############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:pickgene.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings pickgene_1.79.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pickgene.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘pickgene/DESCRIPTION’ ... OK * this is package ‘pickgene’ version ‘1.79.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘pickgene’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") See ‘/home/biocbuild/bbs-3.21-bioc/meat/pickgene.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 do.oddsplot: warning in em.ggb(data[[conditions[1]]], data[[conditions[2]]], theta, theta[1:3], print = TRUE): partial argument match of 'print' to 'printit' pickgene.poly: warning in pickgene.two(y[, i], intensity, geneid = geneID, singlelevel = singlelevel, npick = npickgene, ylab = ylabs[i], ...): partial argument match of 'npick' to 'npickgene' lod.plot: possible error in oddsplot(exp(data[[x]]), exp(data[[y]]), theta, col = col, xlab = xlab, ylab = ylab, chip = ""): unused argument (chip = "") nloglik: no visible binding for global variable ‘.fit.xx’ nloglik: no visible binding for global variable ‘.fit.yy’ nploglik: no visible binding for global variable ‘.fit.xx’ nploglik: no visible binding for global variable ‘.fit.yy’ nploglik: no visible binding for global variable ‘.fit.zz’ s.check1: no visible global function definition for ‘lod’ s.marg: no visible binding for global variable ‘x’ shrinkplot: no visible global function definition for ‘s.fits’ shrinkplot: no visible binding for global variable ‘lims’ Undefined global functions or variables: .fit.xx .fit.yy .fit.zz lims lod s.fits x * checking Rd files ... NOTE prepare_Rd: Simulation.pickgene.Rd:8: Dropping empty section \keyword prepare_Rd: Simulation.pickgene.Rd:5-6: Dropping empty section \usage prepare_Rd: Simulation.pickgene.Rd:7: Dropping empty section \details * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/pickgene.Rcheck/00check.log’ for details.