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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scRepertoire_2.5.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scRepertoire.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 ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.5.6’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    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 ... 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 ... NOTE
clonalSizeDistribution: no visible binding for global variable ‘y’
combineExpression: no visible binding for global variable
  ‘clonalFrequency’
Undefined global functions or variables:
  clonalFrequency y
* 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
StartracDiversity      13.291  0.303  16.636
clonalSizeDistribution 12.778  0.096  17.525
clonalCluster          11.284  0.236  14.191
percentGeneUsage        9.322  0.019  13.026
clonalRarefaction       6.308  0.043   6.758
alluvialClones          4.128  0.064   8.313
positionalProperty      3.927  0.034   5.657
clonalBias              3.609  0.028   6.295
loadContigs             0.427  0.010   6.746
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘scRepertoire’ ...
** this is package ‘scRepertoire’ version ‘2.5.6’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o scRepertoire.so RcppExports.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.197   0.033   0.427 

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.

> # 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 0 | WARN 1 | SKIP 0 | PASS 781 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 781 ]
> 
> proc.time()
   user  system elapsed 
266.172   5.598 392.659