############################################################################## ############################################################################## ### ### 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ptairMS/DESCRIPTION’ ... OK * this is package ‘ptairMS’ version ‘1.14.0’ * 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-3.20-bioc/meat/ptairMS.Rcheck/00install.out’ for details. * 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 ... 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 184.072 3.343 196.744 imputeMat 30.543 0.915 33.039 alignSamples 29.659 1.072 32.251 writeEset 29.700 0.771 31.800 impute 27.775 0.767 30.255 getPeakList 26.819 0.745 28.819 annotation 26.747 0.725 28.793 convert_to_mzML 23.100 1.084 25.844 plot 21.943 0.536 23.884 plotTIC 20.502 0.602 22.334 plotRaw 20.275 0.641 22.257 plotCalib 19.838 0.541 21.404 plotFeatures 19.400 0.570 21.122 rmPeakList 19.200 0.463 20.597 updatePtrSet 19.133 0.432 20.634 defineKnots 18.749 0.448 20.514 resetSampleMetadata 18.050 0.535 19.671 exportSampleMetada 18.129 0.450 19.617 setSampleMetadata 18.056 0.409 19.928 importSampleMetadata 18.043 0.402 19.889 getSampleMetadata 17.919 0.462 20.129 getDirectory 17.843 0.494 18.868 changeTimeLimits 17.461 0.422 18.821 getFileNames 17.219 0.498 18.778 createPtrSet 16.213 0.673 17.780 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00check.log’ for details.