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CHECK report for MDTS on tokay1

This page was generated on 2019-04-13 11:28:58 -0400 (Sat, 13 Apr 2019).

Package 902/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MDTS 1.2.0
Jack M.. Fu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MDTS
Branch: RELEASE_3_8
Last Commit: 5d78cee
Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MDTS
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MDTS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MDTS_1.2.0.tar.gz
StartedAt: 2019-04-13 03:35:46 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:40:08 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 261.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MDTS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MDTS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MDTS_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MDTS.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'plot'
.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 'plot'
.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 plot queryHits rect
  rgb segments seqlevels seqlevels<- subjectHits text
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "rgb")
  importFrom("graphics", "hist", "layout", "par", "plot", "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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MDTS_1.2.0.tar.gz && rm -rf MDTS.buildbin-libdir && mkdir MDTS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MDTS.buildbin-libdir MDTS_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MDTS_1.2.0.zip && rm MDTS_1.2.0.tar.gz MDTS_1.2.0.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 23326  100 23326    0     0   406k      0 --:--:-- --:--:-- --:--:--  438k

install for i386

* installing *source* package 'MDTS' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'MDTS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MDTS' as MDTS_1.2.0.zip
* DONE (MDTS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MDTS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MDTS.Rcheck/tests_i386/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.03    0.31    7.32 

MDTS.Rcheck/tests_x64/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.62    0.39    7.00 

Example timings

MDTS.Rcheck/examples_i386/MDTS-Ex.timings

nameusersystemelapsed
calcBins0.050.020.08
calcCounts0.010.000.03
calcMD0.080.040.13
denovoDeletions4.600.044.64
getMetaData0.040.030.22
normalizeCounts0.070.000.06
segmentMD3.980.003.98
visualizeDeletion000

MDTS.Rcheck/examples_x64/MDTS-Ex.timings

nameusersystemelapsed
calcBins0.050.000.05
calcCounts0.000.020.01
calcMD0.080.010.10
denovoDeletions3.510.003.51
getMetaData0.030.040.14
normalizeCounts0.080.000.08
segmentMD2.910.002.91
visualizeDeletion000