* using log directory ‘/srv/hornik/tmp/CRAN/curesurv.Rcheck’ * using R Under development (unstable) (2024-07-18 r86905) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (1+b1) Debian flang-new version 18.1.8 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘curesurv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘curesurv’ version ‘0.1.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/7s] NOTE Maintainer: ‘Juste Goungounga ’ New submission License components with restrictions and base license permitting such: GPL (>= 3) + file LICENSE File 'LICENSE': YEAR: 2022 COPYRIGHT HOLDER: curesurv authors Possibly misspelled words in DESCRIPTION: Boussari (15:322) al (15:135, 15:334) et (15:132, 15:331) * 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 ‘curesurv’ can be installed ... [14s/14s] 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 ... [33s/33s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: curesurv.Rd: Surv Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... [6s/6s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/16s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘Vignette_tneh.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN/curesurv.Rcheck/vign_test/curesurv/vignettes/Vignette_tneh_files/figure-html/plotpredictnocov-1.png 1920x1536 pixels, 3x8 bits/pixel, RGB Input IDAT size = 116531 bytes Input file size = 116777 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 101531 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 = 101531 Output IDAT size = 101531 bytes (15000 bytes decrease) Output file size = 101609 bytes (15168 bytes = 12.99% decrease) ** Processing: /srv/hornik/tmp/CRAN/curesurv.Rcheck/vign_test/curesurv/vignettes/Vignette_tneh_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 49486 bytes Input file size = 49636 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39917 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 = 39917 Output IDAT size = 39917 bytes (9569 bytes decrease) Output file size = 39995 bytes (9641 bytes = 19.42% decrease) ** Processing: /srv/hornik/tmp/CRAN/curesurv.Rcheck/vign_test/curesurv/vignettes/Vignette_tneh_files/figure-html/predict_tnehcov-1.png 1920x1920 pixels, 3x8 bits/pixel, RGB Input IDAT size = 246709 bytes Input file size = 247147 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 199296 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 = 199296 Output IDAT size = 199296 bytes (47413 bytes decrease) Output file size = 199374 bytes (47773 bytes = 19.33% decrease) ** Processing: /srv/hornik/tmp/CRAN/curesurv.Rcheck/vign_test/curesurv/vignettes/Vignette_tneh_files/figure-html/predicted_to_plot_by_age-1.png 1920x1536 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 62994 bytes Input file size = 63936 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 58301 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 58031 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 = 58031 Output IDAT size = 58031 bytes (4963 bytes decrease) Output file size = 58109 bytes (5827 bytes = 9.11% decrease) ** Processing: /srv/hornik/tmp/CRAN/curesurv.Rcheck/vign_test/curesurv/vignettes/Vignette_tneh_files/figure-html/plot_for_specific_age-1.png 1920x1536 pixels, 3x8 bits/pixel, RGB Input IDAT size = 142812 bytes Input file size = 143094 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 125993 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 = 125993 Output IDAT size = 125993 bytes (16819 bytes decrease) Output file size = 126071 bytes (17023 bytes = 11.90% decrease) ** Processing: /srv/hornik/tmp/CRAN/curesurv.Rcheck/vign_test/curesurv/vignettes/Vignette_tneh_files/figure-html/plot_for_specific_age_2-1.png 1920x1536 pixels, 3x8 bits/pixel, RGB Input IDAT size = 110997 bytes Input file size = 111231 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 96406 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 = 96406 Output IDAT size = 96406 bytes (14591 bytes decrease) Output file size = 96484 bytes (14747 bytes = 13.26% decrease) --- finished re-building ‘Vignette_tneh.Rmd’ --- re-building ‘vignette_mixture.Rmd’ using rmarkdown Error: processing vignette 'vignette_mixture.Rmd' failed with diagnostics: there is no package called ‘bookdown’ --- failed re-building ‘vignette_mixture.Rmd’ SUMMARY: processing the following file failed: ‘vignette_mixture.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [5s/5s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Text line contains an invalid character. l.645 ^^? A funny symbol that I can't read has just been input. Continue, and I'll forget that it ever happened. ! Undefined control sequence. frac{d ln(\Tau (x))}{dx} = \frac {\Tau '(x)}{\Tau (x)} l.947 ...au(x))}{dx} = \frac{\Tau'(x)}{\Tau(x)}}{} . ! Undefined control sequence. \Tau '(x) l.947 ...au(x))}{dx} = \frac{\Tau'(x)}{\Tau(x)}}{} . ! Undefined control sequence. \Tau (x) l.947 ...au(x))}{dx} = \frac{\Tau'(x)}{\Tau(x)}}{} . * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [2s/2s] NOTE Found the following HTML validation problems: curesurv.html:38:25 (curesurv.Rd:189): Warning: unescaped & or unknown entity "τ" * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘curesurv-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 4 NOTEs