beadarray 2.20.1
Mark Dunning
| 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/beadarray | | Last Changed Rev: 112515 / Revision: 116712 | | Last Changed Date: 2016-01-13 08:34:26 -0800 (Wed, 13 Jan 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings beadarray_2.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/beadarray.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 ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.20.1’
* 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 : .local: no visible global function
definition for ‘ggplot’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘aes’
boxplot,ExpressionSetIllumina : .local: no visible binding for global
variable ‘Var2’
boxplot,ExpressionSetIllumina : .local: no visible binding for global
variable ‘value’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘geom_boxplot’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘scale_fill_discrete’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘facet_wrap’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘theme’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘element_blank’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘element_text’
boxplot,ExpressionSetIllumina : .local: no visible global function
definition for ‘ylab’
plot,limmaResults-ANY : .local: no visible global function definition
for ‘ggplot’
plot,limmaResults-ANY : .local: no visible global function definition
for ‘aes’
plot,limmaResults-ANY : .local: no visible global function definition
for ‘geom_point’
plot,limmaResults-ANY : .local: no visible global function definition
for ‘facet_wrap’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘ggplot’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘aes’
plotMA,ExpressionSetIllumina : .local: no visible binding for global
variable ‘value.1’
plotMA,ExpressionSetIllumina : .local: no visible binding for global
variable ‘value’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘stat_binhex’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘theme_bw’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘xlab’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘ylab’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘facet_wrap’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘theme’
plotMA,ExpressionSetIllumina : .local: no visible global function
definition for ‘ggtitle’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [331s/337s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 54.988 0.032 55.223
summarize 34.129 0.124 34.345
limmaDE 23.106 0.012 23.185
calculateOutlierStats 20.112 0.280 20.463
outlierplot 15.107 0.112 15.263
calculateDetection 14.961 0.008 14.999
controlProbeDetection 13.849 0.044 15.568
insertSectionData 12.356 0.128 12.529
identifyControlBeads 12.470 0.008 13.503
makeQCTable 12.168 0.179 12.363
maplots 11.857 0.032 11.921
normaliseIllumina 11.283 0.092 11.392
poscontPlot 10.879 0.072 10.963
quickSummary 8.005 0.048 8.047
imageplot 7.293 0.072 8.167
showArrayMask 6.959 0.076 7.031
annotationInterface 6.930 0.083 7.031
addFeatureData 6.843 0.057 6.989
combine 5.565 0.063 6.346
* 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-3.2-bioc/meat/beadarray.Rcheck/00check.log’
for details.
* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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 -std=gnu99 -I/home/biocbuild/bbs-3.2-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 -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)