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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:megadepth.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings megadepth_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/megadepth.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘megadepth/DESCRIPTION’ ... OK
* this is package ‘megadepth’ version ‘1.0.3’
* 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 ‘megadepth’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
get_coverage 16.196  0.504  20.105
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK

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###
### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL megadepth
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘megadepth’ ...
** using staged installation
** R
** 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 (megadepth)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(megadepth)
> 
> ## Install the latest version if necessary
> install_megadepth(force = TRUE)
The latest megadepth version is 1.1.0c
megadepth has been installed to /home/biocbuild/bin
> 
> test_check("megadepth")
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test.bam"
Read 96 records
# of overlapping pairs: 27
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.1.0c
building whole annotation region map done
2 chromosomes for annotated regions read
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test.bam"
Read 92 records
# of overlapping pairs: 27
Processing /tmp/RtmpIbUf0j/test.bam.all.bw
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test3.bam"
Read 12 records
# of overlapping pairs: 3
building whole annotation region map done
2 chromosomes for annotated regions read
Processing http://stingray.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing /tmp/RtmpIbUf0j/test.bam.all.bw
Processing BAM: "/home/biocbuild/bbs-3.12-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 100 ]
> 
> proc.time()
   user  system elapsed 
  9.848   3.184  18.877