############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneXtendeR_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneXtendeR.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘geneXtendeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geneXtendeR’ version ‘1.34.0’ * 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 ‘geneXtendeR’ can be installed ... WARNING Found the following significant warnings: annotate.c:159:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] annotate.c:191:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] annotate.c:199:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] annotate.c:208:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] annotate.c:228:97: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] extract_peaks.c:202:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] See ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... INFO installed size is 11.4Mb sub-directories of 1Mb or more: data 5.8Mb doc 1.9Mb extdata 3.5Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘rtracklayer’ A package should be listed in only one of these fields. * 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 ... NOTE Namespaces in Imports field not imported from: ‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’ 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 .geneXtender: no visible binding for global variable ‘type’ .geneXtender: no visible binding for global variable ‘seqid’ .geneXtender: no visible binding for global variable ‘gene_id’ .geneXtender: no visible binding for global variable ‘gene_name’ annotate_n: no visible binding for global variable ‘..I’ annotate_n: no visible binding for global variable ‘seqid’ diffGO: no visible binding for global variable ‘rat’ gene_annotate: no visible global function definition for ‘.’ gene_annotate: no visible binding for global variable ‘Distance-of-Gene-to-Nearest-Peak’ gene_annotate: no visible global function definition for ‘sd’ gene_annotate: no visible binding for global variable ‘Chromosome’ gene_annotate: no visible binding for global variable ‘Gene-Start’ gene_annotate: no visible binding for global variable ‘Gene-End’ gene_annotate: no visible binding for global variable ‘Gene-ID’ gene_annotate: no visible binding for global variable ‘Gene-Name’ gene_annotate: no visible binding for global variable ‘Peaks-on-Gene-Body’ gene_annotate: no visible binding for global variable ‘Number-of-Peaks-Associated-with-Gene’ gene_lookup: no visible binding for global variable ‘gene_name_id’ gene_lookup: no visible binding for global variable ‘gene_id’ gene_lookup : internal_find: no visible binding for global variable ‘Chromosome’ gene_lookup : internal_find: no visible binding for global variable ‘distance’ gene_lookup : internal_find: no visible global function definition for ‘na.omit’ gene_lookup: no visible binding for global variable ‘..I’ gene_lookup: no visible binding for global variable ‘distance’ makeWordCloud: no visible binding for global variable ‘rat’ meanPeakLength: no visible binding for global variable ‘rat’ peaksInput: no visible binding for global variable ‘chr’ peaksInput: no visible global function definition for ‘na.omit’ peaksMerge: no visible binding for global variable ‘chr’ peaksMerge: no visible binding for global variable ‘g’ peaksMerge: no visible global function definition for ‘.’ plotWordFreq : geneXtender: no visible binding for global variable ‘type’ plotWordFreq : geneXtender: no visible binding for global variable ‘seqid’ plotWordFreq : geneXtender: no visible binding for global variable ‘gene_id’ plotWordFreq : geneXtender: no visible binding for global variable ‘gene_name’ Undefined global functions or variables: . ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id na.omit rat sd seqid type Consider adding importFrom("stats", "na.omit", "sd") 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 LazyData ... WARNING LazyData DB of 5.7 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE Files named as vignettes but with no recognized vignette engine: ‘vignettes/geneXtendeR.Rnw’ (Is a VignetteBuilder field missing?) * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed meanPeakLengthPlot 13.308 1.828 17.018 hotspotPlot 9.668 0.483 11.538 annotate 7.551 0.139 9.504 cumlinePlot 6.798 0.278 8.874 barChart 6.637 0.302 8.722 linePlot 6.648 0.244 8.760 gene_annotate 6.433 0.206 8.084 makeNetwork 6.240 0.306 8.319 distinct 5.989 0.248 8.015 plotWordFreq 5.839 0.285 7.743 diffGO 5.777 0.279 7.845 makeWordCloud 5.654 0.339 7.783 peakLengthBoxplot 5.386 0.295 7.480 gene_lookup 5.270 0.104 7.293 meanPeakLength 5.194 0.167 7.142 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 6 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneXtendeR.Rcheck/00check.log’ for details.