,7 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", @@ -1011,14 +1011,14 @@ }, "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", @@ -1283,7 +1283,7 @@ }, "dqrng": { "Package": "dqrng", - "Version": "0.3.2", + "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1292,7 +1292,7 @@ "Rcpp", "sitmo" ], - "Hash": "824df2aeba88d701df5e79018b35b815" + "Hash": "b31198e6268008976689b196bf9d883f" }, "dtplyr": { "Package": "dtplyr", @@ -1330,17 +1330,6 @@ ], "Hash": "20783ecb7e7cea3f351e8b21153e3eb8" }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, "evaluate": { "Package": "evaluate", "Version": "0.23", @@ -1366,10 +1355,10 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastDummies": { "Package": "fastDummies", @@ -1386,10 +1375,10 @@ }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "RSPM", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fishpond": { "Package": "fishpond", @@ -2351,13 +2340,13 @@ }, "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", @@ -2626,14 +2615,14 @@ }, "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", @@ -2737,7 +2726,7 @@ }, "reticulate": { "Package": "reticulate", - "Version": "1.36.1", + "Version": "1.37.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2755,7 +2744,7 @@ "utils", "withr" ], - "Hash": "e037fb5dc364efdaf616eb6bc05aaca2" + "Hash": "9465d3bc6ec44eeaa52527ac2cba4020" }, "rhdf5": { "Package": "rhdf5", @@ -2793,7 +2782,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.27", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2812,7 +2801,7 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "rprojroot": { "Package": "rprojroot", @@ -3264,7 +3253,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -3273,7 +3262,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -3331,14 +3320,15 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "6d538cff441f0f1f36db2209ac7495ac" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "tensor": { "Package": "tensor", @@ -3470,13 +3460,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.50", + "Version": "0.51", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "be7a76845222ad20adb761f462eed3ea" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "tximport": { "Package": "tximport", @@ -3628,7 +3618,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -3636,7 +3626,7 @@ "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "317a0538d32f4a009658bcedb7923f4b" }, "xml2": { "Package": "xml2", diff --git a/docker/renv_slim.lock b/docker/renv_slim.lock index 03961f3..b3c30d1 100644 --- a/docker/renv_slim.lock +++ b/docker/renv_slim.lock @@ -66,15 +66,29 @@ ], "Hash": "ef32d07aafdd12f24c5827374ae3590d" }, + "BiocIO": { + "Package": "BiocIO", + "Version": "1.14.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "R", + "S4Vectors", + "methods", + "tools" + ], + "Hash": "f97a7ef01d364cf20d1946d43a3d526f" + }, "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", @@ -142,6 +156,26 @@ ], "Hash": "b892e27fc9659a4c8f8787d34c37b8b2" }, + "Biostrings": { + "Package": "Biostrings", + "Version": "2.72.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDb", + "IRanges", + "R", + "S4Vectors", + "XVector", + "crayon", + "grDevices", + "methods", + "stats", + "utils" + ], + "Hash": "48618c7c7b90b503837824ebcfee6363" + }, "Cairo": { "Package": "Cairo", "Version": "1.6-2", @@ -271,6 +305,28 @@ ], "Hash": "c3c792a7b7f2677be56e8632c5b7543d" }, + "GenomicAlignments": { + "Package": "GenomicAlignments", + "Version": "1.40.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "BiocParallel", + "Biostrings", + "GenomeInfoDb", + "GenomicRanges", + "IRanges", + "R", + "Rsamtools", + "S4Vectors", + "SummarizedExperiment", + "methods", + "stats", + "utils" + ], + "Hash": "e539709764587c581b31e446dc84d7b8" + }, "GenomicRanges": { "Package": "GenomicRanges", "Version": "1.56.0", @@ -431,6 +487,18 @@ ], "Hash": "45f0398006e83a5b10b72a90663d8d8c" }, + "RCurl": { + "Package": "RCurl", + "Version": "1.98-1.14", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bitops", + "methods" + ], + "Hash": "47f648d288079d0c696804ad4e55197e" + }, "RSpectra": { "Package": "RSpectra", "Version": "0.16-1", @@ -535,6 +603,41 @@ ], "Hash": "c92ba8b9a2c5c9ff600a1062a3b7b727" }, + "Rhtslib": { + "Package": "Rhtslib", + "Version": "3.0.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "tools", + "zlibbioc" + ], + "Hash": "5d6514cd44a0106581e3310f3972a82e" + }, + "Rsamtools": { + "Package": "Rsamtools", + "Version": "2.20.