############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeomxTools_3.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeomxTools.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘GeomxTools/DESCRIPTION’ ... OK * this is package ‘GeomxTools’ version ‘3.12.1’ * package encoding: UTF-8 * 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 ‘GeomxTools’ can be installed ... OK * checking installed package size ... INFO installed size is 19.4Mb sub-directories of 1Mb or more: extdata 18.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 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 aggregateCounts: no visible binding for global variable ‘TargetName’ hkNorm: no visible binding for global variable ‘TargetName’ mixedModelDE: multiple local function definitions for ‘deFunc’ with different formal arguments qgrubbs: no visible global function definition for ‘qtable’ readNanoStringGeoMxSet: no visible global function definition for ‘read.table’ readPKCFile: no visible binding for global variable ‘RTS_ID’ readPKCFile: no visible binding for global variable ‘Module’ setGrubbsFlags: no visible binding for global variable ‘TargetName’ setGrubbsFlags : : no visible binding for global variable ‘Module’ setProbeRatioFlags: no visible binding for global variable ‘TargetName’ setTargetFlags: no visible global function definition for ‘analtye’ subtractBackground : : no visible binding for global variable ‘Module’ setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global function definition for ‘setSigFuncs<-’ signatureScores,NanoStringGeoMxSet: no visible global function definition for ‘assayDataElement2’ signatureScores,NanoStringGeoMxSet: no visible global function definition for ‘.sigCalc’ Undefined global functions or variables: .sigCalc Module RTS_ID TargetName analtye assayDataElement2 qtable read.table setSigFuncs<- Consider adding importFrom("utils", "read.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: NanoStringGeoMxSet-class.Rd: ExpressionSet-class, AnnotatedDataFrame, MIAME, SignatureSet, ExpressionSet readPKCFile.Rd: DataFrame-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mixedModelDE 163.127 2.321 186.286 normalize-NanoStringGeoMxSet-method 125.698 2.060 0.327 readNanoStringGeoMxSet 102.492 5.648 118.698 writeNanoStringGeoMxSet 42.209 2.345 46.225 NanoStringGeoMxSet-class 40.598 1.836 44.566 setQCFlags-NanoStringGeoMxSet-method 36.229 0.448 39.778 setBioProbeQCFlags 35.443 0.285 37.332 aggregateCounts 29.015 0.189 29.703 readPKCFile 24.698 1.844 29.922 plotConcordance 15.399 0.444 17.128 as.SpatialExperiment 12.210 0.578 13.116 as.Seurat 8.673 0.182 9.395 plotNormFactorConcordance 8.677 0.062 9.398 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’