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CHECK report for MDTS on malbec1

This page was generated on 2021-05-06 12:28:09 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MDTS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1027/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MDTS 1.10.0  (landing page)
Jack M.. Fu
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MDTS
Branch: RELEASE_3_12
Last Commit: f64bdf7
Last Changed Date: 2020-10-27 11:32:52 -0400 (Tue, 27 Oct 2020)
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: MDTS
Version: 1.10.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MDTS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MDTS_1.10.0.tar.gz
StartedAt: 2021-05-06 03:09:33 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:12:44 -0400 (Thu, 06 May 2021)
EllapsedTime: 190.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MDTS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MDTS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MDTS_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MDTS.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 ‘MDTS/DESCRIPTION’ ... OK
* this is package ‘MDTS’ version ‘1.10.0’
* 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 ‘MDTS’ 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 ... NOTE
.extractCovBins: no visible global function definition for ‘seqlevels’
.mappabilityHelper: no visible global function definition for
  ‘subjectHits’
.mappabilityHelper: no visible global function definition for
  ‘queryHits’
.pullReads: no visible global function definition for ‘as’
.visualize: no visible global function definition for ‘rect’
.visualize: no visible global function definition for ‘segments’
.visualize: no visible global function definition for ‘text’
.visualize: no visible global function definition for ‘par’
.visualize: no visible global function definition for ‘rgb’
.visualizeFamily: no visible global function definition for ‘rgb’
.visualizeFamily: no visible global function definition for ‘layout’
.visualizeFamily: no visible global function definition for ‘par’
.visualizeFamily: no visible global function definition for ‘text’
.visualizeFamily: no visible global function definition for ‘hist’
.visualizeFamily: no visible global function definition for ‘rect’
calcBins: no visible global function definition for ‘seqlevels<-’
calcBins: no visible global function definition for ‘seqlevels’
calcBins: no visible global function definition for ‘import’
calcBins: no visible global function definition for ‘queryHits’
calcBins: no visible global function definition for ‘subjectHits’
visualizeDeletion: no visible global function definition for
  ‘subjectHits’
visualizeDeletion: no visible global function definition for ‘pdf’
visualizeDeletion: no visible global function definition for ‘dev.new’
visualizeDeletion: no visible binding for global variable ‘pD’
visualizeDeletion: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as dev.new dev.off hist import layout pD par pdf queryHits rect rgb
  segments seqlevels seqlevels<- subjectHits text
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "rgb")
  importFrom("graphics", "hist", "layout", "par", "rect", "segments",
             "text")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘test-all.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MDTS.Rcheck/00check.log’
for details.



Installation output

MDTS.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MDTS’ ...
** 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 (MDTS)

Tests output

MDTS.Rcheck/tests/test-all.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)
> test_check('MDTS')
Loading required package: MDTS
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  8.980   0.256   9.246 

Example timings

MDTS.Rcheck/MDTS-Ex.timings

nameusersystemelapsed
calcBins0.1240.0000.135
calcCounts0.0040.0040.010
calcMD0.1800.0000.184
denovoDeletions2.3640.0242.393
getMetaData0.0920.0120.425
normalizeCounts0.1520.0080.159
segmentMD2.9800.0082.993
visualizeDeletion000