* using log directory 'd:/RCompile/CRANincoming/R-devel/aaSEA.Rcheck' * using R Under development (unstable) (2025-11-24 r89059 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'aaSEA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'aaSEA' version '1.1.2' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Raja Sekhara Reddy D.M ' New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: al (7:421) et (7:418) CRAN repository db overrides: X-CRAN-Comment: Archived on 2022-06-21 as check problems were not corrected despite reminders. No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: person(given = c("Raja", "Sekhara", "Reddy"), family = "D.M", role = c("aut", "cre"), email = "raja.duvvuru@gmail.com") as necessary. Package has a VignetteBuilder field but no prebuilt vignette index. * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'aaSEA' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'aaSEA' Warning: replacing previous import 'seqinr::a' by 'shiny::a' when loading 'aaSEA' Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'aaSEA' Warning: replacing previous import 'DT::JS' by 'networkD3::JS' when loading 'aaSEA' See 'd:/RCompile/CRANincoming/R-devel/aaSEA.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... WARNING checkRd: (5) Cruciani.Rd:9: \item in \describe must have non-empty label checkRd: (5) Fasgai.Rd:9: \item in \describe must have non-empty label checkRd: (5) Kidera.Rd:9: \item in \describe must have non-empty label * 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 ... WARNING Variables with usage in Rd file 'AAindex.Rd' but not in code: 'AAindex' Variables with usage in Rd file 'Cruciani.Rd' but not in code: 'Cruciani' Variables with usage in Rd file 'Fasgai.Rd' but not in code: 'Fasgai' Variables with usage in Rd file 'Kidera.Rd' but not in code: 'Kidera' Variables with usage in Rd file 'corSubFile.Rd' but not in code: 'corSubFile' * 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 ... OK * checking LazyData ... NOTE 'LazyDataCompression' is specified without 'LazyData' * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'aaSEA_Documentation.Rmd' * checking examples ... ERROR Running examples in 'aaSEA-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getCorPropChange > ### Title: Get property changes associated with correlated substitutions > ### Aliases: getCorPropChange > > ### ** Examples > > getCorPropChange(corSubFile = corSubFile, propertyDF = "Cruciani", propertyIndex = 1) Error in getCorPropChange(corSubFile = corSubFile, propertyDF = "Cruciani", : object 'Cruciani' not found Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... WARNING Directory 'inst/doc' does not exist. Package vignette without corresponding single PDF/HTML: 'aaSEA_Documentation.Rmd' * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'aaSEA_Documentation.Rmd' using rmarkdown Quitting from aaSEA_Documentation.Rmd:82-85 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `getPropChange()`: ! object 'Cruciani' not found --- Backtrace: ▆ 1. └─aaSEA::getPropChange(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics: object 'Cruciani' not found --- failed re-building 'aaSEA_Documentation.Rmd' SUMMARY: processing the following file failed: 'aaSEA_Documentation.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [12s] OK * checking HTML version of manual ... NOTE Found the following HTML validation problems: Cruciani.html:39:1 (Cruciani.Rd:9): Warning: trimming empty
Fasgai.html:39:1 (Fasgai.Rd:9): Warning: trimming empty
Kidera.html:39:1 (Kidera.Rd:9): Warning: trimming empty
aaSEA.html:205:1 (Cruciani.Rd:9): Warning: trimming empty
aaSEA.html:239:1 (Fasgai.Rd:9): Warning: trimming empty
aaSEA.html:279:1 (Kidera.Rd:9): Warning: trimming empty
* DONE Status: 2 ERRORs, 5 WARNINGs, 3 NOTEs