############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:Spectra.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings Spectra_1.19.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Spectra.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘Spectra/DESCRIPTION’ ... OK * this is package ‘Spectra’ version ‘1.19.4’ * 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 ‘Spectra’ can be installed ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .Call("_H5Dclose", ..., PACKAGE = "rhdf5") .Call("_H5Dopen", ..., PACKAGE = "rhdf5") .Call("_H5Dread", ..., PACKAGE = "rhdf5") .Call("_H5Fclose", ..., PACKAGE = "rhdf5") .Call("_H5Fopen", ..., PACKAGE = "rhdf5") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'MsBackend.Rd': ‘[MsCoreUtils:matching]{MsCoreUtils::closest()}’ Non-topic package-anchored link(s) in Rd file 'addProcessing.Rd': ‘[MsCoreUtils:matching]{MsCoreUtils::common()}’ Non-topic package-anchored link(s) in Rd file 'joinPeaks.Rd': ‘[MsCoreUtils:matching]{MsCoreUtils::join()}’ Non-topic package-anchored link(s) in Rd file 'spectra-plotting.Rd': ‘[MsCoreUtils:matching]{MsCoreUtils::common()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed estimatePrecursorMz 50.157 0.969 49.237 plotMzDelta 7.355 0.701 7.624 addProcessing 7.004 0.598 9.112 combinePeaks 6.132 1.246 4.589 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/Spectra.Rcheck/00check.log’ for details.