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "BiocParallel", + "Biostrings", + "GenomeInfoDb", + "GenomicRanges", + "IRanges", + "R", + "Rhtslib", + "S4Vectors", + "XVector", + "bitops", + "methods", + "stats", + "utils", + "zlibbioc" + ], + "Hash": "9762f24dcbdbd1626173c516bb64792c" + }, "Rtsne": { "Package": "Rtsne", "Version": "0.17", @@ -611,7 +714,7 @@ }, "SparseArray": { "Package": "SparseArray", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -625,9 +728,10 @@ "XVector", "matrixStats", "methods", - "stats" + "stats", + "utils" ], - "Hash": "84697af365cd2a6367fa5d2c1086298c" + "Hash": "c309b75cfb1f52407e40ebbd151af932" }, "SummarizedExperiment": { "Package": "SummarizedExperiment", @@ -667,6 +771,18 @@ ], "Hash": "83d45b690bffd09d1980c224ef329f5b" }, + "XML": { + "Package": "XML", + "Version": "3.99-0.16.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods", + "utils" + ], + "Hash": "da3098169c887914551b607c66fe2a28" + }, "XVector": { "Package": "XVector", "Version": "0.44.0", @@ -806,6 +922,13 @@ ], "Hash": "9fe98599ca456d6552421db0d6772d8f" }, + "bitops": { + "Package": "bitops", + "Version": "1.0-7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b7d8d8ee39869c18d8846a184dd8a1af" + }, "blob": { "Package": "blob", "Version": "1.2.4", @@ -839,14 +962,13 @@ }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -856,7 +978,7 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", @@ -882,14 +1004,14 @@ }, "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", @@ -1095,7 +1217,7 @@ }, "dqrng": { "Package": "dqrng", - "Version": "0.3.2", + "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1104,7 +1226,7 @@ "Rcpp", "sitmo" ], - "Hash": "824df2aeba88d701df5e79018b35b815" + "Hash": "b31198e6268008976689b196bf9d883f" }, "dtplyr": { "Package": "dtplyr", @@ -1142,17 +1264,6 @@ ], "Hash": "20783ecb7e7cea3f351e8b21153e3eb8" }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, "evaluate": { "Package": "evaluate", "Version": "0.23", @@ -1178,17 +1289,17 @@ }, "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", @@ -1939,13 +2050,13 @@ }, "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", @@ -2103,14 +2214,14 @@ }, "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", @@ -2212,6 +2323,22 @@ ], "Hash": "bb5996d0bd962d214a11140d77589917" }, + "restfulr": { + "Package": "restfulr", + "Version": "0.0.15", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "RCurl", + "S4Vectors", + "XML", + "methods", + "rjson", + "yaml" + ], + "Hash": "44651c1e68eda9d462610aca9f15a815" + }, "rhdf5": { "Package": "rhdf5", "Version": "2.48.0", @@ -2235,6 +2362,16 @@ ], "Hash": "99e15369f8fb17dc188377234de13fc6" }, + "rjson": { + "Package": "rjson", + "Version": "0.2.21", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "f9da75e6444e95a1baf8ca24909d63b9" + }, "rlang": { "Package": "rlang", "Version": "1.1.3", @@ -2248,7 +2385,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.27", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2267,7 +2404,7 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "rstudioapi": { "Package": "rstudioapi", @@ -2287,6 +2424,33 @@ ], "Hash": "b462187d887abc519894874486dbd6fd" }, + "rtracklayer": { + "Package": "rtracklayer", + "Version": "1.64.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "BiocIO", + "Biostrings", + "GenomeInfoDb", + "GenomicAlignments", + "GenomicRanges", + "IRanges", + "R", + "Rsamtools", + "S4Vectors", + "XML", + "XVector", + "curl", + "httr", + "methods", + "restfulr", + "tools", + "zlibbioc" + ], + "Hash": "3d6f004fce582bd7d68e2e18d44abbc1" + }, "rvest": { "Package": "rvest", "Version": "1.0.4", @@ -2493,7 +2657,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2502,7 +2666,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -2544,14 +2708,15 @@ }, "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", @@ -2676,13 +2841,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.50", + "Version": "0.51", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "be7a76845222ad20adb761f462eed3ea" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "tximport": { "Package": "tximport", @@ -2834,7 +2999,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2842,7 +3007,7 @@ "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "317a0538d32f4a009658bcedb7923f4b" }, "xml2": { "Package": "xml2", diff --git a/docker/renv_zellkonverter.lock b/docker/renv_zellkonverter.lock index f8977b0..f0f3eaa 100644 --- a/docker/renv_zellkonverter.lock +++ b/docker/renv_zellkonverter.