############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:recoup.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings recoup_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/recoup.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 ‘recoup/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘recoup’ version ‘1.35.0’ * package encoding: UTF-8 * 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 ‘recoup’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck/00install.out’ for details. * 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 ... 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 dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 Unexported objects imported by ':::' calls: ‘biomaRt:::.generateFilterXML’ ‘biomaRt:::.setResultColNames’ ‘biomaRt:::martCheck’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘biomaRt:::martVSchema’ ‘txdbmaker:::GFF_FEATURE_TYPES’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘makeHorizontalAnnotation’ * 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 readBamIntervals: no visible binding for global variable ‘bam.file’ recoupCorrelation: no visible binding for global variable ‘Index’ recoupCorrelation: no visible binding for global variable ‘Coverage’ recoupCorrelation: no visible binding for global variable ‘Condition’ recoupCorrelation: no visible binding for global variable ‘Design’ recoupHeatmap : : no visible global function definition for ‘grid.text’ recoupProfile: no visible binding for global variable ‘Signal’ recoupProfile: no visible binding for global variable ‘Condition’ recoupProfile: no visible binding for global variable ‘Design’ Undefined global functions or variables: Condition Coverage Design Index Signal bam.file grid.text * checking Rd files ... NOTE checkRd: (-1) recoup.Rd:210-211: Lost braces 210 | \code{region}{Minimum flank is 0bp and maximum is | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: coverageRef.Rd: makeGRangesFromDataFrame recoup.Rd: GRanges, findOverlaps, ggplot, Heatmap, makeGRangesFromDataFrame recoupPlot.Rd: draw rpMatrix.Rd: makeGRangesFromDataFrame 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 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 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. 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 LazyData ... 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 mergeRuns 27.246 8.451 27.124 profileMatrix 15.034 5.670 12.197 recoup 11.408 4.833 11.419 simpleGetSet 11.405 4.259 11.194 recoupPlot 10.959 4.385 11.039 sliceObj 10.451 4.714 10.481 kmeansDesign 10.527 4.094 10.579 recoupHeatmap 7.357 2.313 8.746 recoupCorrelation 7.345 2.288 8.909 recoupProfile 7.541 2.084 8.878 coverageRef 6.350 0.392 6.755 getAnnotation 2.118 0.304 5.897 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck/00check.log’ for details.