Package: methVisual

Version: 1.38.0

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_1.38.0.tar.gz

StartedAt: 2020-04-15 03:46:34 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:48:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 110.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methVisual.Rcheck

Warnings: 1

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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_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/methVisual.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.38.0’
* 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-3.10-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
MethylQC: no visible global function definition for ‘score’
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 score
* 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-3.10-bioc/meat/methVisual.Rcheck/00check.log’
for details.

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### Running command:
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###   /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
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘methVisual’
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
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘methVisual’
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘methVisual’
** testing if installed package keeps a record of temporary installation path
* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.508	0.245	0.733
MethAlignNW	1.227	0.184	1.393
MethDataInput	0.023	0.008	0.030
MethLollipops	0.011	0.003	0.014
MethylQC	1.003	0.147	1.133
cgInAlign	0.002	0.003	0.005
cgMethFinder	0.001	0.000	0.001
coversionGenom	0.000	0.001	0.001
findNonAligned	0.004	0.003	0.007
heatMapMeth	0.104	0.013	0.117
makeDataMethGFF	0.429	0.114	0.531
makeLocalExpDir	0.016	0.006	0.021
makeTabFilePath	0.012	0.002	0.015
matrixSNP	0.267	0.178	0.425
methCA	0.017	0.005	0.022
methData	0.002	0.002	0.004
methFisherTest	0.048	0.006	0.053
methWhitneyUTest	0.006	0.002	0.008
plotAbsMethyl	0.004	0.003	0.007
plotMatrixSNP	0.505	0.290	0.771
readBisulfFASTA	0.04	0.01	0.05
selectRefSeq	0.012	0.005	0.017