example("SpatialExperiment") requires suggested packages but doesn't check for this #163
Description
These examples depend on the suggested packages DropletUtils and ** BumpyMatrix** but don't check that these are installed/available.
I'm not certain, but I don't think this is expected/correct behaviour.
FWIW my quick read of WRE is that these should have a if(require(pkgname)) guarding the relevant examples which is consistent with the advice in https://r-pkgs.org/dependencies-in-practice.html#sec-dependencies-in-suggests-in-examples-and-vignettes
# Using renv to mock a new R installation with empty package library
renv::init()
#> - Linking packages into the project library ... [55/84] ��������[56/84] ��������[57/84] ��������[58/84] ��������[59/84] ��������[60/84] ��������[61/84] ��������[62/84] ��������[63/84] ��������[64/84] ��������[65/84] ��������[66/84] ��������[67/84] ��������[68/84] ��������[69/84] ��������[70/84] ��������[71/84] ��������[72/84] ��������[73/84] ��������[74/84] ��������[75/84] ��������[76/84] ��������[77/84] ��������[78/84] ��������[79/84] ��������[80/84] ��������[81/84] ��������[82/84] ��������[83/84] ��������[84/84] Done!
#> The following package(s) will be updated in the lockfile:
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#> # Bioconductor ---------------------------------------------------------------
#> - GenomeInfoDbData [* -> 1.2.13]
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#> # Bioconductor 3.20 ----------------------------------------------------------
#> - Biobase [* -> 2.66.0]
#> - BiocFileCache [* -> 2.14.0]
#> - BiocGenerics [* -> 0.52.0]
#> - BiocVersion [* -> 3.20.0]
#> - DelayedArray [* -> 0.32.0]
#> - GenomeInfoDb [* -> 1.42.1]
#> - GenomicRanges [* -> 1.58.0]
#> - IRanges [* -> 2.40.1]
#> - MatrixGenerics [* -> 1.18.1]
#> - S4Arrays [* -> 1.6.0]
#> - S4Vectors [* -> 0.44.0]
#> - SingleCellExperiment [* -> 1.28.1]
#> - SparseArray [* -> 1.6.0]
#> - SpatialExperiment [* -> 1.16.0]
#> - SummarizedExperiment [* -> 1.36.0]
#> - UCSC.utils [* -> 1.2.0]
#> - XVector [* -> 0.46.0]
#> - zlibbioc [* -> 1.52.0]
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#> # CRAN -----------------------------------------------------------------------
#> - abind [* -> 1.4-8]
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#> - bit [* -> 4.5.0.1]
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#> - cli [* -> 3.6.3]
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#> - curl [* -> 6.1.0]
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#> - highr [* -> 0.11]
#> - htmltools [* -> 0.5.8.1]
#> - httr [* -> 1.4.7]
#> - jquerylib [* -> 0.1.4]
#> - jsonlite [* -> 1.8.9]
#> - knitr [* -> 1.49]
#> - lattice [* -> 0.22-6]
#> - lifecycle [* -> 1.0.4]
#> - magick [* -> 2.8.5]
#> - magrittr [* -> 2.0.3]
#> - Matrix [* -> 1.7-1]
#> - matrixStats [* -> 1.5.0]
#> - memoise [* -> 2.0.1]
#> - mime [* -> 0.12]
#> - openssl [* -> 2.3.1]
#> - pillar [* -> 1.10.1]
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#> - Rcpp [* -> 1.0.14]
#> - renv [* -> 1.0.11]
#> - rjson [* -> 0.2.23]
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#> - rmarkdown [* -> 2.29]
#> - RSQLite [* -> 2.3.9]
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#> - sessioninfo [* -> 1.2.2]
#> - stringi [* -> 1.8.4]
#> - stringr [* -> 1.5.1]
#> - sys [* -> 3.4.3]
#> - tibble [* -> 3.2.1]
#> - tidyr [* -> 1.3.1]
#> - tidyselect [* -> 1.2.1]
#> - tinytex [* -> 0.54]
#> - utf8 [* -> 1.2.4]
#> - vctrs [* -> 0.6.5]
#> - withr [* -> 3.0.2]
#> - xfun [* -> 0.50]
#> - yaml [* -> 2.3.10]
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#> The version of R recorded in the lockfile will be updated:
#> - R [* -> 4.4.2]
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install.packages("BiocManager")
#> The following package(s) will be installed:
#> - BiocManager [1.30.25]
#> These packages will be installed into "/private/var/folders/z7/48jz0mzd6ms7zdv4vhkgns_c001kx2/T/Rtmp7ajbf9/reprex-ff59599d1f8c-ivory-pewee/renv/library/macos/R-4.4/aarch64-apple-darwin20".
#>
#> # Installing packages --------------------------------------------------------
#> - Installing BiocManager ... OK [linked from cache]
#> Successfully installed 1 package in 4.3 milliseconds.
BiocManager::install("SpatialExperiment", ask = FALSE)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> BioCsoft: https://bioconductor.org/packages/3.20/bioc
#> BioCann: https://bioconductor.org/packages/3.20/data/annotation
#> BioCexp: https://bioconductor.org/packages/3.20/data/experiment
#> BioCworkflows: https://bioconductor.org/packages/3.20/workflows
#> BioCbooks: https://bioconductor.org/packages/3.20/books
#> CRAN: https://packagemanager.posit.co/cran/latest
#> Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)
#> Warning: package(s) not installed when version(s) same as or greater than current; use
#> `force = TRUE` to re-install: 'SpatialExperiment'
#> Old packages: 'rlang', 'SparseArray'
#>
#> The downloaded binary packages are in
#> /var/folders/z7/48jz0mzd6ms7zdv4vhkgns_c001kx2/T//RtmpULLNjL/downloaded_packages
library(SpatialExperiment)
#> Loading required package: SingleCellExperiment
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
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#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
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#> Attaching package: 'BiocGenerics'
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#> IQR, mad, sd, var, xtabs
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#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
#> table, tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
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#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
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#> findMatches
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#> expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
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#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
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#> rowMedians
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#> anyMissing, rowMedians
example("SpatialExperiment")
#>
#> SptlEx> #########################################################
#> SptlEx> # Example 1: Spot-based ST (10x Visium) using constructor
#> SptlEx> #########################################################
#> SptlEx>
#> SptlEx> dir <- system.file(
#> SptlEx+ file.path("extdata", "10xVisium", "section1", "outs"),
#> SptlEx+ package = "SpatialExperiment")
#>
#> SptlEx> # read in counts
#> SptlEx> fnm <- file.path(dir, "raw_feature_bc_matrix")
#>
#> SptlEx> sce <- DropletUtils::read10xCounts(fnm)
#> Error in loadNamespace(x): there is no package called 'DropletUtils'Created on 2025-01-21 with reprex v2.1.1
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os macOS Sequoia 15.0.1
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Australia/Melbourne
#> date 2025-01-21
#> pandoc 3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#>
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#>
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#> P ── Loaded and on-disk path mismatch.
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