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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1931/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scRepertoire 2.5.3  (landing page)
Nick Borcherding
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/scRepertoire
git_branch: devel
git_last_commit: 526c298
git_last_commit_date: 2025-07-25 13:33:26 -0400 (Fri, 25 Jul 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 scRepertoire on nebbiolo2

To the developers/maintainers of the scRepertoire package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scRepertoire.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: scRepertoire
Version: 2.5.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRepertoire_2.5.3.tar.gz
StartedAt: 2025-09-22 04:06:42 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 04:21:04 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 861.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: scRepertoire.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRepertoire_2.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.5.3’
* 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 ‘scRepertoire’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... NOTE
.calculatePairwiseIndices: no visible global function definition for
  ‘combn’
clonalSizeDistribution: no visible binding for global variable ‘y’
Undefined global functions or variables:
  combn y
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'StartracDiversity.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'alluvialClones.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalAbundance.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalBias.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalDiversity.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalHomeostasis.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalLength.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalNetwork.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalOccupy.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalOverlap.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalProportion.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalQuant.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalRarefaction.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalScatter.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'clonalSizeDistribution.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'percentAA.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'percentGeneUsage.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'percentKmer.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'positionalEntropy.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

Non-topic package-anchored link(s) in Rd file 'positionalProperty.Rd':
  ‘[grDevices:palettes]{hcl.pals}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
clonalCluster          14.038  0.761   8.345
StartracDiversity      10.428  0.328  10.757
clonalSizeDistribution  9.105  0.081   9.187
percentGeneUsage        6.858  0.041   6.900
* 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:
  
      union
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-clonalScatter.R:76:3'): Plotting output has the correct components ──
  plot_output$labels$fill (`actual`) not equal to "class" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('class')
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.


Installation output

scRepertoire.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scRepertoire
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scRepertoire’ ...
** this is package ‘scRepertoire’ version ‘2.5.3’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scRepertoire.so RcppExports.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-scRepertoire/00new/scRepertoire/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'floor' 
Note: wrong number of arguments to 'floor' 
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scRepertoire)

Tests output

scRepertoire.Rcheck/tests/spelling.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.157   0.030   0.175 

scRepertoire.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(scRepertoire)
Loading required package: ggplot2
> 
> test_check("scRepertoire")

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-clonalScatter.R:76:3'): Plotting output has the correct components ──
plot_output$labels$fill (`actual`) not equal to "class" (`expected`).

`actual` is NULL
`expected` is a character vector ('class')

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ]
Error: Test failures
Execution halted

Example timings

scRepertoire.Rcheck/scRepertoire-Ex.timings

nameusersystemelapsed
StartracDiversity10.428 0.32810.757
addVariable0.8080.0370.845
alluvialClones2.8710.0722.944
annotateInvariant1.5730.0111.583
clonalAbundance1.7000.0141.713
clonalBias2.8050.0572.861
clonalCluster14.038 0.761 8.345
clonalCompare2.5510.0352.586
clonalDiversity1.7740.0461.820
clonalHomeostasis1.1460.0031.150
clonalLength1.8000.0211.821
clonalNetwork0.0010.0000.000
clonalOccupy1.7370.0171.756
clonalOverlap1.0390.0071.046
clonalOverlay1.8970.0091.906
clonalProportion1.1430.0001.143
clonalQuant1.2290.0001.229
clonalRarefaction4.1020.0044.107
clonalScatter1.1720.0041.176
clonalSizeDistribution9.1050.0819.187
combineBCR4.2490.0231.820
combineExpression2.2830.0462.330
combineTCR0.7790.0000.779
createHTOContigList000
exportClones000
getCirclize1.4460.0391.485
highlightClones1.2680.0001.269
loadContigs0.6610.0271.838
percentAA2.2610.0432.305
percentGeneUsage6.8580.0416.900
percentKmer1.5380.0161.553
positionalEntropy1.5550.0061.561
positionalProperty2.4840.0162.499
quietVDJgenes0.0790.0000.079
subsetClones0.8650.0000.866