############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Dune.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Dune_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Dune.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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 ‘Dune/DESCRIPTION’ ... OK * this is package ‘Dune’ version ‘1.19.0’ * package encoding: UTF-8 * checking package namespace information ... NOTE Found export directive that requires package ‘methods’: ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * 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 ‘Dune’ can be installed ... OK * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .metricTrend: no visible binding for global variable ‘.’ .metricTrend: no visible binding for global variable ‘step’ .metricTrend: no visible binding for global variable ‘change’ .metricTrend: no visible binding for global variable ‘value’ .plotMetric: no visible binding for global variable ‘label2’ .plotMetric: no visible binding for global variable ‘metric’ .plotMetric: no visible binding for global variable ‘label1’ ARIImp : f: no visible binding for global variable ‘cells’ ConfusionEvolution : : no visible binding for global variable ‘Freq’ ConfusionEvolution : : no visible binding for global variable ‘total_x’ ConfusionEvolution : : no visible binding for global variable ‘total_y’ ConfusionEvolution: no visible binding for global variable ‘overlap’ ConfusionEvolution: no visible binding for global variable ‘Freq’ ConfusionEvolution: no visible binding for global variable ‘step’ ConfusionPlot: no visible binding for global variable ‘Freq’ ConfusionPlot: no visible binding for global variable ‘total_x’ ConfusionPlot: no visible binding for global variable ‘total_y’ ConfusionPlot: no visible binding for global variable ‘overlap’ NMIImp : f: no visible binding for global variable ‘cells’ intermediateMat: no visible binding for global variable ‘cells’ plotPrePost: no visible binding for global variable ‘Nb’ Undefined global functions or variables: . Freq Nb cells change label1 label2 metric overlap step total_x total_y value Consider adding importFrom("stats", "step") 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: ARItrend.Rd: ggplot ConfusionEvolution.Rd: transition_states, animate ConfusionPlot.Rd: ggplot Dune.Rd: SummarizedExperiment NMItrend.Rd: ggplot plotARIs.Rd: ggplot plotNMIs.Rd: ggplot plotPrePost.Rd: ggplot 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Dune 9.513 0.175 9.750 ARItrend 5.917 0.048 5.980 plotARIs 5.711 0.036 5.762 plotNMIs 5.533 0.111 5.682 NMItrend 5.458 0.051 5.540 ARIImp 5.332 0.080 5.427 plotPrePost 5.333 0.051 5.420 functionTracking 5.370 0.012 5.395 intermediateMat 5.230 0.024 5.265 clusterConversion 5.161 0.047 5.227 NMIImp 5.111 0.028 5.157 whenToStop 5.084 0.052 5.158 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/Dune.Rcheck/00check.log’ for details.