############################################################################## ############################################################################## ### ### 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_2.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/beadarray.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘beadarray/DESCRIPTION’ ... OK * this is package ‘beadarray’ version ‘2.56.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: 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 ... 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 27.054 0.155 27.208 summarize 6.406 0.520 6.927 * 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-3.20-bioc/meat/beadarray.Rcheck/00check.log’ for details.