From f80414305fb3ec22b4a4d6f41125afe286067ab6 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 11:51:17 +1100 Subject: [PATCH 01/23] Add qs2 to lockfile --- renv.lock | 2153 +++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 2096 insertions(+), 57 deletions(-) diff --git a/renv.lock b/renv.lock index bd94859..4adbb2f 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.5.1", + "Version": "4.5.0", "Repositories": [ { "Name": "BioCsoft", @@ -50,6 +50,63 @@ "Repository": "CRAN", "Encoding": "UTF-8" }, + "BiocGenerics": { + "Package": "BiocGenerics", + "Version": "0.56.0", + "Source": "Bioconductor", + "Title": "S4 generic functions used in Bioconductor", + "Description": "The package defines many S4 generic functions used in Bioconductor.", + "biocViews": "Infrastructure", + "URL": "https://bioconductor.org/packages/BiocGenerics", + "BugReports": "https://github.com/Bioconductor/BiocGenerics/issues", + "License": 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RMarkdown / HTML.), Phylis Atieno [ctb] (Translated 'Introduction to BiocParallel' vignette from Sweave to Rmarkdown / HTML.), Sergio Oller [ctb] (Improved bpmapply() efficiency., ORCID: )", + "Maintainer": "Jiefei Wang " + }, "BiocVersion": { "Package": "BiocVersion", "Version": "3.22.0", @@ -104,6 +224,121 @@ "Author": "Martin Morgan [aut], Marcel Ramos [ctb], Bioconductor Package Maintainer [ctb, cre]", "Maintainer": "Bioconductor Package Maintainer " }, + "Biostrings": { + "Package": "Biostrings", + "Version": "2.78.0", + "Source": "Bioconductor", + "Title": "Efficient manipulation of biological strings", + "Description": "Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.", + "biocViews": "SequenceMatching, Alignment, Sequencing, Genetics, DataImport, DataRepresentation, Infrastructure", + "URL": "https://bioconductor.org/packages/Biostrings", + "BugReports": 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Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.", + "biocViews": "Infrastructure, DataRepresentation", + "URL": "https://bioconductor.org/packages/IRanges", + "BugReports": "https://github.com/Bioconductor/IRanges/issues", + "License": "Artistic-2.0", + "Encoding": "UTF-8", + "Authors@R": "c( person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"hpages.on.github@gmail.com\"), person(\"Patrick\", \"Aboyoun\", role=\"aut\"), person(\"Michael\", \"Lawrence\", role=\"aut\"))", + "Depends": [ + "R (>= 4.0.0)", + "methods", + "utils", + "stats", + "BiocGenerics (>= 0.53.2)", + "S4Vectors (>= 0.47.6)" + ], + "Imports": [ + "stats4" + ], + "LinkingTo": [ + "S4Vectors" + ], + "Suggests": [ + "XVector", + "GenomicRanges", + "Rsamtools", + "GenomicAlignments", + "GenomicFeatures", + "BSgenome.Celegans.UCSC.ce2", + "pasillaBamSubset", + "RUnit", + "BiocStyle" + ], + "Collate": "thread-control.R range-squeezers.R Vector-class-leftovers.R DataFrameList-class.R DataFrameList-utils.R AtomicList-class.R AtomicList-utils.R Ranges-and-RangesList-classes.R IPosRanges-class.R IPosRanges-comparison.R IntegerRangesList-class.R IRanges-class.R IRanges-constructor.R makeIRangesFromDataFrame.R IRanges-utils.R Rle-class-leftovers.R IPos-class.R subsetting-utils.R Grouping-class.R Views-class.R RleViews-class.R RleViews-summarization.R extractList.R seqapply.R multisplit.R SimpleGrouping-class.R IRangesList-class.R IPosList-class.R ViewsList-class.R RleViewsList-class.R RleViewsList-utils.R RangedSelection-class.R MaskCollection-class.R read.Mask.R CompressedList-class.R CompressedList-comparison.R CompressedHitsList-class.R CompressedDataFrameList-class.R CompressedAtomicList-class.R CompressedAtomicList-summarization.R CompressedGrouping-class.R CompressedRangesList-class.R Hits-class-leftovers.R NCList-class.R findOverlaps-methods.R windows-methods.R intra-range-methods.R inter-range-methods.R reverse-methods.R coverage-methods.R cvg-methods.R slice-methods.R setops-methods.R nearest-methods.R cbind-Rle-methods.R tile-methods.R extractListFragments.R zzz.R", + "git_url": "https://git.bioconductor.org/packages/IRanges", + "git_branch": "RELEASE_3_22", + "git_last_commit": "964a290", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "yes", + "Author": "Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut]", + "Maintainer": "Hervé Pagès " + }, "KernSmooth": { "Package": "KernSmooth", "Version": "2.23-26", @@ -331,7 +745,8 @@ "NeedsCompilation": "yes", "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", "Maintainer": "Brian Ripley ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "MASS": { "Package": "MASS", @@ -367,7 +782,8 @@ "NeedsCompilation": "yes", "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. 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Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.", + "License": "GPL (>= 2)", + "Depends": [ + "R (>= 2.15.1)" + ], + "Suggests": [ + "zoo", + "testthat" + ], + "Imports": [ + "Rcpp" + ], + "LinkingTo": [ + "Rcpp" + ], + "RoxygenNote": "6.0.1", + "NeedsCompilation": "yes", + "Author": "Kevin Ushey [aut, cre]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, "RcppTOML": { "Package": "RcppTOML", "Version": "0.2.3", @@ -980,6 +1425,102 @@ "Maintainer": "Georgi N. Boshnakov ", "Repository": "RSPM" }, + "Rhtslib": { + "Package": "Rhtslib", + "Version": "3.6.0", + "Source": "Bioconductor", + "Title": "HTSlib high-throughput sequencing library as an R package", + "Description": "This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package=\"Rhtslib\", \"Rhtslib\").", + "biocViews": "DataImport, Sequencing", + "URL": "https://bioconductor.org/packages/Rhtslib, http://www.htslib.org/", + "BugReports": "https://github.com/Bioconductor/Rhtslib/issues", + "License": "LGPL (>= 2)", + "Copyright": "Unless otherwise noted in the file, all files outside src/htslib-1.18 or inst/include copyright Bioconductor; for files inside src/htslib-1.18 or inst/include, see file src/htslib-1.18/LICENSE.", + "Encoding": "UTF-8", + "Authors@R": "c( person(\"Nathaniel\", \"Hayden\", role=c(\"led\", \"aut\"), email=\"nhayden@fredhutch.org\"), person(\"Martin\", \"Morgan\", role=\"aut\", email=\"martin.morgan@roswellpark.org\"), person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"hpages.on.github@gmail.com\"), person(\"Tomas\", \"Kalibera\", role=\"ctb\"), person(\"Jeroen\", \"Ooms\", role=\"ctb\"))", + "Imports": [ + "tools" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "BiocStyle" + ], + "SystemRequirements": "libbz2 & liblzma & libcurl (with header files), GNU make", + "StagedInstall": "no", + "VignetteBuilder": "knitr", + "git_url": "https://git.bioconductor.org/packages/Rhtslib", + "git_branch": "RELEASE_3_22", + "git_last_commit": "c4b7268", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "yes", + "Author": "Nathaniel Hayden [led, aut], Martin Morgan [aut], Hervé Pagès [aut, cre], Tomas Kalibera [ctb], Jeroen Ooms [ctb]", + "Maintainer": "Hervé Pagès " + }, + "Rsamtools": { + "Package": "Rsamtools", + "Version": "2.26.0", + "Source": "Bioconductor", + "Type": "Package", + "Title": "Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import", + "Description": "This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.", + "biocViews": "DataImport, Sequencing, Coverage, Alignment, QualityControl", + "URL": "https://bioconductor.org/packages/Rsamtools", + "Video": "https://www.youtube.com/watch?v=Rfon-DQYbWA&list=UUqaMSQd_h-2EDGsU6WDiX0Q", + "BugReports": "https://github.com/Bioconductor/Rsamtools/issues", + "License": "Artistic-2.0 | file LICENSE", + "Encoding": "UTF-8", + "Authors@R": "c( person(\"Martin\", \"Morgan\", role = \"aut\"), person(\"Hervé\", \"Pagès\", role = \"aut\"), person(\"Valerie\", \"Obenchain\", role = \"aut\"), person(\"Nathaniel\", \"Hayden\", role = \"aut\"), person(\"Busayo\", \"Samuel\", role = \"ctb\", comment = \"Converted Rsamtools vignette from Sweave to RMarkdown / HTML.