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CHECK report for Ringo on malbec1

This page was generated on 2018-04-12 13:07:56 -0400 (Thu, 12 Apr 2018).

Package 1180/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ringo 1.42.1
J. Toedling
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Ringo
Branch: RELEASE_3_6
Last Commit: 505228e
Last Changed Date: 2018-04-02 13:46:50 -0400 (Mon, 02 Apr 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Ringo
Version: 1.42.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.42.1.tar.gz
StartedAt: 2018-04-12 02:27:21 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:29:27 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 126.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.42.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Ringo.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ringo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ringo’ version ‘1.42.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘RColorBrewer’ ‘limma’ ‘Matrix’ ‘grid’ ‘lattice’
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 ‘Ringo’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
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 ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘mclust’ ‘rtracklayer’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘limma’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘Matrix’ ‘RColorBrewer’ ‘grid’ ‘lattice’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘clusters’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
asExprSet: no visible global function definition for ‘featureNames<-’
asExprSet: no visible global function definition for ‘featureData<-’
autocor: no visible global function definition for ‘featureNames’
autocor: no visible global function definition for ‘exprs’
autocor : <anonymous>: no visible global function definition for
  ‘matchpt’
autocor: no visible global function definition for ‘cor’
chersToBED: no visible global function definition for ‘write.table’
chipAlongChrom: no visible global function definition for
  ‘featureNames’
chipAlongChrom: no visible global function definition for ‘exprs’
chipAlongChrom: no visible global function definition for ‘brewer.pal’
chipAlongChrom: no visible global function definition for
  ‘pushViewport’
chipAlongChrom: no visible global function definition for ‘viewport’
chipAlongChrom: no visible global function definition for ‘grid.layout’
chipAlongChrom: no visible global function definition for
  ‘dataViewport’
chipAlongChrom: no visible global function definition for ‘grid.yaxis’
chipAlongChrom: no visible global function definition for ‘gpar’
chipAlongChrom: no visible global function definition for ‘grid.text’
chipAlongChrom: no visible global function definition for ‘unit’
chipAlongChrom: no visible global function definition for ‘draw.key’
chipAlongChrom: no visible global function definition for ‘sampleNames’
chipAlongChrom: no visible global function definition for ‘strwidth’
chipAlongChrom: no visible global function definition for ‘strheight’
chipAlongChrom: no visible global function definition for ‘popViewport’
chipAlongChrom: no visible global function definition for ‘grid.lines’
chipAlongChrom: no visible global function definition for
  ‘grid.segments’
chipAlongChrom: no visible global function definition for ‘arrow’
chipAlongChrom1: no visible global function definition for
  ‘featureNames’
chipAlongChrom1: no visible global function definition for ‘exprs’
chipAlongChrom1: no visible global function definition for ‘colors’
chipAlongChrom1: no visible global function definition for ‘brewer.pal’
chipAlongChrom1: no visible global function definition for ‘axis’
chipAlongChrom1: no visible global function definition for ‘mtext’
chipAlongChrom1: no visible global function definition for ‘abline’
chipAlongChrom1: no visible global function definition for ‘lines’
chipAlongChrom1: no visible global function definition for ‘points’
chipAlongChrom1: no visible global function definition for ‘rug’
chipAlongChrom1: no visible global function definition for
  ‘sampleNames’
chipAlongChrom1: no visible global function definition for ‘legend’
compute.gc: no visible global function definition for ‘listLen’
computeRunningMedians: no visible global function definition for
  ‘varLabels’
computeRunningMedians: no visible global function definition for
  ‘pData’
computeRunningMedians: no visible global function definition for
  ‘sampleNames’
computeRunningMedians: no visible global function definition for
  ‘exprs’
computeRunningMedians: no visible global function definition for
  ‘featureNames’
computeRunningMedians: no visible global function definition for
  ‘phenoData’
computeRunningMedians: no visible global function definition for
  ‘featureNames<-’
computeRunningMedians: no visible global function definition for
  ‘featureData<-’
computeRunningMedians: no visible global function definition for
  ‘featureData’
computeRunningMedians: no visible global function definition for
  ‘sampleNames<-’
computeSlidingT: no visible global function definition for ‘exprs’
computeSlidingT: no visible global function definition for
  ‘featureNames’
computeSlidingT: no visible global function definition for
  ‘sampleNames’
computeSlidingT: no visible binding for global variable ‘median’
computeSlidingT: no visible global function definition for ‘median’
computeSlidingT: no visible global function definition for
  ‘featureNames<-’
computeSlidingT: no visible global function definition for
  ‘featureData<-’
computeSlidingT: no visible global function definition for
  ‘featureData’
computeSlidingT: no visible global function definition for
  ‘sampleNames<-’
corPlot: no visible global function definition for ‘exprs’
corPlot: no visible global function definition for ‘relevel’
corPlot: no visible global function definition for ‘pairs’
corPlot : <anonymous>: no visible global function definition for ‘par’
corPlot : <anonymous>: no visible global function definition for
  ‘abline’
exportCCData: no visible global function definition for ‘exprs’
exportCCData: no visible global function definition for ‘exprs<-’
exportCCData: no visible global function definition for
  ‘package.version’
exportCCData: no visible global function definition for ‘write.table’
exportCherList: no visible global function definition for ‘IRanges’
exportCherList: no visible global function definition for ‘GenomicData’
exportCherList: no visible global function definition for ‘export’
findChersOnSmoothed: no visible global function definition for ‘pData’
findChersOnSmoothed: no visible global function definition for
  ‘sampleNames’
findChersOnSmoothed: no visible global function definition for
  ‘featureNames’
findChersOnSmoothed : <anonymous>: no visible global function
  definition for ‘exprs’
ftr2xys: no visible global function definition for ‘read.delim’
ftr2xys: no visible global function definition for ‘write.table’
image.RGList: no visible global function definition for
  ‘colorRampPalette’
image.RGList: no visible global function definition for ‘brewer.pal’
image.RGList: no visible global function definition for ‘quantile’
image.RGList: no visible global function definition for ‘points’
merge.RGList: no visible global function definition for ‘makeUnique’
newVP: no visible global function definition for ‘pushViewport’
newVP: no visible global function definition for ‘viewport’
newVP: no visible global function definition for ‘grid.layout’
newVP: no visible global function definition for ‘grid.text’
