############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeomxTools_3.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * 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 13.5Mb sub-directories of 1Mb or more: extdata 12.7Mb * 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 loading without being on the library search path ... 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 62.162 0.716 63.287 normalize-NanoStringGeoMxSet-method 48.788 0.600 0.157 readNanoStringGeoMxSet 40.772 0.664 41.438 NanoStringGeoMxSet-class 17.357 0.628 18.029 writeNanoStringGeoMxSet 16.263 0.384 16.647 setQCFlags-NanoStringGeoMxSet-method 14.477 0.076 14.547 setBioProbeQCFlags 14.436 0.048 14.478 aggregateCounts 11.317 0.196 11.514 readPKCFile 8.996 0.163 9.161 as.SpatialExperiment 5.989 0.308 6.297 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using ‘UTF-8’... OK ‘GeomxSet_coercions.Rmd’ using ‘UTF-8’... OK ‘Protein_in_GeomxTools.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck/00check.log’ for details.