############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:dittoSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dittoSeq_1.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/dittoSeq.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dittoSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dittoSeq’ version ‘1.20.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘dittoSeq’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: addDimReduction.Rd: SingleCellExperiment-class addPrcomp.Rd: SingleCellExperiment-class dittoDimPlot.Rd: ggrepel, SingleCellExperiment dittoFreqPlot.Rd: geom_violin dittoHeatmap.Rd: pheatmap dittoHex.Rd: ggrepel dittoPlot.Rd: geom_violin dittoPlotVarsAcrossGroups.Rd: geom_violin dittoScatterPlot.Rd: ggrepel importDittoBulk.Rd: SummarizedExperiment-class, SingleCellExperiment-class setBulk.Rd: SingleCellExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘dittoSeq-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dittoBarPlot > ### Title: Outputs a stacked bar plot to show the percent composition of > ### samples, groups, clusters, or other groupings > ### Aliases: dittoBarPlot > > ### ** Examples > > example(importDittoBulk, echo = FALSE) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: 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 Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, 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")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians > myRNA class: SingleCellExperiment dim: 1000 60 metadata(0): assays(2): counts logcounts rownames(1000): gene1 gene2 ... gene999 gene1000 rowData names(0): colnames(60): sample1 sample2 ... sample59 sample60 colData names(7): conditions timepoint ... score1 score2 reducedDimNames(2): pca tsne mainExpName: NULL altExpNames(0): > > dittoBarPlot(myRNA, "clustering", group.by = "groups") > dittoBarPlot(myRNA, "clustering", group.by = "groups", + scale = "count") > > # Reordering the x-axis groupings to have "C" (#3) come first > dittoBarPlot(myRNA, "clustering", group.by = "groups", + x.reorder = c(3,1,2,4)) > > ### Accessing underlying data: > # as dataframe > dittoBarPlot(myRNA, "clustering", group.by = "groups", + data.out = TRUE) $p $data label grouping count label.count.total.per.facet percent 1 1 A 5 18 0.27777778 2 2 A 6 18 0.33333333 3 3 A 1 18 0.05555556 4 4 A 6 18 0.33333333 5 1 B 6 16 0.37500000 6 2 B 6 16 0.37500000 7 3 B 1 16 0.06250000 8 4 B 3 16 0.18750000 9 1 C 3 10 0.30000000 10 2 C 2 10 0.20000000 11 3 C 3 10 0.30000000 12 4 C 2 10 0.20000000 13 1 D 5 16 0.31250000 14 2 D 4 16 0.25000000 15 3 D 2 16 0.12500000 16 4 D 5 16 0.31250000 > # through hovering the cursor over the relevant parts of the plot > if (requireNamespace("plotly", quietly = TRUE)) { + dittoBarPlot(myRNA, "clustering", group.by = "groups", + do.hover = TRUE) + } Error in pm[[2]] : subscript out of bounds Calls: dittoBarPlot -> -> ggplotly.ggplot -> gg2list Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1. ├─testthat::expect_type(...) at test-multis.R:67:5 2. │ └─testthat::quasi_label(enquo(object), arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─dittoSeq::multi_dittoDimPlot(object = sce, conts_3, do.hover = TRUE) 5. └─base::lapply(...) 6. └─dittoSeq (local) FUN(X[[i]], ...) 7. └─dittoSeq::dittoDimPlot(...) 8. └─dittoSeq::dittoScatterPlot(...) 9. ├─plotly::ggplotly(p, tooltip = "text") 10. └─plotly:::ggplotly.ggplot(p, tooltip = "text") 11. └─plotly::gg2list(...) [ FAIL 6 | WARN 14 | SKIP 1 | PASS 831 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/dittoSeq.Rcheck/00check.log’ for details.