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This page was generated on 2021-09-20 15:04:47 -0400 (Mon, 20 Sep 2021).

CHECK results for DAMEfinder on nebbiolo1

To the developers/maintainers of the DAMEfinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DAMEfinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 440/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAMEfinder 1.4.0  (landing page)
Stephany Orjuela
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/DAMEfinder
git_branch: RELEASE_3_13
git_last_commit: a0da475
git_last_commit_date: 2021-05-19 12:49:06 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DAMEfinder
Version: 1.4.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DAMEfinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DAMEfinder_1.4.0.tar.gz
StartedAt: 2021-09-19 09:26:53 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:31:39 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 286.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DAMEfinder.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DAMEfinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DAMEfinder_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DAMEfinder.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAMEfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAMEfinder’ version ‘1.4.0’
* 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 ‘DAMEfinder’ 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 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
extract_bams 33.043  1.776  34.826
* 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

DAMEfinder.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DAMEfinder
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘DAMEfinder’ ...
** using staged installation
** R
** data
** 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 (DAMEfinder)

Tests output

DAMEfinder.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(DAMEfinder)
> 
> test_check("DAMEfinder")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 71.370   2.809  74.163 

Example timings

DAMEfinder.Rcheck/DAMEfinder-Ex.timings

nameusersystemelapsed
calc_asm1.3060.0801.351
calc_derivedasm2.8530.1082.962
dame_track0.8510.0120.862
dame_track_mean0.6880.0200.708
extract_bams33.043 1.77634.826
find_dames0.5780.0600.638
get_tstats0.2470.0080.255
methyl_MDS_plot0.3950.0320.427
methyl_circle_plot4.6890.1644.853
methyl_circle_plotCpG4.2860.5604.846
read_tuples0.0890.0140.074