Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:00 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the beadarray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beadarray.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 134/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
beadarray 2.48.0 (landing page) Mark Dunning
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: beadarray |
Version: 2.48.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:beadarray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings beadarray_2.48.0.tar.gz |
StartedAt: 2023-04-10 18:56:52 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:02:53 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 361.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: beadarray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:beadarray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings beadarray_2.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/beadarray.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘beadarray/DESCRIPTION’ ... OK * this is package ‘beadarray’ version ‘2.48.0’ * 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 ‘Negative’ 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: IMAGE.TYPE.RASTER 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 LazyData ... 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 43.813 0.432 44.432 summarize 18.749 1.526 20.419 limmaDE 13.013 0.293 13.364 calculateOutlierStats 10.670 0.597 11.304 normaliseIllumina 9.671 0.684 10.396 calculateDetection 9.540 0.578 10.168 outlierplot 9.282 0.362 9.715 controlProbeDetection 7.143 0.325 7.491 identifyControlBeads 6.703 0.131 6.856 insertSectionData 6.484 0.269 6.773 addFeatureData 6.486 0.228 7.153 makeQCTable 6.300 0.337 6.705 annotationInterface 6.312 0.294 6.652 poscontPlot 6.010 0.260 6.312 * 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-3.16-bioc/meat/beadarray.Rcheck/00check.log’ for details.
beadarray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL beadarray ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘beadarray’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c BASH.c -o BASH.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c HULK.c -o HULK.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c findAllOutliers.c -o findAllOutliers.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c imageProcessing.c -o imageProcessing.o clang -mmacosx-version-min=10.13 -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/4.2/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 | 0.000 | 0.002 | 0.002 | |
BASHCompact | 0.000 | 0.001 | 0.001 | |
BASHDiffuse | 0.000 | 0.001 | 0.001 | |
BASHExtended | 0 | 0 | 0 | |
GEO | 0.000 | 0.000 | 0.001 | |
GEOtemplate | 0.002 | 0.001 | 0.003 | |
HULK | 0.000 | 0.000 | 0.001 | |
addFeatureData | 6.486 | 0.228 | 7.153 | |
annotationInterface | 6.312 | 0.294 | 6.652 | |
backgroundCorrectSingleSection | 0.000 | 0.001 | 0.000 | |
beadarrayUsersGuide | 0.002 | 0.000 | 0.003 | |
boxplot | 3.018 | 0.175 | 3.207 | |
calculateDetection | 9.540 | 0.578 | 10.168 | |
calculateOutlierStats | 10.670 | 0.597 | 11.304 | |
class-beadLevelData | 2.381 | 0.128 | 2.524 | |
class-illuminaChannel | 0.003 | 0.000 | 0.003 | |
combine | 3.668 | 0.155 | 3.839 | |
controlProbeDetection | 7.143 | 0.325 | 7.491 | |
createTargetsFile | 0 | 0 | 0 | |
expressionQCPipeline | 0.028 | 0.001 | 0.029 | |
generateNeighbours | 0.000 | 0.000 | 0.001 | |
getBeadData | 1.906 | 0.081 | 1.999 | |
identifyControlBeads | 6.703 | 0.131 | 6.856 | |
illuminaOutlierMethod | 2.324 | 0.170 | 2.507 | |
imageplot | 4.576 | 0.287 | 4.923 | |
insertBeadData | 2.509 | 0.104 | 2.622 | |
insertSectionData | 6.484 | 0.269 | 6.773 | |
limmaDE | 13.013 | 0.293 | 13.364 | |
makeControlProfile | 0.324 | 0.010 | 0.338 | |
makeQCTable | 6.300 | 0.337 | 6.705 | |
maplots | 3.860 | 0.589 | 4.465 | |
medianNormalise | 1.440 | 0.044 | 1.493 | |
metrics | 2.225 | 0.220 | 2.458 | |
noOutlierMethod | 1.702 | 0.026 | 1.738 | |
normaliseIllumina | 9.671 | 0.684 | 10.396 | |
numBeads | 1.745 | 0.029 | 1.800 | |
outlierplot | 9.282 | 0.362 | 9.715 | |
plotBeadIntensities | 3.087 | 0.142 | 3.248 | |
plotBeadLocations | 2.843 | 0.116 | 2.979 | |
plotChipLayout | 0.001 | 0.000 | 0.000 | |
plotMAXY | 0.000 | 0.001 | 0.000 | |
poscontPlot | 6.010 | 0.260 | 6.312 | |
quickSummary | 4.657 | 0.150 | 4.822 | |
readBeadSummaryData | 0 | 0 | 0 | |
sectionNames | 1.599 | 0.064 | 1.670 | |
showArrayMask | 4.660 | 0.288 | 4.962 | |
squeezedVarOutlierMethod | 43.813 | 0.432 | 44.432 | |
summarize | 18.749 | 1.526 | 20.419 | |
transformationFunctions | 2.098 | 0.148 | 2.258 | |
weightsOutlierMethod | 0.000 | 0.000 | 0.001 | |