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", @@ -609,7 +609,7 @@ }, "SparseArray": { "Package": "SparseArray", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -623,9 +623,10 @@ "XVector", "matrixStats", "methods", - "stats" + "stats", + "utils" ], - "Hash": "84697af365cd2a6367fa5d2c1086298c" + "Hash": "c309b75cfb1f52407e40ebbd151af932" }, "SummarizedExperiment": { "Package": "SummarizedExperiment", @@ -837,14 +838,13 @@ }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -854,7 +854,7 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", @@ -880,14 +880,14 @@ }, "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", @@ -1104,7 +1104,7 @@ }, "dqrng": { "Package": "dqrng", - "Version": "0.3.2", + "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1113,7 +1113,7 @@ "Rcpp", "sitmo" ], - "Hash": "824df2aeba88d701df5e79018b35b815" + "Hash": "b31198e6268008976689b196bf9d883f" }, "dtplyr": { "Package": "dtplyr", @@ -1151,17 +1151,6 @@ ], "Hash": "20783ecb7e7cea3f351e8b21153e3eb8" }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, "evaluate": { "Package": "evaluate", "Version": "0.23", @@ -1187,17 +1176,17 @@ }, "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" }, "filelock": { "Package": "filelock", @@ -1968,13 +1957,13 @@ }, "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", @@ -2132,14 +2121,14 @@ }, "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", @@ -2243,7 +2232,7 @@ }, "reticulate": { "Package": "reticulate", - "Version": "1.36.1", + "Version": "1.37.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2261,7 +2250,7 @@ "utils", "withr" ], - "Hash": "e037fb5dc364efdaf616eb6bc05aaca2" + "Hash": "9465d3bc6ec44eeaa52527ac2cba4020" }, "rhdf5": { "Package": "rhdf5", @@ -2299,7 +2288,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.27", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2318,7 +2307,7 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "rprojroot": { "Package": "rprojroot", @@ -2554,7 +2543,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2563,7 +2552,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -2605,14 +2594,15 @@ }, "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", @@ -2737,13 +2727,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.50", + "Version": "0.51", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "be7a76845222ad20adb761f462eed3ea" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "tximport": { "Package": "tximport", @@ -2895,7 +2885,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -2903,7 +2893,7 @@ "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "317a0538d32f4a009658bcedb7923f4b" }, "xml2": { "Package": "xml2", diff --git a/renv.lock b/renv.lock index 4d21e76..56f1613 100644 --- a/renv.lock +++ b/renv.lock @@ -184,13 +184,13 @@ }, "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", @@ -826,7 +826,7 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.8.2.1", + "Version": "0.12.8.3.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -836,7 +836,7 @@ "stats", "utils" ], - "Hash": "d5448fb24fb114c4da1275a37a571f37" + "Hash": "1eb4a0603478b5557b77d75534251371" }, "RcppEigen": { "Package": "RcppEigen", @@ -1035,7 +1035,7 @@ }, "Seurat": { "Package": "Seurat", - "Version": "5.0.3", + "Version": "5.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1098,11 +1098,11 @@ "utils", "uwot" ], - "Hash": "f5325a968489ef65254a51d74dc0c520" + "Hash": "aa2040fec3d03e3e598e0b406a84a104" }, "SeuratObject": { "Package": "SeuratObject", - "Version": "5.0.1", + "Version": "5.0.2", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1125,7 +1125,7 @@ "tools", "utils" ], - "Hash": "424c2b9e50b053c86fc38f17e09917da" + "Hash": "e9b70412b7e04571b46101f5dcbaacad" }, "SingleCellExperiment": { "Package": "SingleCellExperiment", @@ -1169,7 +1169,7 @@ }, "SparseArray": { "Package": "SparseArray", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -1183,9 +1183,10 @@ "XVector", "matrixStats", "methods", - "stats" + "stats", + "utils" ], - "Hash": "84697af365cd2a6367fa5d2c1086298c" + "Hash": "c309b75cfb1f52407e40ebbd151af932" }, "SummarizedExperiment": { "Package": "SummarizedExperiment", @@ -1281,7 +1282,7 @@ }, "alabaster.base": { "Package": "alabaster.base", - "Version": "1.4.0", + "Version": "1.4.