############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tradeSeq_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tradeSeq.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 ‘tradeSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tradeSeq’ version ‘1.21.0’ * 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 ‘tradeSeq’ 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 ... NOTE Warning: program compiled against libxml 212 using older 211 Namespaces in Imports field not imported from: ‘Biobase’ ‘igraph’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .earlyDETest: no visible binding for global variable ‘X1’ .earlyDETest: no visible binding for global variable ‘X2’ .findKnots: no visible binding for global variable ‘t1’ .findKnots: no visible binding for global variable ‘l1’ .plotGeneCount: no visible binding for global variable ‘dim1’ .plotGeneCount: no visible binding for global variable ‘dim2’ .plotSmoothers: no visible binding for global variable ‘time’ .plotSmoothers: no visible binding for global variable ‘gene_count’ .plotSmoothers: no visible binding for global variable ‘lineage’ .plotSmoothers_conditions: no visible binding for global variable ‘time’ .plotSmoothers_conditions: no visible binding for global variable ‘gene_count’ .plotSmoothers_conditions: no visible binding for global variable ‘lineage’ .plotSmoothers_conditions: no visible binding for global variable ‘pCol’ .plotSmoothers_sce: no visible binding for global variable ‘time’ .plotSmoothers_sce: no visible binding for global variable ‘gene_count’ .plotSmoothers_sce: no visible binding for global variable ‘lineage’ .plotSmoothers_sce: no visible binding for global variable ‘pCol’ Undefined global functions or variables: X1 X2 dim1 dim2 gene_count l1 lineage pCol t1 time Consider adding importFrom("stats", "time") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) fitGAM.Rd:151-154: Lost braces in \itemize; meant \describe ? checkRd: (-1) fitGAM.Rd:155-156: Lost braces in \itemize; meant \describe ? checkRd: (-1) fitGAM.Rd:157-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) fitGAM.Rd:159-160: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: fitGAM.Rd: gamObject gamList.Rd: gamObject plotGeneCount.Rd: SlingshotDataSet, SingleCellExperiment, ggplot plotSmoothers.Rd: geom_line, geom_point, labs, 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 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 conditionTest 98.351 0.301 98.816 associationTest 63.433 0.618 80.291 plotSmoothers 61.753 0.247 63.552 plotGeneCount 58.955 0.256 59.321 fitGAM 58.140 0.172 58.427 plot_evalutateK_results 31.633 0.254 33.769 evaluateK 30.292 0.147 30.493 * 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/tradeSeq.Rcheck/00check.log’ for details.