* using log directory ‘/srv/hornik/tmp/CRAN/BioPred.Rcheck’ * using R Under development (unstable) (2024-05-29 r86642) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘BioPred/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioPred’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Zihuan Liu ’ New submission Possibly misspelled words in DESCRIPTION: BioPred (3:8) XGBoost (10:73) The Title field starts with the package name. The Title field should be in title case. Current version is: ‘BioPred: an R package for biomarkers analysis in precision medicine’ In title case that is: ‘BioPred: An R Package for Biomarkers Analysis in Precision Medicine’ * 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 ‘BioPred’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [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 ... [10s/10s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [2s/2s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [5s/5s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘Tutorial.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN/BioPred.Rcheck/vign_test/BioPred/vignettes/Tutorial_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 8943 bytes Input file size = 9033 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6962 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6962 Output IDAT size = 6962 bytes (1981 bytes decrease) Output file size = 7040 bytes (1993 bytes = 22.06% decrease) ** Processing: /srv/hornik/tmp/CRAN/BioPred.Rcheck/vign_test/BioPred/vignettes/Tutorial_files/figure-html/unnamed-chunk-9-1.png 576x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 22259 bytes Input file size = 23141 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20635 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20635 Output IDAT size = 20635 bytes (1624 bytes decrease) Output file size = 20713 bytes (2428 bytes = 10.49% decrease) ** Processing: /srv/hornik/tmp/CRAN/BioPred.Rcheck/vign_test/BioPred/vignettes/Tutorial_files/figure-html/unnamed-chunk-10-1.png 768x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 129640 bytes Input file size = 129898 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99748 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99748 Output IDAT size = 99748 bytes (29892 bytes decrease) Output file size = 99826 bytes (30072 bytes = 23.15% decrease) Quitting from lines 152-156 [unnamed-chunk-11] (Tutorial.Rmd) Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: invalid 'row.names' length --- failed re-building ‘Tutorial.Rmd’ SUMMARY: processing the following file failed: ‘Tutorial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] 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, 1 NOTE