############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:genoCN.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings genoCN_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/genoCN.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘genoCN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genoCN’ version ‘1.56.0’ * 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 ‘genoCN’ can be installed ... WARNING Found the following significant warnings: utility.c:155:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] See ‘/home/biocbuild/bbs-3.19-bioc/meat/genoCN.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE genoCNA: no visible binding for global variable ‘init.Para.CNA’ genoCNV: no visible binding for global variable ‘init.Para.CNV’ Undefined global functions or variables: init.Para.CNA init.Para.CNV * checking Rd files ... NOTE checkRd: (-1) genoCNA.Rd:60: Escaped LaTeX specials: \_ checkRd: (-1) genoCNA.Rd:61: Escaped LaTeX specials: \_ checkRd: (-1) genoCNV.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) init.Para.CNA.Rd:14-16: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:17-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:20-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:30-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNA.Rd:42-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:14-16: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:17-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:20-22: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:30-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) init.Para.CNV.Rd:42-46: Lost braces in \itemize; meant \describe ? * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genoCNA 5.389 0.148 5.536 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/genoCN.Rcheck/00check.log’ for details.