############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:condiments.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings condiments_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/condiments.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘condiments/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘condiments’ 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 ‘condiments’ 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 .condition_sling: no visible binding for global variable ‘.’ .condition_sling : : no visible binding for global variable ‘.’ .distinct_inputs: no visible binding for global variable ‘Samples’ .distinct_inputs: no visible binding for global variable ‘.’ .fateSelectionTest: no visible binding for global variable ‘pair’ .fateSelectionTest: no visible binding for global variable ‘statistic’ .fateSelectionTest: no visible binding for global variable ‘p.value’ .multiple_samples: no visible binding for global variable ‘p.value’ .progressionTest: no visible binding for global variable ‘lineage’ .progressionTest: no visible binding for global variable ‘statistic’ .progressionTest: no visible binding for global variable ‘p.value’ .topologyTest_multipleSamples: no visible binding for global variable ‘p.value’ fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding for global variable ‘condition’ progressionTest_multipleSamples,SlingshotDataSet: no visible binding for global variable ‘condition’ Undefined global functions or variables: . Samples condition lineage p.value pair statistic * 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 topologyTest_multipleSamples 5.428 0.044 5.481 topologyTest 5.363 0.008 5.380 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/condiments.Rcheck/00check.log’ for details.