* using log directory ‘/srv/hornik/tmp/CRAN_pretest/TECAT.Rcheck’ * using R Under development (unstable) (2025-04-02 r88103) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘TECAT/DESCRIPTION’ ... OK * this is package ‘TECAT’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/3s] NOTE Maintainer: ‘Jake Reed ’ New submission Non-FOSS package license (file LICENSE) Possibly misspelled words in DESCRIPTION: TECAT (10:8, 16:54) Telomere (4:44, 9:25, 13:29) seqkit (16:13) telomere (8:2, 11:29, 12:15) telomeres (10:56) telomeric (13:10) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Jake", family = "Reed", role = c("aut", "cre"), email = "hreed.ga@gmail.com"), person(given = c("Kevin", "R."), family = "Coombes", role = "aut"), person(given = "Mark", family = "Oelkuct", role = "aut")) as necessary. * 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 whether package ‘TECAT’ can be installed ... [9s/9s] 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 ... [3s/3s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [3s/3s] 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 ... [13s/13s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/3s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [264s/264s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘ONT_example_vignette.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/TECAT.Rcheck/vign_test/TECAT/vignettes/ONT_example_vignette_files/figure-html/plot_threshold_data-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19765 bytes Input file size = 19867 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16507 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 = 16507 Output IDAT size = 16507 bytes (3258 bytes decrease) Output file size = 16585 bytes (3282 bytes = 16.52% decrease) ** Processing: /srv/hornik/tmp/CRAN_pretest/TECAT.Rcheck/vign_test/TECAT/vignettes/ONT_example_vignette_files/figure-html/check_lengths-1.png 288x288 pixels, 8 bits/pixel, 211 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 1810 bytes Input file size = 2533 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 1504 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 1498 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 = 1 f = 0 IDAT size = 1498 Output IDAT size = 1498 bytes (312 bytes decrease) Output file size = 1576 bytes (957 bytes = 37.78% decrease) Quitting from ONT_example_vignette.Rmd:483-536 [truncate] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ONT_example_vignette.Rmd' failed with diagnostics: Join columns in `x` must be present in the data. ✖ Problem with `telo_name`. --- failed re-building ‘ONT_example_vignette.Rmd’ SUMMARY: processing the following file failed: ‘ONT_example_vignette.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