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CHECK report for beadarray on celaya2

This page was generated on 2019-04-09 12:51:25 -0400 (Tue, 09 Apr 2019).

Package 118/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.33.2
Mark Dunning
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/beadarray
Branch: master
Last Commit: ad3d461
Last Changed Date: 2019-01-28 07:09:18 -0400 (Mon, 28 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: beadarray
Version: 2.33.2
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_2.33.2.tar.gz
StartedAt: 2019-04-09 00:05:41 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:16:02 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 620.9 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

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### Running 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_2.33.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/beadarray.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.33.2’
* 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 or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 57.834  1.553  60.396
summarize                35.152  6.028  41.591
limmaDE                  35.567  0.626  37.268
normaliseIllumina        18.704  1.976  20.686
outlierplot              18.808  1.680  20.741
calculateOutlierStats    15.258  2.609  17.875
calculateDetection       15.029  2.061  17.090
controlProbeDetection    12.269  1.266  13.537
makeQCTable              10.472  2.240  13.347
identifyControlBeads     12.034  0.637  12.679
poscontPlot              11.098  0.999  12.405
insertSectionData        10.189  1.671  12.095
imageplot                 9.073  1.073  10.621
showArrayMask             7.661  1.517   9.245
maplots                   6.245  2.914   9.240
addFeatureData            8.418  0.661   9.163
quickSummary              7.260  1.027   8.376
annotationInterface       7.026  0.909   7.936
transformationFunctions   4.301  1.027   5.328
insertBeadData            4.526  0.669   5.262
boxplot                   4.711  0.477   5.188
illuminaOutlierMethod     4.151  0.900   5.172
plotBeadIntensities       4.240  0.784   5.029
* 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-3.9-bioc/meat/beadarray.Rcheck/00check.log’
for details.



Installation output

beadarray.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL beadarray
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘beadarray’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c BASH.c -o BASH.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c HULK.c -o HULK.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c findAllOutliers.c -o findAllOutliers.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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/3.6/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)

Tests output


Example timings

beadarray.Rcheck/beadarray-Ex.timings

nameusersystemelapsed
BASH0.0000.0010.001
BASHCompact000
BASHDiffuse0.0000.0000.001
BASHExtended0.0000.0010.001
GEO000
GEOtemplate0.0030.0020.004
HULK000
addFeatureData8.4180.6619.163
annotationInterface7.0260.9097.936
backgroundCorrectSingleSection0.0010.0010.001
beadarrayUsersGuide0.0020.0010.002
boxplot4.7110.4775.188
calculateDetection15.029 2.06117.090
calculateOutlierStats15.258 2.60917.875
class-beadLevelData3.3680.7144.082
class-illuminaChannel0.0030.0010.003
combine3.8590.8724.731
controlProbeDetection12.269 1.26613.537
createTargetsFile000
expressionQCPipeline0.0370.0020.038
generateNeighbours0.0010.0010.000
getBeadData3.3140.6073.921
identifyControlBeads12.034 0.63712.679
illuminaOutlierMethod4.1510.9005.172
imageplot 9.073 1.07310.621
insertBeadData4.5260.6695.262
insertSectionData10.189 1.67112.095
limmaDE35.567 0.62637.268
makeControlProfile0.5580.0110.653
makeQCTable10.472 2.24013.347
maplots6.2452.9149.240
medianNormalise1.8900.2332.123
metrics2.3700.3822.752
noOutlierMethod2.4510.3002.750
normaliseIllumina18.704 1.97620.686
numBeads2.7450.3713.116
outlierplot18.808 1.68020.741
plotBeadIntensities4.2400.7845.029
plotBeadLocations3.9770.6124.589
plotChipLayout0.0000.0000.001
plotMAXY0.0000.0010.001
poscontPlot11.098 0.99912.405
quickSummary7.2601.0278.376
readBeadSummaryData0.0010.0000.001
sectionNames2.5280.3622.902
showArrayMask7.6611.5179.245
squeezedVarOutlierMethod57.834 1.55360.396
summarize35.152 6.02841.591
transformationFunctions4.3011.0275.328
weightsOutlierMethod000