############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flagme.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flagme_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'flagme/DESCRIPTION' ... OK * this is package 'flagme' version '1.50.0' * checking package namespace information ... NOTE Namespace with empty importFrom: 'gcspikelite' * 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 * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... OK * 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 ... WARNING man/plotMultipleSpectra.Rd: non-ASCII input and no declared encoding problem found in 'plotMultipleSpectra.Rd' * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/flagme/libs/i386/flagme.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/flagme/libs/x64/flagme.dll': 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. 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMultipleSpectra 34.11 0.44 94.89 peaksAlignment 22.41 0.30 73.01 ndpRT 21.50 0.27 80.50 corPrt 21.48 0.15 82.97 dynRT 21.22 0.31 69.04 plotSpectra 21.16 0.36 69.13 retFatMatrix 13.28 0.09 42.00 addXCMSPeaks 8.50 0.20 29.05 imputePeaks 8.26 0.08 10.33 plot 7.38 0.06 7.44 calcTimeDiffs 6.55 0.27 18.23 addAMDISPeaks 5.67 0.41 23.36 progressiveAlignment 5.65 0.24 5.88 rmaFitUnit 5.68 0.06 5.75 gatherInfo 5.56 0.02 5.58 multipleAlignment 5.53 0.01 5.55 clusterAlignment 5.03 0.17 5.20 compress 5.05 0.13 5.18 peaksDataset 4.98 0.13 5.11 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMultipleSpectra 34.66 0.95 97.83 plotSpectra 23.92 0.69 78.08 peaksAlignment 23.41 0.66 77.12 ndpRT 22.69 0.50 74.17 dynRT 22.86 0.31 118.41 corPrt 21.29 0.57 288.89 retFatMatrix 14.74 0.42 47.86 imputePeaks 8.92 0.15 9.08 addXCMSPeaks 8.45 0.12 33.34 plot 7.67 0.16 7.84 calcTimeDiffs 6.77 0.13 6.89 rmaFitUnit 6.75 0.14 6.89 progressiveAlignment 6.53 0.12 6.66 multipleAlignment 5.75 0.07 5.81 gatherInfo 5.55 0.05 5.59 compress 5.17 0.18 5.36 clusterAlignment 5.26 0.08 6.56 addAMDISPeaks 5.03 0.21 5.23 normDotProduct 5.17 0.03 5.21 peaksDataset 5.00 0.09 5.11 addChromaTOFPeaks 3.81 0.06 10.35 * 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 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck/00check.log' for details.