############################################################################## ############################################################################## ### ### 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_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flagme.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 ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.62.0’ * 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 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 whether 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 Rd file 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link or links in Rd file 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link or links in Rd file '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 152.190 32.934 103.673 addXCMSPeaks 80.869 16.447 72.081 corPrt 78.787 17.384 70.559 peaksAlignment-class 78.252 16.979 70.365 progressiveAlignment-class 77.359 17.077 68.069 dynRT 76.982 17.121 67.852 ndpRT 76.747 16.988 68.020 retFatMatrix 76.907 16.808 67.602 plotAlignment-peaksAlignment-method 76.409 17.043 69.181 plotFrags 75.585 17.015 66.887 imputePeaks 18.696 0.297 19.464 plotChrom-peaksDataset-method 16.509 0.338 17.098 calcTimeDiffs 13.133 0.347 13.761 gatherInfo 12.287 0.266 12.655 rmaFitUnit 12.046 0.328 12.450 multipleAlignment-class 12.189 0.167 12.800 dp 11.345 0.221 11.625 clusterAlignment 11.193 0.202 11.493 normDotProduct 10.239 0.219 10.702 plotClustAlignment-clusterAlignment-method 10.156 0.204 10.772 addAMDISPeaks 9.580 0.299 10.132 peaksDataset 9.439 0.210 9.979 addChromaTOFPeaks 7.228 0.275 7.732 plotImage 6.131 0.165 6.476 parseChromaTOF 5.606 0.054 5.749 parseELU 5.121 0.027 5.398 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck/00check.log’ for details.