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CHECK report for MDTS on tokay2

This page was generated on 2020-10-17 11:57:01 -0400 (Sat, 17 Oct 2020).

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 1014/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MDTS 1.8.0
Jack M.. Fu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MDTS
Branch: RELEASE_3_11
Last Commit: 80d165b
Last Changed Date: 2020-04-27 15:14:29 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MDTS
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MDTS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MDTS_1.8.0.tar.gz
StartedAt: 2020-10-17 05:44:56 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:49:30 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 274.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MDTS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MDTS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MDTS_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MDTS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MDTS/DESCRIPTION' ... OK
* this is package 'MDTS' version '1.8.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MDTS.Rcheck/00check.log'
for details.



Installation output

MDTS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MDTS_1.8.0.tar.gz && rm -rf MDTS.buildbin-libdir && mkdir MDTS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MDTS.buildbin-libdir MDTS_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MDTS_1.8.0.zip && rm MDTS_1.8.0.tar.gz MDTS_1.8.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 23193  100 23193    0     0   473k      0 --:--:-- --:--:-- --:--:--  552k

install for i386

* installing *source* package 'MDTS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MDTS'
    finding HTML links ... done
    MDTS-package                            html  
    calcBins                                html  
    calcCounts                              html  
    calcMD                                  html  
    denovoDeletions                         html  
    getMetaData                             html  
    normalizeCounts                         html  
    segmentMD                               html  
    visualizeDeletion                       html  
** 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

install for x64

* installing *source* package 'MDTS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MDTS' as MDTS_1.8.0.zip
* DONE (MDTS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MDTS' successfully unpacked and MD5 sums checked

Tests output

MDTS.Rcheck/tests_i386/test-all.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.79    0.73    9.50 

MDTS.Rcheck/tests_x64/test-all.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.01    0.40   12.40 

Example timings

MDTS.Rcheck/examples_i386/MDTS-Ex.timings

nameusersystemelapsed
calcBins0.060.000.06
calcCounts0.000.020.02
calcMD0.100.060.16
denovoDeletions4.760.054.81
getMetaData0.030.030.33
normalizeCounts0.130.010.14
segmentMD4.860.004.86
visualizeDeletion000

MDTS.Rcheck/examples_x64/MDTS-Ex.timings

nameusersystemelapsed
calcBins0.090.010.11
calcCounts0.020.000.01
calcMD0.160.020.17
denovoDeletions4.170.014.19
getMetaData0.030.000.10
normalizeCounts0.160.010.18
segmentMD4.870.004.89
visualizeDeletion000