newVP: no visible global function definition for ‘gpar’
newVP: no visible global function definition for ‘popViewport’
nimblegenScale : tukey.biweight: no visible global function definition
  for ‘median’
normalizeBetweenArraysVSN: no visible global function definition for
  ‘exprs’
oneChannelVSN: no visible global function definition for ‘predict’
pair2xys: no visible global function definition for ‘read.delim’
pair2xys: no visible global function definition for ‘write.table’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.scatter: no visible global function definition for ‘points’
panel.scatter: no visible global function definition for ‘abline’
plot.cher: no visible global function definition for ‘sampleNames’
plot.cher: no visible global function definition for ‘rug’
plot.cher: no visible global function definition for ‘legend’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘convertWidth’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘stringWidth’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘grid.rect’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘unit’
plotAlongChromLegend : formatRow: no visible binding for global
  variable ‘gpar’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘grid.text’
plotAlongChromLegend : formatRow: no visible global function definition
  for ‘gpar’
plotAlongChromLegend: no visible global function definition for
  ‘pushViewport’
plotAlongChromLegend: no visible global function definition for
  ‘viewport’
plotAlongChromLegend: no visible global function definition for
  ‘popViewport’
plotBM: no visible global function definition for ‘arrows’
plotBM: no visible global function definition for ‘axis’
plotFeatures: no visible global function definition for ‘pushViewport’
plotFeatures: no visible global function definition for ‘dataViewport’
plotFeatures: no visible global function definition for ‘grid.segments’
plotFeatures: no visible global function definition for ‘gpar’
plotFeatures: no visible global function definition for ‘listLen’
plotFeatures: no visible global function definition for ‘grid.rect’
plotFeatures: no visible global function definition for ‘convertWidth’
plotFeatures: no visible global function definition for ‘stringWidth’
plotFeatures: no visible global function definition for ‘grid.text’
plotFeatures: no visible global function definition for ‘popViewport’
plotOneChIPSample: no visible global function definition for ‘unit’
plotOneChIPSample: no visible global function definition for ‘quantile’
plotOneChIPSample: no visible global function definition for
  ‘pushViewport’
plotOneChIPSample: no visible global function definition for
  ‘dataViewport’
plotOneChIPSample: no visible global function definition for
  ‘grid.yaxis’
plotOneChIPSample: no visible global function definition for ‘gpar’
plotOneChIPSample: no visible global function definition for
  ‘grid.text’
plotOneChIPSample: no visible global function definition for
  ‘grid.lines’
plotOneChIPSample: no visible global function definition for
  ‘grid.polyline’
plotOneChIPSample: no visible global function definition for
  ‘grid.points’
plotOneChIPSample: no visible global function definition for
  ‘popViewport’
posToProbeAnno: no visible global function definition for ‘read.delim’
preprocess: no visible global function definition for
  ‘normalizeWithinArrays’
preprocess: no visible global function definition for
  ‘normalizeBetweenArrays’
quantilesOverPositions: no visible global function definition for
  ‘exprs’
quantilesOverPositions : <anonymous>: no visible global function
  definition for ‘approx’
quantilesOverPositions: no visible global function definition for
  ‘sampleNames’
quantilesOverPositions : <anonymous>: no visible binding for global
  variable ‘quantile’
quantilesOverPositions: no visible global function definition for
  ‘density’
quantilesOverPositions: no visible global function definition for
  ‘approx’
readNgIntensitiesTxt: no visible global function definition for
  ‘read.table’
readNgIntensitiesTxt: no visible global function definition for
  ‘removeExt’
readNimblegen: no visible global function definition for ‘readTargets’
readNimblegen: no visible global function definition for
  ‘readSpotTypes’
readNimblegen: no visible global function definition for
  ‘controlStatus’
sigGOTable: no visible global function definition for ‘mappedkeys’
sigGOTable: no visible binding for global variable ‘annFUN.gene2GO’
sigGOTable: no visible binding for global variable ‘annFUN.org’
sigGOTable: no visible global function definition for ‘runTest’
sigGOTable: no visible global function definition for ‘GenTable’
sigGOTable: no visible global function definition for ‘usedGO’
sigGOTable: no visible binding for global variable ‘p.value’
splitAndSimplify: no visible global function definition for ‘listLen’
takeMeanOverGroups: no visible global function definition for ‘pData’
takeMeanOverGroups: no visible global function definition for ‘exprs’
takeMeanOverGroups: no visible global function definition for
  ‘featureNames<-’
takeMeanOverGroups: no visible global function definition for
  ‘featureNames’
twoGaussiansNull: no visible binding for global variable
  ‘p.adjust.methods’
twoGaussiansNull: no visible global function definition for ‘Mclust’
twoGaussiansNull: no visible global function definition for ‘na.omit’
twoGaussiansNull: no visible global function definition for ‘pnorm’
upperBoundNull: no visible global function definition for ‘na.omit’
upperBoundNull: no visible global function definition for ‘quantile’
cbind2,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘featureNames’
cbind2,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘exprs’
cbind2,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘sampleNames’
plot,cher-ExpressionSet: no visible global function definition for
  ‘sampleNames’
plot,qop-ANY: no visible global function definition for ‘axis’
plot,qop-ANY: no visible global function definition for ‘rainbow’
plot,qop-ANY: no visible global function definition for ‘lines’
plot,qop-ANY: no visible global function definition for ‘legend’
Undefined global functions or variables:
  GenTable GenomicData IRanges Mclust abline addVigs2WinMenu
  annFUN.gene2GO annFUN.org approx arrow arrows axis brewer.pal
  colorRampPalette colors controlStatus convertWidth cor dataViewport
  density draw.key export exprs exprs<- featureData featureData<-
  featureNames featureNames<- gpar grid.layout grid.lines grid.points
  grid.polyline grid.rect grid.segments grid.text grid.yaxis legend
  lines listLen makeUnique mappedkeys matchpt median mtext na.omit
  normalizeBetweenArrays normalizeWithinArrays p.adjust.methods p.value
  pData package.version pairs par phenoData pnorm points popViewport
  predict pushViewport quantile rainbow read.delim read.table
  readSpotTypes readTargets relevel removeExt rug runTest sampleNames
  sampleNames<- strheight stringWidth strwidth text unit usedGO
  varLabels viewport write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "colors", "rainbow")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "pairs", "par", "points", "rug", "strheight",
             "strwidth", "text")
  importFrom("stats", "approx", "cor", "density", "median", "na.omit",
             "p.adjust.methods", "pnorm", "predict", "quantile",
             "relevel")
  importFrom("utils", "read.delim", "read.table", "write.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking compiled code ... 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-3.6-bioc/meat/Ringo.Rcheck/00check.log’
for details.

