############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SingleMoleculeFootprinting_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.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 ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK * this is package ‘SingleMoleculeFootprinting’ version ‘2.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘SingleMoleculeFootprinting’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biostrings::setequal’ by ‘dplyr::setequal’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Biostrings::collapse’ by ‘dplyr::collapse’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Matrix::image’ by ‘graphics::image’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::between’ by ‘plyranges::between’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n_distinct’ by ‘plyranges::n_distinct’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n’ by ‘plyranges::n’ when loading ‘SingleMoleculeFootprinting’ See ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.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 ... 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 Create_MethylationCallingWindows: no visible binding for global variable ‘idx’ GRanges_to_DF: no visible binding for global variable ‘Sample’ GRanges_to_DF: no visible binding for global variable ‘Score’ LowCoverageMethRate_RMSE: no visible binding for global variable ‘Sample’ PlotAvgSMF: no visible binding for global variable ‘MethRate’ PlotSingleMoleculeStack : : no visible binding for global variable ‘Coordinate’ PlotSingleMoleculeStack : : no visible binding for global variable ‘Methylation’ PlotSingleMoleculeStack: no visible binding for global variable ‘Sample’ StateQuantificationPlot: no visible binding for global variable ‘State’ StateQuantificationPlot: no visible binding for global variable ‘Pattern’ StateQuantificationPlot: no visible binding for global variable ‘Bin’ StateQuantificationPlot: no visible binding for global variable ‘Methylation’ Undefined global functions or variables: Bin Coordinate MethRate Methylation Pattern Sample Score State idx * checking Rd files ... OK * 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 ... NOTE S3 methods shown with full name in Rd file 'cbind.fill.Matrix.Rd': ‘cbind.fill.Matrix’ S3 methods shown with full name in Rd file 'rbind.fill.Matrix.Rd': ‘rbind.fill.Matrix’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GetSingleMolMethMat 4.048 1.155 5.205 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’ for details.