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BioC 3.3: CHECK report for RTN on moscato2

This page was generated on 2016-10-13 12:51:43 -0700 (Thu, 13 Oct 2016).

Package 1019/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTN 1.10.0
Mauro Castro
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/RTN
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTN
Version: 1.10.0
Command: rm -rf RTN.buildbin-libdir RTN.Rcheck && mkdir RTN.buildbin-libdir RTN.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTN.buildbin-libdir RTN_1.10.0.tar.gz >RTN.Rcheck\00install.out 2>&1 && cp RTN.Rcheck\00install.out RTN-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RTN.buildbin-libdir --install="check:RTN-install.out" --force-multiarch --no-vignettes --timings RTN_1.10.0.tar.gz
StartedAt: 2016-10-13 08:33:02 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 08:37:45 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 283.2 seconds
RetCode: 0
Status:  OK  
CheckDir: RTN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RTN.buildbin-libdir RTN.Rcheck && mkdir RTN.buildbin-libdir RTN.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTN.buildbin-libdir RTN_1.10.0.tar.gz >RTN.Rcheck\00install.out 2>&1 && cp RTN.Rcheck\00install.out RTN-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RTN.buildbin-libdir --install="check:RTN-install.out" --force-multiarch --no-vignettes --timings RTN_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/RTN.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/RTN.Rcheck/00check.log'
for details.

RTN.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RTN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTN' as RTN_1.10.0.zip
* DONE (RTN)

RTN.Rcheck/examples_i386/RTN-Ex.timings:

nameusersystemelapsed
AVS-class000
RTN.data0.610.000.61
TNA-class000
TNI-class0.720.010.73
avs.evse0.020.000.02
avs.get000
avs.plot1000
avs.plot2000
avs.preprocess000
avs.vse000
tna.get0.560.020.57
tna.graph0.530.010.55
tna.gsea10.660.000.65
tna.gsea20.50.00.5
tna.mra0.720.000.72
tna.overlap0.730.020.75
tna.plot.gsea10.720.000.72
tna.plot.gsea20.880.000.88
tna.shadow0.820.020.84
tna.synergy0.720.000.72
tni.bootstrap0.560.010.57
tni.conditional0.520.020.53
tni.dpi.filter0.500.030.54
tni.get0.490.000.49
tni.graph0.50.00.5
tni.permutation0.530.000.53
tni.preprocess1.330.011.34
tni2tna.preprocess0.500.020.52

RTN.Rcheck/examples_x64/RTN-Ex.timings:

nameusersystemelapsed
AVS-class000
RTN.data0.520.000.52
TNA-class000
TNI-class0.820.000.82
avs.evse000
avs.get000
avs.plot1000
avs.plot2000
avs.preprocess000
avs.vse000
tna.get0.430.020.44
tna.graph0.450.000.45
tna.gsea10.780.000.78
tna.gsea20.390.010.40
tna.mra0.450.000.46
tna.overlap0.480.000.48
tna.plot.gsea10.460.000.45
tna.plot.gsea20.450.020.47
tna.shadow0.670.000.67
tna.synergy0.590.010.61
tni.bootstrap0.630.000.62
tni.conditional0.430.000.44
tni.dpi.filter0.450.020.46
tni.get0.640.000.64
tni.graph0.440.000.44
tni.permutation0.560.030.59
tni.preprocess1.370.001.38
tni2tna.preprocess0.670.000.67