############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PAST_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PAST.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PAST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PAST’ version ‘1.22.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘PAST’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::findMatches’ by ‘utils::findMatches’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PAST.Rcheck/00install.out’ for details. * 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 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 assign_SNPs_to_genes: no visible binding for global variable ‘position’ assign_SNPs_to_genes: no visible binding for global variable ‘Marker_original’ assign_SNPs_to_genes: no visible binding for global variable ‘effect’ assign_SNPs_to_genes: no visible binding for global variable ‘p.value’ assign_SNPs_to_genes: no visible binding for global variable ‘linked_snp_count’ assign_SNPs_to_genes: no visible binding for global variable ‘name’ assign_SNPs_to_genes: no visible binding for global variable ‘marker’ assign_chunk: no visible binding for global variable ‘chromosome’ assign_chunk: no visible global function definition for ‘IRanges’ assign_chunk: no visible binding for global variable ‘position’ assign_chunk: no visible binding for global variable ‘seqid’ assign_chunk: no visible binding for global variable ‘Name’ find_pathway_significance: no visible binding for global variable ‘gene_id’ plot_pathways: no visible binding for global variable ‘running_enrichment_score’ Undefined global functions or variables: IRanges Marker_original Name chromosome effect gene_id linked_snp_count marker name p.value position running_enrichment_score seqid * 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 Undocumented arguments in Rd file 'assign_SNPs_to_genes.Rd' ‘filter_type’ 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 plot_pathways 1.756 0.104 25.706 find_pathway_significance 1.319 0.080 25.845 assign_SNPs_to_genes 1.329 0.058 16.959 * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PAST.Rcheck/00check.log’ for details.