############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tradeSeq_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/tradeSeq.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tradeSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tradeSeq’ version ‘1.12.0’ * 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 R 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 ... NOTE 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 83.665 7.957 97.375 associationTest 47.700 3.352 62.907 plotSmoothers 36.648 6.206 43.028 fitGAM 33.659 5.628 39.466 plotGeneCount 32.562 6.053 38.809 plot_evalutateK_results 20.003 0.511 20.562 evaluateK 17.770 0.567 18.361 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/tradeSeq.Rcheck/00check.log’ for details.