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This page was generated on 2025-09-23 12:07 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
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: 2025-09-22 13:45 -0400 (Mon, 22 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ScreenR
Version: 1.11.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ScreenR_1.11.0.tar.gz
StartedAt: 2025-09-23 11:43:47 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 11:49:20 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 333.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ScreenR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ScreenR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ScreenR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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 ... 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_barcode_trend       38.023  0.575  46.850
plot_zscore_distribution 37.861  0.410  52.969
compute_metrics          21.786  1.219  28.415
find_zscore_hit          18.233  0.224  22.673
find_robust_zscore_hit   17.469  0.541  23.086
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ScreenR.Rcheck/00check.log’
for details.


Installation output

ScreenR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ScreenR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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.

> 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_lost0.2150.0080.224
compute_data_table0.2490.0040.262
compute_explained_variance0.0230.0030.027
compute_metrics21.786 1.21928.415
compute_slope0.0590.0000.059
count_mapped_reads0.0420.0000.042
create_edger_obj0.0310.0000.030
create_screenr_object0.0600.0000.077
filter_by_slope0.1560.0040.161
filter_by_variance1.4390.0051.498
find_camera_hit1.5590.0031.804
find_common_hit0.0470.0000.096
find_roast_hit2.5590.0134.322
find_robust_zscore_hit17.469 0.54123.086
find_zscore_hit18.233 0.22422.673
get_annotation_table0.0210.0000.021
get_count_table0.1060.0000.172
get_data_table0.0410.0000.081
get_groups0.0000.0000.005
get_normalized_count_table0.0680.0000.132
get_replicates0.0010.0000.000
mapped_reads0.0580.0040.126
normalize_data0.0600.0040.132
plot_barcode_hit1.7850.0081.957
plot_barcode_lost0.5650.0000.670
plot_barcode_lost_for_gene2.2430.0083.263
plot_barcode_trend38.023 0.57546.850
plot_boxplot0.6210.0081.257
plot_common_hit0.4010.0000.813
plot_explained_variance0.6590.0000.879
plot_mapped_reads0.2950.0000.372
plot_mapped_reads_distribution2.4730.0003.600
plot_mds0.5110.0040.517
plot_trend2.1850.0163.038
plot_zscore_distribution37.861 0.41052.969
remove_all_zero_row0.0160.0000.032
set_annotation_table0.1930.0000.390
set_count_table0.1970.0000.395
set_data_table0.1980.0000.399
set_groups0.1940.0000.391
set_normalized_count_table0.2710.0000.544
set_replicates0.1880.0000.343