############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pRoloc_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/pRoloc.Rcheck’ * using R version 4.5.2 (2025-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pRoloc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pRoloc’ version ‘1.50.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 28 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘pRoloc’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.1.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 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 ':::' calls which should be '::': ‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’ ‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘MSnbase:::.sameNbCol’ ‘MSnbase:::getVariableName’ ‘MSnbase:::logging’ ‘MSnbase:::nologging’ ‘caret:::predict.plsda’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getAttributesOfInterest0’ ‘getAttributesOfInterestX’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... WARNING checkRd: (7) plsdaOptimisation.Rd:66-81: Tag \donttest not recognized * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'AnnotationParams-class.Rd': ‘getGOFromFeatures’ ‘makeGoSet’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: AnnotationParams-class.Rd: getGOFromFeatures, makeGoSet GenRegRes-class.Rd: MSnSet-class MLearn-methods.Rd: MSnSet-class, xvalSpec, MLearn QSep-class.Rd: MSnSet-class, Versioned-class SpatProtVis-class.Rd: MSnSet-class clustDist.Rd: MSnSet-class getMarkerClasses.Rd: MSnSet-class getMarkers.Rd: MSnSet-class getPredictions.Rd: MSnSet-class highlightOnPlot.Rd: FeaturesOfInterest-class knnClassification.Rd: MSnSet-class, knn knnOptimisation.Rd: MSnSet-class, knn knntlClassification.Rd: MSnSet-class knntlOptimisation.Rd: MSnSet-class ksvmClassification.Rd: MSnSet-class, ksvm ksvmOptimisation.Rd: MSnSet-class, ksvm minMarkers.Rd: MSnSet-class move2Ds.Rd: MSnSetList nbClassification.Rd: MSnSet-class, naiveBayes nbOptimisation.Rd: MSnSet-class, naiveBayes nnetClassification.Rd: MSnSet-class, nnet nnetOptimisation.Rd: MSnSet-class, nnet orgQuants.Rd: MSnSet-class perTurboClassification.Rd: MSnSet-class, ginv perTurboOptimisation.Rd: MSnSet-class, ginv phenoDisco.Rd: filterNA plot2Ds.Rd: MSnSet-class, MSnSetList plsdaClassification.Rd: MSnSet-class, plsda plsdaOptimisation.Rd: MSnSet-class, plsda rfClassification.Rd: MSnSet-class, randomForest rfOptimisation.Rd: MSnSet-class, randomForest sampleMSnSet.Rd: MSnSet-class svmClassification.Rd: MSnSet-class, svm svmOptimisation.Rd: MSnSet-class, svm testMSnSet.Rd: MSnSet-class testMarkers.Rd: MSnSet-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘addGoAnnotations’ ‘flipGoTermId’ ‘getGOEvidenceCodes’ ‘getGOFromFeatures’ ‘goIdToTerm’ ‘goTermToId’ ‘makeGoSet’ ‘prettyGoTermId’ ‘showGOEvidenceCodes’ Undocumented data sets: ‘andy2011params’ ‘dunkley2006params’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 knntlClassification 33.433 2.602 36.304 knntlOptimisation 29.051 2.912 31.680 perTurboOptimisation 27.823 0.146 32.136 perTurboClassification 27.510 0.135 31.328 svmClassification 12.611 0.156 14.726 svmOptimisation 12.566 0.075 14.398 rfOptimisation 11.570 0.247 13.424 ksvmClassification 10.816 0.276 12.570 SpatProtVis-class 10.573 0.261 13.197 rfClassification 10.444 0.251 12.234 nnetOptimisation 10.034 0.068 11.448 nnetClassification 9.938 0.065 11.261 ksvmOptimisation 8.001 0.170 9.333 plot2D 6.278 0.532 7.744 nbClassification 6.220 0.094 7.240 nbOptimisation 6.173 0.062 7.036 move2Ds 4.326 0.265 5.098 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 3 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/pRoloc.Rcheck/00check.log’ for details.