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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:granulator.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings granulator_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/granulator.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘granulator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘granulator’ version ‘1.19.0’
* 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 ‘granulator’ 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 ... 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
deconvolute      61.916  1.268  65.984
plot_benchmark   38.929  0.309  39.561
benchmark        36.624  0.572  45.112
correlate        36.300  0.418  38.872
plot_deconvolute 36.338  0.246  36.880
plot_regress     35.566  0.395  40.233
plot_correlate   35.486  0.256  35.967
plot_proportions 32.099  0.227  32.544
plot_similarity   4.322  0.059   5.173
* 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:
  Differences:
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
  Expected `class(plot_correlate(correl))[1]` to equal "gg".
  Differences:
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  
  [ FAIL 40 | WARN 23 | SKIP 0 | PASS 97 ]
  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-3.23-bioc/meat/granulator.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL granulator
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘granulator’ ...
** this is package ‘granulator’ version ‘1.19.0’
** using staged installation
** R
** data
** 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 (granulator)

R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

> library("testthat")
> library("granulator")
> 
> test_check("granulator")
Saving _problems/test-data-10.R
Saving _problems/test-data-14.R
Saving _problems/test-data-18.R
Saving _problems/test-data-22.R
Saving _problems/test-data-30.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
Saving _problems/test-deconvolution-21.R
Saving _problems/test-deconvolution-22.R
Saving _problems/test-deconvolution-31.R
Saving _problems/test-deconvolution-32.R
Saving _problems/test-deconvolution-40.R
[ FAIL 40 | WARN 23 | SKIP 0 | PASS 97 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-data.R:10:5'): Load data ─────────────────────────────────────
Expected `class(plot_similarity(sigMatrix_ABIS_S0))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:14:5'): Load data ─────────────────────────────────────
Expected `class(plot_similarity(sigMatrix_ABIS_S1))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:18:5'): Load data ─────────────────────────────────────
Expected `class(plot_similarity(sigMatrix_ABIS_S2))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:22:5'): Load data ─────────────────────────────────────
Expected `class(plot_similarity(sigMatrix_ABIS_S3))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:30:5'): Load data ─────────────────────────────────────
Expected `class(plot_similarity(sigList))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
Expected `class(plot_proportions(decon, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
Expected `class(plot_deconvolute(decon))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
Expected `class(plot_regress(bench, method = m, signature = "sig1"))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
Expected `class(plot_benchmark(bench))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
Expected `class(plot_correlate(correl))[1]` to equal "gg".
Differences:
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"

[ FAIL 40 | WARN 23 | SKIP 0 | PASS 97 ]
Error:
! Test failures.
Execution halted