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CHECK report for methVisual on celaya2

This page was generated on 2019-10-16 12:47:55 -0400 (Wed, 16 Oct 2019).

Package 976/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methVisual 1.36.0
Arie Zackay
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/methVisual
Branch: RELEASE_3_9
Last Commit: d842367
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: methVisual
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methVisual.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methVisual_1.36.0.tar.gz
StartedAt: 2019-10-16 04:30:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:33:04 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 148.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methVisual.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methVisual.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methVisual_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methVisual.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methVisual/DESCRIPTION’ ... OK
* this is package ‘methVisual’ version ‘1.36.0’
* 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 ‘methVisual’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed") 
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/methVisual.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’ ‘grid’
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘gsubfn’ ‘plotrix’ ‘sqldf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeDataMethGFF: no visible binding for global variable ‘fn’
plotMatrixSNP: no visible global function definition for ‘color.legend’
Undefined global functions or variables:
  color.legend fn
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/methVisual.Rcheck/00check.log’
for details.



Installation output

methVisual.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methVisual
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘methVisual’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'windows(n, lengthData, ': unused argument (rescale = "fixed") 
** 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 (methVisual)

Tests output


Example timings

methVisual.Rcheck/methVisual-Ex.timings

nameusersystemelapsed
Cooccurrence0.6670.4481.099
MethAlignNW1.4380.3491.772
MethDataInput0.0290.0130.043
MethLollipops0.0130.0060.018
MethylQC1.1210.2791.391
cgInAlign0.0020.0040.007
cgMethFinder0.0010.0000.000
coversionGenom0.0000.0000.001
findNonAligned0.0040.0050.009
heatMapMeth0.1130.0200.133
makeDataMethGFF0.5100.2220.726
makeLocalExpDir0.0170.0100.027
makeTabFilePath0.0200.0070.030
matrixSNP0.3550.3460.688
methCA0.0200.0110.030
methData0.0020.0030.005
methFisherTest0.0460.0110.063
methWhitneyUTest0.0080.0060.014
plotAbsMethyl0.0060.0040.010
plotMatrixSNP0.7640.6391.389
readBisulfFASTA0.0670.0220.088
selectRefSeq0.0200.0120.033