############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.36.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DAPAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DAPAR’ version ‘1.36.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Vignette dependency required without any vignettes:: ‘knitr’ * 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 ‘DAPAR’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Check_Dataset_Validity: no visible global function definition for ‘exprs’ OWAnova: no visible global function definition for ‘aov’ aggregateIterParallel: no visible binding for global variable ‘cond’ averageIntensities: no visible binding for global variable ‘condition’ averageIntensities: no visible binding for global variable ‘feature’ averageIntensities: no visible binding for global variable ‘intensity’ createMSnset: no visible global function definition for ‘installed.packages’ createMSnset: no visible binding for global variable ‘Prostar.loc’ createMSnset2: no visible global function definition for ‘installed.packages’ createMSnset2: no visible binding for global variable ‘Prostar.loc’ diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘x’ diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘y’ diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘g’ display.CC.visNet: no visible binding for global variable ‘layout_nicely’ getTextForGOAnalysis: no visible binding for global variable ‘textGOParams’ getTextForGOAnalysis: no visible binding for global variable ‘input’ globalAdjPval: no visible global function definition for ‘stack’ heatmapForMissingValues: no visible binding for global variable ‘par’ limmaCompleteTest: no visible binding for global variable ‘A’ limmaCompleteTest: no visible binding for global variable ‘B’ limmaCompleteTest: no visible binding for global variable ‘P.Value’ pepa.test: no visible global function definition for ‘nodes<-’ testAnovaModels : : no visible global function definition for ‘TukeyHSD’ visualizeClusters: no visible binding for global variable ‘adjusted_pvalues’ visualizeClusters: no visible binding for global variable ‘Condition’ visualizeClusters: no visible binding for global variable ‘Intensity’ visualizeClusters: no visible binding for global variable ‘FDR_threshold’ visualizeClusters: no visible binding for global variable ‘feature’ wrapperClassic1wayAnova: no visible binding for global variable ‘Pr(>F)1’ wrapperRunClustering: no visible global function definition for ‘str_c’ Undefined global functions or variables: A B Condition FDR_threshold Intensity P.Value Pr(>F)1 Prostar.loc TukeyHSD adjusted_pvalues aov cond condition exprs feature g input installed.packages intensity layout_nicely nodes<- par stack str_c textGOParams x y Consider adding importFrom("graphics", "par") importFrom("stats", "TukeyHSD", "aov") importFrom("utils", "installed.packages", "stack") to your NAMESPACE file. * checking Rd files ... OK * 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 examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed wrapper.compareNormalizationD_HC 114.906 47.898 181.051 wrapper.dapar.impute.mi 34.097 2.096 46.534 barplotEnrichGO_HC 15.890 3.059 23.469 barplotGroupGO_HC 10.925 1.269 14.956 checkClusterability 7.162 3.699 11.909 enrich_GO 9.466 1.175 13.351 group_GO 9.441 1.167 13.386 scatterplotEnrichGO_HC 9.432 1.126 12.868 densityPlotD_HC 6.363 2.608 10.407 CVDistD_HC 6.536 0.608 8.308 wrapper.CVDistD_HC 4.698 1.913 7.648 mvImage 5.641 0.326 7.271 wrapperRunClustering 4.830 0.699 7.302 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck/00check.log’ for details.