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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cicero_1.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cicero.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cicero/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cicero’ version ‘1.17.2’
* 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 ‘cicero’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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
aggregate_nearby_peaks: no visible binding for global variable 'val'
annotate_cds_by_site: no visible binding for global variable 'row_name'
assemble_connections : <anonymous>: no visible global function
  definition for 'patterns'
assemble_connections: no visible binding for global variable 'value'
estimateDispersionsForCellDataSet: no visible global function
  definition for 'cooks.distance'
estimateSizeFactorsSimp: no visible global function definition for
  'sizeFactors<-'
find_overlapping_ccans: no visible binding for global variable 'CCAN'
generate_windows: no visible binding for global variable 'V1'
parametricDispersionFit: no visible global function definition for
  'glm'
parametricDispersionFit: no visible global function definition for
  'Gamma'
plot_accessibility_in_pseudotime: no visible binding for global
  variable 'f_id'
plot_accessibility_in_pseudotime: no visible binding for global
  variable 'Var1'
Undefined global functions or variables:
  CCAN Gamma V1 Var1 cooks.distance f_id glm patterns row_name
  sizeFactors<- val value
Consider adding
  importFrom("stats", "Gamma", "cooks.distance", "glm")
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cicero-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assemble_connections
> ### Title: Combine and reconcile cicero models
> ### Aliases: assemble_connections
> 
> ### ** Examples
> 
>   data("cicero_data")
>   data("human.hg19.genome")
>   sample_genome <- subset(human.hg19.genome, V1 == "chr18")
>   sample_genome$V2[1] <- 100000
>   input_cds <- make_atac_cds(cicero_data, binarize = TRUE)
>   input_cds <- reduceDimension(input_cds, max_components = 2, num_dim=6,
+                                reduction_method = 'tSNE',
+                                norm_method = "none")
>   tsne_coords <- t(reducedDimA(input_cds))
>   row.names(tsne_coords) <- row.names(pData(input_cds))
>   cicero_cds <- make_cicero_cds(input_cds, reduced_coordinates = tsne_coords)
Overlap QC metrics:
Cells per bin: 50
Maximum shared cells bin-bin: 44
Mean shared cells bin-bin: 12.3918128654971
Median shared cells bin-bin: 1
Warning in make_cicero_cds(input_cds, reduced_coordinates = tsne_coords) :
  On average, more than 10% of cells are shared between paired bins.
Error in class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE : 
  'length = 2' in coercion to 'logical(1)'
Calls: make_cicero_cds
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:
  • plotting/connections-plot-with-collapsetranscripts-true.svg
  • plotting/connections-plot-with-comparison-color.svg
  • plotting/connections-plot-with-comparison-peak-color-hex.svg
  • plotting/connections-plot-with-comparison-peak-color.svg
  • plotting/connections-plot-with-comparison.svg
  • plotting/connections-plot-with-gene-model-color.svg
  • plotting/connections-plot-with-gene-model-no-genes.svg
  • plotting/connections-plot-with-gene-model-with-comparison.svg
  • plotting/connections-plot-with-gene-model.svg
  • plotting/peak-color-color-column.svg
  • plotting/peak-color-logical-column.svg
  • plotting/peak-color-type-column.svg
  • plotting/peak-color.svg
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘website.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/cicero.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cicero
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘cicero’ ...
** 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 (cicero)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(cicero)
Loading required package: monocle
Loading required package: Matrix
Loading required package: Biobase
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Loading required package: DDRTree
Loading required package: irlba
Loading required package: Gviz
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("cicero")
[1] "Generating fData ranges"
[1] "Generating feature data ranges"
[1] "Determining overlaps"
[1] "Assigning labels"
[1] "Merging to fData table"
[1] "Generating fData ranges"
[1] "Generating feature data ranges"
[1] "Determining overlaps"
[1] "Assigning labels"
[1] "Merging to fData table"
[1] "Generating fData ranges"
[1] "Reading data file"
[1] "Generating feature data ranges"
[1] "Determining overlaps"
[1] "Assigning labels"
[1] "Merging to fData table"
[ FAIL 4 | WARN 0 | SKIP 19 | PASS 116 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (19)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-aggregate.R:23'): aggregate_nearby_peaks makes a valid cds object not sparse ──
Error in `class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
    ▆
 1. └─cicero::aggregate_nearby_peaks(test_cds2, 10000) at test-aggregate.R:23:2
 2.   ├─base::suppressWarnings(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─monocle::newCellDataSet(...)
