BioC 3.3: CHECK report for RTN on zin2

Package: RTN

Version: 1.10.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RTN_1.10.0.tar.gz

StartedAt: 2016-10-13 06:27:50 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:29:45 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 114.9 seconds

RetCode: 0

Status:  OK

CheckDir: RTN.Rcheck

Warnings: 0

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###
### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RTN_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RTN.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 ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘1.10.0’
* 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 ‘RTN’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.perm.pmin.pooled: no visible global function definition for ‘cor’
.perm.pmin.separate: no visible global function definition for ‘cor’
avsplot1: no visible global function definition for ‘pdf’
avsplot1: no visible global function definition for ‘layout’
avsplot1: no visible global function definition for ‘par’
avsplot1: no visible global function definition for ‘plot’
avsplot1: no visible global function definition for ‘axis’
avsplot1: no visible global function definition for ‘lines’
avsplot1: no visible global function definition for ‘hist’
avsplot1: no visible global function definition for ‘boxplot’
avsplot1: no visible global function definition for ‘mtext’
avsplot1: no visible global function definition for ‘points’
avsplot1: no visible global function definition for ‘dev.off’
avsplot2: no visible global function definition for ‘pdf’
avsplot2: no visible global function definition for ‘layout’
avsplot2: no visible global function definition for ‘par’
avsplot2: no visible global function definition for ‘plot.new’
avsplot2: no visible global function definition for ‘abline’
avsplot2: no visible global function definition for ‘boxplot’
avsplot2: no visible global function definition for ‘axis’
avsplot2: no visible global function definition for ‘mtext’
avsplot2: no visible global function definition for ‘points’
avsplot2: no visible global function definition for ‘image’
avsplot2: no visible global function definition for ‘dev.off’
buildRandomAVS: no visible global function definition for ‘data’
buildRandomAVS: no visible global function definition for
  ‘txtProgressBar’
buildRandomAVS : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
cdt.stability: no visible global function definition for
  ‘txtProgressBar’
cdt.stability: no visible global function definition for
  ‘setTxtProgressBar’
checkModuationEffect: no visible global function definition for ‘qnorm’
checkModuationEffect: no visible global function definition for ‘pnorm’
checkModuationEffect: no visible global function definition for
  ‘p.adjust’
cv.filter: no visible binding for global variable ‘sd’
data.integration: no visible global function definition for ‘aggregate’
data.integration : <anonymous>: no visible global function definition
  for ‘aggregate’
drcircle: no visible global function definition for ‘polygon’
eqtlTest: no visible global function definition for ‘formula’
eqtlTest: no visible global function definition for ‘lm’
eqtlTest: no visible global function definition for ‘manova’
eqtlTest: no visible global function definition for ‘anova’
eqtlTestDetailed: no visible global function definition for ‘formula’
eqtlTestDetailed: no visible global function definition for ‘lm’
eqtlTestDetailed: no visible global function definition for ‘manova’
eqtlTestDetailed: no visible global function definition for ‘anova’
eqtlTestDetailed: no visible global function definition for ‘aov’
eqtlTestDetailedAnova : <anonymous>: no visible global function
  definition for ‘formula’
eqtlTestDetailedAnova : <anonymous>: no visible global function
  definition for ‘aov’
eqtlTestDetailedAnova: no visible global function definition for ‘cor’
evsea: no visible global function definition for ‘txtProgressBar’
evsea : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
evseaproxy: no visible global function definition for ‘txtProgressBar’
evseaproxy : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
getLdPop: no visible global function definition for ‘txtProgressBar’
getLdPop: no visible global function definition for ‘setTxtProgressBar’
getRandomAvsRanges: no visible global function definition for
  ‘txtProgressBar’
getRandomAvsRanges : <anonymous>: no visible global function definition
  for ‘setTxtProgressBar’
getldata: no visible global function definition for ‘data’
gsea1tna: no visible global function definition for ‘txtProgressBar’
gsea1tna: no visible global function definition for ‘setTxtProgressBar’
gsea2tna: no visible global function definition for ‘txtProgressBar’
gsea2tna: no visible global function definition for ‘setTxtProgressBar’
gsplot1 : get.alpha: no visible global function definition for
  ‘col2rgb’
gsplot1 : get.alpha: no visible global function definition for ‘rgb’
gsplot1: no visible global function definition for ‘palette’
gsplot1: no visible global function definition for ‘colorRampPalette’
gsplot1: no visible global function definition for ‘layout’
gsplot1: no visible global function definition for ‘par’
gsplot1: no visible global function definition for ‘plot’
gsplot1: no visible global function definition for ‘abline’
gsplot1: no visible global function definition for ‘lines’
gsplot1: no visible global function definition for ‘axis’
gsplot1: no visible global function definition for ‘legend’
gsplot1: no visible global function definition for ‘segments’
gsplot1: no visible global function definition for ‘title’
gsplot2 : get.alpha: no visible global function definition for
  ‘col2rgb’
gsplot2 : get.alpha: no visible global function definition for ‘rgb’
gsplot2: no visible global function definition for ‘layout’
gsplot2: no visible global function definition for ‘par’
gsplot2: no visible global function definition for ‘plot’
gsplot2: no visible global function definition for ‘abline’
gsplot2: no visible global function definition for ‘lines’
gsplot2: no visible global function definition for ‘axis’
gsplot2: no visible global function definition for ‘legend’
gsplot2: no visible global function definition for ‘segments’
gsplot2: no visible global function definition for ‘title’
gsplot2: no visible global function definition for ‘points’
hyperGeoTest4RTN: no visible global function definition for ‘phyper’
make.plot1: no visible global function definition for ‘pdf’
make.plot1: no visible global function definition for ‘dev.off’
make.plot2: no visible global function definition for ‘pdf’
make.plot2: no visible global function definition for ‘dev.off’
maprset: no visible global function definition for ‘txtProgressBar’
maprset : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
miMdTfStats: no visible global function definition for ‘txtProgressBar’
