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BioC 3.4: CHECK report for dyebias on malbec1

This page was generated on 2017-04-15 16:09:50 -0400 (Sat, 15 Apr 2017).

Package 353/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dyebias 1.34.0
Philip Lijnzaad
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/dyebias
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dyebias
Version: 1.34.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings dyebias_1.34.0.tar.gz
StartedAt: 2017-04-14 22:13:51 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:14:28 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 37.3 seconds
RetCode: 0
Status:  OK 
CheckDir: dyebias.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings dyebias_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/dyebias.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebias/DESCRIPTION’ ... OK
* this is package ‘dyebias’ version ‘1.34.0’
* 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 ‘dyebias’ 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.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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:
  ‘limma’ ‘methods’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘marray’
  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
.check.reporter.labels: no visible global function definition for
  ‘maLabels’
.check.reporter.labels: no visible global function definition for
  ‘maGnames’
.check.reporter.labels: no visible global function definition for
  ‘maNspots’
.check.slide.labels: no visible global function definition for
  ‘maNsamples’
.check.slide.labels: no visible global function definition for
  ‘maLabels’
.check.slide.labels: no visible global function definition for
  ‘maTargets’
.find.estimators: no visible global function definition for ‘quantile’
.limma.to.dataframe: no visible global function definition for ‘is’
.limma.to.dataframe: no visible global function definition for ‘eBayes’
.limma.to.dataframe: no visible global function definition for
  ‘p.adjust’
.mann.kendall: no visible global function definition for ‘cor.test’
.merge.dyebias: no visible global function definition for ‘maLabels’
.merge.dyebias: no visible global function definition for ‘maGnames’
.monotonicity: no visible global function definition for ‘maNsamples’
.monotonicity : <anonymous>: no visible global function definition for
  ‘maM’
.monotonicity : slope: no visible global function definition for
  ‘lsfit’
.rg.subsets: no visible global function definition for ‘quantile’
.set.design: no visible global function definition for ‘modelMatrix’
.set.design : <anonymous>: no visible global function definition for
  ‘modelMatrix’
.set.output: no visible global function definition for ‘X11’
.set.output: no visible global function definition for ‘quartz’
.set.output: no visible global function definition for ‘pdf’
.set.output: no visible global function definition for ‘png’
.set.output: no visible global function definition for ‘postscript’
.slide.bias: no visible global function definition for ‘maNsamples’
.slide.bias: no visible global function definition for ‘maLabels’
.slide.bias: no visible global function definition for ‘maTargets’
.slide.bias: no visible global function definition for ‘maM’
.slide.bias.order: no visible binding for global variable ‘median’
dyebias.application.subset: no visible global function definition for
  ‘maInfo’
dyebias.application.subset: no visible global function definition for
  ‘maTargets’
dyebias.application.subset: no visible global function definition for
  ‘maNspots’
dyebias.application.subset: no visible global function definition for
  ‘maNsamples’
dyebias.application.subset: no visible global function definition for
  ‘maRb’
dyebias.application.subset: no visible global function definition for
  ‘maGb’
dyebias.application.subset: no visible global function definition for
  ‘maRf’
dyebias.application.subset: no visible global function definition for
  ‘maGf’
dyebias.apply.correction: no visible global function definition for
  ‘maM’
dyebias.apply.correction: no visible global function definition for
  ‘maNspots’
dyebias.apply.correction: no visible global function definition for
  ‘maNsamples’
dyebias.apply.correction: no visible global function definition for
  ‘maLabels’
dyebias.apply.correction: no visible global function definition for
  ‘maGnames’
dyebias.apply.correction: no visible global function definition for
  ‘maInfo’
dyebias.apply.correction: no visible global function definition for
  ‘maTargets’
dyebias.apply.correction: no visible global function definition for
  ‘median’
dyebias.apply.correction: no visible global function definition for
