##############################################################################
##############################################################################
###
### 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 -> <Anonymous> -> 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL dittoSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘dittoSeq’ ...
** this is package ‘dittoSeq’ version ‘1.20.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (dittoSeq)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
> test_check("dittoSeq")
Loading required package: dittoSeq
Loading required package: ggplot2
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 6 | WARN 14 | SKIP 1 | PASS 831 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• MASS available (1): 'test-utils.R:23:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-hover.R:12:9'): Showing hover.data works for ScatterPlot (with cells.use) ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-hover.R:12:9
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─dittoSeq::dittoScatterPlot(...)
 5.   ├─plotly::ggplotly(p, tooltip = "text")
 6.   └─plotly:::ggplotly.ggplot(p, tooltip = "text")
 7.     └─plotly::gg2list(...)
── Error ('test-hover.R:32:9'): Showing hover.data works for DimPlot (with cells.use) ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-hover.R:32:9
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─dittoSeq::dittoDimPlot(...)
 5.   └─dittoSeq::dittoScatterPlot(...)
 6.     ├─plotly::ggplotly(p, tooltip = "text")
 7.     └─plotly:::ggplotly.ggplot(p, tooltip = "text")
 8.       └─plotly::gg2list(...)
── Error ('test-hover.R:52:9'): Showing hover.data works for BarPlot (with cells.use) ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-hover.R:52:9
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─dittoSeq::dittoBarPlot(...)
 5.   ├─plotly::ggplotly(p, tooltip = "text")
 6.   └─plotly:::ggplotly.ggplot(p, tooltip = "text")
 7.     └─plotly::gg2list(...)
── Error ('test-hover.R:78:9'): Showing hover.data works for Plot (with cells.use) ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-hover.R:78:9
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─dittoSeq::dittoPlot(...)
 5.   └─dittoSeq:::.warn_or_jitter_plotly(p, plots)
 6.     ├─plotly::ggplotly(p, tooltip = "text")
 7.     └─plotly:::ggplotly.ggplot(p, tooltip = "text")
 8.       └─plotly::gg2list(...)
── Error ('test-hover.R:120:9'): Showing hover.data works for VarsAcrossGroups (with cells.use) ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_s3_class(...) at test-hover.R:120:9
 2. │ └─testthat::quasi_label(enquo(object), arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─dittoSeq::dittoPlotVarsAcrossGroups(...)
 5.   └─dittoSeq:::.warn_or_jitter_plotly(p, plots)
 6.     ├─plotly::ggplotly(p, tooltip = "text")
 7.     └─plotly:::ggplotly.ggplot(p, tooltip = "text")
 8.       └─plotly::gg2list(...)
── Error ('test-multis.R:67:5'): multi Plot&DimPlot messaage & output plots as a list when data.out or do.hover given ──
<subscriptOutOfBoundsError/error/condition>
Error in `pm[[2]]`: subscript out of bounds
Backtrace:
     ▆
  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