miMdTfStats : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
miMdTfStats : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
miMdTfStats : <anonymous> : <anonymous>: no visible global function
  definition for ‘sd’
miMdTfStats: no visible binding for global variable ‘median’
miMdTfStats: no visible binding for global variable ‘sd’
miThresholdMd: no visible global function definition for
  ‘txtProgressBar’
miThresholdMd : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
miThresholdMd : <anonymous>: no visible global function definition for
  ‘quantile’
miThresholdMd: no visible global function definition for ‘median’
miThresholdMdTf: no visible global function definition for
  ‘txtProgressBar’
miThresholdMdTf : <anonymous>: no visible global function definition
  for ‘setTxtProgressBar’
miThresholdMdTf : <anonymous>: no visible binding for global variable
  ‘quantile’
miThresholdMdTf: no visible binding for global variable ‘median’
miThresholdMdTf: no visible global function definition for ‘median’
multiHyperGeoTest4RTN: no visible global function definition for
  ‘txtProgressBar’
multiHyperGeoTest4RTN : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multiHyperGeoTest4RTN: no visible global function definition for
  ‘p.adjust’
p.adjust.cdt: no visible global function definition for ‘p.adjust’
pairwiseShadow: no visible global function definition for
  ‘txtProgressBar’
pairwiseShadow : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
pairwiseSynergy: no visible global function definition for
  ‘txtProgressBar’
pairwiseSynergy : <anonymous>: no visible global function definition
  for ‘setTxtProgressBar’
run.gsea1: no visible global function definition for ‘p.adjust’
run.gsea2: no visible global function definition for ‘p.adjust’
run.overlap: no visible global function definition for ‘p.adjust’
run.shadow: no visible binding for global variable ‘median’
run.shadow: no visible global function definition for ‘p.adjust’
run.synergy: no visible binding for global variable ‘median’
run.synergy: no visible global function definition for ‘p.adjust’
setregs1: no visible global function definition for ‘quantile’
setregs1 : <anonymous>: no visible global function definition for
  ‘median’
shtest: no visible global function definition for ‘quantile’
shtest: no visible global function definition for ‘shapiro.test’
tna.duplicate.remover: no visible global function definition for
  ‘aggregate’
tna.hyper: no visible global function definition for ‘phyper’
tna.hyper.pairs: no visible global function definition for
  ‘txtProgressBar’
tna.hyper.pairs: no visible global function definition for
  ‘setTxtProgressBar’
tna.hyper.pairs: no visible global function definition for ‘p.adjust’
tni.boot: no visible global function definition for ‘txtProgressBar’
tni.boot: no visible global function definition for ‘setTxtProgressBar’
tni.boot : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
tni.cor: no visible global function definition for ‘cor’
tni.perm.pooled: no visible global function definition for
  ‘txtProgressBar’
tni.perm.pooled: no visible global function definition for
  ‘setTxtProgressBar’
tni.perm.pooled : <anonymous>: no visible global function definition
  for ‘setTxtProgressBar’
tni.perm.pooled: no visible global function definition for ‘p.adjust’
tni.perm.separate : <anonymous>: no visible global function definition
  for ‘p.adjust’
tni.perm.separate: no visible global function definition for
  ‘txtProgressBar’
tni.perm.separate : <anonymous>: no visible global function definition
  for ‘setTxtProgressBar’
tni.perm.separate: no visible global function definition for ‘p.adjust’
tni.phyper : phtest: no visible global function definition for ‘phyper’
tni.phyper: no visible global function definition for ‘p.adjust’
tni.pmin: no visible global function definition for ‘cor’
vsea: no visible global function definition for ‘txtProgressBar’
vsea : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
vseformat : <anonymous>: no visible global function definition for ‘sd’
vseformat : <anonymous>: no visible global function definition for
  ‘median’
vseformat: no visible global function definition for ‘pnorm’
vseformat: no visible global function definition for ‘qnorm’
vseformat : <anonymous>: no visible global function definition for
  ‘coef’
vsereport: no visible global function definition for ‘boxplot’
avs.evse,AVS: no visible global function definition for
  ‘txtProgressBar’
avs.evse,AVS : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
tna.graph,TNA: no visible global function definition for ‘quantile’
tni.conditional,TNI: no visible global function definition for ‘median’
tni.conditional,TNI: no visible global function definition for
  ‘model.matrix’
tni.conditional,TNI : <anonymous>: no visible global function
  definition for ‘shapiro.test’
tni.conditional,TNI : <anonymous>: no visible global function
  definition for ‘coef’
tni.conditional,TNI: no visible global function definition for
  ‘txtProgressBar’
tni.conditional,TNI: no visible global function definition for
  ‘setTxtProgressBar’
tni.conditional,TNI : <anonymous>: no visible global function
  definition for ‘phyper’
tni.conditional,TNI : <anonymous>: no visible global function
  definition for ‘ks.test’
tni.conditional,TNI : <anonymous>: no visible global function
  definition for ‘median’
tni.conditional,TNI : <anonymous>: no visible global function
  definition for ‘sd’
tni.graph,TNI : <anonymous>: no visible global function definition for
  ‘median’
tni.graph,TNI: no visible global function definition for ‘quantile’
tni.graph,TNI: no visible global function definition for ‘hclust’
tni.graph,TNI: no visible global function definition for ‘as.dist’
tni.graph,TNI: no visible global function definition for ‘cor’
tni.preprocess,TNI: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline aggregate anova aov as.dist axis boxplot coef col2rgb
  colorRampPalette cor data dev.off formula hclust hist image ks.test
  layout legend lines lm manova median model.matrix mtext p.adjust
  palette par pdf phyper plot plot.new pnorm points polygon qnorm
  quantile rgb sd segments setTxtProgressBar shapiro.test title
  txtProgressBar
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
             "palette", "pdf", "rgb")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "image",
             "layout", "legend", "lines", "mtext", "par", "plot",
             "plot.new", "points", "polygon", "segments", "title")
  importFrom("stats", "aggregate", "anova", "aov", "as.dist", "coef",
             "cor", "formula", "hclust", "ks.test", "lm", "manova",
             "median", "model.matrix", "p.adjust", "phyper", "pnorm",
             "qnorm", "quantile", "sd", "shapiro.test")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/RTN.Rcheck/00check.log’
for details.

