############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:traviz.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings traviz_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/traviz.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘traviz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘traviz’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘traviz’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Invalid license file pointers: LICENSE * 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 ... NOTE .plotGeneCount: no visible binding for global variable ‘dim1’ .plotGeneCount: no visible binding for global variable ‘dim2’ .plotSmoothers: no visible binding for global variable ‘time’ .plotSmoothers: no visible binding for global variable ‘gene_count’ .plotSmoothers: no visible binding for global variable ‘lineage’ .plotSmoothers_conditions: no visible binding for global variable ‘time’ .plotSmoothers_conditions: no visible binding for global variable ‘gene_count’ .plotSmoothers_conditions: no visible binding for global variable ‘lineage’ .plotSmoothers_conditions: no visible binding for global variable ‘pCol’ .plotSmoothers_sce: no visible binding for global variable ‘time’ .plotSmoothers_sce: no visible binding for global variable ‘gene_count’ .plotSmoothers_sce: no visible binding for global variable ‘lineage’ .plotSmoothers_sce: no visible binding for global variable ‘pCol’ plot3d.SlingshotDataSet : : no visible binding for global variable ‘weighted.mean’ plot,SlingshotDataSet-ANY : : no visible binding for global variable ‘weighted.mean’ plotExpression,matrix-SlingshotDataSet-character: no visible global function definition for ‘loess’ plotExpression,matrix-SlingshotDataSet-character: no visible binding for global variable ‘lineage’ Undefined global functions or variables: dim1 dim2 gene_count lineage loess pCol time weighted.mean Consider adding importFrom("stats", "loess", "time", "weighted.mean") to your NAMESPACE file. * 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: plotExpression.Rd: geom_line, geom_point plotGeneCount.Rd: SlingshotDataSet, SingleCellExperiment, ggplot plotSmoothers.Rd: geom_line, geom_point, labs, ggplot 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘traviz-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot-SlingshotDataSet > ### Title: Plot Slingshot output > ### Aliases: plot-SlingshotDataSet plot,SlingshotDataSet,ANY-method > ### lines,SlingshotDataSet-method > > ### ** Examples > > library(slingshot) Loading required package: princurve Loading required package: TrajectoryUtils 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’: 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 > data("slingshotExample", package="slingshot") > rd <- slingshotExample$rd > cl <- slingshotExample$cl > pto <- slingshot(rd, cl, start.clus = "1") Error in loadNamespace(x) : there is no package called ‘DelayedMatrixStats’ Calls: slingshot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart 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: 2. ├─slingshot::as.PseudotimeOrdering(crv) 3. ├─slingshot::as.PseudotimeOrdering(crv) 4. │ └─slingshot (local) .local(x, ...) 5. │ └─TrajectoryUtils::rowmean(reducedDim(sds), slingClusterLabels(sds)) 6. │ └─TrajectoryUtils:::.rowstats_w(...) 7. ├─base::loadNamespace(x) 8. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 9. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 10. │ │ └─base (local) doWithOneRestart(return(expr), restart) 11. │ └─base::stop(cond) 12. └─base (local) ``(``) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘slingshot.Rmd’ using rmarkdown Quitting from lines 29-37 [unnamed-chunk-2] (slingshot.Rmd) Error: processing vignette 'slingshot.Rmd' failed with diagnostics: there is no package called 'DelayedMatrixStats' --- failed re-building ‘slingshot.Rmd’ --- re-building ‘traviz.Rmd’ using rmarkdown --- finished re-building ‘traviz.Rmd’ SUMMARY: processing the following file failed: ‘slingshot.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/traviz.Rcheck/00check.log’ for details.