##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:traviz.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings traviz_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/traviz.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘traviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘traviz’ version ‘1.11.0’
* 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 ‘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 : <anonymous>: no visible binding for global
  variable ‘weighted.mean’
plot,SlingshotDataSet-ANY : <anonymous>: 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 ... OK
* 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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) `<fn>`(`<pckgNtFE>`)
  
  [ 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/traviz.Rcheck/00check.log’
for details.