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BioC 3.4: CHECK report for motifRG on zin1

This page was generated on 2016-09-21 03:37:46 -0700 (Wed, 21 Sep 2016).

Package 776/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifRG 1.17.0
Zizhen Yao
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/motifRG
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifRG
Version: 1.17.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings motifRG_1.17.0.tar.gz
StartedAt: 2016-09-20 09:33:16 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:36:32 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 195.7 seconds
RetCode: 0
Status:  OK 
CheckDir: motifRG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings motifRG_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/motifRG.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifRG/DESCRIPTION’ ... OK
* this is package ‘motifRG’ version ‘1.17.0’
* 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 : <anonymous>: no visible global function definition for
  ‘glm.fit’
getScore : <anonymous>: 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
findMotif 103.98 22.244  57.453
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/motifRG.Rcheck/00check.log’
for details.


motifRG.Rcheck/00install.out:

* installing *source* package ‘motifRG’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifRG)

motifRG.Rcheck/motifRG-Ex.timings:

nameusersystemelapsed
findMotif103.980 22.244 57.453
motifLatexTable0.2560.0480.306
plotMotif0.0600.0000.059
refinePWMMotif1.9880.0242.023
summaryMotif0.0400.0000.036