############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings bigmelon_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/bigmelon.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 ‘bigmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bigmelon’ version ‘1.32.0’ * 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 ‘bigmelon’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'readPepo(barcodes = sets[!is.na(sets)], ': unused argument (barcodes = sets[!is.na(sets)]) See ‘/home/biocbuild/bbs-3.20-bioc/meat/bigmelon.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 ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ 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 whether startup messages can be suppressed ... NOTE No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... WARNING Missing or unexported object: ‘GEOquery::gunzip’ Unexported objects imported by ':::' calls: ‘bumphunter:::greaterOrEqual’ ‘minfi:::pickCompProbes’ ‘minfi:::projectCellType’ ‘wateRmelon:::.impose’ ‘wateRmelon:::.normalizeQuantiles2’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bigpepo: possible error in readPepo(barcodes = sets[!is.na(sets)], manifest = manifest, n = TRUE, oob = FALSE, idatdir = path, ): unused argument (barcodes = sets[!is.na(sets)]) bumphunterEngine.gdsn: no visible binding for global variable ‘locfitByCluster’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParRegistered’ bumphunterEngine.gdsn: no visible global function definition for ‘registerDoSEQ’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParWorkers’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParName’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParVersion’ bumphunterEngine.gdsn: no visible global function definition for ‘smoother’ bumphunterEngine.gdsn: no visible global function definition for ‘regionFinder’ bumphunterEngine.gdsn: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn: no visible global function definition for ‘iter’ bumphunterEngine.gdsn: no visible binding for global variable ‘regionFinder’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘iter’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘iter’ es2gds: no visible global function definition for ‘colData’ estimateCellCounts.gds: no visible global function definition for ‘colData’ idats2gds: no visible binding for global variable ‘ChipType’ Undefined global functions or variables: %dorng% ChipType colData foreach getDoParName getDoParRegistered getDoParVersion getDoParWorkers iter locfitByCluster regionFinder registerDoSEQ smoother * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘bigpepo’ ‘dim.gdsn.class’ ‘dimnames.gds.class’ ‘dimnames.gdsn.class’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Functions or methods with usage in Rd file 'bigPepo.Rd' but not in code: ‘bigPepo’ Codoc mismatches from Rd file 'iadd.Rd': iadd Code: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL, idatpath = NULL, ...) Docs: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL, ...) Argument names in code not in docs: idatpath Mismatches in argument names: Position: 6 Code: idatpath Docs: ... * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'bigPepo.Rd' ‘path’ ‘gds’ ‘manifest’ ‘chunksize’ ‘force’ ‘...’ Undocumented arguments in Rd file 'dim.gds.class.Rd' ‘gfile’ ‘v’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 iadd 18.79 0.676 19.616 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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: 5 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck/00check.log’ for details.