############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicInteractionNodes.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicInteractionNodes_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicInteractionNodes.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 ‘GenomicInteractionNodes/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicInteractionNodes’ version ‘1.6.0’ * 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 ‘GenomicInteractionNodes’ can be installed ... OK * 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 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 ... OK * 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 ... ERROR Running examples in ‘GenomicInteractionNodes-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: enrichmentAnalysis > ### Title: Gene ontology enrichment analysis > ### Aliases: enrichmentAnalysis > > ### ** Examples > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## for human hg19 Loading required package: GenomicFeatures Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(org.Hs.eg.db) ## used to convert gene_id to gene_symbol > library(GO.db) > set.seed(123) > node_regions <- createRandomNodes(TxDb.Hsapiens.UCSC.hg19.knownGene) 403 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this message. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 20 out-of-bound ranges located on sequence chr22. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 20 out-of-bound ranges located on sequence chr22. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 20 out-of-bound ranges located on sequence chr22. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > node_regions <- + annotateNodes(node_regions, + TxDb.Hsapiens.UCSC.hg19.knownGene, + org.Hs.eg.db) 403 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this message. > enr <- enrichmentAnalysis(node_regions, org.Hs.eg.db, onto="BP") Using `select()` to retreive the GO terms. 'select()' returned 1:many mapping between keys and columns * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1157409 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. [1] TRUE > require("org.Hs.eg.db") || stop("unable to load Package:org.Hs.eg.db") Loading required package: org.Hs.eg.db [1] TRUE > require("GO.db") || stop("unable to load Package:GO.db") Loading required package: GO.db [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat [1] TRUE > test_check("GenomicInteractionNodes") * 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: 2 ERRORs See ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicInteractionNodes.Rcheck/00check.log’ for details.