############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpaceTrooper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpaceTrooper_0.99.44.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceTrooper.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpaceTrooper/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpaceTrooper’ version ‘0.99.44’ * 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 ‘SpaceTrooper’ can be installed ... OK * checking installed package size ... INFO installed size is 7.6Mb sub-directories of 1Mb or more: extdata 7.2Mb * 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 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 .checkFovPositionVersion: no visible global function definition for ‘metadata<-’ .checkOutliers: no visible global function definition for ‘metadata<-’ .computeOutliersQCScore: no visible global function definition for ‘metadata<-’ computeTrainDF: no visible binding for global variable ‘spe’ readCosmxProteinSPE: no visible global function definition for ‘metadata<-’ readCosmxSPE: no visible global function definition for ‘metadata<-’ readPolygons: no visible binding for global variable ‘n_points’ readXeniumSPE: no visible global function definition for ‘metadata<-’ Undefined global functions or variables: metadata<- n_points spe * 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: computeTrainDF.Rd: SpatialExperiment-class dot-computeCosmxProteinTrainSet.Rd: SpatialExperiment-class dot-computeCosmxTrainSet.Rd: SpatialExperiment-class dot-computeXenMerTrainSet.Rd: SpatialExperiment-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 * 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 ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... * checking PDF version of manual without index ... ERROR * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceTrooper.Rcheck/00check.log’ for details.