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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:IWTomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings IWTomics_1.33.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/IWTomics.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 ‘IWTomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IWTomics’ version ‘1.33.0’
* 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 ‘IWTomics’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    0.99.0 First submission
  Cannot process chunk/lines:
    0.99.11 Revised package
  Cannot process chunk/lines:
    0.99.12 Fixed bug in plotTest and plotSummary
  Cannot process chunk/lines:
    1.1.1 Fixed bug in IWTomicsTest statistics=variance
  Cannot process chunk/lines:
    1.1.2 Fixed alpha
  Cannot process chunk/lines:
    1.1.3 Fixed bug in IWTomicsData constructor
  Cannot process chunk/lines:
    1.3.3 Citation added
* 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 ... 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 ... WARNING
checkRd: (-1) IWTomicsData-class.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:97-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:103-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IWTomicsData-class.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (5) IWTomicsData-class.Rd:122-126: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:127-170: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:177-179: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:180-182: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:183-186: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:187-189: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:190-193: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:194-196: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:197-200: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:201-204: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:205-208: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:209-211: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:212-214: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:215-217: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:218-220: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:221-223: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:224-226: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:227-229: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:230-234: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:235-237: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:238-248: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:256-261: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:269-274: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:275-280: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:281-286: \item in \describe must have non-empty label
checkRd: (5) IWTomicsData-class.Rd:292-299: \item in \describe must have non-empty label
* 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 ‘IWTomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IWTomicsData-class
> ### Title: Class '"IWTomicsData"'
> ### Aliases: IWTomicsData-class IWTomicsData
> ###   IWTomicsData,GRangesList,list-method
> ###   IWTomicsData,character,data.frame-method
> ###   IWTomicsData,character,character-method
> ###   IWTomicsData,character,matrix-method nRegions nFeatures lengthRegions
> ###   lengthFeatures resolution metadata regions features idRegions
> ###   idFeatures nameRegions nameFeatures alignment testInput nTests
> ###   idRegionsTest idFeaturesTest adjusted_pval
> ###   [,IWTomicsData,ANY,ANY,ANY-method c,IWTomicsData-method
> ###   merge,IWTomicsData,IWTomicsData-method rbind,IWTomicsData-method
> ###   cbind,IWTomicsData-method show,IWTomicsData-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> examples_path <- system.file("extdata",package="IWTomics")
> datasets=read.table(file.path(examples_path,"datasets.txt"),
+                     sep="\t",header=TRUE,stringsAsFactors=FALSE)
> features_datasetsBED=read.table(file.path(examples_path,"features_datasetsBED.txt"),
+                                 sep="\t",header=TRUE,stringsAsFactors=FALSE)
> features_datasetsTable=read.table(file.path(examples_path,"features_datasetsTable.txt"),
+                                   sep="\t",header=TRUE,stringsAsFactors=FALSE)
> data(regions_example)
> data(features_example)
> 
> ## -------------------------------------------------------------------------------------------
> ## CONSTRUCTION
> ## -------------------------------------------------------------------------------------------
> ## Get genomic regions for four region datasets, 
> ## and two features for each region dataset
> 
> ## From BED files (check for consistency, time consuming) 
> regionsFeaturesBED=IWTomicsData(datasets$regionFile,features_datasetsBED[,3:6],
+                                 'center',datasets$id,datasets$name,
+                                 features_datasetsBED$id,features_datasetsBED$name,
+                                 path=file.path(examples_path,'files'))
Reading region dataset 'Elements 1'...
Reading region dataset 'Elements 2'...
Reading region dataset 'Elements 3'...
Reading region dataset 'Controls'...
Reading feature 'Feature 1'...
   Region dataset 'Elements 1'...
   Region dataset 'Elements 2'...
   Region dataset 'Elements 3'...
   Region dataset 'Controls'...
Reading feature 'Feature 2'...
   Region dataset 'Elements 1'...
   Region dataset 'Elements 2'...
   Region dataset 'Elements 3'...
   Region dataset 'Controls'...
> regionsFeaturesBED
IWTomicsData object with 4 region datasets with center alignment, and 2 features:
Regions:                        
 Elements 1:  25 regions
 Elements 2:  20 regions
 Elements 3:  28 regions
   Controls:  35 regions
Features:                               
 Feature 1:  2000 bp resolution
 Feature 2:  2000 bp resolution
No tests present.> 
> ## From Table files (less checks for consistency, more efficient)
> regionsFeaturesTable=IWTomicsData(datasets$regionFile,features_datasetsTable[,3:6],
+                                   'center',datasets$id,datasets$name,
+                                   features_datasetsTable$id,features_datasetsTable$name,
+                                   path=file.path(examples_path,'files'))
Reading region dataset 'Elements 1'...
Reading region dataset 'Elements 2'...
Reading region dataset 'Elements 3'...
Reading region dataset 'Controls'...
Reading feature 'Feature 1'...
   Region dataset 'Elements 1'...
   Region dataset 'Elements 2'...
   Region dataset 'Elements 3'...
   Region dataset 'Controls'...
Reading feature 'Feature 2'...
   Region dataset 'Elements 1'...
   Region dataset 'Elements 2'...
   Region dataset 'Elements 3'...
   Region dataset 'Controls'...
> regionsFeaturesTable
IWTomicsData object with 4 region datasets with center alignment, and 2 features:
Regions:                        
 Elements 1:  25 regions
 Elements 2:  20 regions
 Elements 3:  28 regions
   Controls:  35 regions
Features:                               
 Feature 1:  2000 bp resolution
 Feature 2:  2000 bp resolution
No tests present.> 
> ## From genomic regions datasets and feature measurements.
> regionsFeatures=IWTomicsData(regions_example,features_example,alignment='center')
Error in S4Vectors:::load_package_gracefully("XVector", "by the range() method ",  : 
  Could not load package XVector. Is it installed?

  Note that the XVector package is required by the range() method for
  CompressedIRangesList objects. Please install it with:

    BiocManager::install("XVector")
Calls: IWTomicsData ... .local -> .range_CompressedIRangesList -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
IWTomics-package 8.434  1.121   9.557
* 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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/IWTomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL IWTomics
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘IWTomics’ ...
** this is package ‘IWTomics’ version ‘1.33.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘IWTomics’
** 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 (IWTomics)