############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings geneXtendeR_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/geneXtendeR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘geneXtendeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geneXtendeR’ version ‘1.26.0’ * 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:106:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] annotate.c:116:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_number.c:98:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_number.c:108:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] See ‘/home/biocbuild/bbs-3.17-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 9.9Mb sub-directories of 1Mb or more: data 5.8Mb doc 1.8Mb extdata 2.1Mb * 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 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 ... 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 5.8 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 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 30.902 1.395 34.705 hotspotPlot 21.428 1.207 25.002 annotate 15.468 0.895 18.869 barChart 14.740 0.708 17.847 cumlinePlot 14.536 0.749 17.701 linePlot 14.491 0.559 17.531 makeNetwork 11.934 0.707 15.140 gene_annotate 11.371 0.636 14.400 makeWordCloud 11.317 0.614 14.325 diffGO 11.088 0.668 14.170 distinct 10.908 0.692 13.974 plotWordFreq 10.655 0.616 13.675 peakLengthBoxplot 10.358 0.652 13.506 gene_lookup 10.165 0.596 13.158 meanPeakLength 9.739 0.539 12.661 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/geneXtendeR.Rcheck/00check.log’ for details.