Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 148/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
beadarray 2.54.0 (landing page) Mark Dunning
| kjohnson3 | macOS 13.6.5 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: 2.54.0 |
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_2.54.0.tar.gz |
StartedAt: 2024-05-06 19:50:21 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 19:53:04 -0400 (Mon, 06 May 2024) |
EllapsedTime: 162.8 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_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/beadarray.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘beadarray/DESCRIPTION’ ... OK * this is package ‘beadarray’ version ‘2.54.0’ * 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-1500.1.0.2.5)’ * 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: addTo assayDataEnvLock autoplot closePage dbGetQuery dbListFields dbListTables genesymbol ggbio hwrite hwriteImage IMAGE.TYPE.RASTER lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT metaTemplate Negative newCustomReport newFigure newParagraph newSection newTable normalize.invariantset normalize.qspline Nozzle.R1 openPage opts platformSigs plotIdeogram PROBEQUALITY PROTECTION.PUBLIC qplot theme_blank tracks value value.1 Var1 Var2 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 ... 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 28.951 0.123 29.078 summarize 6.805 0.582 7.416 outlierplot 5.015 0.231 5.304 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/Resources/library’ * installing *source* package ‘beadarray’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/4.4-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 | 0 | 0 | |
BASHCompact | 0 | 0 | 0 | |
BASHDiffuse | 0 | 0 | 0 | |
BASHExtended | 0.000 | 0.001 | 0.000 | |
GEO | 0 | 0 | 0 | |
GEOtemplate | 0.001 | 0.000 | 0.001 | |
HULK | 0 | 0 | 0 | |
addFeatureData | 2.935 | 0.055 | 3.001 | |
annotationInterface | 2.817 | 0.071 | 2.888 | |
backgroundCorrectSingleSection | 0 | 0 | 0 | |
beadarrayUsersGuide | 0.001 | 0.001 | 0.001 | |
boxplot | 1.340 | 0.050 | 1.391 | |
calculateDetection | 4.199 | 0.306 | 4.509 | |
calculateOutlierStats | 4.430 | 0.238 | 4.668 | |
class-beadLevelData | 1.165 | 0.053 | 1.218 | |
class-illuminaChannel | 0.001 | 0.000 | 0.001 | |
combine | 1.646 | 0.090 | 1.737 | |
controlProbeDetection | 3.045 | 0.125 | 3.171 | |
createTargetsFile | 0 | 0 | 0 | |
expressionQCPipeline | 0.006 | 0.001 | 0.007 | |
generateNeighbours | 0 | 0 | 0 | |
getBeadData | 0.955 | 0.050 | 1.006 | |
identifyControlBeads | 3.002 | 0.081 | 3.086 | |
illuminaOutlierMethod | 1.036 | 0.092 | 1.129 | |
imageplot | 2.108 | 0.156 | 2.297 | |
insertBeadData | 0.958 | 0.101 | 1.062 | |
insertSectionData | 2.755 | 0.211 | 2.967 | |
limmaDE | 4.064 | 0.109 | 4.174 | |
makeControlProfile | 0.327 | 0.033 | 0.360 | |
makeQCTable | 2.623 | 0.170 | 2.793 | |
maplots | 1.874 | 0.146 | 2.021 | |
medianNormalise | 0.782 | 0.031 | 0.814 | |
metrics | 0.892 | 0.024 | 0.916 | |
noOutlierMethod | 0.899 | 0.024 | 0.923 | |
normaliseIllumina | 4.359 | 0.240 | 4.610 | |
numBeads | 0.910 | 0.027 | 1.098 | |
outlierplot | 5.015 | 0.231 | 5.304 | |
plotBeadIntensities | 1.536 | 0.064 | 1.603 | |
plotBeadLocations | 1.414 | 0.051 | 1.465 | |
plotChipLayout | 0 | 0 | 0 | |
plotMAXY | 0 | 0 | 0 | |
poscontPlot | 2.839 | 0.103 | 2.946 | |
quickSummary | 2.276 | 0.112 | 2.388 | |
readBeadSummaryData | 0 | 0 | 0 | |
sectionNames | 0.908 | 0.019 | 0.927 | |
showArrayMask | 2.403 | 0.168 | 2.578 | |
squeezedVarOutlierMethod | 28.951 | 0.123 | 29.078 | |
summarize | 6.805 | 0.582 | 7.416 | |
transformationFunctions | 1.533 | 0.113 | 1.646 | |
weightsOutlierMethod | 0 | 0 | 0 | |