############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BubbleTree_2.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BubbleTree.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BubbleTree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BubbleTree’ version ‘2.32.0’ * 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 ‘BubbleTree’ can be installed ... OK * checking installed package size ... NOTE installed size is 23.8Mb sub-directories of 1Mb or more: data 23.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 annoByOverlap,Annotate: no visible binding for global variable 'queryHits' Undefined global functions or variables: queryHits * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘BubbleTree-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeRBD > ### Title: makeRBD > ### Aliases: makeRBD makeRBD,RBD-method makeRBD > > ### ** Examples > > > # load sample files > load(system.file("data", "cnv.gr.rda", package="BubbleTree")) > load(system.file("data", "snp.gr.rda", package="BubbleTree")) > > # load annotations > load(system.file("data", "centromere.dat.rda", package="BubbleTree")) > load(system.file("data", "cyto.gr.rda", package="BubbleTree")) > load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree")) > load(system.file("data", "vol.genes.rda", package="BubbleTree")) > load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree")) > > > # initialize RBD object > r <- new("RBD", unimodal.kurtosis=-0.1) > > # create new RBD object with GenomicRanges objects for SNPs and CNVs > rbd <- makeRBD(r, snp.gr, cnv.gr) > head(rbd) seqnames start end width strand seg.id num.mark lrr kurtosis 1 chr1 65625 2066855 2001231 * 1 548 0.1997 0.1830119 2 chr1 2075796 38489397 36413602 * 2 5284 -0.4146 -1.9020390 3 chr1 38511244 39761601 1250358 * 3 72 -0.0511 -2.0000000 4 chr1 39763396 39982177 218782 * 4 112 0.0401 -0.9912620 5 chr1 39988109 43905367 3917259 * 5 601 0.0372 -1.4809979 6 chr1 43905709 44128685 222977 * 6 53 0.2822 -2.0000000 hds hds.sd het.cnt seg.size 1 0.01220 0.05007095 71 0.24809178 2 0.35600 0.06296830 501 2.39218420 3 0.15555 0.03471894 2 0.03259600 4 0.12060 0.06761821 4 0.05070489 5 0.14560 0.06186714 47 0.27208605 6 0.07280 0.05176022 2 0.02399428 > > # create a new prediction > btreepredictor <- new("BTreePredictor", rbd=rbd, max.ploidy=6, prev.grid=seq(0.2,1, by=0.01)) > pred <- btpredict(btreepredictor) > > # create rbd plot > btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10) > btree <- drawBTree(btreeplotter, pred@rbd) Warning in drawBTree(btreeplotter, pred@rbd) : More ploidy might be suggested: 1.6, 1.6, 2.2, 1.7, 1.9, 1.5, 1.7, 2.2, 1.9, 2.1, 1.7 > print(btree) > > # create rbd.adj plot > btreeplotter <- new("BTreePlotter", branch.col="gray50") > btree <- drawBTree(btreeplotter, pred@rbd.adj) Warning in drawBTree(btreeplotter, pred@rbd.adj) : More ploidy might be suggested: 1.8, 1.9, 2.1, 2, 2.2, 2.9, 2.3, 2.6, 1.8, 1.9, 2, 2.3, 3, 2.6, 2.9, 2.3 > print(btree) * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/BubbleTree.Rcheck/00check.log’ for details.