##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:spiky.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings spiky_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/spiky.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘spiky/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spiky’ version ‘1.8.0’
* 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 ‘spiky’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.4Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata  12.9Mb
* 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 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
.toGRs: warning in grep("(chrom|seqnames|start|end)1", colnames(x), val
  = TRUE): partial argument match of 'val' to 'value'
.toGRs: warning in grep("(chrom|seqnames|start|end)2", colnames(x), val
  = TRUE): partial argument match of 'val' to 'value'
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
scan_genomic_contigs 13.356  1.688  15.046
scan_genomic_bedpe   13.434  0.912  14.346
model_bam_standards   6.313  0.576   6.889
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘spiky_vignette.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘spiky_vignette.Rmd’
  ...
Loading required package: usethis

> load_all("./")

  When sourcing ‘spiky_vignette.R’:
Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/tmp/RtmpL4urW8/file2ce2527b73010c/vignettes'.
ℹ Are you in your project directory and does your project have a 'DESCRIPTION'
  file?
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/spiky.Rcheck/00check.log’
for details.