############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PANR_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PANR.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘PANR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PANR’ version ‘1.51.0’ * 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 ‘PANR’ can be installed ... OK * 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 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 SNR2p,BetaMixture-numeric_Or_integer: no visible global function definition for ‘runif’ SNR2p,BetaMixture-numeric_Or_integer: no visible global function definition for ‘pbeta’ p2SNR,BetaMixture-numeric_Or_integer: no visible global function definition for ‘qbeta’ Undefined global functions or variables: pbeta qbeta runif Consider adding importFrom("stats", "pbeta", "qbeta", "runif") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) assoScore.Rd:33: Lost braces 33 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) buildPAN.Rd:27: Lost braces 27 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) exportPAN.Rd:34: Lost braces 34 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) fitBM.Rd:28: Lost braces 28 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) fitNULL.Rd:37: Lost braces 37 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) infer.Rd:27: Lost braces 27 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) pvclustModule.Rd:38: Lost braces 38 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) viewNestedModules.Rd:30: Lost braces 30 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ checkRd: (-1) viewPAN.Rd:33: Lost braces 33 | a logical value to switch on (if \code{TRUE}) or off {if \code{FALSE}} detailed | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fitNULL 7.346 0.054 7.401 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/PANR.Rcheck/00check.log’ for details.