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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CAGEr_2.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.5.0’
* 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 ‘CAGEr’ 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 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 ‘CAGEr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterCTSS
> ### Title: Cluster CTSSs into tag clusters
> ### Aliases: clusterCTSS clusterCTSS,CAGEexp-method
> 
> ### ** Examples
> 
> 
> # Using 'distclu', notice argument 'maxDist'
> ce <- clusterCTSS( exampleCAGEexp, threshold = 50, thresholdIsTpm = TRUE
+            , nrPassThreshold = 1, method = "distclu", maxDist = 20
+            , removeSingletons = TRUE, keepSingletonsAbove = 100)

Filtering out CTSSs below threshold...
Clustering...
	-> Zf.unfertilized.egg
	-> Zf.high
	-> Zf.30p.dome
	-> Zf.prim6.rep1
	-> Zf.prim6.rep2
> tagClustersGR(ce, "Zf.30p.dome")
TagClusters object with 88 ranges and 4 metadata columns:
     seqnames            ranges strand |            score   nr_ctss
        <Rle>         <IRanges>  <Rle> |            <Rle> <integer>
   1    chr17 26453632-26453722      + | 1194.07800791544        14
   2    chr17 26564522-26564589      + | 1505.62283034387        15
   3    chr17 26564610-26564614      + | 180.571402714547         3
   4    chr17 26595639-26595805      + | 7099.05702175236        36
   5    chr17 26596033-26596070      + | 490.202040074153         8
  ..      ...               ...    ... .              ...       ...
  84    chr17 31802467-31802468      + | 77.0002365314291         2
  85    chr17          32249369      + | 103.571166183118         1
  86    chr17 32364966-32364987      + | 128.575090100563         3
  87    chr17 32566467-32566493      + | 128.446193727075         3
  88    chr17 32706111-32706247      + | 9235.46741649492        53
     dominant_ctss tpm.dominant_ctss
         <integer>             <Rle>
   1      26453701  393.295792264432
   2      26564585   287.56899462406
   3      26564610  103.571166183118
   4      26595750   2804.3982647548
   5      26596070  129.738486436885
  ..           ...               ...
  84      31802467  51.4459571956458
  85      32249369  103.571166183118
  86      32364987   77.466531428997
  87      32566467  51.4459571956458
  88      32706231  1085.31882195528
  -------
  seqinfo: 26 sequences (1 circular) from danRer7 genome
> 
> # Using 'paraclu', notice arguments 'maxLength' and 'minStability'
> ce <- clusterCTSS( exampleCAGEexp, threshold = 50, thresholdIsTpm = TRUE
+            , nrPassThreshold = 1, method = "paraclu"
+            , removeSingletons = TRUE, keepSingletonsAbove = 100
+            , maxLength = 500, minStability = 1
+            , reduceToNonoverlapping = TRUE)

Filtering out CTSSs below threshold...
Clustering...
	-> Zf.unfertilized.egg
	-> Zf.high
	-> Zf.30p.dome
	-> Zf.prim6.rep1
	-> Zf.prim6.rep2
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CAGE_Resources.Rmd’ using ‘UTF-8’... OK
  ‘CAGEexp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CAGEr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘CAGEr’ ...
** 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 (CAGEr)