############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SingleMoleculeFootprinting_2.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SingleMoleculeFootprinting.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK * this is package ‘SingleMoleculeFootprinting’ version ‘2.3.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 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 ... OK * 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: ‘qs’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘qs’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .detect.footprints: no visible binding for global variable ‘occupancy’ .detect.footprints: no visible binding for global variable ‘biological.state’ AggregateFootprints : : no visible binding for global variable ‘TF’ AggregateFootprints : : no visible binding for global variable ‘biological.state’ AnnotateFootprints: no visible binding for global variable ‘biological.state’ Create_MethylationCallingWindows: no visible binding for global variable ‘.’ Create_MethylationCallingWindows: no visible binding for global variable ‘idx’ DetectFootprints: no visible binding for global variable ‘partition.nr’ DetectFootprints: no visible binding for global variable ‘partition.coverage’ DetectFootprints: no visible binding for global variable ‘nr.cytosines’ DetectFootprints: no visible binding for global variable ‘biological.state’ FootprintCharter: no visible binding for global variable ‘partition.coverage’ FootprintCharter: no visible binding for global variable ‘partition.nr’ FootprintCharter: no visible binding for global variable ‘.’ GRanges_to_DF: no visible global function definition for ‘matches’ 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’ MethSM.to.dense: no visible binding for global variable ‘.’ PlotAvgSMF: no visible binding for global variable ‘MethRate’ PlotFootprints: no visible binding for global variable ‘partition.nr’ PlotFootprints: no visible binding for global variable ‘biological.state’ PlotFootprints: no visible binding for global variable ‘partition.coverage’ PlotFootprints: no visible binding for global variable ‘TF’ PlotFootprints: no visible binding for global variable ‘coordinate’ PlotFootprints: no visible binding for global variable ‘bulk.SMF’ PlotSingleMoleculeStack : : no visible binding for global variable ‘Coordinate’ PlotSingleMoleculeStack : : no visible binding for global variable ‘Methylation’ PlotSingleMoleculeStack: no visible binding for global variable ‘Sample’ Plot_FootprintCharter_SM: no visible binding for global variable ‘biological.state’ Plot_FootprintCharter_SM: no visible binding for global variable ‘partition.nr’ Plot_FootprintCharter_SM: no visible binding for global variable ‘partition.coverage’ Plot_FootprintCharter_SM: no visible binding for global variable ‘partition.coverage.cumsum’ Plot_FootprintCharter_SM: no visible binding for global variable ‘d’ Plot_FootprintCharter_SM: no visible binding for global variable ‘read.idx’ StateQuantificationPlot: no visible binding for global variable ‘State’ StateQuantificationPlot: no visible binding for global variable ‘Pattern’ StateQuantificationPlot: no visible binding for global variable ‘.’ 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 TF biological.state bulk.SMF coordinate d idx matches nr.cytosines occupancy partition.coverage partition.coverage.cumsum partition.nr read.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 ... 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 ‘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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’ for details.