##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:escape.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings escape_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/escape.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘escape/DESCRIPTION’ ... OK
* this is package ‘escape’ version ‘2.0.0’
* 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 ‘escape’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getGeneSets 6.753  0.144    6.91
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • pcaEnrichment/pcaenrichment-facetby-plot.svg
  • pcaEnrichment/pcaenrichment-hex-plot.svg
  • ridgeEnrichment/ridgeenrichment-facet-plot.svg
  • ridgeEnrichment/ridgeenrichment-gradient-facet-plot.svg
  • ridgeEnrichment/ridgeenrichment-gradient-plot.svg
  • ridgeEnrichment/ridgeenrichment-gradient-reorder-plot.svg
  • ridgeEnrichment/ridgeenrichment-order-plot.svg
  • ridgeEnrichment/ridgeenrichment-rugadded-plot.svg
  • scatterEnrichment/scatterenrichment-facet-plot.svg
  • scatterEnrichment/scatterenrichment-hex-plot.svg
  • scatterEnrichment/scatterenrichment-scale-plot.svg
  • splitEnrichment/splitenrichment-facet-plot.svg
  • splitEnrichment/splitenrichment-mean-plot.svg
  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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/escape.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL escape
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘escape’ ...
** using staged installation
** R
** data
** 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 (escape)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.211   0.021   0.221 

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(escape)
> 
> test_check("escape")
[1] "Calculating features per cell..."
[1] "Normalizing enrichment scores per cell..."
[1] "Calculating features per cell..."
[1] "Normalizing enrichment scores per cell..."
Picking joint bandwidth of 9.72
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
Notch went outside hinges
ℹ Do you want `notch = FALSE`?
Notch went outside hinges
ℹ Do you want `notch = FALSE`?
[ FAIL 1 | WARN 0 | SKIP 7 | PASS 17 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (7): 'test-densityEnrichment.R:9:3', 'test-geyserEnrichment.R:8:3',
  'test-heatmapEnrichment.R:7:3', 'test-pcaEnrichment.R:9:3',
  'test-ridgeEnrichment.R:8:3', 'test-scatterEnrichment.R:7:3',
  'test-splitEnrichment.R:7:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-performPCA.R:13:3'): performPCA works ────────────────────────
output$PCA not equal to getdata("performPCA", "performPCA_PCAvalues").
68/170 mismatches (average diff: 2.59)
[69] -0.408 -  0.408 == -0.817
[70]  2.435 - -2.435 ==  4.870
[71]  0.745 - -0.745 ==  1.490
[72]  4.293 - -4.293 ==  8.586
[73] -1.497 -  1.497 == -2.993
[74]  2.343 - -2.343 ==  4.686
[75] -1.769 -  1.769 == -3.538
[76]  0.568 - -0.568 ==  1.136
[77] -1.935 -  1.935 == -3.870
...

[ FAIL 1 | WARN 0 | SKIP 7 | PASS 17 ]
Deleting unused snapshots:
• densityEnrichment/denistyenrichment-group-by-plot.svg
• geyserEnrichment/geyserenrichment-facet-plot.svg
• geyserEnrichment/geyserenrichment-gradient-facet-plot.svg
• geyserEnrichment/geyserenrichment-gradient-plot.svg
• geyserEnrichment/geyserenrichment-gradient-reorder-plot.svg
• geyserEnrichment/geyserenrichment-order-plot.svg
• geyserEnrichment/geyserenrichment-scale-plot.svg
• heatmapEnrichment/heatmapenrichment-clustercolumns-plot.svg
• heatmapEnrichment/heatmapenrichment-clusterrows-plot.svg
• heatmapEnrichment/heatmapenrichment-facet-plot.svg
• heatmapEnrichment/heatmapenrichment-scale-plot.svg
• pcaEnrichment/pcaenrichment-addfactors-plot.svg
• pcaEnrichment/pcaenrichment-facetby-addfactors-plot.svg
• pcaEnrichment/pcaenrichment-facetby-plot.svg
• pcaEnrichment/pcaenrichment-hex-plot.svg
• ridgeEnrichment/ridgeenrichment-facet-plot.svg
• ridgeEnrichment/ridgeenrichment-gradient-facet-plot.svg
• ridgeEnrichment/ridgeenrichment-gradient-plot.svg
• ridgeEnrichment/ridgeenrichment-gradient-reorder-plot.svg
• ridgeEnrichment/ridgeenrichment-order-plot.svg
• ridgeEnrichment/ridgeenrichment-rugadded-plot.svg
• scatterEnrichment/scatterenrichment-facet-plot.svg
• scatterEnrichment/scatterenrichment-hex-plot.svg
• scatterEnrichment/scatterenrichment-scale-plot.svg
• splitEnrichment/splitenrichment-facet-plot.svg
• splitEnrichment/splitenrichment-mean-plot.svg
Error: Test failures
Execution halted