* installing *source* package ‘RTN’ ...
** 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 (RTN)

name	user	system	elapsed
AVS-class	0.001	0.000	0.000
RTN.data	0.404	0.004	0.409
TNA-class	0.001	0.000	0.000
TNI-class	0.549	0.000	0.550
avs.evse	0.001	0.000	0.001
avs.get	0	0	0
avs.plot1	0.001	0.000	0.000
avs.plot2	0.001	0.000	0.001
avs.preprocess	0	0	0
avs.vse	0.001	0.000	0.000
tna.get	0.362	0.004	0.366
tna.graph	0.364	0.000	0.364
tna.gsea1	0.504	0.012	0.516
tna.gsea2	0.346	0.000	0.346
tna.mra	0.37	0.00	0.37
tna.overlap	0.373	0.000	0.373
tna.plot.gsea1	0.348	0.004	0.356
tna.plot.gsea2	0.349	0.016	0.365
tna.shadow	0.362	0.004	0.366
tna.synergy	0.355	0.004	0.359
tni.bootstrap	0.359	0.000	0.358
tni.conditional	0.364	0.000	0.364
tni.dpi.filter	0.348	0.008	0.356
tni.get	0.358	0.004	0.362
tni.graph	0.363	0.000	0.363
tni.permutation	0.358	0.000	0.358
tni.preprocess	0.871	0.024	0.894
tni2tna.preprocess	0.533	0.004	0.538