Mark Dunning
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/beadarray |
| git_branch: devel |
| git_last_commit: a89dbc2 |
| git_last_commit_date: 2025-04-15 09:37:46 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 | ||||
| Package 156/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beadarray 2.59.0 (landing page) Mark Dunning
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the beadarray package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: beadarray |
| Version: 2.59.0 |
| 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_2.59.0.tar.gz |
| StartedAt: 2025-08-29 19:18:28 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 19:25:21 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 412.4 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_2.59.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.59.0’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) createTargetsFile.Rd:49: Lost braces
49 | code{metricsflag}: This gives the key word that can be used to identify metrics files.
| ^
checkRd: (-1) readBeadSummaryData.Rd:70: Escaped LaTeX specials: \_
checkRd: (-1) readBeadSummaryData.Rd:71: Escaped LaTeX specials: \_ \_
checkRd: (-1) readBeadSummaryData.Rd:76: Escaped LaTeX specials: \_ \_
checkRd: (-1) sampleSheet.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'class-ExpressionSetIllumina.Rd':
‘[Biobase:class.eSet]{eSet}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
squeezedVarOutlierMethod 43.187 0.573 44.149
summarize 21.956 1.560 23.813
limmaDE 16.674 0.317 17.091
normaliseIllumina 14.375 0.899 15.375
calculateOutlierStats 10.428 0.744 11.239
calculateDetection 10.308 0.484 10.854
outlierplot 10.281 0.413 10.842
controlProbeDetection 7.551 0.305 7.912
insertSectionData 6.958 0.316 7.313
identifyControlBeads 6.950 0.175 7.160
makeQCTable 6.518 0.302 6.875
annotationInterface 5.794 0.327 6.169
addFeatureData 5.872 0.246 6.194
poscontPlot 5.734 0.276 6.060
showArrayMask 5.489 0.367 5.908
quickSummary 5.455 0.246 5.760
imageplot 4.962 0.346 5.388
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 7 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘beadarray’ ... ** this is package ‘beadarray’ version ‘2.59.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BASH.c -o BASH.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HULK.c -o HULK.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findAllOutliers.c -o findAllOutliers.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imageProcessing.c -o imageProcessing.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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 | 0.001 | |
| BASHCompact | 0 | 0 | 0 | |
| BASHDiffuse | 0 | 0 | 0 | |
| BASHExtended | 0.001 | 0.001 | 0.001 | |
| GEO | 0.000 | 0.001 | 0.000 | |
| GEOtemplate | 0.002 | 0.002 | 0.003 | |
| HULK | 0.000 | 0.001 | 0.000 | |
| addFeatureData | 5.872 | 0.246 | 6.194 | |
| annotationInterface | 5.794 | 0.327 | 6.169 | |
| backgroundCorrectSingleSection | 0.000 | 0.001 | 0.001 | |
| beadarrayUsersGuide | 0.002 | 0.001 | 0.003 | |
| boxplot | 3.124 | 0.240 | 3.412 | |
| calculateDetection | 10.308 | 0.484 | 10.854 | |
| calculateOutlierStats | 10.428 | 0.744 | 11.239 | |
| class-beadLevelData | 2.036 | 0.134 | 2.182 | |
| class-illuminaChannel | 0.003 | 0.000 | 0.003 | |
| combine | 2.334 | 0.160 | 2.505 | |
| controlProbeDetection | 7.551 | 0.305 | 7.912 | |
| createTargetsFile | 0.000 | 0.000 | 0.001 | |
| expressionQCPipeline | 0.029 | 0.002 | 0.031 | |
| generateNeighbours | 0 | 0 | 0 | |
| getBeadData | 1.637 | 0.082 | 1.732 | |
| identifyControlBeads | 6.950 | 0.175 | 7.160 | |
| illuminaOutlierMethod | 2.072 | 0.187 | 2.280 | |
| imageplot | 4.962 | 0.346 | 5.388 | |
| insertBeadData | 2.314 | 0.112 | 2.455 | |
| insertSectionData | 6.958 | 0.316 | 7.313 | |
| limmaDE | 16.674 | 0.317 | 17.091 | |
| makeControlProfile | 0.415 | 0.015 | 0.434 | |
| makeQCTable | 6.518 | 0.302 | 6.875 | |
| maplots | 4.391 | 0.536 | 4.968 | |
| medianNormalise | 1.225 | 0.132 | 1.373 | |
| metrics | 1.465 | 0.034 | 1.518 | |
| noOutlierMethod | 1.372 | 0.026 | 1.411 | |
| normaliseIllumina | 14.375 | 0.899 | 15.375 | |
| numBeads | 1.500 | 0.033 | 1.549 | |
| outlierplot | 10.281 | 0.413 | 10.842 | |
| plotBeadIntensities | 2.869 | 0.183 | 3.074 | |
| plotBeadLocations | 1.684 | 0.152 | 1.859 | |
| plotChipLayout | 0.000 | 0.000 | 0.001 | |
| plotMAXY | 0 | 0 | 0 | |
| poscontPlot | 5.734 | 0.276 | 6.060 | |
| quickSummary | 5.455 | 0.246 | 5.760 | |
| readBeadSummaryData | 0.000 | 0.001 | 0.001 | |
| sectionNames | 1.454 | 0.052 | 1.538 | |
| showArrayMask | 5.489 | 0.367 | 5.908 | |
| squeezedVarOutlierMethod | 43.187 | 0.573 | 44.149 | |
| summarize | 21.956 | 1.560 | 23.813 | |
| transformationFunctions | 3.187 | 0.201 | 3.422 | |
| weightsOutlierMethod | 0.000 | 0.000 | 0.001 | |