############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ptairMS’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’ See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * 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 ... WARNING '::' or ':::' imports not declared from: ‘htmlwidgets’ ‘plyr’ There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’ ‘processFileTemporalNominalMass’ ‘tofToMz’ * 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 line endings in C/C++/Fortran sources/headers ... 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 detectPeak 99.467 2.780 104.613 writeEset 19.752 0.845 20.689 imputeMat 18.409 0.879 19.394 alignSamples 16.867 1.136 18.081 getPeakList 16.822 0.689 18.097 annotation 15.608 0.881 16.580 impute 15.080 0.768 15.927 convert_to_mzML 14.281 0.565 14.993 plotRaw 12.657 0.555 13.252 plotTIC 12.542 0.459 13.058 plot 12.373 0.446 12.854 resetSampleMetadata 11.549 0.481 12.071 setSampleMetadata 11.458 0.481 12.084 updatePtrSet 11.384 0.473 11.979 importSampleMetadata 11.238 0.372 11.644 defineKnots 11.270 0.320 11.639 plotCalib 10.964 0.522 11.541 plotFeatures 10.910 0.497 11.513 getFileNames 10.610 0.376 12.720 rmPeakList 10.469 0.450 10.986 getDirectory 10.402 0.381 11.631 createPtrSet 9.986 0.331 10.364 exportSampleMetada 9.699 0.389 12.127 changeTimeLimits 8.926 0.598 9.669 getSampleMetadata 8.470 0.417 9.000 * 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: 1. └─ptairMS (local) test_alignSamples() 2. └─testthat::expect_equal(nrow(Biobase::exprs(eset)), 1) at test-alignment.R:40:3 ── Failure ('test-annotation.R:32:1'): annotateVOC function and findIsotope ──── Biobase::fData(bacteria.eset)[1, "isotope"] not equal to row.names(Biobase::fData(bacteria.eset))[2]. 1/1 mismatches x[1]: "60.0514" y[1]: "59.0608" Backtrace: ▆ 1. └─ptairMS (local) test_annotateVOC_and_isotope() 2. └─testthat::expect_equal(...) at test-annotation.R:28:3 [ FAIL 3 | WARN 0 | SKIP 0 | PASS 56 ] 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, 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00check.log’ for details.