Mark Dunning
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/beadarray |
| git_branch: RELEASE_3_18 |
| git_last_commit: 3a4da33 |
| git_last_commit_date: 2023-10-24 09:36:14 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:06 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 146/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| beadarray 2.52.0 (landing page) Mark Dunning
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the beadarray package: - 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: 2.52.0 |
| 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_2.52.0.tar.gz |
| StartedAt: 2024-04-17 06:36:21 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 06:45:06 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 524.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: beadarray.Rcheck |
| Warnings: 0 |
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### 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_2.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/beadarray.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.52.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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) 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 ... 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 86.855 0.938 90.110
summarize 23.470 2.398 26.578
normaliseIllumina 14.436 0.876 15.569
outlierplot 13.298 1.222 15.164
calculateDetection 12.791 0.791 13.913
calculateOutlierStats 12.004 1.546 13.946
limmaDE 11.651 0.319 12.204
poscontPlot 10.438 0.374 10.993
controlProbeDetection 10.253 0.451 10.838
makeQCTable 8.724 0.620 9.573
annotationInterface 8.302 0.313 9.118
identifyControlBeads 8.131 0.404 8.937
showArrayMask 7.688 0.567 9.056
insertSectionData 7.140 0.726 9.275
addFeatureData 7.649 0.211 8.148
quickSummary 7.140 0.455 7.803
imageplot 6.865 0.672 7.747
maplots 5.286 0.479 5.877
plotBeadIntensities 4.618 0.503 5.685
transformationFunctions 4.854 0.263 5.213
combine 4.742 0.298 5.157
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/Resources/library’ * installing *source* package ‘beadarray’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BASH.c -o BASH.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HULK.c -o HULK.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c determiningGridPositions.c -o determiningGridPositions.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findAllOutliers.c -o findAllOutliers.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imageProcessing.c -o imageProcessing.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 | 0.001 | 0.001 | |
| BASHCompact | 0.001 | 0.000 | 0.000 | |
| BASHDiffuse | 0 | 0 | 0 | |
| BASHExtended | 0 | 0 | 0 | |
| GEO | 0.000 | 0.001 | 0.001 | |
| GEOtemplate | 0.003 | 0.002 | 0.005 | |
| HULK | 0.000 | 0.001 | 0.000 | |
| addFeatureData | 7.649 | 0.211 | 8.148 | |
| annotationInterface | 8.302 | 0.313 | 9.118 | |
| backgroundCorrectSingleSection | 0 | 0 | 0 | |
| beadarrayUsersGuide | 0.002 | 0.000 | 0.003 | |
| boxplot | 4.306 | 0.213 | 4.623 | |
| calculateDetection | 12.791 | 0.791 | 13.913 | |
| calculateOutlierStats | 12.004 | 1.546 | 13.946 | |
| class-beadLevelData | 3.718 | 0.241 | 4.090 | |
| class-illuminaChannel | 0.003 | 0.000 | 0.003 | |
| combine | 4.742 | 0.298 | 5.157 | |
| controlProbeDetection | 10.253 | 0.451 | 10.838 | |
| createTargetsFile | 0 | 0 | 0 | |
| expressionQCPipeline | 0.031 | 0.002 | 0.033 | |
| generateNeighbours | 0 | 0 | 0 | |
| getBeadData | 3.774 | 0.207 | 4.027 | |
| identifyControlBeads | 8.131 | 0.404 | 8.937 | |
| illuminaOutlierMethod | 3.824 | 0.394 | 4.304 | |
| imageplot | 6.865 | 0.672 | 7.747 | |
| insertBeadData | 4.133 | 0.335 | 4.545 | |
| insertSectionData | 7.140 | 0.726 | 9.275 | |
| limmaDE | 11.651 | 0.319 | 12.204 | |
| makeControlProfile | 0.380 | 0.011 | 0.406 | |
| makeQCTable | 8.724 | 0.620 | 9.573 | |
| maplots | 5.286 | 0.479 | 5.877 | |
| medianNormalise | 2.402 | 0.056 | 2.501 | |
| metrics | 2.676 | 0.068 | 2.781 | |
| noOutlierMethod | 2.791 | 0.084 | 2.931 | |
| normaliseIllumina | 14.436 | 0.876 | 15.569 | |
| numBeads | 2.985 | 0.160 | 3.198 | |
| outlierplot | 13.298 | 1.222 | 15.164 | |
| plotBeadIntensities | 4.618 | 0.503 | 5.685 | |
| plotBeadLocations | 3.109 | 0.209 | 3.606 | |
| plotChipLayout | 0.000 | 0.001 | 0.001 | |
| plotMAXY | 0.000 | 0.001 | 0.000 | |
| poscontPlot | 10.438 | 0.374 | 10.993 | |
| quickSummary | 7.140 | 0.455 | 7.803 | |
| readBeadSummaryData | 0.000 | 0.000 | 0.001 | |
| sectionNames | 3.011 | 0.086 | 3.174 | |
| showArrayMask | 7.688 | 0.567 | 9.056 | |
| squeezedVarOutlierMethod | 86.855 | 0.938 | 90.110 | |
| summarize | 23.470 | 2.398 | 26.578 | |
| transformationFunctions | 4.854 | 0.263 | 5.213 | |
| weightsOutlierMethod | 0.000 | 0.001 | 0.001 | |