Mark Dunning
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/beadarray |
| Branch: master |
| Last Commit: 1ec2778 |
| Last Changed Date: 2019-10-29 13:34:41 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:30:04 -0500 (Thu, 16 Jan 2020).
| Package 127/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| beadarray 2.37.0 Mark Dunning
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: beadarray |
| Version: 2.37.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:beadarray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings beadarray_2.37.0.tar.gz |
| StartedAt: 2020-01-16 02:02:03 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:14:01 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 718.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beadarray.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:beadarray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings beadarray_2.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/beadarray.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.37.0’
* 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
Package in Depends field not imported from: ‘hexbin’
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.
* 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 binding for global variable ‘ID’
combinedControlPlot: no visible binding for global variable
‘Log2Intensity’
combinedControlPlot: no visible binding for global variable
‘ControlType’
combinedControlPlot: no visible binding for global variable ‘Masked’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
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 binding for global variable ‘Var1’
imageplot: no visible binding for global variable ‘Var2’
imageplot: no visible binding for global variable ‘value’
makeReport: no visible binding for global variable ‘Nozzle.R1’
makeReport: no visible binding for global variable ‘ggbio’
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 ‘newFigure’
makeReport: no visible binding for global variable ‘IMAGE.TYPE.RASTER’
makeReport: no visible binding for global variable ‘PROTECTION.PUBLIC’
makeReport: no visible binding for global variable ‘value’
makeReport: no visible global function definition for ‘writeReport’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
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’
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 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 binding for global variable
‘Var2’
boxplot,ExpressionSetIllumina: no visible binding for global variable
‘value’
plotMA,ExpressionSetIllumina: no visible binding for global variable
‘value.1’
plotMA,ExpressionSetIllumina: no visible binding for global variable
‘value’
Undefined global functions or variables:
Control ControlType ID IMAGE.TYPE.RASTER Log2Intensity Masked
Negative Nozzle.R1 PROBEQUALITY PROTECTION.PUBLIC Var1 Var2 addTo
assayDataEnvLock autoplot closePage dbGetQuery dbListFields
dbListTables genesymbol ggbio hwrite hwriteImage
lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn
lumiRatIDMapping_dbconn lumiT metaTemplate newCustomReport newFigure
newParagraph newSection newTable normalize.invariantset
normalize.qspline openPage opts platformSigs plotIdeogram qplot
theme_blank tracks value value.1 vsn2 writeReport
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 59.134 1.289 61.122
summarize 38.701 5.760 45.066
limmaDE 38.604 1.076 45.235
normaliseIllumina 21.777 2.520 24.524
outlierplot 21.157 1.961 23.365
calculateDetection 18.478 2.273 20.760
calculateOutlierStats 17.955 2.649 20.623
controlProbeDetection 13.416 1.567 15.006
identifyControlBeads 13.450 0.835 14.388
insertSectionData 11.848 2.078 14.087
makeQCTable 11.764 2.085 14.879
poscontPlot 11.711 1.657 13.392
quickSummary 9.926 1.397 11.328
addFeatureData 10.180 0.743 11.702
showArrayMask 8.806 1.936 10.887
imageplot 9.120 1.314 10.589
annotationInterface 8.995 1.136 10.181
maplots 6.966 2.673 10.203
combine 5.350 1.001 6.354
transformationFunctions 4.889 1.228 6.433
boxplot 5.440 0.588 6.096
plotBeadIntensities 4.663 0.806 5.495
insertBeadData 4.577 0.839 5.420
* 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-3.11-bioc/meat/beadarray.Rcheck/00check.log’
for details.
beadarray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL beadarray ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘beadarray’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASH.c -o BASH.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c HULK.c -o HULK.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findAllOutliers.c -o findAllOutliers.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c imageProcessing.c -o imageProcessing.o clang -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 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-beadarray/00new/beadarray/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (beadarray)
beadarray.Rcheck/beadarray-Ex.timings
| name | user | system | elapsed | |
| BASH | 0.001 | 0.001 | 0.002 | |
| BASHCompact | 0.001 | 0.001 | 0.001 | |
| BASHDiffuse | 0.000 | 0.001 | 0.001 | |
| BASHExtended | 0.001 | 0.001 | 0.000 | |
| GEO | 0.001 | 0.000 | 0.001 | |
| GEOtemplate | 0.004 | 0.002 | 0.006 | |
| HULK | 0.001 | 0.001 | 0.001 | |
| addFeatureData | 10.180 | 0.743 | 11.702 | |
| annotationInterface | 8.995 | 1.136 | 10.181 | |
| backgroundCorrectSingleSection | 0.000 | 0.001 | 0.001 | |
| beadarrayUsersGuide | 0.003 | 0.000 | 0.004 | |
| boxplot | 5.440 | 0.588 | 6.096 | |
| calculateDetection | 18.478 | 2.273 | 20.760 | |
| calculateOutlierStats | 17.955 | 2.649 | 20.623 | |
| class-beadLevelData | 3.485 | 0.682 | 4.169 | |
| class-illuminaChannel | 0.005 | 0.001 | 0.006 | |
| combine | 5.350 | 1.001 | 6.354 | |
| controlProbeDetection | 13.416 | 1.567 | 15.006 | |
| createTargetsFile | 0.000 | 0.000 | 0.001 | |
| expressionQCPipeline | 0.048 | 0.002 | 0.049 | |
| generateNeighbours | 0.000 | 0.000 | 0.001 | |
| getBeadData | 3.684 | 0.602 | 4.291 | |
| identifyControlBeads | 13.450 | 0.835 | 14.388 | |
| illuminaOutlierMethod | 4.14 | 0.86 | 5.00 | |
| imageplot | 9.120 | 1.314 | 10.589 | |
| insertBeadData | 4.577 | 0.839 | 5.420 | |
| insertSectionData | 11.848 | 2.078 | 14.087 | |
| limmaDE | 38.604 | 1.076 | 45.235 | |
| makeControlProfile | 0.791 | 0.072 | 1.018 | |
| makeQCTable | 11.764 | 2.085 | 14.879 | |
| maplots | 6.966 | 2.673 | 10.203 | |
| medianNormalise | 2.208 | 0.315 | 2.746 | |
| metrics | 2.911 | 0.475 | 3.556 | |
| noOutlierMethod | 2.814 | 0.342 | 3.210 | |
| normaliseIllumina | 21.777 | 2.520 | 24.524 | |
| numBeads | 2.770 | 0.412 | 3.183 | |
| outlierplot | 21.157 | 1.961 | 23.365 | |
| plotBeadIntensities | 4.663 | 0.806 | 5.495 | |
| plotBeadLocations | 2.998 | 0.675 | 3.686 | |
| plotChipLayout | 0.000 | 0.000 | 0.001 | |
| plotMAXY | 0 | 0 | 0 | |
| poscontPlot | 11.711 | 1.657 | 13.392 | |
| quickSummary | 9.926 | 1.397 | 11.328 | |
| readBeadSummaryData | 0.001 | 0.001 | 0.001 | |
| sectionNames | 2.811 | 0.364 | 3.178 | |
| showArrayMask | 8.806 | 1.936 | 10.887 | |
| squeezedVarOutlierMethod | 59.134 | 1.289 | 61.122 | |
| summarize | 38.701 | 5.760 | 45.066 | |
| transformationFunctions | 4.889 | 1.228 | 6.433 | |
| weightsOutlierMethod | 0.000 | 0.000 | 0.001 | |