############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SingleMoleculeFootprinting_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck’ * using R Under development (unstable) (2024-11-24 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 ‘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 27 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: program compiled against libxml 212 using older 211 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 ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ 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’ Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ 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 ... 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 * 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 .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 ‘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’ 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’ 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’ Plot_FootprintCharter_SM: no visible global function definition for ‘unnest’ Plot_FootprintCharter_SM: no visible binding for global variable ‘x.axis.breaks’ 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 TF biological.state bulk.SMF coordinate d idx nr.cytosines occupancy partition.coverage partition.coverage.cumsum partition.nr read.idx unnest x.axis.breaks * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 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 ... ERROR Running examples in ‘SingleMoleculeFootprinting-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: FootprintCharter > ### Title: Run FootprintCharter > ### Aliases: FootprintCharter > > ### ** Examples > > > Methylation = qs::qread(system.file("extdata", "Methylation_4.qs", package="SingleMoleculeFootprinting")) > MethSM = Methylation[[2]] > RegionOfInterest = GenomicRanges::GRanges("chr6", IRanges::IRanges(88106000, 88106500)) > RegionOfInterest = IRanges::resize(RegionOfInterest, 80, "center") > > FootprintCharter( + MethSM = MethSM, + RegionOfInterest = RegionOfInterest, + coverage = 30, + k = 16, + n = 5, + TF.length = c(5,75), + nucleosome.length = c(120,1000), + cytosine.coverage.thr = 5, + verbose = TRUE + ) -> FC_results 1. Pooling molecules from all samples 2. Computing sliding windows Discarding 1973/2233 molecules that do not entirely cover the RegionOfInterest Discarding 41/59 cytosines that are NA in more than 0% of the reads Discarding 0/260 molecules that have NAs in more than 0% of the remaining cytosines 3. computing distance matrix *** caught segfault *** address 0x65747562697284, cause 'memory not mapped' Traceback: 1: parallelDist::parDist(x = MethSM_smoothed, method = "euclidean", threads = 1) 2: FootprintCharter(MethSM = MethSM, RegionOfInterest = RegionOfInterest, coverage = 30, k = 16, n = 5, TF.length = c(5, 75), nucleosome.length = c(120, 1000), cytosine.coverage.thr = 5, verbose = TRUE) An irrecoverable exception occurred. R is aborting now ... * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 5 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’ for details.