Installation output

Ringo.Rcheck/00install.out

* installing *source* package ‘Ringo’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mmeansd.cpp -o mmeansd.o
mmeansd.cpp: In function ‘SEXPREC* moving_mean_sd(SEXP, SEXP, SEXP)’:
mmeansd.cpp:29:24: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
     int * x, nval, hs, is, i;
                        ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mmedian.cpp -o mmedian.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c region_overlap.c -o region_overlap.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ringo_init.c -o ringo_init.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/Ringo.Rcheck/Ringo/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Ringo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Ringo)

Tests output

Example timings

Ringo.Rcheck/Ringo-Ex.timings

nameusersystemelapsed
arrayImage0.0880.0000.087
asExprSet0.6160.0120.625
autocorr0.0960.0000.097
cherByThreshold0.0080.0000.006
cherClass0.4000.0080.408
chipAlongChrom0.8880.0040.892
chipAlongChromOld0.0360.0000.034
computeRunningMedians0.3680.0000.369
compute_gc0.0040.0000.001
compute_sliding_t0.0480.0000.048
corrPlot0.0280.0000.026
exportCherList000
features2Probes0.6840.0160.699
findChersOnSmoothed0.1160.0000.117
ftr2xys000
newCER0.0000.0000.001
nonzero0.0160.0000.017
plotAutocorr000
plotBM0.0400.0000.041
posToProbeAnnoEnvironment0.0720.0120.087
preprocess0.3400.0000.344
probeAnnoClass0.0160.0000.019
qopS4000
quantilesOverPositions0.6280.0320.661
readNimblegen0.0960.0000.097
regionoverlap0.0040.0000.004
relateCERs000
sigGOTable000
sliding_meansd0.0040.0000.002
sliding_quantile0.0160.0000.014
twoGaussiansNull0.1320.0000.132
upperBoundNull0.0520.0000.051
validProbeAnno0.0160.0000.015