############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.56.0’ * 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 ‘flagme’ 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 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘xcms:::rectUnique’ 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 addXCMSPeaks: no visible global function definition for ‘bpparam’ addXCMSPeaks: no visible global function definition for ‘sampnames’ addXCMSPeaks : : : no visible global function definition for ‘setNames’ importSpec : : no visible global function definition for ‘setNames’ Undefined global functions or variables: bpparam sampnames setNames Consider adding importFrom("stats", "setNames") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link or links in documentation object 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link or links in documentation object 'plotClustAlignment-clusterAlignment-method.Rd': ‘plotAlignment’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘plotAlignment’ ‘plotChrom’ ‘plotClustAlignment’ Undocumented S4 methods: generic 'show' and siglist 'betweenAlignment' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAlignedFrags 133.687 26.366 115.101 addXCMSPeaks 73.910 13.354 80.748 corPrt 72.006 13.763 78.426 dynRT 71.113 13.884 74.789 retFatMatrix 69.761 14.037 76.109 plotFrags 69.633 13.855 74.506 progressiveAlignment-class 69.150 14.141 75.589 ndpRT 68.931 14.106 78.193 plotAlignment-peaksAlignment-method 68.599 14.058 74.782 peaksAlignment-class 68.719 13.677 75.996 imputePeaks 15.999 0.438 21.927 plotChrom-peaksDataset-method 13.804 0.361 17.836 calcTimeDiffs 11.792 0.411 16.313 rmaFitUnit 11.666 0.400 14.994 gatherInfo 10.610 0.296 14.226 multipleAlignment-class 10.547 0.280 14.551 normDotProduct 9.735 0.256 12.912 clusterAlignment 9.605 0.171 12.836 plotClustAlignment-clusterAlignment-method 9.569 0.169 12.347 dp 9.425 0.308 12.971 peaksDataset 8.850 0.247 11.871 addAMDISPeaks 7.731 0.278 11.090 plotImage 6.017 0.168 7.691 addChromaTOFPeaks 5.820 0.261 8.133 parseChromaTOF 5.643 0.058 7.659 parseELU 5.021 0.027 6.438 * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/flagme.Rcheck/00check.log’ for details.