Ringo 1.34.0
J. Toedling
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Ringo | | Last Changed Rev: 109589 / Revision: 110496 | | 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 | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Ringo_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Ringo.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [17s/17s] 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’ ‘grid’ ‘lattice’ ‘limma’ ‘Matrix’ ‘RColorBrewer’
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 ... [12s/12s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/Ringo.Rcheck/00check.log’
for details.
* installing *source* package ‘Ringo’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c mmeansd.cpp -o mmeansd.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c mmedian.cpp -o mmedian.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c region_overlap.c -o region_overlap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c ringo_init.c -o ringo_init.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)