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BioC 3.2: CHECK report for Ringo on zin1

This page was generated on 2016-04-23 10:10:39 -0700 (Sat, 23 Apr 2016).

Package 885/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ringo 1.34.0
J. Toedling
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Ringo
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Ringo
Version: 1.34.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.34.0.tar.gz
StartedAt: 2016-04-23 04:48:23 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:50:13 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 110.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Ringo_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Ringo.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.34.0’
* 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 ... [11s/11s] 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’
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 ‘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 ‘brewer.pal’
chipAlongChrom1: no visible global function definition for
  ‘sampleNames’
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 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’
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’
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’
image.RGList: no visible global function definition for ‘brewer.pal’
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’
normalizeBetweenArraysVSN: no visible global function definition for
  ‘exprs’
plot.cher: no visible global function definition for ‘sampleNames’
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’
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
  ‘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’
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: no visible global function definition for
  ‘sampleNames’
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 global function definition for ‘Mclust’
cbind2,ExpressionSet-ExpressionSet : .local: no visible global function
  definition for ‘featureNames’
cbind2,ExpressionSet-ExpressionSet : .local: no visible global function
  definition for ‘exprs’
cbind2,ExpressionSet-ExpressionSet : .local: no visible global function
  definition for ‘sampleNames’
plot,cher-ExpressionSet : .local: no visible global function definition
  for ‘sampleNames’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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-3.2-bioc/meat/Ringo.Rcheck/00check.log’
for details.


Ringo.Rcheck/00install.out:

* installing *source* package ‘Ringo’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-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:27:24: warning: variable ‘is’ set but not used [-Wunused-but-set-variable]
     int * x, nval, hs, is, i;
                        ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c region_overlap.c -o region_overlap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)

Ringo.Rcheck/Ringo-Ex.timings:

nameusersystemelapsed
arrayImage0.0800.0040.084
asExprSet0.1360.0000.136
autocorr0.1090.0040.113
cherByThreshold0.0050.0000.004
cherClass0.3530.0040.357
chipAlongChrom0.1080.0000.108
chipAlongChromOld0.0350.0000.035
computeRunningMedians0.1910.0040.195
compute_gc0.0010.0000.001
compute_sliding_t0.0520.0000.052
corrPlot0.0240.0040.028
exportCherList0.0000.0000.001
features2Probes0.8420.0120.853
findChersOnSmoothed0.0670.0000.071
ftr2xys0.0010.0000.000
newCER0.0010.0000.002
nonzero0.0100.0000.009
plotAutocorr0.0000.0000.001
plotBM0.0060.0000.011
posToProbeAnnoEnvironment0.0270.0000.026
preprocess0.1890.0040.193
probeAnnoClass0.0150.0000.016
qopS40.0010.0000.000
quantilesOverPositions0.4620.0000.461
readNimblegen0.0600.0040.065
regionoverlap0.0050.0000.005
relateCERs000
sigGOTable0.0010.0000.001
sliding_meansd0.0020.0000.002
sliding_quantile0.0110.0000.011
twoGaussiansNull0.1350.0000.135
upperBoundNull0.0500.0000.052
validProbeAnno0.0160.0000.016