\"), person(\"Bioconductor Package Maintainer\", email = \"maintainer@bioconductor.org\", role = \"cre\"))", + "Depends": [ + "R (>= 3.5.0)", + "methods", + "Seqinfo", + "GenomicRanges (>= 1.61.1)", + "Biostrings (>= 2.77.2)" + ], + "Imports": [ + "utils", + "BiocGenerics (>= 0.25.1)", + "S4Vectors (>= 0.17.25)", + "IRanges (>= 2.13.12)", + "XVector (>= 0.19.7)", + "bitops", + "BiocParallel", + "stats" + ], + "Suggests": [ + "GenomicAlignments", + "ShortRead (>= 1.19.10)", + "GenomicFeatures", + "VariantAnnotation", + "TxDb.Dmelanogaster.UCSC.dm3.ensGene", + "TxDb.Hsapiens.UCSC.hg18.knownGene", + "RNAseqData.HNRNPC.bam.chr14", + "BSgenome.Hsapiens.UCSC.hg19", + "RUnit", + "BiocStyle", + "knitr" + ], + "LinkingTo": [ + "Rhtslib (>= 3.3.1)", + "S4Vectors", + "IRanges", + "XVector", + "Biostrings" + ], + "LazyLoad": "yes", + "SystemRequirements": "GNU make", + "VignetteBuilder": "knitr", + "git_url": "https://git.bioconductor.org/packages/Rsamtools", + "git_branch": "RELEASE_3_22", + "git_last_commit": "ea99fb0", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "yes", + "Author": "Martin Morgan [aut], Hervé Pagès [aut], Valerie Obenchain [aut], Nathaniel Hayden [aut], Busayo Samuel [ctb] (Converted Rsamtools vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre]", + "Maintainer": "Bioconductor Package Maintainer " + }, "Rtsne": { "Package": "Rtsne", "Version": "0.17", @@ -1004,10 +1545,54 @@ ], "RoxygenNote": "7.2.3", "NeedsCompilation": "yes", - "Author": "Jesse Krijthe [aut, cre], Laurens van der Maaten [cph] (Author of original C++ code)", - "Maintainer": "Jesse Krijthe ", - "License_is_FOSS": "yes", - "Repository": "CRAN" + "Author": "Jesse Krijthe [aut, cre], Laurens van der Maaten [cph] (Author of original C++ code)", + "Maintainer": "Jesse Krijthe ", + "License_is_FOSS": "yes", + "Repository": "CRAN" + }, + "S4Vectors": { + "Package": "S4Vectors", + "Version": "0.48.0", + "Source": "Bioconductor", + "Title": "Foundation of vector-like and list-like containers in Bioconductor", + "Description": "The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).", + "biocViews": "Infrastructure, DataRepresentation", + "URL": "https://bioconductor.org/packages/S4Vectors", + "BugReports": "https://github.com/Bioconductor/S4Vectors/issues", + "License": "Artistic-2.0", + "Encoding": "UTF-8", + "Authors@R": "c( person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"hpages.on.github@gmail.com\"), person(\"Michael\", \"Lawrence\", role=\"aut\"), person(\"Patrick\", \"Aboyoun\", role=\"aut\"), person(\"Aaron\", \"Lun\", role=\"ctb\"), person(\"Beryl\", \"Kanali\", role=\"ctb\", comment=\"Converted vignettes from Sweave to RMarkdown\"))", + "Depends": [ + "R (>= 4.0.0)", + "methods", + "utils", + "stats", + "stats4", + "BiocGenerics (>= 0.53.2)" + ], + "Suggests": [ + "IRanges", + "GenomicRanges", + "SummarizedExperiment", + "Matrix", + "DelayedArray", + "ShortRead", + "graph", + "data.table", + "RUnit", + "BiocStyle", + "knitr" + ], + "VignetteBuilder": "knitr", + "Collate": "S4-utils.R show-utils.R utils.R normarg-utils.R bindROWS.R LLint-class.R isSorted.R subsetting-utils.R vector-utils.R integer-utils.R character-utils.R raw-utils.R eval-utils.R map_ranges_to_runs.R RectangularData-class.R Annotated-class.R DataFrame_OR_NULL-class.R Vector-class.R Vector-comparison.R Vector-setops.R Vector-merge.R Hits-class.R Hits-comparison.R Hits-setops.R Rle-class.R Rle-utils.R Factor-class.R List-class.R List-comparison.R splitAsList.R List-utils.R SimpleList-class.R HitsList-class.R DataFrame-class.R DataFrame-combine.R DataFrame-comparison.R DataFrame-utils.R DataFrameFactor-class.R TransposedDataFrame-class.R Pairs-class.R FilterRules-class.R stack-methods.R expand-methods.R aggregate-methods.R shiftApply-methods.R zzz.R", + "git_url": "https://git.bioconductor.org/packages/S4Vectors", + "git_branch": "RELEASE_3_22", + "git_last_commit": "c4f37f0", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "yes", + "Author": "Hervé Pagès [aut, cre], Michael Lawrence [aut], Patrick Aboyoun [aut], Aaron Lun [ctb], Beryl Kanali [ctb] (Converted vignettes from Sweave to RMarkdown)", + "Maintainer": "Hervé Pagès " }, "S7": { "Package": "S7", @@ -1048,6 +1633,52 @@ "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, + "Seqinfo": { + "Package": "Seqinfo", + "Version": "1.0.0", + "Source": "Bioconductor", + "Title": "A simple S4 class for storing basic information about a collection of genomic sequences", + "Description": "The Seqinfo class stores the names, lengths, circularity flags, and genomes for a particular collection of sequences. These sequences are typically the chromosomes and/or scaffolds of a specific genome assembly of a given organism. Seqinfo objects are rarely used as standalone objects. Instead, they are used as part of higher-level objects to represent their seqinfo() component. Examples of such higher-level objects are GRanges, RangedSummarizedExperiment, VCF, GAlignments, etc... defined in other Bioconductor infrastructure packages.", + "biocViews": "Infrastructure, DataRepresentation, GenomeAssembly, Annotation, GenomeAnnotation", + "URL": "https://bioconductor.org/packages/Seqinfo", + "BugReports": "https://github.com/Bioconductor/Seqinfo/issues", + "License": "Artistic-2.0", + "Encoding": "UTF-8", + "Authors@R": "person(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"), email=\"hpages.on.github@gmail.com\", comment=c(ORCID=\"0009-0002-8272-4522\"))", + "Depends": [ + "methods", + "BiocGenerics" + ], + "Imports": [ + "stats", + "S4Vectors (>= 0.47.6)", + "IRanges" + ], + "Suggests": [ + "GenomeInfoDb", + "GenomicRanges", + "BSgenome", + "GenomicFeatures", + "TxDb.Hsapiens.UCSC.hg38.knownGene", + "TxDb.Dmelanogaster.UCSC.dm3.ensGene", + "BSgenome.Hsapiens.UCSC.hg38", + "BSgenome.Celegans.UCSC.ce2", + "RUnit", + "knitr", + "rmarkdown", + "BiocStyle" + ], + "VignetteBuilder": "knitr", + "Collate": "utils.R rankSeqlevels.R seqinfo.R sortSeqlevels.R Seqinfo-class.R seqlevelsInUse.R GenomeDescription-class.R zzz.R", + "git_url": "https://git.bioconductor.org/packages/Seqinfo", + "git_branch": "RELEASE_3_22", + "git_last_commit": "9fc5a61", + "git_last_commit_date": "2025-10-29", + "Repository": "Bioconductor 3.22", + "NeedsCompilation": "no", + "Author": "Hervé Pagès [aut, cre] (ORCID: )", + "Maintainer": "Hervé Pagès " + }, "Seurat": { "Package": "Seurat", "Version": "5.4.0", @@ -1264,6 +1895,89 @@ "RemoteRef": "master", "RemoteSha": "5c61db78cdd624636e161406d5d42aeb2c0f1205" }, + "Signac": { + "Package": "Signac", + "Version": "1.16.0", + "Source": "GitHub", + "Title": "Analysis of Single-Cell Chromatin Data", + "Date": "2025-10-10", + "Authors@R": "c( person(given = 'Tim', family = 'Stuart', email = 'stuartt@a-star.edu.sg', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')), person(given = 'Avi', family = 'Srivastava', email = 'asrivastava@wistar.org', role = 'aut', comment = c(ORCID = '0000-0001-9798-2079')), person(given = 'Paul', family = 'Hoffman', email = 'phoffman@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-7693-8957')), person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9448-8833')) )", + "Description": "A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. 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This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 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back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.", + "License": "MIT + file LICENSE", + "URL": "https://dbplyr.tidyverse.org/, https://github.com/tidyverse/dbplyr", + "BugReports": "https://github.com/tidyverse/dbplyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "blob (>= 1.2.0)", + "cli (>= 3.6.1)", + "DBI (>= 1.1.3)", + "dplyr (>= 1.1.2)", + "glue (>= 1.6.2)", + "lifecycle (>= 1.0.3)", + "magrittr", + "methods", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "R6 (>= 2.2.2)", + "rlang (>= 1.1.1)", + "tibble (>= 3.2.1)", + "tidyr (>= 1.3.0)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "bit64", + "covr", + "knitr", + "Lahman", + "nycflights13", + "odbc (>= 1.4.2)", + "RMariaDB (>= 1.2.2)", + "rmarkdown", + "RPostgres (>= 1.4.5)", + "RPostgreSQL", + "RSQLite (>= 2.3.8)", + "testthat (>= 3.1.10)" ], - "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", - "License": "MPL-2.0 | file LICENSE", - "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", - "BugReports": "https://github.com/Rdatatable/data.table/issues", "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", "Encoding": "UTF-8", - "ByteCompile": "TRUE", - "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\", email=\"j.gorecki@wit.edu.pl\"), person(\"Michael\",\"Chirico\", role=\"aut\", email=\"michaelchirico4@gmail.com\", comment = c(ORCID=\"0000-0003-0787-087X\")), 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\"aut\"), person(\"Mark\", \"Fairbanks\", role = \"aut\"), person(\"Ryan\", \"Dickerson\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.", + "License": "MIT + file LICENSE", + "URL": "https://dtplyr.tidyverse.org, https://github.com/tidyverse/dtplyr", + "BugReports": "https://github.com/tidyverse/dtplyr/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "data.table (>= 1.13.0)", + "dplyr (>= 1.1.0)", + "glue", + "lifecycle", + "rlang (>= 1.0.4)", + "tibble", + "tidyselect (>= 1.2.0)", + "vctrs (>= 0.4.1)" + ], + "Suggests": [ + "bench", + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.2)", + "tidyr (>= 1.1.0)", + "waldo (>= 0.3.