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CHECK report for megadepth on malbec1

This page was generated on 2021-05-06 12:28:10 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the megadepth package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1034/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
megadepth 1.0.3  (landing page)
David Zhang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/megadepth
Branch: RELEASE_3_12
Last Commit: 4cef55c
Last Changed Date: 2021-02-02 15:33:32 -0400 (Tue, 02 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: megadepth
Version: 1.0.3
Command: /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
StartedAt: 2021-05-06 03:11:27 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:13:48 -0400 (Thu, 06 May 2021)
EllapsedTime: 140.5 seconds
RetCode: 0
Status:   OK  
CheckDir: megadepth.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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


Installation output

megadepth.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL megadepth
###
##############################################################################
##############################################################################


* 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)

Tests output

megadepth.Rcheck/tests/testthat.Rout


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 

Example timings

megadepth.Rcheck/megadepth-Ex.timings

nameusersystemelapsed
bam_to_bigwig1.3680.5283.812
bam_to_junctions0.3120.0761.706
get_coverage16.196 0.50420.105
install_megadepth0.2760.1321.506
megadepth_cmd0.3240.3442.006
read_coverage0.6160.1642.284
read_junction_table0.3440.1601.584