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BioC 3.4: CHECK report for PWMEnrich on zin1

This page was generated on 2016-09-21 03:37:49 -0700 (Wed, 21 Sep 2016).

Package 945/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.9.2
Robert Stojnic
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PWMEnrich
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 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: PWMEnrich
Version: 4.9.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_4.9.2.tar.gz
StartedAt: 2016-09-20 10:56:33 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:58:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 97.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_4.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/PWMEnrich.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 ‘PWMEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PWMEnrich’ version ‘4.9.2’
* 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 ‘PWMEnrich’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.4Mb
* 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
* 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' calls in package code:
  ‘PWMEnrich.Dmelanogaster.background’ ‘PWMEnrich.Hsapiens.background’
  ‘PWMEnrich.Mmusculus.background’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colMedians: no visible binding for global variable ‘median’
colSds: no visible binding for global variable ‘sd’
getPromoters: no visible global function definition for
  ‘providerVersion’
getPromoters: no visible global function definition for ‘data’
gevPerSequence: no visible global function definition for ‘predict.lm’
logNormPval: no visible global function definition for ‘plnorm’
makePWMGEVBackground : <anonymous>: no visible global function
  definition for ‘lm’
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for ‘dlnorm’
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for ‘plnorm’
makePWMLognBackground: no visible binding for global variable ‘sd’
makePWMLognBackground: no visible global function definition for
  ‘quantile’
makePWMLognBackground: no visible global function definition for
  ‘median’
makePWMLognBackground: no visible global function definition for
  ‘optimize’
makePWMPvalCutoffBackground: no visible global function definition for
  ‘quantile’
makePWMPvalCutoffBackground: no visible global function definition for
  ‘ecdf’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘na.omit’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘quantile’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘ecdf’
matrixShuffleZscorePerSequence: no visible binding for global variable
  ‘sd’
motifEcdf : <anonymous>: no visible global function definition for
  ‘na.omit’
motifEcdf: no visible binding for global variable ‘ecdf’
motifEnrichment: no visible binding for global variable ‘qlnorm’
motifEnrichment : <anonymous>: no visible global function definition
  for ‘pchisq’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
  ‘mclapply’
motifSimilarity: no visible binding for global variable ‘sd’
plotMotifScores: no visible global function definition for ‘palette’
plotMotifScores: no visible global function definition for ‘col2rgb’
plotMotifScores: no visible global function definition for ‘rgb’
plotMotifScores: no visible global function definition for ‘par’
plotMotifScores: no visible global function definition for ‘lines’
plotMotifScores: no visible global function definition for ‘polygon’
plotMotifScores: no visible global function definition for ‘rect’
plotMotifScores: no visible global function definition for ‘text’
registerCoresPWMEnrich: no visible global function definition for
  ‘detectCores’
tryAllMotifAlignments : <anonymous>: no visible global function
  definition for ‘cor’
Undefined global functions or variables:
  col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
  na.omit optimize palette par pchisq plnorm polygon predict.lm
  providerVersion qlnorm quantile rect rgb sd text
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
  importFrom("graphics", "lines", "par", "polygon", "rect", "text")
  importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
             "optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
             "quantile", "sd")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.


PWMEnrich.Rcheck/00install.out:

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

PWMEnrich.Rcheck/PWMEnrich-Ex.timings:

nameusersystemelapsed
PFMtoPWM2.1720.2242.423
PWMUnscaled0.3720.0040.377
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method2.3760.0002.386
makeBackground0.0040.0000.004
makePWMCutoffBackground0.0000.0000.001
makePWMEmpiricalBackground000
makePWMGEVBackground0.0000.0000.001
makePWMLognBackground0.0000.0000.001
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors0.0000.0000.002
motifDiffEnrichment2.5440.0002.541
motifEnrichment3.5240.0003.531
motifIC0.0400.0000.046
motifRankingForGroup-commaMotifEnrichmentResults-method2.0360.0002.040
motifRankingForSequence-commaMotifEnrichmentResults-method1.8600.0041.867
motifScores3.8160.0123.831
motifSimilarity0.0560.0000.056
plot0.1640.0040.167
plotMotifScores0.060.000.06
plotTopMotifsGroup-commaMotifEnrichmentResults-method2.1560.0082.167
plotTopMotifsSequence-commaMotifEnrichmentResults-method2.1840.0042.192
readMotifs0.0760.0040.080
registerCoresPWMEnrich0.0000.0000.001
reverseComplement0.0120.0000.015
scanWithPWM0.0320.0000.034
sequenceReport-commaMotifEnrichmentResults-method2.8360.0122.867
toPWM2.1720.1682.342
useBigMemoryPWMEnrich0.0000.0000.001