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -1295,7 +1296,7 @@ "rhdf5", "utils" ], - "Hash": "dff0dcd23d2ca7ce1d90e513cb6a6c63" + "Hash": "a4208190d6be247ff0a9d020e0caf4f3" }, "alabaster.matrix": { "Package": "alabaster.matrix", @@ -1548,14 +1549,13 @@ }, "broom": { "Package": "broom", - "Version": "1.0.5", + "Version": "1.0.6", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "backports", "dplyr", - "ellipsis", "generics", "glue", "lifecycle", @@ -1565,7 +1565,7 @@ "tibble", "tidyr" ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" + "Hash": "a4652c36d1f8abfc3ddf4774f768c934" }, "bslib": { "Package": "bslib", @@ -1602,14 +1602,14 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", @@ -1986,7 +1986,7 @@ }, "dqrng": { "Package": "dqrng", - "Version": "0.3.2", + "Version": "0.4.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1995,7 +1995,7 @@ "Rcpp", "sitmo" ], - "Hash": "824df2aeba88d701df5e79018b35b815" + "Hash": "b31198e6268008976689b196bf9d883f" }, "dtplyr": { "Package": "dtplyr", @@ -2065,17 +2065,6 @@ ], "Hash": "f465598eee872acd692ea6ba2cfc4c94" }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, "ensembldb": { "Package": "ensembldb", "Version": "2.28.0", @@ -2128,10 +2117,10 @@ }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "RSPM", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastDummies": { "Package": "fastDummies", @@ -2148,10 +2137,10 @@ }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Repository": "RSPM", + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "filelock": { "Package": "filelock", @@ -3356,13 +3345,13 @@ }, "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", @@ -3415,7 +3404,7 @@ }, "paws.common": { "Package": "paws.common", - "Version": "0.7.2", + "Version": "0.7.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -3430,17 +3419,17 @@ "utils", "xml2" ], - "Hash": "c66dfa46eb607d3171f89596d7529446" + "Hash": "cac0fa401210ea975f052359afa894e2" }, "paws.storage": { "Package": "paws.storage", - "Version": "0.5.0", + "Version": "0.6.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "paws.common" ], - "Hash": "e4a5655c4172112449f7f501c60ed671" + "Hash": "86a93407f22e5855723b83988a142dcb" }, "pbapply": { "Package": "pbapply", @@ -3717,14 +3706,14 @@ }, "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", @@ -3854,9 +3843,9 @@ }, "reticulate": { "Package": "reticulate", - "Version": "1.36.1", + "Version": "1.37.0", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "Matrix", "R", @@ -3872,7 +3861,7 @@ "utils", "withr" ], - "Hash": "e037fb5dc364efdaf616eb6bc05aaca2" + "Hash": "9465d3bc6ec44eeaa52527ac2cba4020" }, "rhdf5": { "Package": "rhdf5", @@ -3920,9 +3909,9 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.27", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", "Requirements": [ "R", "bslib", @@ -3939,7 +3928,7 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "rprojroot": { "Package": "rprojroot", @@ -4444,7 +4433,7 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -4453,7 +4442,7 @@ "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -4523,14 +4512,15 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "6d538cff441f0f1f36db2209ac7495ac" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "tensor": { "Package": "tensor", @@ -4691,13 +4681,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.50", + "Version": "0.51", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "xfun" ], - "Hash": "be7a76845222ad20adb761f462eed3ea" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "tweenr": { "Package": "tweenr", @@ -4882,7 +4872,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.44", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -4890,7 +4880,7 @@ "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "317a0538d32f4a009658bcedb7923f4b" }, "xml2": { "Package": "xml2", From 419b38df98eb9028f3578d7f9fc5a92d75d7c2b4 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Thu, 23 May 2024 08:22:30 -0400 Subject: [PATCH 3/3] add a tag for PRs so GHA doesn't warn --- .github/workflows/build-docker.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-docker.yaml b/.github/workflows/build-docker.yaml index 291c6c4..34a80f2 100644 --- a/.github/workflows/build-docker.yaml +++ b/.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