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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPOTlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPOTlight_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SPOTlight.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 ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘1.13.0’
* 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 ‘SPOTlight’ 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 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 ... 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:
  plotTopicProfiles.Rd: NMFfit
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 ... OK
* 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:
  y[1]: "gg"
  ── Failure ('test-utils.R:133:5'): .plot_image() SPE ───────────────────────────
  class(plt)[1] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  ── Failure ('test-utils.R:139:5'): .plot_image() SPE ───────────────────────────
  class(plt)[1] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  
  [ FAIL 16 | WARN 3 | SKIP 0 | PASS 301 ]
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SPOTlight.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPOTlight
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SPOTlight’ ...
** this is package ‘SPOTlight’ version ‘1.13.0’
** 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 (SPOTlight)

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.

> set.seed(321)
> library(testthat)
> library(SPOTlight)
> # plotImage() ----
> test_check("SPOTlight")
[ FAIL 16 | WARN 3 | SKIP 0 | PASS 301 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotImage.R:11:5'): plotImage path ───────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotImage.R:20:5'): plotImage array ──────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotImage.R:49:5'): plotImage SPE ────────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:20:5'): plotSpatialScatterpie with matrix and bad colnames ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:30:5'): plotSpatialScatterpie with matrix and bad colnames ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:40:5'): plotSpatialScatterpie - image ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:50:5'): plotSpatialScatterpie - type subset ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:61:5'): plotSpatialScatterpie - alpha ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:72:5'): plotSpatialScatterpie - pie_scale ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:90:5'): plotSpatialScatterpie - image ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:102:5'): plotSpatialScatterpie - spots on image ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:124:5'): plotSpatialScatterpie - rotate 90 degrees ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:145:3'): plotSpatialScatterpie - mirror veritcal ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:165:3'): plotSpatialScatterpie - mirror horizontal ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-utils.R:133:5'): .plot_image() SPE ───────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-utils.R:139:5'): .plot_image() SPE ───────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"

[ FAIL 16 | WARN 3 | SKIP 0 | PASS 301 ]
Error: Test failures
Execution halted