############################################################################## ############################################################################## ### ### 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_3.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeomxTools/DESCRIPTION’ ... OK * this is package ‘GeomxTools’ version ‘3.4.0’ * 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 ... NOTE installed size is 19.3Mb sub-directories of 1Mb or more: extdata 18.4Mb * 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 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 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’ 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 setSigFuncs<- * checking Rd files ... WARNING checkRd: (5) NanoStringGeoMxSet-class.Rd:109-112: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:113-116: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:117-120: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:121-124: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:125-128: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:129-132: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:133-136: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:137-140: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:141-144: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:145-149: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:150-154: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:155-158: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:159-162: \item in \describe must have non-empty label checkRd: (5) NanoStringGeoMxSet-class.Rd:163-166: \item in \describe must have non-empty label * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mixedModelDE 153.597 3.031 208.161 normalize-NanoStringGeoMxSet-method 117.450 2.555 0.344 readNanoStringGeoMxSet 95.279 3.655 125.668 writeNanoStringGeoMxSet 39.249 1.412 50.936 NanoStringGeoMxSet-class 37.753 1.481 53.824 setBioProbeQCFlags 35.578 0.163 44.213 setQCFlags-NanoStringGeoMxSet-method 35.392 0.193 44.135 aggregateCounts 28.265 0.431 38.168 readPKCFile 19.767 0.830 26.666 as.SpatialExperiment 11.700 0.596 16.505 plotConcordance 10.433 0.582 14.094 as.Seurat 6.857 0.214 9.117 plotNormFactorConcordance 5.790 0.041 7.396 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’