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [cre, aut], Maximilian Girlich [aut], Mark Fairbanks [aut], Ryan Dickerson [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "edgeR": { "Package": "edgeR", "Version": "4.8.2", @@ -3082,6 +4126,25 @@ "Maintainer": "Winston Chang ", "Repository": "CRAN" }, + "fastmatch": { + "Package": "fastmatch", + "Version": "1.1-8", + "Source": "Repository", + "Title": "Fast 'match()' Function", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.nz, ORCID: )", + "Authors@R": "person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.nz\", ORCID=\"0000-0003-2297-1732\"))", + "Maintainer": "Simon Urbanek ", + "Description": "Package providing a fast match() replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match() function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.", + "License": "GPL-2", + "Depends": [ + "R (>= 2.3.0)" + ], + "URL": "https://www.rforge.net/fastmatch", + "BugReports": "https://github.com/s-u/fastmatch/issues/", + "NeedsCompilation": "yes", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, "fitdistrplus": { "Package": "fitdistrplus", "Version": "1.2-6", @@ -3178,6 +4241,48 @@ "Maintainer": "Richard Iannone ", "Repository": "CRAN" }, + "forcats": { + "Package": "forcats", + "Version": "1.0.1", + "Source": "Repository", + "Title": "Tools for Working with Categorical Variables (Factors)", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').", + "License": "MIT + file LICENSE", + "URL": "https://forcats.tidyverse.org/, https://github.com/tidyverse/forcats", + "BugReports": "https://github.com/tidyverse/forcats/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle", + "magrittr", + "rlang (>= 1.0.0)", + "tibble" + ], + "Suggests": [ + "covr", + "dplyr", + "ggplot2", + "knitr", + "readr", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "forecast": { "Package": "forecast", "Version": "9.0.1", @@ -3234,6 +4339,35 @@ "Maintainer": "Rob Hyndman ", "Repository": "CRAN" }, + "formatR": { + "Package": "formatR", + "Version": "1.14", + "Source": "Repository", + "Type": "Package", + "Title": "Format R Code Automatically", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Ed\", \"Lee\", role = \"ctb\"), person(\"Eugene\", \"Ha\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Pavel\", \"Krivitsky\", role = \"ctb\"), person() )", + "Description": "Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package (see tidy_app()).", + "Depends": [ + "R (>= 3.2.3)" + ], + "Suggests": [ + "rstudioapi", + "shiny", + "testit", + "rmarkdown", + "knitr" + ], + "License": "GPL", + "URL": "https://github.com/yihui/formatR", + "BugReports": "https://github.com/yihui/formatR/issues", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Ed Lee [ctb], Eugene Ha [ctb], Kohske Takahashi [ctb], Pavel Krivitsky [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" + }, "fracdiff": { "Package": "fracdiff", "Version": "1.5-3", @@ -3303,6 +4437,62 @@ "Maintainer": "Jeroen Ooms ", "Repository": "CRAN" }, + "futile.logger": { + "Package": "futile.logger", + "Version": "1.4.9", + "Source": "Repository", + "Type": "Package", + "Title": "A Logging Utility for R", + "Date": "2025-12-22", + "Maintainer": "Brian Lee Yung Rowe ", + "Authors@R": "person(given=c(\"Brian\", \"Lee\", \"Yung\"), family=\"Rowe\", role=c(\"aut\", \"cre\"), email=\"r@zatonovo.com\")", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "utils", + "lambda.r (>= 1.1.0)", + "futile.options" + ], + "Suggests": [ + "testit", + "jsonlite", + "httr", + "crayon", + "rsyslog", + "glue" + ], + "Description": "Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.", + "License": "LGPL-3", + "LazyLoad": "yes", + "NeedsCompilation": "no", + "ByteCompile": "yes", + "Collate": "'options.R' 'appender.R' 'constants.R' 'layout.R' 'logger.R' 'scat.R' 'util.R' 'futile.logger-package.R'", + "RoxygenNote": "7.1.2", + "URL": "https://github.com/zatonovo/futile.logger", + "Author": "Brian Lee Yung Rowe [aut, cre]", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "futile.options": { + "Package": "futile.options", + "Version": "1.0.1", + "Source": "Repository", + "Type": "Package", + "Title": "Futile Options Management", + "Date": "2018-04-20", + "Author": "Brian Lee Yung Rowe", + "Maintainer": "Brian Lee Yung Rowe ", + "Depends": [ + "R (>= 2.8.0)" + ], + "Description": "A scoped options management framework. Used in other packages.", + "License": "LGPL-3", + "LazyLoad": "yes", + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, "future": { "Package": "future", "Version": "1.69.0", @@ -3379,6 +4569,55 @@ "Maintainer": "Henrik Bengtsson ", "Repository": "CRAN" }, + "gargle": { + "Package": "gargle", + "Version": "1.6.1", + "Source": "Repository", + "Title": "Utilities for Working with Google APIs", + "Authors@R": "c( person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Craig\", \"Citro\", , \"craigcitro@google.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Google Inc\", role = \"cph\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides utilities for working with Google APIs . This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.", + "License": "MIT + file LICENSE", + "URL": "https://gargle.r-lib.org, https://github.com/r-lib/gargle", + "BugReports": "https://github.com/r-lib/gargle/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli (>= 3.0.1)", + "fs (>= 1.3.1)", + "glue (>= 1.3.0)", + "httr (>= 1.4.5)", + "jsonlite", + "lifecycle (>= 0.2.0)", + "openssl", + "rappdirs", + "rlang (>= 1.1.0)", + "stats", + "utils", + "withr" + ], + "Suggests": [ + "aws.ec2metadata", + "aws.signature", + "covr", + "httpuv", + "knitr", + "rmarkdown", + "sodium", + "spelling", + "testthat (>= 3.1.7)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Jennifer Bryan [aut, cre] (ORCID: ), Craig Citro [aut], Hadley Wickham [aut] (ORCID: ), Google Inc [cph], Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, "generics": { "Package": "generics", "Version": "0.1.4", @@ -3670,6 +4909,33 @@ "Maintainer": "Claus O. Wilke ", "Repository": "CRAN" }, + "ggseqlogo": { + "Package": "ggseqlogo", + "Version": "0.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos", + "Date": "2025-12-22", + "Description": "The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.", + "License": "LGPL", + "URL": "https://github.com/omarwagih/ggseqlogo", + "BugReports": "https://github.com/omarwagih/ggseqlogo/issues", + "Encoding": "UTF-8", + "Imports": [ + "ggplot2" + ], + "RoxygenNote": "7.2.3", + "Suggests": [ + "knitr", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Repository": "CRAN", + "Authors@R": "person(\"Omar\", \"Wagih\", , \"omarwagih@gmail.com\", role = c(\"aut\", \"cre\"))", + "Author": "Omar Wagih [aut, cre]", + "Maintainer": "Omar Wagih " + }, "globals": { "Package": "globals", "Version": "0.19.0", @@ -3731,35 +4997,134 @@ "Config/Needs/website": "bench, forcats, ggbeeswarm, ggplot2, R.utils, rprintf, tidyr, tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "NeedsCompilation": "yes", - "Author": "Jim Hester [aut] (), Jennifer Bryan [aut, cre] (), Posit Software, PBC [cph, fnd]", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Jennifer Bryan [aut, cre] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "goftest": { + "Package": "goftest", + "Version": "1.2-3", + "Source": "Repository", + "Type": "Package", + "Title": "Classical Goodness-of-Fit Tests for Univariate Distributions", + "Date": "2021-10-07", + "Authors@R": "c(person(\"Julian\", \"Faraway\", role = \"aut\"), person(\"George\", \"Marsaglia\", role = \"aut\"), person(\"John\", \"Marsaglia\", role = \"aut\"), person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\"))", + "Depends": [ + "R (>= 3.3)" + ], + "Imports": [ + "stats" + ], + "Description": "Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms.", + "URL": "https://github.com/baddstats/goftest", + "BugReports": "https://github.com/baddstats/goftest/issues", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Author": "Julian Faraway [aut], George Marsaglia [aut], John Marsaglia [aut], Adrian Baddeley [aut, cre]", + "Maintainer": "Adrian Baddeley ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "googledrive": { + "Package": "googledrive", + "Version": "2.1.2", + "Source": "Repository", + "Title": "An Interface to Google Drive", + "Authors@R": "c( person(\"Lucy\", \"D'Agostino McGowan\", , role = \"aut\"), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Manage Google Drive files from R.", + "License": "MIT + file LICENSE", + "URL": "https://googledrive.tidyverse.org, https://github.com/tidyverse/googledrive", + "BugReports": "https://github.com/tidyverse/googledrive/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "gargle (>= 1.6.0)", + "glue (>= 1.4.2)", + "httr", + "jsonlite", + "lifecycle", + "magrittr", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "rlang (>= 1.0.2)", + "tibble (>= 2.0.0)", + "utils", + "uuid", + "vctrs (>= 0.3.0)", + "withr" + ], + "Suggests": [ + "curl", + "dplyr (>= 1.0.0)", + "knitr", + "rmarkdown", + "spelling", + "testthat (>= 3.1.5)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Lucy D'Agostino McGowan [aut], Jennifer Bryan [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, - "goftest": { - "Package": "goftest", - "Version": "1.2-3", + "googlesheets4": { + "Package": "googlesheets4", + "Version": "1.1.2", "Source": "Repository", - "Type": "Package", - "Title": "Classical Goodness-of-Fit Tests for Univariate Distributions", - "Date": "2021-10-07", - "Authors@R": "c(person(\"Julian\", \"Faraway\", role = \"aut\"), person(\"George\", \"Marsaglia\", role = \"aut\"), person(\"John\", \"Marsaglia\", role = \"aut\"), person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\"))", + "Title": "Access Google Sheets using the Sheets API V4", + "Authors@R": "c( person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Interact with Google Sheets through the Sheets API v4 . \"API\" is an acronym for \"application programming interface\"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The \"v4\" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.", + "License": "MIT + file