############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings beadarray_2.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/beadarray.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed squeezedVarOutlierMethod 51.297 0.120 51.417 summarize 22.402 0.836 23.238 limmaDE 13.403 0.099 13.503 normaliseIllumina 12.555 0.204 12.759 calculateOutlierStats 11.528 0.692 12.219 controlProbeDetection 11.292 0.167 11.460 outlierplot 10.447 0.376 10.823 identifyControlBeads 10.705 0.064 10.769 insertSectionData 9.258 0.249 9.505 calculateDetection 9.171 0.178 9.349 poscontPlot 8.882 0.087 8.971 makeQCTable 8.741 0.224 8.965 annotationInterface 6.179 0.513 6.692 quickSummary 6.518 0.055 6.574 imageplot 6.422 0.119 6.542 addFeatureData 5.361 0.263 5.629 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ImageProcessing.rnw’... OK ‘beadarray.rnw’... OK ‘beadlevel.rnw’... OK ‘beadsummary.rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/beadarray.Rcheck/00check.log’ for details.