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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpaceTrooper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpaceTrooper_0.99.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceTrooper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpaceTrooper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpaceTrooper’ version ‘0.99.3’
* 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 ‘SpaceTrooper’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
* 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 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 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
.checkFovPositionVersion: no visible global function definition for
  ‘metadata<-’
readCosmxProteinSPE: no visible global function definition for
  ‘metadata<-’
readCosmxSPE: no visible global function definition for ‘metadata<-’
readXeniumSPE: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
  metadata<-
* 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:
  computeTrainDF.Rd: SpatialExperiment-class
  dot-computeCosmxProteinTrainSet.Rd: SpatialExperiment-class
  dot-computeCosmxTrainSet.Rd: SpatialExperiment-class
  dot-computeXenMerTrainSet.Rd: SpatialExperiment-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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SpaceTrooper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qcFlagPlots
> ### Title: qcFlagPlots
> ### Aliases: qcFlagPlots
> 
> ### ** Examples
> 
> 
> example(readAndAddPolygonsToSPE)

rAAPTS> example(readCosmxSPE)

rdCSPE> cospath <- system.file(file.path("extdata", "CosMx_DBKero_Tiny"),
rdCSPE+    package="SpaceTrooper")

rdCSPE> spe <- readCosmxSPE(cospath, sampleName="DBKero_Tiny")

rAAPTS> spe <- readAndAddPolygonsToSPE(spe)