LICENSE", + "URL": "https://googlesheets4.tidyverse.org, https://github.com/tidyverse/googlesheets4", + "BugReports": "https://github.com/tidyverse/googlesheets4/issues", "Depends": [ - "R (>= 3.3)" + "R (>= 3.6)" ], "Imports": [ - "stats" + "cellranger", + "cli (>= 3.0.0)", + "curl", + "gargle (>= 1.6.0)", + "glue (>= 1.3.0)", + "googledrive (>= 2.1.0)", + "httr", + "ids", + "lifecycle", + "magrittr", + "methods", + "purrr", + "rematch2", + "rlang (>= 1.0.2)", + "tibble (>= 2.1.1)", + "utils", + "vctrs (>= 0.2.3)", + "withr" ], - "Description": "Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms.", - "URL": "https://github.com/baddstats/goftest", - "BugReports": "https://github.com/baddstats/goftest/issues", - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Author": "Julian Faraway [aut], George Marsaglia [aut], John Marsaglia [aut], Adrian Baddeley [aut, cre]", - "Maintainer": "Adrian Baddeley ", - "Repository": "CRAN", - "Encoding": "UTF-8" + "Suggests": [ + "readr", + "rmarkdown", + "spelling", + "testthat (>= 3.1.7)" + ], + "ByteCompile": "true", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "no", + "Author": "Jennifer Bryan [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" }, "gplots": { "Package": "gplots", @@ -3934,6 +5299,55 @@ "Maintainer": "Ben Bolker ", "Repository": "CRAN" }, + "haven": { + "Package": "haven", + "Version": "2.5.5", + "Source": "Repository", + "Title": "Import and Export 'SPSS', 'Stata' and 'SAS' Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Evan\", \"Miller\", role = c(\"aut\", \"cph\"), comment = \"Author of included ReadStat code\"), person(\"Danny\", \"Smith\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Import foreign statistical formats into R via the embedded 'ReadStat' C library, .", + "License": "MIT + file LICENSE", + "URL": "https://haven.tidyverse.org, https://github.com/tidyverse/haven, https://github.com/WizardMac/ReadStat", + "BugReports": "https://github.com/tidyverse/haven/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "forcats (>= 0.2.0)", + "hms", + "lifecycle", + "methods", + "readr (>= 0.1.0)", + "rlang (>= 0.4.0)", + "tibble", + "tidyselect", + "vctrs (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "crayon", + "fs", + "knitr", + "pillar (>= 1.4.0)", + "rmarkdown", + "testthat (>= 3.0.0)", + "utf8" + ], + "LinkingTo": [ + "cpp11" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "GNU make, zlib: zlib1g-dev (deb), zlib-devel (rpm)", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), Danny Smith [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "hdf5r": { "Package": "hdf5r", "Version": "1.3.12", @@ -4248,6 +5662,34 @@ "Repository": "CRAN", "Encoding": "UTF-8" }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository", + "Title": "Generate Random Identifiers", + "Authors@R": "person(\"Rich\", \"FitzJohn\", role = c(\"aut\", \"cre\"), email = \"rich.fitzjohn@gmail.com\")", + "Description": "Generate random or human readable and pronounceable identifiers.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/richfitz/ids", + "BugReports": "https://github.com/richfitz/ids/issues", + "Imports": [ + "openssl", + "uuid" + ], + "Suggests": [ + "knitr", + "rcorpora", + "rmarkdown", + "testthat" + ], + "RoxygenNote": "6.0.1", + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Rich FitzJohn [aut, cre]", + "Maintainer": "Rich FitzJohn ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, "igraph": { "Package": "igraph", "Version": "2.2.2", @@ -4575,6 +6017,31 @@ "Repository": "CRAN", "Encoding": "UTF-8" }, + "lambda.r": { + "Package": "lambda.r", + "Version": "1.2.4", + "Source": "Repository", + "Type": "Package", + "Title": "Modeling Data with Functional Programming", + "Date": "2019-09-15", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "formatR" + ], + "Suggests": [ + "testit" + ], + "Author": "Brian Lee Yung Rowe", + "Maintainer": "Brian Lee Yung Rowe ", + "Description": "A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.", + "License": "LGPL-3", + "LazyLoad": "yes", + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, "later": { "Package": "later", "Version": "1.4.8", @@ -4652,7 +6119,8 @@ "NeedsCompilation": "yes", "Author": "Deepayan Sarkar [aut, cre] (), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)", "Maintainer": "Deepayan Sarkar ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "lazyeval": { "Package": "lazyeval", @@ -5238,7 +6706,8 @@ "NeedsCompilation": "yes", "Author": "Simon Wood [aut, cre]", "Maintainer": "Simon Wood ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "microbenchmark": { "Package": "microbenchmark", @@ -5510,7 +6979,8 @@ "NeedsCompilation": "yes", "Author": "Brian Ripley [aut, cre, cph], William Venables [cph]", "Maintainer": "Brian Ripley ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "numDeriv": { "Package": "numDeriv", @@ -6091,6 +7561,46 @@ "Maintainer": "Gabor Csardi ", "Repository": "CRAN" }, + "processx": { + "Package": "processx", + "Version": "3.8.6", + "Source": "Repository", + "Title": "Execute and Control System Processes", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Ascent Digital Services\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.", + "License": "MIT + file LICENSE", + "URL": "https://processx.r-lib.org, https://github.com/r-lib/processx", + "BugReports": "https://github.com/r-lib/processx/issues", + "Depends": [ + "R (>= 3.4.0)" + ], + "Imports": [ + "ps (>= 1.2.0)", + "R6", + "utils" + ], + "Suggests": [ + "callr (>= 3.7.3)", + "cli (>= 3.3.0)", + "codetools", + "covr", + "curl", + "debugme", + "parallel", + "rlang (>= 1.0.2)", + "testthat (>= 3.0.0)", + "webfakes", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1.9000", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre, cph] (), Winston Chang [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, "progress": { "Package": "progress", "Version": "1.2.3", @@ -6220,6 +7730,46 @@ "Maintainer": "Barret Schloerke ", "Repository": "CRAN" }, + "ps": { + "Package": "ps", + "Version": "1.9.2", + "Source": "Repository", + "Title": "List, Query, Manipulate System Processes", + "Authors@R": "c( person(\"Jay\", \"Loden\", role = \"aut\"), person(\"Dave\", \"Daeschler\", role = \"aut\"), person(\"Giampaolo\", \"Rodola'\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/ps, https://ps.r-lib.org/", + "BugReports": "https://github.com/r-lib/ps/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "curl", + "pillar", + "pingr", + "processx (>= 3.1.0)", + "R6", + "rlang", + "testthat (>= 3.0.0)", + "webfakes", + "withr" + ], + "Biarch": "true", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-28", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Jay Loden [aut], Dave Daeschler [aut], Giampaolo Rodola' [aut], Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, "purrr": { "Package": "purrr", "Version": "1.2.1", @@ -6308,6 +7858,43 @@ "Author": "Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Yousef Saad [ctb] (author of sparskit2), Victor Chernozhukov [ctb] (contributions to extreme value inference code), Ivan Fernandez-Val [ctb] (contributions to extreme value inference code), Martin Maechler [ctb] (tweaks (src/chlfct.f, 'tiny','Large'), ), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)", "Encoding": "UTF-8" }, + "ragg": { + "Package": "ragg", + "Version": "1.5.2", + "Source": "Repository", + "Type": "Package", + "Title": "Graphic Devices Based on AGG", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Maintainer": "Thomas Lin Pedersen ", + "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://ragg.r-lib.org, https://github.com/r-lib/ragg", + "BugReports": "https://github.com/r-lib/ragg/issues", + "Imports": [ + "systemfonts (>= 1.0.3)", + "textshaping (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "graphics", + "grid", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "systemfonts", + "textshaping" + ], + "Config/build/compilation-database": "true", + "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg, libwebp, libwebpmux", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit Software, PBC [cph, fnd] (ROR: )", + "Repository": "CRAN" + }, "rappdirs": { "Package": "rappdirs", "Version": "0.3.4", @@ -6425,6 +8012,46 @@ "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.5", + "Source": "Repository", + "Title": "Read Excel Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", + "Description": "Import excel files into R. Supports '.xls' via the embedded 'libxls' C library and '.xlsx' via the embedded 'RapidXML' C++ library . Works on Windows, Mac and Linux without external dependencies.", + "License": "MIT + file LICENSE", + "URL": "https://readxl.tidyverse.org, https://github.com/tidyverse/readxl", + "BugReports": "https://github.com/tidyverse/readxl/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cellranger", + "tibble (>= 2.0.1)", + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.6)", + "withr" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.0)", + "progress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, tidyverse", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Note": "libxls v1.6.3 c199d13", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Posit, PBC [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, "reformulas": { "Package": "reformulas", "Version": "0.4.4", @@ -6436,23 +8063,68 @@ "License": "GPL-3", "Encoding": "UTF-8", "Imports": [ - "stats", - "methods", - "Matrix", - "Rdpack" + "stats", + "methods", + "Matrix", + "Rdpack" + ], + "RdMacros": "Rdpack", + "Suggests": [ + "lme4", + "tinytest", + "glmmTMB", + "Formula" + ], + "RoxygenNote": "7.3.3", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Ben Bolker [aut, cre] (ORCID: ), Anna Ly [ctb] (ORCID: )", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository", + "Title": "Match Regular Expressions with a Nicer 'API'", + "Author": "Gabor Csardi", + "Maintainer": "Gabor Csardi ", + "Description": "A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/gaborcsardi/rematch", + "BugReports": "https://github.com/gaborcsardi/rematch/issues", + "RoxygenNote": "5.0.1.9000", + "Suggests": [ + "covr", + "testthat" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository", + "Title": "Tidy Output from Regular Expression Matching", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", email = \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Matthew\", \"Lincoln\", email = \"matthew.d.lincoln@gmail.com\", role = c(\"ctb\")))", + "Description": "Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames.", + "License": "MIT + file LICENSE", + "LazyData": "true", + "URL": "https://github.com/r-lib/rematch2#readme", + "BugReports": "https://github.com/r-lib/rematch2/issues", + "RoxygenNote": "7.1.0", + "Imports": [ + "tibble" ], - "RdMacros": "Rdpack", "Suggests": [ - "lme4", - "tinytest", - "glmmTMB", - "Formula" + "covr", + "testthat" ], - "RoxygenNote": "7.3.3", - "Config/testthat/edition": "3", + "Encoding": "UTF-8", "NeedsCompilation": "no", - "Author": "Ben Bolker [aut, cre] (ORCID: ), Anna Ly [ctb] (ORCID: )", - "Maintainer": "Ben Bolker ", + "Author": "Gábor Csárdi [aut, cre], Matthew Lincoln [ctb]", + "Maintainer": "Gábor Csárdi ", "Repository": "CRAN" }, "renv": { @@ -6508,6 +8180,58 @@ "Maintainer": "Kevin Ushey ", "Repository": "RSPM" }, + "reprex": { + "Package": "reprex", + "Version": "2.1.1", + "Source": "Repository", + "Title": "Prepare Reproducible Example Code via the Clipboard", + "Authors@R": "c( person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as and , or in email. The user's clipboard is the default source of input code and the default target for rendered output. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.", + "License": "MIT + file LICENSE", + "URL": "https://reprex.tidyverse.org, https://github.com/tidyverse/reprex", + "BugReports": "https://github.com/tidyverse/reprex/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "callr (>= 3.6.0)", + "cli (>= 3.2.0)", + "clipr (>= 0.4.0)", + "fs", + "glue", + "knitr (>= 1.23)", + "lifecycle", + "rlang (>= 1.0.0)", + "rmarkdown", + "rstudioapi", + "utils", + "withr (>= 2.3.0)" + ], + "Suggests": [ + "covr", + "fortunes", + "miniUI", + "rprojroot", + "sessioninfo", + "shiny", + "spelling", + "styler (>= 1.2.0)", + "testthat (>= 3.2.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "dplyr, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Config/testthat/start-first": "knitr-options, venues, reprex", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "SystemRequirements": "pandoc (>= 2.0) - https://pandoc.org/", + "NeedsCompilation": "no", + "Author": "Jennifer Bryan [aut, cre] (), Jim Hester [aut] (), David Robinson [aut], Hadley Wickham [aut] (), Christophe Dervieux [aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, "reshape2": { "Package": "reshape2", "Version": "1.4.5", @@ -6821,6 +8545,57 @@ "Author": "Kevin Ushey [aut, cre], JJ Allaire [aut], Hadley Wickham [aut], Gary Ritchie [aut], RStudio [cph]", "Repository": "CRAN" }, + "rvest": { + "Package": "rvest", + "Version": "1.0.5", + "Source": "Repository", + "Title": "Easily Harvest (Scrape) Web Pages", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.", + "License": "MIT + file LICENSE", + "URL": "https://rvest.tidyverse.org/, https://github.com/tidyverse/rvest", + "BugReports": "https://github.com/tidyverse/rvest/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli", + "glue", + "httr (>= 0.5)", + "lifecycle (>= 1.0.3)", + "magrittr", + "rlang (>= 1.1.0)", + "selectr", + "tibble", + "xml2 (>= 1.4.0)" + ], + "Suggests": [ + "chromote", + "covr", + "knitr", + "purrr", + "R6", + "readr", + "repurrrsive", + "rmarkdown", + "spelling", + "stringi (>= 0.3.1)", + "testthat (>= 3.0.2)", + "tidyr", + "webfakes" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "sass": { "Package": "sass", "Version": "0.4.10", @@ -7004,6 +8779,36 @@ "Maintainer": "Saket Choudhary ", "Repository": "CRAN" }, + "selectr": { + "Package": "selectr", + "Version": "0.5-1", + "Source": "Repository", + "Type": "Package", + "Title": "Translate CSS Selectors to XPath Expressions", + "Authors@R": "c(person(\"Simon\", \"Potter\", role = c(\"aut\", \"trl\", \"cre\"), email = \"simon@sjp.co.nz\"), person(\"Simon\", \"Sapin\", role = \"aut\"), person(\"Ian\", \"Bicking\", role = \"aut\"))", + "License": "BSD_3_clause + file LICENCE", + "Depends": [ + "R (>= 3.0)" + ], + "Imports": [ + "methods", + "stringr", + "R6" + ], + "Suggests": [ + "testthat", + "XML", + "xml2" + ], + "URL": "https://sjp.co.nz/projects/selectr/", + "BugReports": "https://github.com/sjp/selectr/issues", + "Description": "Translates a CSS selector into an equivalent XPath expression. This allows us to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package 'cssselect' ().", + "NeedsCompilation": "no", + "Author": "Simon Potter [aut, trl, cre], Simon Sapin [aut], Ian Bicking [aut]", + "Maintainer": "Simon Potter ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, "shiny": { "Package": "shiny", "Version": "1.13.0", @@ -7141,6 +8946,27 @@ "Maintainer": "Winston Chang ", "Repository": "CRAN" }, + "shinyhelper": { + "Package": "shinyhelper", + "Version": "0.3.2", + "Source": "Repository", + "Type": "Package", + "Title": "Easily Add Markdown Help Files to 'shiny' App Elements", + "Authors@R": "person(\"Chris\", \"Mason-Thom\", email = \"christopher.w.thom@outlook.com\", role=c(\"aut\",\"cre\"))", + "BugReports": "https://github.com/cwthom/shinyhelper/issues", + "Description": "Creates a lightweight way to add markdown helpfiles to 'shiny' apps, using modal dialog boxes, with no need to observe each help button separately.", + "License": "GPL-3", + "Imports": [ + "shiny", + "markdown" + ], + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Chris Mason-Thom [aut, cre]", + "Maintainer": "Chris Mason-Thom ", + "Repository": "CRAN" + }, "shinyjs": { "Package": "shinyjs", "Version": "2.1.1", @@ -7175,6 +9001,28 @@ "Maintainer": "Dean Attali ", "Repository": "CRAN" }, + "shinythemes": { + "Package": "shinythemes", + "Version": "1.2.0", + "Source": "Repository", + "Title": "Themes for Shiny", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch themes\"), person(\"Lukasz\", \"Dziedzic\", role = c(\"ctb\", \"cph\"), comment = \"Lato font\"), person(\"Nathan\", \"Willis\", role = c(\"ctb\", \"cph\"), comment = \"News Cycle font\"), person(family = \"Google Corporation\", role = c(\"ctb\", \"cph\"), comment = \"Open Sans and Roboto fonts\"), person(\"Matt\", \"McInerney\", role = c(\"ctb\", \"cph\"), comment = \"Raleway font\"), person(family = \"Adobe Systems Incorporated\", role = c(\"ctb\", \"cph\"), comment = \"Source Sans Pro font\"), person(family = \"Canonical Ltd\", role = c(\"ctb\", \"cph\"), comment = \"Ubuntu font\") )", + "Description": "Themes for use with Shiny. Includes several Bootstrap themes from , which are packaged for use with Shiny applications.", + "Depends": [ + "R (>= 3.0.0)" + ], + "Imports": [ + "shiny (>= 0.11)" + ], + "URL": "https://rstudio.github.io/shinythemes/", + "License": "GPL-3 | file LICENSE", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut, cre], RStudio [cph], Thomas Park [ctb, cph] (Bootswatch themes), Lukasz Dziedzic [ctb, cph] (Lato font), Nathan Willis [ctb, cph] (News Cycle font), Google Corporation [ctb, cph] (Open Sans and Roboto fonts), Matt McInerney [ctb, cph] (Raleway font), Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font), Canonical Ltd [ctb, cph] (Ubuntu font)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, "sisal": { "Package": "sisal", "Version": "0.49", @@ -7249,6 +9097,29 @@ "Maintainer": "James Balamuta ", "Repository": "CRAN" }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Title": "Simple Network of Workstations", + "Author": "Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova", + "Description": "Support for simple parallel computing in R.", + "Maintainer": "Luke Tierney ", + "Suggests": [ + "rlecuyer" + ], + "Enhances": [ + "Rmpi" + ], + "License": "GPL", + "Depends": [ + "R (>= 2.13.1)", + "utils" + ], + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, "snowflakeauth": { "Package": "snowflakeauth", "Version": "0.2.2", @@ -7808,7 +9679,8 @@ "NeedsCompilation": "yes", "Author": "Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009), Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]", "Maintainer": "Terry M Therneau ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "sys": { "Package": "sys", @@ -7896,6 +9768,50 @@ "Maintainer": "Jonathan Rougier ", "Encoding": "UTF-8" }, + "textshaping": { + "Package": "textshaping", + "Version": "1.0.5", + "Source": "Repository", + "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/textshaping", + "BugReports": "https://github.com/r-lib/textshaping/issues", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "lifecycle", + "stats", + "stringi", + "systemfonts (>= 1.3.0)", + "utils" + ], + "Suggests": [ + "covr", + "grDevices", + "grid", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.1)", + "systemfonts (>= 1.