############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings geneXtendeR_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.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 ‘geneXtendeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geneXtendeR’ version ‘1.32.0’ * 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:159:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] annotate.c:191:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] annotate.c:199:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] annotate.c:208:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] annotate.c:228:83: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 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:202:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 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-3.20-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... NOTE 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 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 5.7 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 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 29.383 0.313 31.670 hotspotPlot 17.800 0.213 19.998 annotate 16.005 1.626 19.695 barChart 14.888 1.927 18.892 cumlinePlot 14.792 0.685 17.531 linePlot 14.056 0.664 16.749 gene_annotate 12.051 0.094 14.069 makeNetwork 11.082 0.348 13.402 distinct 10.998 0.251 13.300 makeWordCloud 10.927 0.225 13.143 diffGO 10.626 0.350 12.941 plotWordFreq 10.205 0.105 12.349 meanPeakLength 9.805 0.178 11.908 peakLengthBoxplot 9.500 0.076 11.550 gene_lookup 8.848 0.115 10.930 * 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, 7 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck/00check.log’ for details.