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### Running command:
###
###   /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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SPOTlight.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘1.7.0’
* 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 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
SPOTlight         18.352  0.532  21.627
plotTopicProfiles 16.401  0.213  19.121
runDeconvolution  13.524  0.118  15.707
trainNMF          12.496  0.114  14.649
data              11.398  0.135  13.512
* 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:
    6.     ├─SeuratObject::.CreateStdAssay(...)
    7.     └─SeuratObject:::.CreateStdAssay.list(...)
    8.       ├─methods::new(...)
    9.       │ ├─methods::initialize(value, ...)
   10.       │ └─methods::initialize(value, ...)
   11.       └─SeuratObject::LogMap(y = cells.all)
   12.         └─methods::new(...)
   13.           ├─methods::initialize(value, ...)
   14.           └─methods::initialize(value, ...)
   15.             └─methods (local) initMatrix(.Object, ...)
   16.               └─methods::validObject(.Object)
  
  [ FAIL 6 | WARN 2 | SKIP 0 | PASS 151 ]
  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
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘SPOTlight’ ...
** 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 6 | WARN 2 | SKIP 0 | PASS 151 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SPOTlight.R:12:1'): (code run outside of `test_that()`) ────────
Error in `validObject(.Object)`: invalid class "LogMap" object: Duplicate rownames not allowed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(SeuratObject::CreateSeuratObject(counts = counts(sce))) at test-SPOTlight.R:12:1
  2. │ └─base::withCallingHandlers(...)
  3. ├─SeuratObject::CreateSeuratObject(counts = counts(sce))
  4. └─SeuratObject:::CreateSeuratObject.default(counts = counts(sce))
  5.   └─SeuratObject::CreateAssay5Object(...)
  6.     ├─SeuratObject::.CreateStdAssay(...)
  7.     └─SeuratObject:::.CreateStdAssay.list(...)
  8.       ├─methods::new(...)
  9.       │ ├─methods::initialize(value, ...)
 10.       │ └─methods::initialize(value, ...)
 11.       └─SeuratObject::LogMap(y = cells.all)
 12.         └─methods::new(...)
 13.           ├─methods::initialize(value, ...)
 14.           └─methods::initialize(value, ...)
 15.             └─methods (local) initMatrix(.Object, ...)
 16.               └─methods::validObject(.Object)
── Failure ('test-plotInteractions.R:57:5'): plotInteractions(), which = 'heatmap', tunning ──
`min` not equal to "#FFFF00".
Lengths differ: 0 is not 1
── Failure ('test-plotInteractions.R:59:5'): plotInteractions(), which = 'heatmap', tunning ──
`max` not equal to "#FF0000".
Lengths differ: 0 is not 1
── Failure ('test-plotInteractions.R:61:5'): plotInteractions(), which = 'heatmap', tunning ──
`na` not equal to "grey50".
1/1 mismatches
x[1]: "#FF7F00"
y[1]: "grey50"
── Error ('test-runDeconvolution.R:12:1'): (code run outside of `test_that()`) ──
Error in `validObject(.Object)`: invalid class "LogMap" object: Duplicate rownames not allowed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(SeuratObject::CreateSeuratObject(counts = SingleCellExperiment::counts(sce))) at test-runDeconvolution.R:12:1
  2. │ └─base::withCallingHandlers(...)
  3. ├─SeuratObject::CreateSeuratObject(counts = SingleCellExperiment::counts(sce))
  4. └─SeuratObject:::CreateSeuratObject.default(counts = SingleCellExperiment::counts(sce))
  5.   └─SeuratObject::CreateAssay5Object(...)
  6.     ├─SeuratObject::.CreateStdAssay(...)
  7.     └─SeuratObject:::.CreateStdAssay.list(...)
  8.       ├─methods::new(...)
  9.       │ ├─methods::initialize(value, ...)
 10.       │ └─methods::initialize(value, ...)
 11.       └─SeuratObject::LogMap(y = cells.all)
 12.         └─methods::new(...)
 13.           ├─methods::initialize(value, ...)
 14.           └─methods::initialize(value, ...)
 15.             └─methods (local) initMatrix(.Object, ...)
 16.               └─methods::validObject(.Object)
── Error ('test-trainNMF.R:8:1'): (code run outside of `test_that()`) ──────────
Error in `validObject(.Object)`: invalid class "LogMap" object: Duplicate rownames not allowed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(SeuratObject::CreateSeuratObject(counts = counts(sce))) at test-trainNMF.R:8:1
  2. │ └─base::withCallingHandlers(...)
  3. ├─SeuratObject::CreateSeuratObject(counts = counts(sce))
  4. └─SeuratObject:::CreateSeuratObject.default(counts = counts(sce))
  5.   └─SeuratObject::CreateAssay5Object(...)
  6.     ├─SeuratObject::.CreateStdAssay(...)
  7.     └─SeuratObject:::.CreateStdAssay.list(...)
  8.       ├─methods::new(...)
  9.       │ ├─methods::initialize(value, ...)
 10.       │ └─methods::initialize(value, ...)
 11.       └─SeuratObject::LogMap(y = cells.all)
 12.         └─methods::new(...)
 13.           ├─methods::initialize(value, ...)
 14.           └─methods::initialize(value, ...)
 15.             └─methods (local) initMatrix(.Object, ...)
 16.               └─methods::validObject(.Object)

[ FAIL 6 | WARN 2 | SKIP 0 | PASS 151 ]
Error: Test failures
Execution halted