############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings imcRtools_1.15.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/imcRtools.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 ‘imcRtools/DESCRIPTION’ ... OK * this is package ‘imcRtools’ version ‘1.15.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 29 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘imcRtools’ 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 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 .generateInteractionsPlot: no visible binding for global variable ‘weight’ .valid.plotInteractions.input: no visible binding for global variable ‘from_label’ .valid.plotInteractions.input: no visible binding for global variable ‘to_label’ .valid.plotInteractions.input: no visible global function definition for ‘n_distinct’ .valid.plotInteractions.input: no visible global function definition for ‘capture.output’ plotInteractions: no visible binding for global variable ‘from_label’ plotInteractions: no visible binding for global variable ‘to_label’ plotInteractions: no visible binding for global variable ‘weight’ plotInteractions: no visible global function definition for ‘everything’ Undefined global functions or variables: capture.output everything from_label n_distinct to_label weight Consider adding importFrom("utils", "capture.output") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) aggregateNeighbors.Rd:52: Lost braces; missing escapes or markup? 52 | \code{summarize_by = "metadata"} or "{statistic}_aggregatedExpression" when | ^ checkRd: (-1) testInteractions.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotSpatial.Rd: ggraph readImagefromTXT.Rd: Image-class, CytoImageList-class readSCEfromTXT.Rd: SingleCellExperiment-class read_cpout.Rd: SpatialExperiment-class, SingleCellExperiment-class read_steinbock.Rd: SpatialExperiment-class, SingleCellExperiment-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 testInteractions 211.079 4.782 211.503 read_steinbock 22.692 4.366 21.803 buildSpatialGraph 12.397 1.238 13.707 plotInteractions 9.252 0.169 9.322 plotSpatial 6.141 0.180 6.341 plotSpatialContext 6.187 0.065 6.269 filterSpatialContext 5.538 0.248 5.801 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/imcRtools.Rcheck/00check.log’ for details.