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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 912/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
granulator 1.17.0  (landing page)
Sabina Pfister
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/granulator
git_branch: devel
git_last_commit: 0a7bef1
git_last_commit_date: 2025-04-15 12:27:55 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for granulator on lconway

To the developers/maintainers of the granulator package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/granulator.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: granulator
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2025-09-26 21:37:05 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 21:45:22 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 496.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: granulator.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/granulator.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘granulator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘granulator’ version ‘1.17.0’
* 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      61.504  0.446  69.125
plot_deconvolute 39.304  0.332  47.765
plot_correlate   38.167  0.312  47.261
plot_regress     35.211  0.250  35.679
plot_benchmark   34.641  0.243  37.188
plot_proportions 32.952  0.275  33.474
benchmark        32.669  0.269  33.188
correlate        31.948  0.233  32.373
* 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-deconvolution.R:32:9'): Deconvolution methods ────────────────
  class(plot_benchmark(bench))[1] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  ── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
  class(plot_correlate(correl))[1] not equal to "gg".
  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-3.22-bioc/meat/granulator.Rcheck/00check.log’
for details.


Installation output

granulator.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL granulator
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘granulator’ ...
** this is package ‘granulator’ version ‘1.17.0’
** 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)

Tests output

granulator.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
[ FAIL 40 | WARN 23 | SKIP 0 | PASS 97 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-data.R:10:5'): Load data ─────────────────────────────────────
class(plot_similarity(sigMatrix_ABIS_S0))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:14:5'): Load data ─────────────────────────────────────
class(plot_similarity(sigMatrix_ABIS_S1))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:18:5'): Load data ─────────────────────────────────────
class(plot_similarity(sigMatrix_ABIS_S2))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:22:5'): Load data ─────────────────────────────────────
class(plot_similarity(sigMatrix_ABIS_S3))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-data.R:30:5'): Load data ─────────────────────────────────────
class(plot_similarity(sigList))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:21:9'): Deconvolution methods ────────────────
class(plot_proportions(decon, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:22:9'): Deconvolution methods ────────────────
class(plot_deconvolute(decon))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:31:9'): Deconvolution methods ────────────────
class(plot_regress(bench, method = m, signature = "sig1"))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:32:9'): Deconvolution methods ────────────────
class(plot_benchmark(bench))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-deconvolution.R:40:9'): Deconvolution methods ────────────────
class(plot_correlate(correl))[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"

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

Example timings

granulator.Rcheck/granulator-Ex.timings

nameusersystemelapsed
benchmark32.669 0.26933.188
correlate31.948 0.23332.373
deconvolute61.504 0.44669.125
get_TPM0.0010.0000.002
get_decon_methods000
load_ABIS0.0120.0060.018
plot_benchmark34.641 0.24337.188
plot_correlate38.167 0.31247.261
plot_deconvolute39.304 0.33247.765
plot_proportions32.952 0.27533.474
plot_regress35.211 0.25035.679
plot_similarity3.9080.0273.957