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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpaceTrooper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpaceTrooper_0.99.4.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpaceTrooper.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘SpaceTrooper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpaceTrooper’ version ‘0.99.4’
* 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 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 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
.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
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Error in `vec_slice()`:
! `x` must be a vector, not `NULL`.
Backtrace:
     ▆
  1. ├─SpaceTrooper::qcFlagPlots(spe, fov = 16, theme = "dark")
  2. │ └─cowplot::plot_grid(ggp1, ggp2, ggp3, ncol = 2)
  3. │   └─cowplot::align_plots(...)
  4. │     └─base::lapply(...)
  5. │       └─cowplot (local) FUN(X[[i]], ...)
  6. │         ├─cowplot::as_gtable(x)
  7. │         └─cowplot:::as_gtable.default(x)
  8. │           ├─cowplot::as_grob(plot)
  9. │           └─cowplot:::as_grob.ggplot(plot)
 10. │             └─ggplot2::ggplotGrob(plot)
 11. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
 12. │               │ └─ggplot2:::attach_plot_env(data@plot@plot_env)
 13. │               │   └─base::options(ggplot2_plot_env = env)
 14. │               ├─ggplot2::ggplot_build(x)
 15. │               └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
 16. │                 └─plot@guides$build(npscales, plot@layers, plot@labels, data, plot@theme)
 17. │                   └─ggplot2 (local) build(..., self = self)
 18. │                     └─guides$process_layers(layers, layer_data, theme)
 19. │                       └─ggplot2 (local) process_layers(..., self = self)
 20. │                         └─base::Map(...)
 21. │                           └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 22. │                             └─ggplot2 (local) `<fn>`(guide = dots[[1L]][[1L]], param = dots[[2L]][[1L]])
 23. │                               └─guide$process_layers(param, layers, data, theme)
 24. │                                 └─ggplot2 (local) process_layers(..., self = self)
 25. │                                   └─self$get_layer_key(params, layers[include], data[include], theme)
 26. │                                     └─ggplot2 (local) get_layer_key(...)
 27. │                                       └─base::Map(...)
 28. │                                         └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 29. │                                           └─ggplot2 (local) `<fn>`(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]])
 30. │                                             └─layer$compute_geom_2(key, single_params, theme)
 31. │                                               └─ggplot2 (local) compute_geom_2(..., self = self)
 32. │                                                 └─ggproto_parent(Layer, self)$compute_geom_2(data, params, ...)
 33. │                                                   └─ggplot2 (local) compute_geom_2(..., self = self)
 34. │                                                     └─self$geom$use_defaults(...)
 35. │                                                       └─ggplot2 (local) use_defaults(..., self = self)
 36. │                                                         └─vctrs::vec_slice(data, order(unlist(index)))
 37. └─vctrs:::stop_scalar_type(`<fn>`(NULL), "x", `<env>`)
 38.   └─vctrs:::stop_vctrs(...)
 39.     └─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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SpaceTrooper.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SpaceTrooper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SpaceTrooper’ ...
** this is package ‘SpaceTrooper’ version ‘0.99.4’
** 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 (2025-08-23 r88802) -- "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.

> # 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 
 22.817   1.303  24.279