############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BiocOncoTK_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BiocOncoTK.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 ‘BiocOncoTK/DESCRIPTION’ ... OK * this is package ‘BiocOncoTK’ version ‘1.22.0’ * 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 ... NOTE Found the following hidden files and directories: .dockstore.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BiocOncoTK’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: data 2.2Mb pamphlets 4.5Mb * 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 ... NOTE ggscat_av: warning in png(file = tempfile()): partial argument match of 'file' to 'filename' .flexbi: no visible binding for global variable ‘v1’ .flexbi: no visible binding for global variable ‘v2’ .rainfall.bq.df: no visible global function definition for ‘seqlengths’ .rainfall.maeGRL.df: no visible global function definition for ‘genome’ .rainfall.maeGRL.df: no visible global function definition for ‘seqlengths’ acronym_to_system: no visible binding for global variable ‘map_tcga_ncit’ add_sym: no visible global function definition for ‘mapIds’ bipg_tests: no visible global function definition for ‘new’ checkCache_patel: no visible global function definition for ‘BiocFileCache’ chrbounds_basic: no visible global function definition for ‘seqlengths’ ggFeatDens : : no visible binding for global variable ‘Consequence’ ggFeatDens: no visible binding for global variable ‘tfstart’ ggFeatureSegs: no visible binding for global variable ‘symbol’ ggMutDens : : no visible binding for global variable ‘Consequence’ ggMutDens: no visible binding for global variable ‘project_short_name’ ggbox: no visible binding for global variable ‘acronym’ ggbox: no visible binding for global variable ‘symbol’ ggbox: no visible binding for global variable ‘log2ex’ ggbox: no visible binding for global variable ‘msicode’ ggscat: no visible binding for global variable ‘acronym’ ggscat: no visible binding for global variable ‘symbol’ ggscat: no visible binding for global variable ‘msival’ ggscat: no visible binding for global variable ‘log2ex’ ggscat_av: no visible binding for global variable ‘acronym’ ggscat_av: no visible binding for global variable ‘symbol’ ggscat_av: no visible binding for global variable ‘msival’ ggscat_av: no visible binding for global variable ‘tmsi’ ggscat_av: no visible binding for global variable ‘log2exa’ mc3toGR : : no visible binding for global variable ‘Consequence’ multiviz: no visible binding for global variable ‘acronym’ multiviz: no visible binding for global variable ‘msival’ prc: no visible binding for global variable ‘acronym’ prc: no visible global function definition for ‘right_join’ rainfall: no visible global function definition for ‘genome’ tumNorSet : : no visible global function definition for ‘pancan_SE’ Undefined global functions or variables: BiocFileCache Consequence acronym genome log2ex log2exa mapIds map_tcga_ncit msicode msival new pancan_SE project_short_name right_join seqlengths symbol tfstart tmsi v1 v2 Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Note: found 46 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 429185 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 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: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr * 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, 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/BiocOncoTK.Rcheck/00check.log’ for details.