############################################################################## ############################################################################## ### ### 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88129) * using platform: aarch64-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 Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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-3.21-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 ... NOTE Non-topic package-anchored link(s) in Rd file 'detectPeak.Rd': ‘[ptairMS]{ptrSet}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 98.670 5.670 104.494 writeEset 18.368 1.263 19.635 imputeMat 16.759 1.384 18.209 alignSamples 16.624 1.455 18.099 getPeakList 16.604 1.203 18.940 impute 16.437 1.133 18.856 annotation 14.579 1.121 15.704 convert_to_mzML 13.957 0.738 14.698 plotTIC 13.027 0.891 13.948 rmPeakList 12.468 0.921 13.391 plotFeatures 12.330 0.959 13.321 updatePtrSet 12.469 0.782 13.355 plot 12.096 0.946 13.053 defineKnots 11.929 0.791 12.795 plotRaw 11.339 0.777 12.142 getSampleMetadata 10.543 0.754 12.474 importSampleMetadata 10.337 0.804 11.710 plotCalib 10.255 0.809 11.180 resetSampleMetadata 10.248 0.808 11.072 getFileNames 10.154 0.743 10.908 createPtrSet 10.086 0.762 10.887 setSampleMetadata 10.258 0.507 10.779 changeTimeLimits 9.183 0.869 10.052 exportSampleMetada 8.941 0.413 9.354 getDirectory 7.099 0.490 7.735 * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ptairMS.Rcheck/00check.log’ for details.