############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GRaNIE_1.3.34.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.3.34’ * 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 ‘GRaNIE’ 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 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 .getFinalListOfTFs: no visible binding for global variable ‘external_gene_name’ .getFinalListOfTFs: no visible binding for global variable ‘ensembl_gene_id’ .getFinalListOfTFs: no visible binding for global variable ‘SYMBOL’ .makeObjectCompatible: no visible binding for global variable ‘TF.name’ .performIHW: no visible binding for global variable ‘adj_pvalue’ .printGene: no visible binding for global variable ‘gene.ENSEMBL’ .printTF: no visible binding for global variable ‘TF.ID’ getGRNSummary: no visible binding for global variable ‘pval’ Undefined global functions or variables: SYMBOL TF.ID TF.name adj_pvalue ensembl_gene_id external_gene_name gene.ENSEMBL pval * 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 ... WARNING Documented arguments not in \usage in documentation object 'plotCorrelations': ‘peak_gene_max_adjP’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotCommunitiesEnrichment 10.478 0.751 13.375 generateStatsSummary 9.266 0.536 9.982 plotPCA_all 7.968 0.864 9.899 plotCommunitiesStats 8.144 0.615 9.761 calculateCommunitiesEnrichment 7.452 0.628 8.305 addConnections_TF_peak 7.219 0.692 9.626 add_TF_gene_correlation 7.242 0.616 8.413 nPeaks 6.788 0.564 8.993 plotCorrelations 6.694 0.608 7.982 loadExampleObject 6.659 0.640 8.504 getGRNSummary 6.657 0.600 8.758 plotDiagnosticPlots_peakGene 6.602 0.552 7.334 getTopNodes 6.583 0.508 7.402 getParameters 6.445 0.515 7.967 calculateTFEnrichment 6.392 0.551 8.244 overlapPeaksAndTFBS 6.252 0.364 8.019 nGenes 6.050 0.560 6.887 calculateGeneralEnrichment 6.197 0.360 7.216 build_eGRN_graph 5.980 0.419 6.781 nTFs 5.886 0.499 7.776 plotDiagnosticPlots_TFPeaks 5.863 0.464 6.507 visualizeGRN 5.814 0.476 6.467 calculateCommunitiesStats 5.175 0.460 5.990 plotGeneralEnrichment 4.802 0.540 5.513 plotTFEnrichment 4.905 0.384 5.465 plotGeneralGraphStats 4.756 0.420 5.357 filterData 4.588 0.484 5.245 plot_stats_connectionSummary 4.594 0.400 5.166 filterGRNAndConnectGenes 4.528 0.400 5.100 deleteIntermediateData 4.446 0.396 5.014 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GRaNIE_packageDetails.Rmd’ using ‘UTF-8’... OK ‘GRaNIE_singleCell_eGRNs.Rmd’ using ‘UTF-8’... OK ‘GRaNIE_workflow.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.