############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flagme.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings flagme_1.61.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'flagme/DESCRIPTION' ... OK * this is package 'flagme' version '1.61.0' * 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 whether package 'flagme' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 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 for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/flagme/libs/x64/flagme.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 36.96 3.64 91.58 peaksAlignment-class 23.09 1.53 75.37 addXCMSPeaks 23.05 1.32 70.27 dynRT 21.56 1.83 73.48 ndpRT 21.25 1.99 76.03 corPrt 19.48 1.81 70.01 retFatMatrix 19.56 1.54 66.48 plotFrags 18.67 1.61 64.89 plotAlignment-peaksAlignment-method 18.53 1.59 65.41 progressiveAlignment-class 18.55 1.44 64.99 imputePeaks 10.65 0.65 11.28 dp 9.36 0.36 9.71 rmaFitUnit 9.05 0.52 9.55 plotChrom-peaksDataset-method 8.79 0.39 9.14 gatherInfo 7.99 0.31 8.27 multipleAlignment-class 7.96 0.30 8.23 addAMDISPeaks 6.97 0.16 7.39 calcTimeDiffs 6.44 0.57 7.00 clusterAlignment 6.44 0.43 6.83 plotClustAlignment-clusterAlignment-method 6.32 0.41 6.70 normDotProduct 5.70 0.42 6.88 peaksDataset 5.59 0.36 5.92 * 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/flagme.Rcheck/00check.log' for details.