beadarray 2.24.0
Mark Dunning
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/beadarray | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/beadarray.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘beadarray’ 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
* 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' calls in package code:
‘Nozzle.R1’ ‘affy’ ‘ggbio’ ‘hwriter’ ‘lumi’ ‘vsn’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘ggplot2’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘BeadDataPackR:::combineFiles’ ‘BeadDataPackR:::readHeader’
‘Biobase:::assayDataStorageMode’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘illuminaForeground_6x6’ ‘locsIndicesToGrid’ ‘obtainLocs’
‘simpleXMLparse’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.mergePhenodata: no visible global function definition for ‘new’
.onAttach: no visible global function definition for
‘packageDescription’
addFeatureData: no visible global function definition for ‘is’
addFeatureData: no visible global function definition for ‘new’
analyseDirectory: no visible global function definition for
‘read.table’
calculateDetection: no visible global function definition for
‘txtProgressBar’
calculateDetection: no visible global function definition for
‘setTxtProgressBar’
checkRegistration: no visible global function definition for ‘new’
combinedControlPlot: no visible binding for global variable ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
combinedControlPlot: no visible global function definition for
‘density’
combinedControlPlot: no visible global function definition for ‘ggplot’
combinedControlPlot: no visible global function definition for ‘aes’
combinedControlPlot: no visible binding for global variable ‘ID’
combinedControlPlot: no visible binding for global variable
‘Log2Intensity’
combinedControlPlot: no visible binding for global variable
‘ControlType’
combinedControlPlot: no visible global function definition for
‘geom_boxplot’
combinedControlPlot: no visible global function definition for
‘geom_hline’
combinedControlPlot: no visible global function definition for
‘facet_wrap’
combinedControlPlot: no visible global function definition for
‘geom_point’
combinedControlPlot: no visible binding for global variable ‘Masked’
convertBeadLevelList: no visible global function definition for ‘new’
createGEOMatrix: no visible global function definition for
‘write.table’
createGEOMeta: no visible global function definition for ‘data’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
createTargetsFile: no visible global function definition for
‘read.table’
expressionQCPipeline: no visible global function definition for
‘ggsave’
expressionQCPipeline: no visible global function definition for ‘jpeg’
expressionQCPipeline: no visible global function definition for ‘pdf’
expressionQCPipeline: no visible global function definition for ‘png’
expressionQCPipeline: no visible global function definition for
‘dev.off’
expressionQCPipeline: no visible global function definition for
‘openPage’
expressionQCPipeline: no visible global function definition for
‘hwrite’
expressionQCPipeline: no visible global function definition for
‘hwriteImage’
expressionQCPipeline: no visible global function definition for
‘closePage’
expressionQCPipeline: no visible global function definition for
‘write.csv’
generateE: no visible global function definition for ‘aggregate’
genericBeadIntensityPlot: no visible global function definition for
‘runif’
getPlatformSigs: no visible global function definition for
‘lumiHumanIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
‘dbListTables’
getPlatformSigs: no visible global function definition for
‘dbListFields’
getPlatformSigs: no visible global function definition for ‘dbGetQuery’
getPlatformSigs: no visible global function definition for
‘lumiMouseIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
‘lumiRatIDMapping_dbconn’
imageplot: no visible global function definition for ‘ggplot’
imageplot: no visible global function definition for ‘aes’
imageplot: no visible binding for global variable ‘Var1’
imageplot: no visible binding for global variable ‘Var2’
imageplot: no visible binding for global variable ‘value’
imageplot: no visible global function definition for ‘geom_tile’
imageplot: no visible global function definition for
‘scale_fill_gradient’
imageplot: no visible global function definition for ‘theme’
imageplot: no visible global function definition for ‘element_blank’
limmaDE: no visible global function definition for ‘model.matrix’
limmaDE: no visible global function definition for ‘new’
makeControlProfile: no visible global function definition for
‘packageDescription’
makeReport: no visible global function definition for ‘as’
makeReport: no visible global function definition for ‘newCustomReport’
makeReport: no visible global function definition for ‘newSection’
makeReport: no visible global function definition for ‘newTable’
makeReport: no visible global function definition for ‘newParagraph’
makeReport: no visible global function definition for ‘addTo’
makeReport: no visible global function definition for ‘autoplot’
makeReport: no visible global function definition for ‘plotIdeogram’
makeReport: no visible global function definition for ‘tracks’
makeReport: no visible global function definition for ‘ggsave’
makeReport: no visible global function definition for ‘newFigure’
makeReport: no visible binding for global variable ‘IMAGE.TYPE.RASTER’
makeReport: no visible binding for global variable ‘PROTECTION.PUBLIC’
makeReport: no visible global function definition for ‘ggplot’
makeReport: no visible global function definition for ‘aes’
makeReport: no visible binding for global variable ‘value’
makeReport: no visible global function definition for ‘geom_boxplot’
makeReport: no visible global function definition for ‘facet_wrap’
makeReport: no visible global function definition for ‘writeReport’
maplots: no visible global function definition for ‘ggplot’
maplots: no visible global function definition for ‘aes’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
maplots: no visible global function definition for ‘stat_binhex’
maplots: no visible global function definition for ‘theme_bw’
maplots: no visible global function definition for ‘xlab’
maplots: no visible global function definition for ‘ylab’
maplots: no visible global function definition for ‘facet_wrap’
maplots: no visible global function definition for ‘theme’
maplots: no visible global function definition for ‘ggtitle’
normaliseIllumina: no visible global function definition for ‘new’
normaliseIllumina: no visible global function definition for ‘lumiT’
normaliseIllumina: no visible global function definition for
‘normalize.qspline’
normaliseIllumina: no visible global function definition for ‘vsn2’
normaliseIllumina: no visible global function definition for ‘rsn’
numberOfChannels: no visible global function definition for
‘read.table’
numberOfColumns: no visible global function definition for ‘read.table’
outlierplot2: no visible global function definition for ‘geom_vline’
outlierplot2: no visible global function definition for ‘geom_hline’
plot.smooth.line: no visible global function definition for ‘approx’
plot.smooth.line: no visible global function definition for ‘lowess’
plotBeadIntensities: no visible global function definition for
‘rainbow’
plotBeadLocations2: no visible global function definition for ‘qplot’
plotBeadLocations2: no visible global function definition for ‘opts’
plotBeadLocations2: no visible global function definition for
‘theme_blank’
plotChipLayout: no visible global function definition for ‘rgb’
plotProbe: no visible global function definition for ‘data’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible global function definition for ‘aes’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
plotTIFF: no visible global function definition for ‘col2rgb’
plotTIFF: no visible global function definition for ‘rgb’
poscontPlot: no visible global function definition for ‘rainbow’
rankInvariantNormalise: no visible global function definition for
‘normalize.invariantset’
rankInvariantNormalise: no visible global function definition for
‘predict’
readBeadSummaryData: no visible global function definition for
‘read.table’
readBeadSummaryData: no visible global function definition for ‘new’
readIdatFiles: no visible global function definition for ‘new’
readIllumina: no visible global function definition for ‘new’
readQC: no visible global function definition for ‘read.table’
readQC: no visible global function definition for ‘new’
readSampleSheet: no visible global function definition for ‘read.csv’
setFeatureData: no visible global function definition for
‘packageDescription’
setFeatureData: no visible global function definition for ‘new’
squeezedVarOutlierMethod: no visible global function definition for
‘loess’
squeezedVarOutlierMethod: no visible global function definition for
‘predict’
suggestAnnotation: no visible binding for global variable
‘platformSigs’
suggestAnnotation_Vector: no visible global function definition for
‘data’
suggestAnnotation_Vector: no visible binding for global variable
‘platformSigs’
summarize: no visible global function definition for ‘new’
summarize: no visible global function definition for
‘packageDescription’
viewBeads: no visible global function definition for ‘col2rgb’
viewBeads: no visible global function definition for ‘menu’
viewBeads: no visible global function definition for ‘rgb’
writeOutFiles: no visible global function definition for ‘write.table’
[,ExpressionSetIllumina-ANY: no visible global function definition for
‘assayDataEnvLock’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘ggplot’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘aes’
boxplot,ExpressionSetIllumina: no visible binding for global variable
‘Var2’
boxplot,ExpressionSetIllumina: no visible binding for global variable
‘value’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘geom_boxplot’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘scale_fill_discrete’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘facet_wrap’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘theme’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘element_blank’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘element_text’
boxplot,ExpressionSetIllumina: no visible global function definition
for ‘ylab’
channel,ExpressionSetIllumina-ANY: no visible global function
definition for ‘new’
coerce,ExpressionSet-ExpressionSetIllumina: no visible global function
definition for ‘new’
coerce,limmaResults-GRanges: no visible global function definition for
‘new’
combine,beadLevelData-beadLevelData: no visible global function
definition for ‘new’
initialize,ExpressionSetIllumina: no visible global function definition
for ‘new’
initialize,ExpressionSetIllumina: no visible global function definition
for ‘callNextMethod’
initialize,limmaResults: no visible global function definition for
‘new’
initialize,limmaResults: no visible global function definition for
‘callNextMethod’
plot,limmaResults-ANY: no visible global function definition for
‘ggplot’
plot,limmaResults-ANY: no visible global function definition for ‘aes’
plot,limmaResults-ANY: no visible global function definition for
‘geom_point’
plot,limmaResults-ANY: no visible global function definition for
‘facet_wrap’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘ggplot’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘aes’
plotMA,ExpressionSetIllumina: no visible binding for global variable
‘value.1’
plotMA,ExpressionSetIllumina: no visible binding for global variable
‘value’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘stat_binhex’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘theme_bw’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘xlab’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘ylab’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘facet_wrap’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘theme’
plotMA,ExpressionSetIllumina: no visible global function definition for
‘ggtitle’
show,ExpressionSetIllumina: no visible global function definition for
‘callNextMethod’
show,limmaResults: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
Negative PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo aes aggregate
approx as assayDataEnvLock autoplot callNextMethod closePage col2rgb
data dbGetQuery dbListFields dbListTables density dev.off
element_blank element_text facet_wrap genesymbol geom_boxplot
geom_hline geom_point geom_tile geom_vline ggplot ggsave ggtitle
hwrite hwriteImage is jpeg loess lowess lumiHumanIDMapping_dbconn
lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT menu
metaTemplate model.matrix new newCustomReport newFigure newParagraph
newSection newTable normalize.invariantset normalize.qspline openPage
opts p.adjust packageDescription pdf platformSigs plotIdeogram png
predict qplot rainbow read.csv read.table rgb rsn runif
scale_fill_discrete scale_fill_gradient setTxtProgressBar stat_binhex
theme theme_blank theme_bw tracks txtProgressBar value value.1 vsn2
write.csv write.table writeReport xlab ylab
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png",
"rainbow", "rgb")
importFrom("methods", "as", "callNextMethod", "is", "new")
importFrom("stats", "aggregate", "approx", "density", "loess",
"lowess", "model.matrix", "p.adjust", "predict", "runif")
importFrom("utils", "data", "menu", "packageDescription", "read.csv",
"read.table", "setTxtProgressBar", "txtProgressBar",
"write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 51.652 0.060 51.745
summarize 26.960 0.368 27.344
limmaDE 19.176 0.004 19.197
calculateOutlierStats 15.924 0.136 16.068
outlierplot 13.784 0.084 13.875
maplots 11.672 0.028 11.705
calculateDetection 11.604 0.000 11.611
controlProbeDetection 11.176 0.040 11.221
normaliseIllumina 10.904 0.196 11.666
identifyControlBeads 10.428 0.008 10.442
makeQCTable 9.672 0.060 9.740
insertSectionData 9.296 0.036 9.337
poscontPlot 9.212 0.048 9.266
addFeatureData 7.984 0.108 8.170
quickSummary 7.532 0.084 7.623
annotationInterface 7.012 0.124 7.155
imageplot 5.616 0.008 5.626
showArrayMask 5.292 0.100 5.397
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/beadarray.Rcheck/00check.log’
for details.
* installing *source* package ‘beadarray’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BASH.c -o BASH.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c HULK.c -o HULK.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:196:29: warning: ‘ma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
^
findAllOutliers.c:196:53: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
^
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:226:20: warning: ‘status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
beadStatusStruct *status;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:88:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
^
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
^
imageProcessing.c:251:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
^
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/beadarray.Rcheck/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beadarray)