* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MetabolSSMF.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘MetabolSSMF/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetabolSSMF’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Wenxuan Liu ’ New submission Possibly misspelled words in DESCRIPTION: Metabolomics (7:50) metabolomic (3:52) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Wenxuan", family = "Liu", role = c("aut", "cre"), email = "wenxuan.liu@ucdconnect.ie"), person(given = c("Thomas", "Brendan"), family = "Murphy", role = "aut"), person(given = "Lorraine", family = "Brennan", role = "aut")) as necessary. The Title field should be in title case. Current version is: ‘Simplex-structured matrix factorisation for metabolomic analysis’ In title case that is: ‘Simplex-Structured Matrix Factorisation for Metabolomic Analysis’ Found the following URLs which should use \doi (with the DOI name only): File ‘bootstrap.Rd’: https://doi.org/10.1177/0049124189018002003 File ‘sARI.Rd’: https://doi.org/10.1007/s11634-018-0346-x File ‘ssmf.Rd’: https://doi.org/10.1137/20M1354982 * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘MetabolSSMF’ can be installed ... [4s/4s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘LICENSE.md’ ‘MetabolSSMF.Rproj’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'diversity.Rd': \examples lines wider than 100 characters: membership2 <- matrix(c(0.1, 0.2, 0.3, 0.4, 0.3, 0.2, 0.4, 0.1, 0.2, 0.3, 0.1, 0.4), nrow=3, ncol=4, byrow=TRUE) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... NOTE ‘qpdf’ made some significant size reductions: compacted ‘MetabolSSMF.pdf’ from 689Kb to 542Kb consider running tools::compactPDF() on these files, or build the source package with --compact-vignettes * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [145s/76s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed gap 126.050 0.436 64.578 bootstrap 15.644 0.267 8.362 * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘caroline’ ‘ggsci’ * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘MetabolSSMF.Rmd’ using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'setup'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Warning in eng_r(options) : Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Quitting from lines 68-76 [unnamed-chunk-4] (MetabolSSMF.Rmd) Error: processing vignette 'MetabolSSMF.Rmd' failed with diagnostics: there is no package called 'ggsci' --- failed re-building ‘MetabolSSMF.Rmd’ SUMMARY: processing the following file failed: ‘MetabolSSMF.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 6 NOTEs