Package: motifRG

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifRG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifRG_1.28.0.tar.gz

StartedAt: 2019-10-16 04:49:43 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:57:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 465.4 seconds

RetCode: 0

Status:  OK

CheckDir: motifRG.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifRG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifRG_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/motifRG.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 ‘motifRG/DESCRIPTION’ ... OK
* this is package ‘motifRG’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biostrings', 'IRanges', 'seqLogo', 'parallel', 'grid', 'BSgenome',
  'XVector', 'BSgenome.Hsapiens.UCSC.hg19'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘motifRG’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’ ‘IRanges’ ‘seqLogo’ ‘parallel’ ‘methods’ ‘grid’ ‘graphics’ ‘XVector’
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
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘methods’
  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
bestPWMMatch: no visible global function definition for ‘Rle’
discretize.glm: no visible global function definition for ‘glm.fit’
findMotif : refinePattern: no visible global function definition for
  ‘t.test’
findMotif : refinePattern: no visible global function definition for
  ‘new’
findPatternView: no visible global function definition for ‘as’
getScore: no visible global function definition for ‘binomial’
getScore : : no visible global function definition for
  ‘glm.fit’
getScore : : no visible global function definition for
  ‘summary.glm’
matchPWMCoor: no visible global function definition for ‘as’
matchPWMCoor: no visible global function definition for ‘GRanges’
motifHtmlTable: no visible global function definition for ‘png’
motifHtmlTable: no visible global function definition for ‘par’
motifHtmlTable: no visible global function definition for ‘dev.off’
motifLatexTable: no visible global function definition for ‘pdf’
motifLatexTable: no visible global function definition for ‘par’
motifLatexTable: no visible global function definition for ‘dev.off’
plotPWM: no visible global function definition for ‘axis’
plotPWM: no visible global function definition for ‘par’
plotPWM: no visible global function definition for ‘col2rgb’
plotPWM: no visible global function definition for ‘rgb’
plotPWM: no visible global function definition for ‘points’
plotPair: no visible global function definition for ‘rgb’
plotPair: no visible global function definition for ‘lines’
Undefined global functions or variables:
  GRanges Rle as axis binomial col2rgb dev.off glm.fit lines new par
  pdf png points rgb summary.glm t.test
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "png", "rgb")
  importFrom("graphics", "axis", "lines", "par", "points")
  importFrom("methods", "as", "new")
  importFrom("stats", "binomial", "glm.fit", "summary.glm", "t.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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
Examples with CPU or elapsed time > 5s
            user  system elapsed
findMotif 277.73 276.461 168.532
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/motifRG.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 motifRG
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘motifRG’ ...
** using staged installation
** R
** data
** 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 (motifRG)

name	user	system	elapsed
findMotif	277.730	276.461	168.532
motifLatexTable	0.429	0.071	0.498
plotMotif	0.120	0.008	0.128
refinePWMMotif	3.198	0.718	3.920
summaryMotif	0.075	0.007	0.082