Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:04 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cfDNAPro on nebbiolo1


To the developers/maintainers of the cfDNAPro package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cfDNAPro.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 292/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cfDNAPro 1.2.0  (landing page)
Haichao Wang
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/cfDNAPro
git_branch: RELEASE_3_15
git_last_commit: 01b93a0
git_last_commit_date: 2022-04-26 12:17:25 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cfDNAPro
Version: 1.2.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:cfDNAPro.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings cfDNAPro_1.2.0.tar.gz
StartedAt: 2022-10-18 18:58:52 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:00:56 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 124.7 seconds
RetCode: 0
Status:   OK  
CheckDir: cfDNAPro.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:cfDNAPro.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings cfDNAPro_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/cfDNAPro.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cfDNAPro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cfDNAPro’ version ‘1.2.0’
* 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 ‘cfDNAPro’ 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
* 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

cfDNAPro.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL cfDNAPro
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘cfDNAPro’ ...
** 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 (cfDNAPro)

Tests output

cfDNAPro.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(cfDNAPro)
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> 
> test_check("cfDNAPro")
setting default input_type to picard.
setting default outfmt to df.
setting default input_type to picard.
setting default input_type to picard.
setting default limit to c(35,135).
setting default outfmt to df.
setting the mincount to 0.
setting default input_type to picard.
setting default limit to c(35,135).
setting default outfmt to df.
Setting default mincount to 0.
setting default input_type to picard.
setting default input_type to picard.
setting default outfmt to df.
setting default input_type to picard.
setting default input_type to picard.
setting default limit to c(35,135).
setting default outfmt to df.
setting the mincount to 0.
setting default input_type to picard.
setting default limit to c(35,135).
setting default outfmt to df.
Setting default mincount to 0.
setting default input_type to picard.
setting default mincount as 0.
setting default horizontal lines: y = 81, 112, 170. 
setting the mincount to 0.
 setting the xlim to c(7,13). 
 setting the mincount to 0. 
 setting the xlim to c(7,13). 
 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 16.107   0.591  16.685 

Example timings

cfDNAPro.Rcheck/cfDNAPro-Ex.timings

nameusersystemelapsed
callMetrics1.1910.0971.290
callMode0.4720.0160.489
callPeakDistance1.6510.0241.674
callSize0.3720.0200.391
callValleyDistance1.5770.0241.601
examplePath0.0000.0020.002
plotAllToOne0.4340.0060.439
plotMetrics0.9880.0000.989
plotMode0.6850.0000.685
plotModeSummary0.5710.0040.575
plotPeakDistance1.6780.0241.703
plotSingleGroup0.9460.0040.950
plotValleyDistance1.7780.0441.822