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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CAGEfightR_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.22.0’
* 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 ‘CAGEfightR’ 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 R 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 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CAGEfightR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterUnidirectionally
> ### Title: Unidirectional Clustering (Tag Clustering) of pooled CTSSs.
> ### Aliases: clusterUnidirectionally clusterUnidirectionally,GRanges-method
> ###   clusterUnidirectionally,RangedSummarizedExperiment-method
> ###   clusterUnidirectionally,GPos-method
> 
> ### ** Examples
> 
> data(exampleCTSSs)
> 
> # Calculate pooledTPM, using supplied number of total tags
> exampleCTSSs <- calcTPM(exampleCTSSs,
+                         inputAssay='counts',
+                         outputAssay='TPM',
+                         totalTags='totalTags')
Using supplied library sizes...
Calculating TPM...
> exampleCTSSs <- calcPooled(exampleCTSSs, inputAssay='TPM')
Warning in calcPooled(exampleCTSSs, inputAssay = "TPM") :
  object already has a column named score in rowData: It will be overwritten!
> 
> # Cluster using defaults: slice-threshold of 0 and reduce-distance of 20
> clusterUnidirectionally(exampleCTSSs)
Splitting by strand...
Slice-reduce to find clusters...
Calculating statistics...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CAGEfightR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL CAGEfightR
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘CAGEfightR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (CAGEfightR)