############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bigmelon_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/bigmelon.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bigmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bigmelon’ version ‘1.33.0’ * 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 ‘bigmelon’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 Note: possible error in 'readPepo(barcodes = sets[!is.na(sets)], ': unused argument (barcodes = sets[!is.na(sets)]) See ‘/home/biocbuild/bbs-3.21-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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 Warning: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: bigmelon-normalization.Rd: wateRmelon bigmelon-package.Rd: dasen, wateRmelon, gdsfmt ecc.Rd: convertArray getquantilesandranks.Rd: get.attr.gdsn wm-port.Rd: wateRmelon Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211