* using log directory 'd:/RCompile/CRANincoming/R-devel/myTAI.Rcheck' * using R Under development (unstable) (2024-10-01 r87205 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'myTAI/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'myTAI' version '2.0.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [14s] NOTE Maintainer: 'Hajk-Georg Drost ' New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: Drost (25:120) Transcriptomics (3:21) al (25:129) et (25:126) transcriptome (25:209, 25:312) transcriptomes (25:104) CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-10-01 as issues were not corrected in time. Found the following (possibly) invalid URLs: URL: https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/bby074 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btx835/4772684 From: README.md Status: 403 Message: Forbidden URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty1018/5239655 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/bioinformatics/article/34/9/1589/4772684 From: README.md Status: 403 Message: Forbidden URL: https://academic.oup.com/g3journal/article/13/6/jkad077/7097621 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/gbe/article/10/11/2906/5140197 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/gbe/article/10/8/2037/5061555 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/gbe/article/8/6/1812/2574026 From: inst/doc/Introduction.html inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/gbe/article/9/6/1519/3867914 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msw284 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article/32/1/258/2925575 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article/32/5/1221/1125964 From: inst/doc/Introduction.html README.md Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article/33/11/3031/2272516 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article/33/5/1158/2580081 From: README.md Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article/33/5/1245/2579728 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://academic.oup.com/mbe/article/38/1/31/5900268 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://www.sciencedirect.com/science/article/pii/S0168952507002995 From: inst/doc/Introduction.html inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://www.sciencedirect.com/science/article/pii/S016895251300111X From: inst/doc/Introduction.html inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden URL: https://www.sciencedirect.com/science/article/pii/S0959437X16302040 From: README.md Status: 403 Message: Forbidden URL: https://www.sciencedirect.com/science/article/pii/S0960982222007217 From: inst/doc/Phylostratigraphy.html Status: 403 Message: Forbidden Please use DOIs for the following publisher URLs: https://academic.oup.com/bioinformatics/article/34/9/1589/4772684 https://academic.oup.com/gbe/article/10/11/2906/5140197 https://academic.oup.com/gbe/article/10/8/2037/5061555 https://academic.oup.com/gbe/article/8/6/1812/2574026 https://academic.oup.com/gbe/article/9/6/1519/3867914 https://academic.oup.com/mbe/article/32/1/258/2925575 https://academic.oup.com/mbe/article/32/5/1221/1125964 https://academic.oup.com/mbe/article/33/11/3031/2272516 https://academic.oup.com/mbe/article/33/5/1158/2580081 https://academic.oup.com/mbe/article/33/5/1245/2579728 https://academic.oup.com/mbe/article/38/1/31/5900268 https://www.sciencedirect.com/science/article/pii/S0168952507002995 https://www.sciencedirect.com/science/article/pii/S016895251300111X https://www.sciencedirect.com/science/article/pii/S0959437X16302040 https://www.sciencedirect.com/science/article/pii/S0960982222007217 * 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 serialization versions ... OK * checking whether package 'myTAI' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking installed package size ... 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 ... 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 ... [14s] OK * checking Rd files ... 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [57s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [49s] OK Running 'testthat.R' [49s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [16s] OK * checking HTML version of manual ... [11s] OK * DONE Status: 1 NOTE