############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RNAseqCovarImpute_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘RNAseqCovarImpute/DESCRIPTION’ ... OK * this is package ‘RNAseqCovarImpute’ version ‘1.4.0’ * 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 ‘RNAseqCovarImpute’ 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 combine_rubins: no visible binding for global variable ‘probe’ combine_rubins: no visible binding for global variable ‘i’ combine_rubins: no visible binding for global variable ‘coef_combined’ combine_rubins: no visible binding for global variable ‘rubins_t_bayes’ combine_rubins: no visible binding for global variable ‘combined_p’ combine_rubins: no visible binding for global variable ‘combined_p_bayes’ limmavoom_imputed_data_list_helper: no visible binding for global variable ‘i’ limmavoom_imputed_data_list_helper: no visible binding for global variable ‘lm_predictor’ limmavoom_imputed_data_pca: no visible binding for global variable ‘probe’ lowess_all_gene_bins: no visible binding for global variable ‘gene_bin’ lowess_all_gene_bins: no visible binding for global variable ‘i’ voom_master_lowess: no visible global function definition for ‘is’ voom_master_lowess: no visible global function definition for ‘new’ voom_master_lowess: no visible global function definition for ‘lowess’ voom_master_lowess: no visible global function definition for ‘approxfun’ voom_sx_sy: no visible global function definition for ‘is’ voom_sx_sy: no visible global function definition for ‘new’ Undefined global functions or variables: approxfun coef_combined combined_p combined_p_bayes gene_bin i is lm_predictor lowess new probe rubins_t_bayes Consider adding importFrom("methods", "is", "new") importFrom("stats", "approxfun", "lowess") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Documented arguments not in \usage in Rd file 'impute_gene_bin_helper.Rd': ‘DGE’ ‘param’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 limmavoom_imputed_data_pca 11.885 2.543 11.741 combine_rubins 8.746 1.472 5.187 limmavoom_imputed_data_list 8.457 1.476 6.159 get_gene_bin_intervals 7.976 1.480 4.839 impute_by_gene_bin 7.940 1.415 4.410 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck/00check.log’ for details.