##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:imcRtools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings imcRtools_1.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/imcRtools.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'imcRtools/DESCRIPTION' ... OK
* this is package 'imcRtools' version '1.2.4'
* 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 whether package 'imcRtools' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
testInteractions  170.37   3.83  177.77
read_steinbock     30.54   3.92  108.07
buildSpatialGraph  17.23   1.46   17.99
plotSpatial         7.03   0.08    7.11
filterPixels        5.44   0.72    6.89
read_cpout          4.08   0.94    4.32
* 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:
  Expected match: "'end_cap' must be of type 'geometry'."
  Actual message: "'end_cap' must be of type 'ggraph_geometry'."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test_plotSpatial.R:704:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─imcRtools::plotSpatial(...)
   7.   └─imcRtools:::.valid.plotSpatial.input(...)
  
  [ FAIL 9 | WARN 0 | SKIP 2 | PASS 1658 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.15-bioc/meat/imcRtools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL imcRtools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'imcRtools' ...
** using staged installation
** R
** 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 (imcRtools)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(imcRtools)
Loading required package: SpatialExperiment
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, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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

> 
> test_check("imcRtools")
[ FAIL 9 | WARN 0 | SKIP 2 | PASS 1658 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (2)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plotSpatial.R:237'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:243'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:267'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:405'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:412'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:433'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:465'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:524'): plotSpatial function works ──────────────
`print(p)` produced warnings.
── Failure ('test_plotSpatial.R:704'): plotSpatial function works ──────────────
`plotSpatial(...)` threw an error with unexpected message.
Expected match: "'end_cap' must be of type 'geometry'."
Actual message: "'end_cap' must be of type 'ggraph_geometry'."
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_plotSpatial.R:704:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─imcRtools::plotSpatial(...)
 7.   └─imcRtools:::.valid.plotSpatial.input(...)

[ FAIL 9 | WARN 0 | SKIP 2 | PASS 1658 ]
Error: Test failures
Execution halted