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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scater_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/scater.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.32.0’
* 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 ‘scater’ 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 ... NOTE
checkRd: (-1) plotHeatmap.Rd:87: Lost braces; missing escapes or markup?
    87 | \item{by_exprs_values}{Alias to {by.assay.type}.}
       |                                 ^
* 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
plotReducedDim    11.732  0.344  15.856
plotRLE            9.592  0.250  14.855
runMultiUMAP       8.461  0.077  12.708
projectReducedDim  7.171  0.096  10.743
runUMAP            5.840  0.061   8.993
plotColData        5.205  0.113   7.902
plotExpression     4.083  0.114   6.182
plotScater         3.784  0.172   6.095
plot_reddim        3.321  0.076   5.188
* 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:
  reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE").
  Objects equal but not identical
  ── Failure ('test-red-dim.R:324:5'): runTSNE works with externally computed nearest neighbor results ──
  reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE").
  Objects equal but not identical
  ── Failure ('test-red-dim.R:329:5'): runTSNE works with externally computed nearest neighbor results ──
  reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE").
  Objects equal but not identical
  ── Failure ('test-red-dim.R:333:5'): runTSNE works with externally computed nearest neighbor results ──
  reducedDim(ref, "TSNE") not identical to reducedDim(alt, "TSNE").
  Objects equal but not identical
  
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 795 ]
  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-3.19-bioc/meat/scater.Rcheck/00check.log’
for details.