############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings PhosR_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/PhosR.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 ‘PhosR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhosR’ version ‘1.12.0’ * 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: .travis.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 ‘PhosR’ 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘stringi’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE abundPlot: no visible binding for global variable ‘.’ Undefined global functions or variables: . * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed kinaseSubstratePred 43.221 0.248 43.548 siteAnnotate 42.871 0.120 43.080 kinaseSubstrateScore 29.674 0.092 29.820 minmax 28.069 0.108 28.233 kinaseSubstrateProfile 15.419 0.092 15.540 matANOVA 15.082 0.023 15.137 standardise 14.768 0.012 14.808 plotQC 6.342 0.056 6.415 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > library(PhosR) > > test_check("PhosR") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-pathwayAnalysis.R:74:5'): Case B.2: Expected output ────────── `result1` not identical to pathwayOverrepresent(geneSet, annotation, universe, alter1). 1/12 mismatches x[3]: "0.100641107506833" y[3]: "0.100641107506832" [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ] Error: Test failures Execution halted * 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/PhosR.Rcheck/00check.log’ for details.