── Error ('test-aggregate.R:36'): aggregate_by_cell_bin makes a valid cds object ──
Error in `class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
    ▆
 1. ├─base::suppressMessages(aggregate_by_cell_bin(test_cds, "cell_subtype")) at test-aggregate.R:36:2
 2. │ └─base::withCallingHandlers(...)
 3. └─cicero::aggregate_by_cell_bin(test_cds, "cell_subtype")
 4.   ├─base::suppressWarnings(...)
 5.   │ └─base::withCallingHandlers(...)
 6.   └─monocle::newCellDataSet(...)
── Error ('test-aggregate.R:49'): aggregate_by_cell_bin makes a valid cds object not sparse ──
Error in `class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
    ▆
 1. ├─base::suppressMessages(aggregate_by_cell_bin(test_cds2, "cell_subtype")) at test-aggregate.R:49:2
 2. │ └─base::withCallingHandlers(...)
 3. └─cicero::aggregate_by_cell_bin(test_cds2, "cell_subtype")
 4.   ├─base::suppressWarnings(...)
 5.   │ └─base::withCallingHandlers(...)
 6.   └─monocle::newCellDataSet(...)
── Error ('test-runCicero.R:18'): (code run outside of `test_that()`) ──────────
Error in `class(cellData) != "matrix" && isSparseMatrix(cellData) == FALSE`: 'length = 2' in coercion to 'logical(1)'
Backtrace:
    ▆
 1. └─cicero::make_cicero_cds(...) at test-runCicero.R:18:0
 2.   ├─base::suppressWarnings(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   └─monocle::newCellDataSet(...)

[ FAIL 4 | WARN 0 | SKIP 19 | PASS 116 ]
Deleting unused snapshots:
• plotting/basic-bar-high-breaks.svg
• plotting/basic-bar-one.svg
• plotting/basic-bar.svg
• plotting/basic-connections-all-bp.svg
• plotting/basic-connections-chr-bp1.svg
• plotting/basic-connections-chr.svg
• plotting/basic-connections-comparison-plot.svg
• plotting/basic-connections-high-comparison-cutoff.svg
• plotting/basic-connections-high-cutoff.svg
• plotting/basic-connections-include-axis-track.svg
• plotting/basic-connections-plot-bad-chr.svg
• plotting/basic-connections-plot-comparison-cutoff.svg
• plotting/basic-connections-plot-cutoff.svg
• plotting/basic-connections-plot-dt.svg
• plotting/basic-connections-plot-with-viewpoint-change-colors.svg
• plotting/basic-connections-plot-with-viewpoint-no-comp.svg
• plotting/basic-connections-plot-with-viewpoint.svg
• plotting/basic-connections-plot.svg
• plotting/comparison-connection-color-color-column.svg
• plotting/comparison-connection-color-comparison-connection-width.svg
• plotting/comparison-connection-color-type-column-coaccess-no-legend.svg
• plotting/comparison-connection-color-type-column-coaccess.svg
• plotting/comparison-connection-color-type-column.svg
• plotting/comparison-connection-color.svg
• plotting/comparison-peak-color-color-column.svg
• plotting/comparison-peak-color-logical-column.svg
• plotting/comparison-peak-color-type-column.svg
• plotting/comparison-peak-color.svg
• plotting/comparison-ymax-plus-cutoff.svg
• plotting/comparison-ymax.svg
• plotting/connection-color-color-column.svg
• plotting/connection-color-connection-width.svg
• plotting/connection-color-type-column-coaccess-no-legend.svg
• plotting/connection-color-type-column-coaccess.svg
• plotting/connection-color-type-column.svg
• plotting/connection-color.svg
• plotting/connection-ymax-plus-cutoff.svg
• plotting/connection-ymax.svg
• plotting/connections-plot-with-collapsetranscripts-gene.svg
• plotting/connections-plot-with-collapsetranscripts-longest.svg
• plotting/connections-plot-with-collapsetranscripts-meta.svg
• plotting/connections-plot-with-collapsetranscripts-shortest.svg
• plotting/connections-plot-with-collapsetranscripts-true.svg
• plotting/connections-plot-with-comparison-color.svg
• plotting/connections-plot-with-comparison-peak-color-hex.svg
• plotting/connections-plot-with-comparison-peak-color.svg
• plotting/connections-plot-with-comparison.svg
• plotting/connections-plot-with-gene-model-color.svg
• plotting/connections-plot-with-gene-model-no-genes.svg
• plotting/connections-plot-with-gene-model-with-comparison.svg
• plotting/connections-plot-with-gene-model.svg
• plotting/peak-color-color-column.svg
• plotting/peak-color-logical-column.svg
• plotting/peak-color-type-column.svg
• plotting/peak-color.svg
Error: Test failures
Execution halted