rAAPTS> colData(spe)
DataFrame with 905 rows and 21 columns
               fov    cellID      Area AspectRatio CenterX_local_px
         <integer> <integer> <integer>   <numeric>        <integer>
f16_c1          16         1      5986        1.06             3688
f16_c10         16        10      4507        1.64             3924
f16_c100        16       100     11559        1.13             1795
f16_c101        16       101     14247        0.95             2619
f16_c102        16       102     12217        1.02             2051
...            ...       ...       ...         ...              ...
f16_c95         16        95     16144        1.02             2825
f16_c96         16        96      7159        1.10             3527
f16_c97         16        97      7481        1.19             3615
f16_c98         16        98     10861        0.78             3262
f16_c99         16        99      9137        1.16             3370
         CenterY_local_px     Width    Height Mean.PanCK Max.PanCK Mean.CD68
                <integer> <integer> <integer>  <integer> <integer> <integer>
f16_c1               4194        93        88        442      1295       308
f16_c10              3663        97        59        452      1547        66
f16_c100             2953       140       124       2195     27640        57
f16_c101             2933       140       148       2673     24878        94
f16_c102             2940       128       125       2260     17308        48
...                   ...       ...       ...        ...       ...       ...
f16_c95              2950       168       165       7702     56862        73
f16_c96              2978       108        98       1412     22935      1883
f16_c97              2969       120       101       4058     34509       191
f16_c98              2956       108       138       5615     34270       279
f16_c99              2962       121       104       1422     11330      1538
          Max.CD68 Mean.MembraneStain_B2M Max.MembraneStain_B2M Mean.CD45
         <integer>              <integer>             <integer> <integer>
f16_c1        2670                    472                  4136       110
f16_c10        233                   2017                 10433        47
f16_c100       571                    922                  6042        79
f16_c101      6403                    640                  4620       136
f16_c102       745                    525                  3285        53
...            ...                    ...                   ...       ...
f16_c95       5275                   1006                  5819        95
f16_c96       7764                   5896                 22216       220
f16_c97       4539                   2723                 25953       139
f16_c98       7100                   2856                 13008       135
f16_c99      17126                   3453                 15256       178
          Max.CD45 Mean.DAPI  Max.DAPI   sample_id     cell_id
         <integer> <integer> <integer> <character> <character>
f16_c1        4787       563      1954 DBKero_Tiny      f16_c1
f16_c10        697       151       326 DBKero_Tiny     f16_c10
f16_c100      1022      1155      3276 DBKero_Tiny    f16_c100
f16_c101      8310      1107      3355 DBKero_Tiny    f16_c101
f16_c102       873       976      3181 DBKero_Tiny    f16_c102
...            ...       ...       ...         ...         ...
f16_c95       7556       769      2700 DBKero_Tiny     f16_c95
f16_c96       1270       144       627 DBKero_Tiny     f16_c96
f16_c97       5811       957      2462 DBKero_Tiny     f16_c97
f16_c98       8785      1037      2743 DBKero_Tiny     f16_c98
f16_c99       1774       942      2817 DBKero_Tiny     f16_c99
                     polygons
                         <sf>
f16_c1     f16_c1:FALSE:1:...
f16_c10   f16_c10:FALSE:1:...
f16_c100 f16_c100:FALSE:1:...
f16_c101 f16_c101:FALSE:1:...
f16_c102 f16_c102:FALSE:1:...
...                       ...
f16_c95   f16_c95:FALSE:1:...
f16_c96   f16_c96:FALSE:1:...
f16_c97   f16_c97:FALSE:1:...
f16_c98   f16_c98:FALSE:1:...
f16_c99   f16_c99:FALSE:1:...
> spe <- spatialPerCellQC(spe)
Removing 1 cells with 0 counts!
> spe <- computeThresholdFlags(spe)
> p <- qcFlagPlots(spe, fov=16, theme="dark")
Warning in computeSpatialOutlier(spe, computeBy = "Area_um", method = "both") :
  Distribution is symmetric: mc is for asymmetric distributions. Use scuttle instead.
Warning in computeSpatialOutlier(spe, computeBy = "Mean.DAPI", method = "both") :
  Distribution is symmetric: mc is for asymmetric distributions. Use scuttle instead.
Warning in qcFlagPlots(spe, fov = 16, theme = "dark") :
  No 0 counts or control/total ratio > 0.1 found
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the SpaceTrooper package.
  Please report the issue at
  <https://github.com/drighelli/SpaceTrooper/issues>.
Error in `vec_slice()`:
! `x` must be a vector, not `NULL`.
Backtrace:
     ▆
  1. ├─SpaceTrooper::qcFlagPlots(spe, fov = 16, theme = "dark")
  2. │ └─cowplot::get_legend(legp)
  3. │   └─cowplot::get_plot_component(plot, pattern, return_all = FALSE)
  4. │     ├─cowplot::as_gtable(plot)
  5. │     └─cowplot:::as_gtable.default(plot)
  6. │       ├─cowplot::as_grob(plot)
  7. │       └─cowplot:::as_grob.ggplot(plot)
  8. │         └─ggplot2::ggplotGrob(plot)
  9. │           ├─ggplot2::ggplot_gtable(ggplot_build(x))
 10. │           │ └─ggplot2:::attach_plot_env(data@plot@plot_env)
 11. │           │   └─base::options(ggplot2_plot_env = env)
 12. │           ├─ggplot2::ggplot_build(x)
 13. │           └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
 14. │             └─plot@guides$build(npscales, plot@layers, plot@labels, data, plot@theme)
 15. │               └─ggplot2 (local) build(..., self = self)
 16. │                 └─guides$process_layers(layers, layer_data, theme)
 17. │                   └─ggplot2 (local) process_layers(..., self = self)
 18. │                     └─base::Map(...)
 19. │                       └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 20. │                         └─ggplot2 (local) `<fn>`(guide = dots[[1L]][[1L]], param = dots[[2L]][[1L]])
 21. │                           └─guide$process_layers(param, layers, data, theme)
 22. │                             └─ggplot2 (local) process_layers(..., self = self)
 23. │                               └─self$get_layer_key(params, layers[include], data[include], theme)
 24. │                                 └─ggplot2 (local) get_layer_key(...)
 25. │                                   └─base::Map(...)
 26. │                                     └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 27. │                                       └─ggplot2 (local) `<fn>`(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]])
 28. │                                         └─layer$compute_geom_2(key, single_params, theme)
 29. │                                           └─ggplot2 (local) compute_geom_2(..., self = self)
 30. │                                             └─ggproto_parent(Layer, self)$compute_geom_2(data, params, ...)
 31. │                                               └─ggplot2 (local) compute_geom_2(..., self = self)
 32. │                                                 └─self$geom$use_defaults(...)
 33. │                                                   └─ggplot2 (local) use_defaults(..., self = self)
 34. │                                                     └─vctrs::vec_slice(data, order(unlist(index)))
 35. └─vctrs:::stop_scalar_type(`<fn>`(NULL), "x", `<env>`)
 36.   └─vctrs:::stop_vctrs(...)
 37.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceTrooper.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpaceTrooper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SpaceTrooper’ ...
** this is package ‘SpaceTrooper’ version ‘0.99.3’
** 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 (SpaceTrooper)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SpaceTrooper)
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
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: Seqinfo
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("SpaceTrooper")

rdCSPE> cospath <- system.file(file.path("extdata", "CosMx_DBKero_Tiny"),
rdCSPE+    package="SpaceTrooper")

rdCSPE> spe <- readCosmxSPE(cospath, sampleName="DBKero_Tiny")
Removing 1 cells with 0 counts!
Removing 1 cells with 0 counts!
Removing 1 cells with 0 counts!
Removing 1 cells with 0 counts!
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  8.654   0.361   9.196