############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tricycle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tricycle_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/tricycle.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tricycle/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tricycle’ version ‘1.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘tricycle’ 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 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 circle_scale_legend: no visible binding for global variable ‘x1’ circle_scale_legend: no visible binding for global variable ‘y1’ circle_scale_legend: no visible binding for global variable ‘x2’ circle_scale_legend: no visible binding for global variable ‘y2’ plot_ccposition_den: no visible binding for global variable ‘x’ Undefined global functions or variables: x x1 x2 y1 y2 * checking Rd files ... NOTE checkRd: (-1) estimate_cycle_position.Rd:26: Lost braces; missing escapes or markup? 26 | and stored with name \code{dimred} in {x}. Default: 'tricycleEmbedding'} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: estimate_Schwabe_stage.Rd: SummarizedExperiment-class, SingleCellExperiment-class estimate_cycle_position.Rd: SummarizedExperiment-class, SingleCellExperiment-class neurosphere_example.Rd: SingleCellExperiment-class plot_emb_circle_scale.Rd: SingleCellExperiment-class project_cycle_space.Rd: SummarizedExperiment-class, SingleCellExperiment-class run_pca_cc_genes.Rd: 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/tricycle.Rcheck/00check.log’ for details.