##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings pipeComp_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/pipeComp.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-14 07:04:01 UTC
* checking for file ‘pipeComp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeComp’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘pipeComp’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scrna_describeDatasets: no visible binding for global variable
  ‘cluster’
scrna_describeDatasets: no visible binding for global variable ‘nb’
scrna_describeDatasets : pf: no visible binding for global variable
  ‘.x’
scrna_describeDatasets : rd: no visible binding for global variable ‘y’
scrna_describeDatasets : rd: no visible binding for global variable
  ‘cluster’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘max.lost’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘mean_F1’
scrna_evalPlot_filtering: no visible binding for global variable ‘filt’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘doubletmethod’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘method’
scrna_evalPlot_overall: no visible binding for global variable
  ‘true.nbClusts’
scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’
Undefined global functions or variables:
  .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb
  true.nbClusts y
* 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 ... ERROR
Running examples in ‘pipeComp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: evaluateClustering
> ### Title: evaluateClustering
> ### Aliases: evaluateClustering
> 
> ### ** Examples
> 
> # random data
> dat <- data.frame( 
+  cluster=rep(LETTERS[1:3], each=10),
+  x=c(rnorm(20, 0), rnorm(10, 1)),
+  y=c(rnorm(10, 1), rnorm(20, 0))
+ )
> # clustering
> dat$predicted <- kmeans(dist(dat[,-1]),3)$cluster
> # evaluation
> evaluateClustering(dat$predicted, dat$cluster)
Warning: `clustComp()` was deprecated in aricode 1.1.0.
ℹ Please use `compare_clustering()` instead.
ℹ The deprecated feature was likely used in the pipeComp package.
  Please report the issue at <https://github.com/plger/pipeComp>.
Warning in sort_pairs(c1, c2) : NAs introduced by coercion
Error in sort_pairs(c1, c2) : NA are not supported.
Calls: evaluateClustering ... unlist -> <Anonymous> -> compare_clustering -> sort_pairs
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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/pipeComp.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL pipeComp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘pipeComp’ ...
** this is package ‘pipeComp’ version ‘1.23.0’
** using staged installation
** R
** data
** inst
** 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 (pipeComp)