* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SerolyzeR.Rcheck’ * using R Under development (unstable) (2025-10-19 r88945) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘SerolyzeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SerolyzeR’ version ‘1.3.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] NOTE Maintainer: ‘Jakub Grzywaczewski ’ New maintainer: Jakub Grzywaczewski Old maintainer(s): Tymoteusz Kwiecinski * 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 ‘SerolyzeR’ 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 ... [8s/8s] 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 ... [29s/29s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [53s/53s] OK Running ‘testthat.R’ [52s/52s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s/13s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] NOTE Found the following HTML validation problems: Model.html:228:1 (Model.Rd:158): Warning:
anchor "Usage" already defined Model.html:234:1 (Model.Rd:162): Warning:
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anchor "Arguments" already defined PlateBuilder.html:558:1 (PlateBuilder.Rd:313): Warning: missing before PlateBuilder.html:158:1 (PlateBuilder.Rd:78): Warning:
anchor "Usage" already defined PlateBuilder.html:164:1 (PlateBuilder.Rd:82): Warning:
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anchor "Usage" already defined PlateBuilder.html:294:1 (PlateBuilder.Rd:165): Warning:
anchor "Arguments" already defined PlateBuilder.html:318:1 (PlateBuilder.Rd:179): Warning:
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anchor "Arguments" already defined PlateBuilder.html:474:1 (PlateBuilder.Rd:265): Warning:
anchor "Usage" already defined PlateBuilder.html:480:1 (PlateBuilder.Rd:269): Warning:
anchor "Arguments" already defined PlateBuilder.html:503:1 (PlateBuilder.Rd:282): Warning:
anchor "Usage" already defined PlateBuilder.html:509:1 (PlateBuilder.Rd:286): Warning:
anchor "Arguments" already defined PlateBuilder.html:535:1 (PlateBuilder.Rd:302): Warning:
anchor "Usage" already defined PlateBuilder.html:541:1 (PlateBuilder.Rd:306): Warning:
anchor "Arguments" already defined extract_dilutions_from_layout.html:49:1 (extract_dilutions_from_layout.Rd:12): Warning: missing before extract_sample_names_from_layout.html:52:1 (extract_sample_names_from_layout.Rd:12): Warning: missing before read_intelliflex_format.html:50:1 (read_intelliflex_format.Rd:12): Warning: missing before read_xponent_format.html:69:1 (read_xponent_format.Rd:25): Warning: missing before sort_list_by.html:55:1 (sort_list_by.Rd:15): Warning: missing before verbose_cat.html:50:1 (verbose_cat.Rd:12): Warning: missing before * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs