beadarray 2.21.0
Mark Dunning
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/beadarray.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.21.0’
* 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 ... [11s/11s] 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
combinedControlPlot: no visible binding for global variable ‘Control’
combinedControlPlot: no visible binding for global variable ‘Negative’
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’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
expressionQCPipeline: no visible global function definition for
‘ggsave’
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’
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’
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 ‘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’
outlierplot2: no visible global function definition for ‘geom_vline’
outlierplot2: no visible global function definition for ‘geom_hline’
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’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible global function definition for ‘aes’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
rankInvariantNormalise: no visible global function definition for
‘normalize.invariantset’
suggestAnnotation: no visible binding for global variable
‘platformSigs’
suggestAnnotation_Vector: no visible binding for global variable
‘platformSigs’
[,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’
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’
Undefined global functions or variables:
Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
Negative PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo aes
assayDataEnvLock autoplot closePage dbGetQuery dbListFields
dbListTables element_blank element_text facet_wrap genesymbol
geom_boxplot geom_hline geom_point geom_tile geom_vline ggplot ggsave
ggtitle hwrite hwriteImage lumiHumanIDMapping_dbconn
lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT metaTemplate
newCustomReport newFigure newParagraph newSection newTable
normalize.invariantset normalize.qspline openPage opts platformSigs
plotIdeogram qplot rsn scale_fill_discrete scale_fill_gradient
stat_binhex theme theme_blank theme_bw tracks value value.1 vsn2
writeReport xlab ylab
* 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 ... [330s/331s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 52.983 0.056 53.121
summarize 33.135 0.203 33.394
limmaDE 23.793 0.024 23.818
calculateDetection 20.358 0.016 20.397
calculateOutlierStats 19.428 0.384 20.046
controlProbeDetection 15.555 0.020 15.599
outlierplot 13.277 0.192 13.486
identifyControlBeads 13.140 0.036 13.191
normaliseIllumina 12.201 0.261 12.495
insertSectionData 12.158 0.068 12.258
poscontPlot 11.744 0.084 11.828
maplots 11.481 0.088 11.591
makeQCTable 10.536 0.260 10.799
quickSummary 8.082 0.072 8.154
annotationInterface 7.055 0.156 7.229
addFeatureData 7.012 0.071 7.093
imageplot 6.407 0.060 6.480
combine 5.209 0.091 5.375
showArrayMask 5.038 0.148 5.192
* 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-3.3-bioc/meat/beadarray.Rcheck/00check.log’
for details.
* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c findAllOutliers.c -o findAllOutliers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c imageProcessing.c -o imageProcessing.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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)