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This page was generated on 2021-10-15 15:06:41 -0400 (Fri, 15 Oct 2021).

CHECK results for MDTS on machv2

To the developers/maintainers of the MDTS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MDTS.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 1059/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MDTS 1.12.0  (landing page)
Jack M.. Fu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MDTS
git_branch: RELEASE_3_13
git_last_commit: e0ad157
git_last_commit_date: 2021-05-19 12:33:55 -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: MDTS
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MDTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MDTS_1.12.0.tar.gz
StartedAt: 2021-10-14 20:44:58 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 20:48:33 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 214.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MDTS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MDTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MDTS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MDTS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MDTS/DESCRIPTION’ ... OK
* this is package ‘MDTS’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/MDTS.Rcheck/00check.log’
for details.



Installation output

MDTS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MDTS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 10.245   0.434  10.666 

Example timings

MDTS.Rcheck/MDTS-Ex.timings

nameusersystemelapsed
calcBins0.0850.0040.089
calcCounts0.0060.0120.018
calcMD0.2520.0270.280
denovoDeletions2.2770.0262.305
getMetaData0.0290.0030.422
normalizeCounts0.2040.0050.209
segmentMD2.1190.0152.141
visualizeDeletion000