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "freetype2, harfbuzz, fribidi", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, "tibble": { "Package": "tibble", "Version": "3.3.1", @@ -8055,6 +9971,70 @@ "Maintainer": "Lionel Henry ", "Repository": "CRAN" }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository", + "Title": "Easily Install and Load the 'Tidyverse'", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at .", + "License": "MIT + file LICENSE", + "URL": "https://tidyverse.tidyverse.org, https://github.com/tidyverse/tidyverse", + "BugReports": "https://github.com/tidyverse/tidyverse/issues", + "Depends": [ + "R (>= 3.3)" + ], + "Imports": [ + "broom (>= 1.0.3)", + "conflicted (>= 1.2.0)", + "cli (>= 3.6.0)", + "dbplyr (>= 2.3.0)", + "dplyr (>= 1.1.0)", + "dtplyr (>= 1.2.2)", + "forcats (>= 1.0.0)", + "ggplot2 (>= 3.4.1)", + "googledrive (>= 2.0.0)", + "googlesheets4 (>= 1.0.1)", + "haven (>= 2.5.1)", + "hms (>= 1.1.2)", + "httr (>= 1.4.4)", + "jsonlite (>= 1.8.4)", + "lubridate (>= 1.9.2)", + "magrittr (>= 2.0.3)", + "modelr (>= 0.1.10)", + "pillar (>= 1.8.1)", + "purrr (>= 1.0.1)", + "ragg (>= 1.2.5)", + "readr (>= 2.1.4)", + "readxl (>= 1.4.2)", + "reprex (>= 2.0.2)", + "rlang (>= 1.0.6)", + "rstudioapi (>= 0.14)", + "rvest (>= 1.0.3)", + "stringr (>= 1.5.0)", + "tibble (>= 3.1.8)", + "tidyr (>= 1.3.0)", + "xml2 (>= 1.3.3)" + ], + "Suggests": [ + "covr (>= 3.6.1)", + "feather (>= 0.3.5)", + "glue (>= 1.6.2)", + "mockr (>= 0.2.0)", + "knitr (>= 1.41)", + "rmarkdown (>= 2.20)", + "testthat (>= 3.1.6)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, "timeDate": { "Package": "timeDate", "Version": "4052.112", @@ -8256,6 +10236,25 @@ "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, + "uuid": { + "Package": "uuid", + "Version": "1.2-2", + "Source": "Repository", + "Title": "Tools for Generating and Handling of UUIDs", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, ORCID: ), Theodore Ts'o [aut, cph] (libuuid)", + "Maintainer": "Simon Urbanek ", + "Authors@R": "c(person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\")), person(\"Theodore\",\"Ts'o\", email=\"tytso@thunk.org\", role=c(\"aut\",\"cph\"), comment=\"libuuid\"))", + "Depends": [ + "R (>= 2.9.0)" + ], + "Description": "Tools for generating and handling of UUIDs (Universally Unique Identifiers).", + "License": "MIT + file LICENSE", + "URL": "https://www.rforge.net/uuid", + "BugReports": "https://github.com/s-u/uuid/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, "uwot": { "Package": "uwot", "Version": "0.2.4", @@ -8582,6 +10581,46 @@ "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, + "xml2": { + "Package": "xml2", + "Version": "1.5.2", + "Source": "Repository", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", email = \"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Bindings to 'libxml2' for working with XML data using a simple, consistent interface based on 'XPath' expressions. Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org, https://r-lib.r-universe.dev/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "mockery", + "rmarkdown", + "testthat (>= 3.2.0)", + "xslt" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Jeroen Ooms [aut, cre], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, "xtable": { "Package": "xtable", "Version": "1.8-8", From 385178418f9c0f2af976f7eecdcb231e8f9a41ca Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 13:20:38 +1100 Subject: [PATCH 02/23] Autoload functions in Rprofile --- .Rprofile | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.Rprofile b/.Rprofile index 81b960f..1608bb6 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1 +1,6 @@ source("renv/activate.R") + +# auto-source functions +if (file.exists("functions/prepShinyCellModular.R")) { + source("functions/prepShinyCellModular.R") +} From 0181609db73064105998e619d0d7a330e0aae660 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 13:31:06 +1100 Subject: [PATCH 03/23] Add docker file and build action --- .github/workflows/build_push_docker.yml | 29 +++++++++++++++++++++++++ Dockerfile | 8 +++++++ 2 files changed, 37 insertions(+) create mode 100644 .github/workflows/build_push_docker.yml create mode 100644 Dockerfile diff --git a/.github/workflows/build_push_docker.yml b/.github/workflows/build_push_docker.yml new file mode 100644 index 0000000..96cdd3e --- /dev/null +++ b/.github/workflows/build_push_docker.yml @@ -0,0 +1,29 @@ +name: Build and push Docker image + +on: + push: + branches: [main, bioc_envs] + workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Login to GHCR + uses: docker/login-action@v3 + with: + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Build and push + uses: docker/build-push-action@v5 + with: + context: . + push: true + build-args: | + REPO_URL=https://github.com/${{ github.repository }} + tags: ghcr.io/${{ github.repository_owner }}/shinycellmodular:latest \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..9daff99 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,8 @@ +FROM bioconductor/bioconductor_docker:RELEASE_3_19 + +WORKDIR /app + +ARG REPO_URL +RUN git clone ${REPO_URL} . + +RUN R -e "install.packages('renv'); renv::restore()" \ No newline at end of file From 250ee5f94f09b2b29d31cf7116934369251af46f Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 13:35:10 +1100 Subject: [PATCH 04/23] Pin Bioc to match renv --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 9daff99..e6b9bce 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM bioconductor/bioconductor_docker:RELEASE_3_19 +FROM bioconductor/bioconductor_docker:RELEASE_3_22 WORKDIR /app From 96c01245d9a00cc04598f2fe08b68f2439376e8a Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 13:43:49 +1100 Subject: [PATCH 05/23] Add cmake glpk hdf5 --- Dockerfile | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/Dockerfile b/Dockerfile index e6b9bce..7e69c9b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,13 @@ FROM bioconductor/bioconductor_docker:RELEASE_3_22 +RUN apt-get update && apt-get install -y \ + cmake \ + libglpk-dev \ + libhdf5-dev \ + libcurl4-openssl-dev \ + libssl-dev \ + libxml2-dev + WORKDIR /app ARG REPO_URL From 7ab0f65c9034e4c2f07040eade88df1a76d48e26 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 13:50:50 +1100 Subject: [PATCH 06/23] Install arrow binary directly --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 7e69c9b..ba9e526 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,4 +13,5 @@ WORKDIR /app ARG REPO_URL RUN git clone ${REPO_URL} . +RUN R -e "install.packages('arrow', repos='https://packagemanager.posit.co/cran/latest')" RUN R -e "install.packages('renv'); renv::restore()" \ No newline at end of file From e3ec2ae0360b478fb132968ad7c42bfa8acc5545 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 13:56:10 +1100 Subject: [PATCH 07/23] Exclude arrow from renv for manual install --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ba9e526..2cca04b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,4 +14,4 @@ ARG REPO_URL RUN git clone ${REPO_URL} . RUN R -e "install.packages('arrow', repos='https://packagemanager.posit.co/cran/latest')" -RUN R -e "install.packages('renv'); renv::restore()" \ No newline at end of file +RUN R -e "renv::restore(exclude='arrow')" \ No newline at end of file From 97b3b4f57b65ea2add4b3097d06b5a8e5edcbca9 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 14:32:21 +1100 Subject: [PATCH 08/23] Rework renv install in docker build --- Dockerfile | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2cca04b..e5a10bb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,5 +13,11 @@ WORKDIR /app ARG REPO_URL RUN git clone ${REPO_URL} . -RUN R -e "install.packages('arrow', repos='https://packagemanager.posit.co/cran/latest')" -RUN R -e "renv::restore(exclude='arrow')" \ No newline at end of file +ENV RENV_PATHS_LIBRARY=/app/renv/library + +RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')" +RUN R -e "renv::install('arrow', repos='https://packagemanager.posit.co/cran/latest')" +RUN R -e "renv::restore(exclude='arrow')" 2>&1 | tee /renv_restore.log && cat /renv_restore.log + +RUN chmod -R 775 /app/renv/library + From 004050f94bc70753f5f5621475875b4747ded887 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 15:03:35 +1100 Subject: [PATCH 09/23] Rework renv env in docker build --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index e5a10bb..d95cdb6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -19,5 +19,7 @@ RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')" RUN