##############################################################################
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###
### 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_1.14.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/traviz.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘traviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘traviz’ version ‘1.14.0’
* 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 ... 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) `<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 slingshot.Rmd:28-37 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'DelayedMatrixStats'
---
Backtrace:
     ▆
  1. ├─slingshot::slingshot(rd, cl)
  2. ├─slingshot::slingshot(rd, cl)
  3. │ ├─slingshot::slingshot(...)
  4. │ └─slingshot::slingshot(...)
  5. │   └─slingshot (local) .local(data, clusterLabels, ...)
  6. │     ├─slingshot::getLineages(...)
  7. │     └─slingshot::getLineages(...)
  8. │       ├─slingshot::getLineages(...)
  9. │       └─slingshot::getLineages(...)
 10. │         └─slingshot (local) .local(data, clusterLabels, ...)
 11. │           ├─TrajectoryUtils::createClusterMST(...)
 12. │           └─TrajectoryUtils::createClusterMST(...)
 13. │             └─TrajectoryUtils (local) .local(x, ...)
 14. │               └─TrajectoryUtils (local) FUN(x, clusters)
 15. │                 └─TrajectoryUtils:::.rowstats_w(...)
 16. └─base::loadNamespace(x)
 17.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18.     └─base (local) withOneRestart(expr, restarts[[1L]])
 19.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL traviz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘traviz’ ...
** this is package ‘traviz’ version ‘1.14.0’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (traviz)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(traviz)
> 
> test_check("traviz")
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

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testPlotting.R:10:3'): plotExpression works ─────────────────────────
Error in `(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'DelayedMatrixStats'", 
    call = loadNamespace(x), package = "DelayedMatrixStats", 
    lib.loc = NULL), class = c("packageNotFoundError", "error", 
"condition")))`: error in evaluating the argument 'sds' in selecting a method for function 'plotExpression': there is no package called 'DelayedMatrixStats'
Backtrace:
     ▆
  1. ├─traviz::plotExpression(...) at testPlotting.R:10:3
  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