Ringo 1.40.0
J. Toedling
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/Ringo | | Branch: RELEASE_3_5 | | Last Commit: 6194162 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Ringo.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.40.0’
* 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-3.5-bioc/meat/Ringo.Rcheck/00check.log’
for details.
* installing *source* package ‘Ringo’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mmedian.cpp -o mmedian.o
gcc -I/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/lib -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)