############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flagme_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flagme/DESCRIPTION’ ... OK * this is package ‘flagme’ version ‘1.66.0’ * 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * 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 loading without being on the library search path ... 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(s) in Rd file 'addXCMSPeaks.Rd': ‘[xcms]{findPeaks-matchedFilter}’ ‘[xcms]{findPeaks-centWave}’ ‘[xcms]{peaksDataset}’ Missing link(s) in Rd file 'plotAlignment-peaksAlignment-method.Rd': ‘plotAlignment’ Missing link(s) in Rd file 'plotClustAlignment-clusterAlignment-method.Rd': ‘plotAlignment’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotAlignment-peaksAlignment-method.Rd: plotAlignment plotClustAlignment-clusterAlignment-method.Rd: plotAlignment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotAlignedFrags 97.938 16.174 64.437 addXCMSPeaks 57.551 10.450 50.920 corPrt 52.907 8.086 43.703 peaksAlignment-class 50.241 10.577 44.275 dynRT 50.255 10.015 43.750 plotFrags 52.367 7.401 42.656 plotAlignment-peaksAlignment-method 51.596 7.651 41.801 ndpRT 49.243 8.964 41.683 progressiveAlignment-class 48.990 7.555 40.995 retFatMatrix 48.890 7.333 40.187 imputePeaks 11.587 0.308 11.946 plotChrom-peaksDataset-method 10.632 0.135 10.795 calcTimeDiffs 9.830 0.519 10.377 rmaFitUnit 9.279 0.032 9.336 dp 7.921 0.307 8.250 gatherInfo 7.779 0.447 8.244 clusterAlignment 7.896 0.299 8.216 multipleAlignment-class 7.525 0.136 7.676 peaksDataset 6.751 0.897 7.669 normDotProduct 7.176 0.271 7.467 plotClustAlignment-clusterAlignment-method 6.844 0.040 6.903 addAMDISPeaks 5.455 0.187 5.730 addChromaTOFPeaks 5.277 0.136 5.423 plotImage 5.100 0.036 5.151 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/flagme.Rcheck/00check.log’ for details.