############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bambu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bambu_3.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/bambu.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bambu/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bambu’ version ‘3.9.2’ * 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: tests/testthat/fixtures/.gitkeep 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 ‘bambu’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'GenomicAlignments:::.result' 'xgboost:::predict.xgb.Booster' 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 readCountWeightedMedian: no visible binding for global variable ‘..valuevar’ readCountWeightedMedian: no visible binding for global variable ‘..timesvar’ updateStartEndReadCount: no visible binding for global variable ‘x’ updateStartEndReadCount: no visible binding for global variable ‘y’ updateStartEndReadCount: no visible binding for global variable ‘z’ Undefined global functions or variables: ..timesvar ..valuevar x y z * checking Rd files ... NOTE checkRd: (-1) bambu.Rd:73: Lost braces 73 | \item{defaultModels}{A model object obtained by code{\link{trainBambu}} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: writeBambuOutput.Rd: SummarizedExperiment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bambu 16.632 0.213 16.982 prepareAnnotations 12.420 0.074 12.559 * 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: Component 1: Modes: numeric, character Component 1: target is numeric, current is character Component 2: Modes: numeric, character Component 2: target is numeric, current is character Component 3: Attributes: < target is NULL, current is list > Component 3: target is numeric, current is factor Component 4: Modes: character, numeric Component 4: Attributes: < target is NULL, current is list > ... ── Failure ('test_isore.R:73:5'): isore.combineTranscriptCandidates completes successfully ── Names of `seIsoReCombined` ('start', 'end', 'readCount', 'intronStarts', 'intronEnds', 'chr', 'strand', 'maxTxScore', 'maxTxScore.noFit', 'NSampleReadCount', 'NSampleReadProp', 'NSampleTxScore', 'confidenceType') don't match 'intronStarts', 'intronEnds', 'chr', 'strand', 'maxTxScore', 'maxTxScore.noFit', 'NSampleReadCount', 'NSampleReadProp', 'NSampleTxScore', 'start', 'end', 'readCount', 'confidenceType' [ FAIL 3 | WARN 8 | SKIP 0 | PASS 131 ] Error: Test failures Execution halted * 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, 6 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/bambu.Rcheck/00check.log’ for details.