############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeomxTools_3.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeomxTools.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeomxTools/DESCRIPTION’ ... OK * this is package ‘GeomxTools’ version ‘3.13.0’ * 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 ... INFO installed size is 19.4Mb 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 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 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 ... 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 93.099 1.301 97.309 normalize-NanoStringGeoMxSet-method 74.554 1.156 0.124 readNanoStringGeoMxSet 51.077 1.293 52.506 setQCFlags-NanoStringGeoMxSet-method 22.587 0.104 22.757 writeNanoStringGeoMxSet 21.720 0.243 22.042 NanoStringGeoMxSet-class 21.624 0.235 22.097 setBioProbeQCFlags 21.554 0.211 21.825 aggregateCounts 17.513 0.084 17.646 readPKCFile 10.952 0.104 11.091 as.SpatialExperiment 7.282 0.283 7.585 plotConcordance 6.932 0.622 7.576 as.Seurat 5.003 0.060 5.079 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: `expected`: TRUE ── Failure ('test_protein.R:158:3'): Concordance plots are plotted ───────────── class(fig)[1] == "gg" is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_protein.R:210:3'): QC plots are plotted ────────────────────── class(fig)[1] == "gg" is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 1 | SKIP 0 | PASS 286 ] Error: Test failures Execution halted * 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: 1 ERROR, 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/GeomxTools.Rcheck/00check.log’ for details.