  ‘sd’
dyebias.apply.correction: no visible global function definition for
  ‘var.test’
dyebias.apply.correction: no visible global function definition for
  ‘maA’
dyebias.apply.correction: no visible global function definition for
  ‘maM<-’
dyebias.apply.correction: no visible global function definition for
  ‘maA<-’
dyebias.apply.correction: no visible global function definition for
  ‘is’
dyebias.apply.correction: no visible global function definition for
  ‘maR<-’
dyebias.apply.correction: no visible global function definition for
  ‘maG<-’
dyebias.boxplot: no visible global function definition for ‘maNsamples’
dyebias.boxplot: no visible global function definition for ‘par’
dyebias.boxplot: no visible global function definition for ‘boxplot’
dyebias.boxplot: no visible global function definition for ‘abline’
dyebias.boxplot: no visible global function definition for ‘dev.off’
dyebias.estimate.iGSDBs: no visible global function definition for ‘is’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maLabels’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maGnames’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maNspots’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maNsamples’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maM’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maA’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maInfo’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maTargets’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘new’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘lmFit’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘eBayes’
dyebias.maplot: no visible global function definition for ‘maM’
dyebias.maplot: no visible global function definition for ‘maA’
dyebias.maplot: no visible global function definition for ‘plot’
dyebias.maplot: no visible global function definition for ‘box’
dyebias.maplot: no visible global function definition for ‘abline’
dyebias.maplot: no visible global function definition for ‘points’
dyebias.maplot: no visible global function definition for ‘dev.off’
dyebias.monotonicityplot: no visible global function definition for
  ‘plot’
dyebias.monotonicityplot: no visible global function definition for
  ‘points’
dyebias.monotonicityplot: no visible global function definition for
  ‘dev.off’
dyebias.rgplot: no visible global function definition for ‘maA’
dyebias.rgplot: no visible global function definition for ‘maM’
dyebias.rgplot: no visible global function definition for ‘plot’
dyebias.rgplot: no visible global function definition for ‘axis’
dyebias.rgplot: no visible global function definition for ‘box’
dyebias.rgplot: no visible global function definition for ‘abline’
dyebias.rgplot: no visible global function definition for ‘points’
dyebias.rgplot: no visible global function definition for ‘dev.off’
dyebias.trendplot: no visible global function definition for ‘quantile’
dyebias.trendplot: no visible global function definition for
  ‘maNsamples’
dyebias.trendplot : <anonymous>: no visible global function definition
  for ‘maM’
dyebias.trendplot: no visible binding for global variable ‘median’
dyebias.trendplot: no visible global function definition for ‘matplot’
dyebias.trendplot: no visible global function definition for ‘axis’
dyebias.trendplot: no visible global function definition for ‘matlines’
dyebias.trendplot: no visible global function definition for ‘abline’
dyebias.trendplot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  X11 abline axis box boxplot cor.test dev.off eBayes is lmFit lsfit
  maA maA<- maG<- maGb maGf maGnames maInfo maLabels maM maM<-
  maNsamples maNspots maR<- maRb maRf maTargets matlines matplot median
  modelMatrix new p.adjust par pdf plot png points postscript quantile
  quartz sd var.test
Consider adding
  importFrom("grDevices", "X11", "dev.off", "pdf", "png", "postscript",
             "quartz")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "matlines",
             "matplot", "par", "plot", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "cor.test", "lsfit", "median", "p.adjust",
             "quantile", "sd", "var.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/dyebias.Rcheck/00check.log’
for details.


dyebias.Rcheck/00install.out:

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

dyebias.Rcheck/dyebias-Ex.timings:

nameusersystemelapsed
dyebias.application.subset1.9880.0202.064
dyebias.apply.correction1.6920.0001.693
dyebias.boxplot1.7240.0121.736
dyebias.estimate.iGSDBs0.9440.0040.950
dyebias.monotonicity0.0040.0000.001
dyebias.monotonicityplot0.0000.0000.001
dyebias.rgplot2.3000.0162.316
dyebias.trendplot1.8960.0041.901