R -e "renv::install('arrow', repos='https://packagemanager.posit.co/cran/latest')" RUN R -e "renv::restore(exclude='arrow')" 2>&1 | tee /renv_restore.log && cat /renv_restore.log +RUN printf '\n.libPaths("/app/renv/library/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu")\nif (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")\n' >> /app/.Rprofile + RUN chmod -R 775 /app/renv/library From 9536e8d77aa092cbc279f0cd001aaea33eb81c88 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 15:37:27 +1100 Subject: [PATCH 10/23] Try fix dockerfile again... --- Dockerfile | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index d95cdb6..c23f8c3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,7 +6,9 @@ RUN apt-get update && apt-get install -y \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ - libxml2-dev + libxml2-dev \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* WORKDIR /app @@ -17,9 +19,11 @@ ENV RENV_PATHS_LIBRARY=/app/renv/library RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')" RUN R -e "renv::install('arrow', repos='https://packagemanager.posit.co/cran/latest')" -RUN R -e "renv::restore(exclude='arrow')" 2>&1 | tee /renv_restore.log && cat /renv_restore.log +RUN R -e "renv::restore(exclude='arrow')" 2>&1 | tee /renv_restore.log -RUN printf '\n.libPaths("/app/renv/library/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu")\nif (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")\n' >> /app/.Rprofile +RUN echo 'RENV_CONFIG_AUTOLOADER_ENABLED=FALSE' >> /usr/local/lib/R/etc/Renviron && \ + echo 'R_PROFILE_USER=/app/.Rprofile' >> /usr/local/lib/R/etc/Renviron -RUN chmod -R 775 /app/renv/library +RUN printf '.libPaths("/app/renv/library/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu")\nif (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")\n' > /app/.Rprofile +RUN chmod -R 775 /app/renv/library \ No newline at end of file From 25bd4f85643980d4c4a9adb752187b79e87fd926 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 16:04:35 +1100 Subject: [PATCH 11/23] Fix redundant renv clashing with base --- Dockerfile | 42 ++++++++++++++++++++++++++++++++---------- 1 file changed, 32 insertions(+), 10 deletions(-) diff --git a/Dockerfile b/Dockerfile index c23f8c3..aa1137b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,15 +15,37 @@ WORKDIR /app ARG REPO_URL RUN git clone ${REPO_URL} . -ENV RENV_PATHS_LIBRARY=/app/renv/library - -RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')" -RUN R -e "renv::install('arrow', repos='https://packagemanager.posit.co/cran/latest')" -RUN R -e "renv::restore(exclude='arrow')" 2>&1 | tee /renv_restore.log - -RUN echo 'RENV_CONFIG_AUTOLOADER_ENABLED=FALSE' >> /usr/local/lib/R/etc/Renviron && \ - echo 'R_PROFILE_USER=/app/.Rprofile' >> /usr/local/lib/R/etc/Renviron - -RUN printf '.libPaths("/app/renv/library/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu")\nif (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")\n' > /app/.Rprofile +# disable renv autoloader and set paths before any R execution +RUN echo 'RENV_CONFIG_AUTOLOADER_ENABLED=FALSE' >> /usr/local/lib/R/etc/Renviron + +# install arrow as system package to avoid compile issues and path complications +RUN R -e "install.packages('arrow', \ + repos='https://packagemanager.posit.co/cran/latest', \ + lib='/usr/local/lib/R/site-library')" + +# restore all packages into explicit path, autoloader disabled +RUN R -e " \ + options(renv.config.autoloader.enabled=FALSE); \ + renv::restore( \ + library='/app/renv/library', \ + exclude='arrow', \ + prompt=FALSE \ + )" 2>&1 | tee /renv_restore.log + +# resolve the exact library path and write to Renviron + .Rprofile +RUN R -e " \ + base <- '/app/renv/library'; \ + l1 <- list.files(base, full.names=TRUE)[1]; \ + l2 <- list.files(l1, full.names=TRUE)[1]; \ + lib <- list.files(l2, full.names=TRUE)[1]; \ + stopifnot(dir.exists(lib)); \ + cat('Resolved lib path:', lib, '\n'); \ + write(paste0('R_LIBS_USER=', lib), \ + '/usr/local/lib/R/etc/Renviron', append=TRUE); \ + write(paste0('R_PROFILE_USER=/app/.Rprofile'), \ + '/usr/local/lib/R/etc/Renviron', append=TRUE); \ + writeLines(c( \ + 'if (file.exists(\"/app/functions/prepShinyCellModular.R\")) source(\"/app/functions/prepShinyCellModular.R\")' \ + ), '/app/.Rprofile')" RUN chmod -R 775 /app/renv/library \ No newline at end of file From f1fb873b8e62b08a847f8e02987523b506c45228 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 16:14:06 +1100 Subject: [PATCH 12/23] Attempt 49726746297 to fix R lib pathing --- Dockerfile | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/Dockerfile b/Dockerfile index aa1137b..7727004 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,37 +15,37 @@ WORKDIR /app ARG REPO_URL RUN git clone ${REPO_URL} . -# disable renv autoloader and set paths before any R execution -RUN echo 'RENV_CONFIG_AUTOLOADER_ENABLED=FALSE' >> /usr/local/lib/R/etc/Renviron - -# install arrow as system package to avoid compile issues and path complications -RUN R -e "install.packages('arrow', \ - repos='https://packagemanager.posit.co/cran/latest', \ +# install renv and arrow to system library first +RUN R -e "install.packages( \ + 'https://cran.r-project.org/src/contrib/Archive/renv/renv_1.1.4.tar.gz', \ + repos=NULL, type='source', \ lib='/usr/local/lib/R/site-library')" -# restore all packages into explicit path, autoloader disabled RUN R -e " \ options(renv.config.autoloader.enabled=FALSE); \ + renv::install('arrow', \ + library='/app/renv/library', \ + repos='https://packagemanager.posit.co/cran/latest'); \ renv::restore( \ library='/app/renv/library', \ exclude='arrow', \ prompt=FALSE \ )" 2>&1 | tee /renv_restore.log -# resolve the exact library path and write to Renviron + .Rprofile +# write Renviron and .Rprofile RUN R -e " \ - base <- '/app/renv/library'; \ - l1 <- list.files(base, full.names=TRUE)[1]; \ - l2 <- list.files(l1, full.names=TRUE)[1]; \ - lib <- list.files(l2, full.names=TRUE)[1]; \ + lib <- list.files('/app/renv/library', recursive=TRUE, \ + full.names=TRUE, include.dirs=TRUE); \ + lib <- lib[grepl('x86_64-pc-linux-gnu$', lib)][1]; \ stopifnot(dir.exists(lib)); \ - cat('Resolved lib path:', lib, '\n'); \ - write(paste0('R_LIBS_USER=', lib), \ + cat('lib path:', lib, '\n'); \ + write(c(paste0('R_LIBS_USER=', lib), \ + 'R_PROFILE_USER=/app/.Rprofile'), \ '/usr/local/lib/R/etc/Renviron', append=TRUE); \ - write(paste0('R_PROFILE_USER=/app/.Rprofile'), \ - '/usr/local/lib/R/etc/Renviron', append=TRUE); \ - writeLines(c( \ - 'if (file.exists(\"/app/functions/prepShinyCellModular.R\")) source(\"/app/functions/prepShinyCellModular.R\")' \ - ), '/app/.Rprofile')" + writeLines( \ + 'if (file.exists(\"/app/functions/prepShinyCellModular.R\")) source(\"/app/functions/prepShinyCellModular.R\")', \ + '/app/.Rprofile')" + +RUN echo 'RENV_CONFIG_AUTOLOADER_ENABLED=FALSE' >> /usr/local/lib/R/etc/Renviron RUN chmod -R 775 /app/renv/library \ No newline at end of file From d5e9e45569507bd140a2bfbd2242743580704476 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 16:40:16 +1100 Subject: [PATCH 13/23] Continue wrestling with renv --- Dockerfile | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7727004..1b1fcd6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,10 +26,12 @@ RUN R -e " \ renv::install('arrow', \ library='/app/renv/library', \ repos='https://packagemanager.posit.co/cran/latest'); \ - renv::restore( \ - library='/app/renv/library', \ - exclude='arrow', \ - prompt=FALSE \ + withr::with_libpaths('/app/renv/library', action='replace', \ + renv::restore( \ + library='/app/renv/library', \ + exclude='arrow', \ + prompt=FALSE \ + ) \ )" 2>&1 | tee /renv_restore.log # write Renviron and .Rprofile From 2856edfe2b1eb65aa144166bbfa8ea0ad5910c3d Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 16:45:39 +1100 Subject: [PATCH 14/23] Manually install withr --- Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1b1fcd6..1ead5a4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,7 +16,10 @@ ARG REPO_URL RUN git clone ${REPO_URL} . # install renv and arrow to system library first -RUN R -e "install.packages( \ +RUN R -e "install.packages(c('withr'), \ + repos='https://packagemanager.posit.co/cran/latest', \ + lib='/usr/local/lib/R/site-library'); \ + install.packages( \ 'https://cran.r-project.org/src/contrib/Archive/renv/renv_1.1.4.tar.gz', \ repos=NULL, type='source', \ lib='/usr/local/lib/R/site-library')" From 7f7a7d57e64ec5c7be2f4795b197cd6575a3d344 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:19:29 +1100 Subject: [PATCH 15/23] Forget renv --- Dockerfile | 55 ++++++++++++++++-------------------------------------- 1 file changed, 16 insertions(+), 39 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1ead5a4..512dabc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,42 +15,19 @@ WORKDIR /app ARG REPO_URL RUN git clone ${REPO_URL} . -# install renv and arrow to system library first -RUN R -e "install.packages(c('withr'), \ - repos='https://packagemanager.posit.co/cran/latest', \ - lib='/usr/local/lib/R/site-library'); \ - install.packages( \ - 'https://cran.r-project.org/src/contrib/Archive/renv/renv_1.1.4.tar.gz', \ - repos=NULL, type='source', \ - lib='/usr/local/lib/R/site-library')" - -RUN R -e " \ - options(renv.config.autoloader.enabled=FALSE); \ - renv::install('arrow', \ - library='/app/renv/library', \ - repos='https://packagemanager.posit.co/cran/latest'); \ - withr::with_libpaths('/app/renv/library', action='replace', \ - renv::restore( \ - library='/app/renv/library', \ - exclude='arrow', \ - prompt=FALSE \ - ) \ - )" 2>&1 | tee /renv_restore.log - -# write Renviron and .Rprofile -RUN R -e " \ - lib <- list.files('/app/renv/library', recursive=TRUE, \ - full.names=TRUE, include.dirs=TRUE); \ - lib <- lib[grepl('x86_64-pc-linux-gnu$', lib)][1]; \ - stopifnot(dir.exists(lib)); \ - cat('lib path:', lib, '\n'); \ - write(c(paste0('R_LIBS_USER=', lib), \ - 'R_PROFILE_USER=/app/.Rprofile'), \ - '/usr/local/lib/R/etc/Renviron', append=TRUE); \ - writeLines( \ - 'if (file.exists(\"/app/functions/prepShinyCellModular.R\")) source(\"/app/functions/prepShinyCellModular.R\")', \ - '/app/.Rprofile')" - -RUN echo 'RENV_CONFIG_AUTOLOADER_ENABLED=FALSE' >> /usr/local/lib/R/etc/Renviron - -RUN chmod -R 775 /app/renv/library \ No newline at end of file +RUN R -e "install.packages(c( \ + 'arrow', 'data.table', 'DT', 'ggplot2', 'ggrepel', 'hdf5r', \ + 'ggdendro', 'gridExtra', 'rsconnect', 'shinythemes', 'shinydashboard', \ + 'tidyverse', 'sortable', 'plotly', 'RColorBrewer', 'ggforce', \ + 'shiny', 'shinyhelper', 'shinyjs', 'shinyWidgets' \ + ), repos='https://packagemanager.posit.co/cran/latest')" + +RUN R -e "BiocManager::install(c('limma', 'edgeR'), ask=FALSE)" + +RUN R -e "devtools::install_github('SGDDNB/ShinyCell')" +RUN R -e "devtools::install_github('immunogenomics/presto')" +RUN R -e "devtools::install_github('jmw86069/FlexDotPlot')" +RUN R -e "install.packages('Seurat', repos='https://packagemanager.posit.co/cran/latest')" + +RUN echo 'R_PROFILE_USER=/app/.Rprofile' >> /usr/local/lib/R/etc/Renviron +RUN echo 'if (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")' > /app/.Rprofile \ No newline at end of file From 7dfe390a82b83fb13fd74f5c02f1b0b030bc3134 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:30:59 +1100 Subject: [PATCH 16/23] Just use mamba --- Dockerfile | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/Dockerfile b/Dockerfile index 512dabc..752886f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,33 +1,32 @@ -FROM bioconductor/bioconductor_docker:RELEASE_3_22 +FROM condaforge/mambaforge:latest RUN apt-get update && apt-get install -y \ cmake \ libglpk-dev \ libhdf5-dev \ - libcurl4-openssl-dev \ - libssl-dev \ - libxml2-dev \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* +RUN mamba config append channels conda-forge && \ + mamba config append channels bioconda && \ + mamba install -y \ + r-arrow r-data.table r-dplyr r-dt bioconductor-edger \ + r-ggdendro r-ggforce r-ggplot2 r-ggrepel r-gridextra \ + r-hdf5r r-jsonlite bioconductor-limma r-magrittr \ + r-patchwork r-plotly r-presto r-rcolorbrewer r-rcpp \ + r-rsconnect r-seurat r-seuratobject r-shiny \ + r-shinydashboard r-shinyjs r-shinywidgets r-sortable \ + r-tidyverse r-factominer r-grimport r-xml r-devtools \ + r-shinythemes \ + && mamba clean -afy + +RUN Rscript -e "devtools::install_github('Simon-Leonard/FlexDotPlot')" +RUN Rscript -e "devtools::install_github('SGDDNB/ShinyCell')" + WORKDIR /app ARG REPO_URL RUN git clone ${REPO_URL} . -RUN R -e "install.packages(c( \ - 'arrow', 'data.table', 'DT', 'ggplot2', 'ggrepel', 'hdf5r', \ - 'ggdendro', 'gridExtra', 'rsconnect', 'shinythemes', 'shinydashboard', \ - 'tidyverse', 'sortable', 'plotly', 'RColorBrewer', 'ggforce', \ - 'shiny', 'shinyhelper', 'shinyjs', 'shinyWidgets' \ - ), repos='https://packagemanager.posit.co/cran/latest')" - -RUN R -e "BiocManager::install(c('limma', 'edgeR'), ask=FALSE)" - -RUN R -e "devtools::install_github('SGDDNB/ShinyCell')" -RUN R -e "devtools::install_github('immunogenomics/presto')" -RUN R -e "devtools::install_github('jmw86069/FlexDotPlot')" -RUN R -e "install.packages('Seurat', repos='https://packagemanager.posit.co/cran/latest')" - -RUN echo 'R_PROFILE_USER=/app/.Rprofile' >> /usr/local/lib/R/etc/Renviron +RUN echo 'R_PROFILE_USER=/app/.Rprofile' >> $(R RHOME)/etc/Renviron RUN echo 'if (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")' > /app/.Rprofile \ No newline at end of file From 5fc8a8fc2402e2a15637b5130f8bd24bd9155911 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:36:16 +1100 Subject: [PATCH 17/23] Add timezone --- Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 752886f..8128862 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,8 @@ -FROM condaforge/mambaforge:latest +ENV DEBIAN_FRONTEND=noninteractive +ENV TZ=Australia/Melbourne RUN apt-get update && apt-get install -y \ + tzdata \ cmake \ libglpk-dev \ libhdf5-dev \ From e1af7c62897c2f577c3cf73d44af9801810eb9c5 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:37:24 +1100 Subject: [PATCH 18/23] Add mambaforge image --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 8128862..a713c2c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,3 +1,5 @@ +FROM condaforge/mambaforge:latest + ENV DEBIAN_FRONTEND=noninteractive ENV TZ=Australia/Melbourne From 555e5dc7b0cbe7e67871993160ca38936dd95ae1 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:39:25 +1100 Subject: [PATCH 19/23] mamba to conda --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index a713c2c..8e90970 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,8 +11,8 @@ RUN apt-get update && apt-get install -y \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* -RUN mamba config append channels conda-forge && \ - mamba config append channels bioconda && \ +RUN conda config append channels conda-forge && \ + conda config append channels bioconda && \ mamba install -y \ r-arrow r-data.table r-dplyr r-dt bioconductor-edger \ r-ggdendro r-ggforce r-ggplot2 r-ggrepel r-gridextra \ From 3fde042fc381f18b40e793ddcb09ddc7e1e1e62d Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:41:13 +1100 Subject: [PATCH 20/23] Append channels correctly --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8e90970..7746537 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,8 +11,8 @@ RUN apt-get update && apt-get install -y \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* -RUN conda config append channels conda-forge && \ - conda config append channels bioconda && \ +RUN mamba config --append channels conda-forge && \ + mamba config --append channels bioconda && \ mamba install -y \ r-arrow r-data.table r-dplyr r-dt bioconductor-edger \ r-ggdendro r-ggforce r-ggplot2 r-ggrepel r-gridextra \ From 7c819ec3124c521d1d2550d4227abb8e044f53a9 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 17:44:00 +1100 Subject: [PATCH 21/23] Append channels to conda --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7746537..24c3b66 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,8 +11,8 @@ RUN apt-get update && apt-get install -y \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* -RUN mamba config --append channels conda-forge && \ - mamba config --append channels bioconda && \ +RUN conda config --append channels conda-forge && \ + conda config --append channels bioconda && \ mamba install -y \ r-arrow r-data.table r-dplyr r-dt bioconductor-edger \ r-ggdendro r-ggforce r-ggplot2 r-ggrepel r-gridextra \ From 4e47357a2203bbb48a76a0a17f30b13e384e7071 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 18:09:05 +1100 Subject: [PATCH 22/23] Add shinycellhelper --- Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 24c3b66..6e14ddb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,6 +26,7 @@ RUN conda config --append channels conda-forge && \ RUN Rscript -e "devtools::install_github('Simon-Leonard/FlexDotPlot')" RUN Rscript -e "devtools::install_github('SGDDNB/ShinyCell')" +RUN Rscript -e "devtools::install_github('cwthom/shinyhelper')" WORKDIR /app @@ -33,4 +34,5 @@ ARG REPO_URL RUN git clone ${REPO_URL} . RUN echo 'R_PROFILE_USER=/app/.Rprofile' >> $(R RHOME)/etc/Renviron -RUN echo 'if (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")' > /app/.Rprofile \ No newline at end of file +RUN echo 'if (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")' >> /app/.Rprofile +RUN echo 'if (file.exists("/app/functions/useShinyCellModular.R")) source("/app/functions/useShinyCellModular.R")' >> /app/.Rprofile \ No newline at end of file From ebac1f3481b7e745234ba47e1298a5da1629c586 Mon Sep 17 00:00:00 2001 From: Tyrone Chen Date: Thu, 2 Apr 2026 18:29:30 +1100 Subject: [PATCH 23/23] Set Renviron correctly --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 6e14ddb..38f3ff4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -34,5 +34,5 @@ ARG REPO_URL RUN git clone ${REPO_URL} . RUN echo 'R_PROFILE_USER=/app/.Rprofile' >> $(R RHOME)/etc/Renviron -RUN echo 'if (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")' >> /app/.Rprofile +RUN echo 'if (file.exists("/app/functions/prepShinyCellModular.R")) source("/app/functions/prepShinyCellModular.R")' > /app/.Rprofile RUN echo 'if (file.exists("/app/functions/useShinyCellModular.R")) source("/app/functions/useShinyCellModular.R")' >> /app/.Rprofile \ No newline at end of file