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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:megadepth.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings megadepth_1.15.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/megadepth.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'megadepth/DESCRIPTION' ... OK
* this is package 'megadepth' version '1.15.0'
* 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 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 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 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 7.53   2.28   10.63
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL megadepth
###
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* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 1.2.0
This is not an interactive session, therefore megadepth has been installed temporarily to 
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpoZVz2m/megadepth.exe
> 
> test_check("megadepth")
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/long_reads.bam"
Read 3 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.20-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
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test.bam.all.bw
The latest megadepth version is 1.2.0
Processing F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpoZVz2m/test.bam.all.bw
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test3.bam"
WARNING: writing BigWigs (--bigwig) is not supported on Windows at this time, no BigWig file(s) will be written, but any other options will still be processed.
Read 12 records
# of overlapping pairs: 3
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing https://snaptron.cs.jhu.edu/data/temp/megadepth.test.bam.all.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
unsorted interval: chr10	4359156	4359188
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
total number of annotations in collapsed: 1
Processing F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpoZVz2m/test.bam.all.bw
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
Processing BAM: "F:/biocbuild/bbs-3.20-bioc/R/library/megadepth/tests/test2.bam"
Read 7 records
# of overlapping pairs: 0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
   4.78    6.28   16.50