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This page was generated on 2025-09-25 12:07 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 1931/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ScreenR 1.11.0  (landing page)
Emanuel Michele Soda
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025)
git_url: https://git.bioconductor.org/packages/ScreenR
git_branch: devel
git_last_commit: 8f08b42
git_last_commit_date: 2025-04-15 12:52:25 -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 ScreenR on kjohnson3

To the developers/maintainers of the ScreenR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ScreenR.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: ScreenR
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ScreenR_1.11.0.tar.gz
StartedAt: 2025-09-24 21:37:55 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 21:39:23 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 88.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ScreenR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ScreenR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ScreenR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.11.0’
* 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 ‘ScreenR’ 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 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 ... NOTE
checkRd: (-1) annotation_table.Rd:25: Lost braces
    25 |                  \url{https://cellecta.com/}{cellecta}}
       |                                             ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'compute_camera.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'select_number_barcode.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'unique_gene_symbols.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plot_zscore_distribution 10.566  2.414  13.966
plot_barcode_trend       10.959  1.934  13.362
compute_metrics           6.794  0.629   7.547
find_zscore_hit           5.223  1.229   6.567
find_robust_zscore_hit    5.055  1.083   6.337
* 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:
  `expected`: "gg"             
  ── Failure ('test-visualization.R:179:5'): plot_zscore_distribution ────────────
  class(p)[1] (`actual`) not equal to "gg" (`expected`).
  
  `actual`:   "ggplot2::ggplot"
  `expected`: "gg"             
  ── Failure ('test-visualization.R:263:5'): Plot common Hit ─────────────────────
  "gg" (`actual`) not equal to class(plot)[1] (`expected`).
  
  `actual`:   "gg"             
  `expected`: "ggplot2::ggplot"
  
  [ FAIL 11 | WARN 253 | SKIP 0 | PASS 53 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ScreenR.Rcheck/00check.log’
for details.


Installation output

ScreenR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ScreenR’ ...
** this is package ‘ScreenR’ version ‘1.11.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ScreenR)

Tests output

ScreenR.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: aarch64-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(ScreenR)

Welcome to ScreenR
--------------------------

See ?ScreenR for a list of
available functions.

Enjoy!

> 
> test_check("ScreenR")
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
Using classic mode.
[ FAIL 11 | WARN 253 | SKIP 0 | PASS 53 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-MDS.R:52:5'): plot_mds NULL ──────────────────────────────────
class(plot)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-MDS.R:61:5'): plot_mds ───────────────────────────────────────
class(plot)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-MDS.R:70:5'): plot_explained_variance ────────────────────────
class(plot)[[1]] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-MDS.R:81:5'): plot_explained_variance CUM ────────────────────
class(plot)[[1]] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:57:5'): plot trend hit ───────────────────────
class(plot)[[1]] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:71:5'): Plot Boxplot violinplot ──────────────
class(p)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:85:5'): Plot Boxplot boxplot ─────────────────
class(p)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:102:5'): plot_barcode_lost_for_gene ──────────
class(p)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:108:5'): plot_barcode_lost_for_gene ──────────
class(p)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:179:5'): plot_zscore_distribution ────────────
class(p)[1] (`actual`) not equal to "gg" (`expected`).

`actual`:   "ggplot2::ggplot"
`expected`: "gg"             
── Failure ('test-visualization.R:263:5'): Plot common Hit ─────────────────────
"gg" (`actual`) not equal to class(plot)[1] (`expected`).

`actual`:   "gg"             
`expected`: "ggplot2::ggplot"

[ FAIL 11 | WARN 253 | SKIP 0 | PASS 53 ]
Error: Test failures
Execution halted

Example timings

ScreenR.Rcheck/ScreenR-Ex.timings

nameusersystemelapsed
barcode_lost0.0730.0040.078
compute_data_table0.0880.0020.092
compute_explained_variance0.0080.0010.008
compute_metrics6.7940.6297.547
compute_slope0.0130.0000.014
count_mapped_reads0.010.000.01
create_edger_obj0.0070.0010.007
create_screenr_object0.0120.0000.012
filter_by_slope0.0370.0010.039
filter_by_variance0.4290.0180.447
find_camera_hit0.4430.0210.491
find_common_hit0.0080.0000.008
find_roast_hit0.6200.0450.671
find_robust_zscore_hit5.0551.0836.337
find_zscore_hit5.2231.2296.567
get_annotation_table0.0040.0000.004
get_count_table0.0310.0080.039
get_data_table0.0080.0000.009
get_groups000
get_normalized_count_table0.0130.0010.014
get_replicates000
mapped_reads0.0160.0000.016
normalize_data0.0110.0000.012
plot_barcode_hit0.5130.0330.547
plot_barcode_lost0.1340.0040.137
plot_barcode_lost_for_gene0.5180.0060.527
plot_barcode_trend10.959 1.93413.362
plot_boxplot0.1350.0030.141
plot_common_hit0.0860.0010.089
plot_explained_variance0.1390.0020.155
plot_mapped_reads0.0660.0010.068
plot_mapped_reads_distribution0.5710.0160.652
plot_mds0.1260.0010.142
plot_trend0.6330.3211.001
plot_zscore_distribution10.566 2.41413.966
remove_all_zero_row0.0040.0000.004
set_annotation_table0.0330.0000.032
set_count_table0.0340.0000.036
set_data_table0.0360.0010.038
set_groups0.0320.0000.033
set_normalized_count_table0.0470.0010.048
set_replicates0.0310.0000.032