diff --git a/R/vcfR_to_tidy_functions.R b/R/vcfR_to_tidy_functions.R index 149c14a..61e14a8 100644 --- a/R/vcfR_to_tidy_functions.R +++ b/R/vcfR_to_tidy_functions.R @@ -17,7 +17,8 @@ #' with very large data sets, they provide a good framework for handling and filtering #' large variant data sets. For some background #' on the benefits of such "tidy" data frames, see -#' \doi{doi.org/10.18637/jss.v059.i10}. +#' \doi{10.18637/jss.v059.i10}. +# ' \doi{doi.org/10.18637/jss.v059.i10}. # ' \doi{doi.org/10.18637/jss.v059.i10}{this article}. # ' \href{https://doi.org/10.18637/jss.v059.i10}{this article}. # ' \href{https://www.jstatsoft.org/article/view/v059i10}{this article}. diff --git a/cran-comments.md b/cran-comments.md index f58e120..322f4f6 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,19 @@ -## Submission -This submission includes updates to the package vcfR. +## Resubmission +The previous submission was returned from CRAN with the following comment. + +Found the following (possibly) invalid DOIs: + DOI: doi.org/10.18637/jss.v059.i10 + From: man/vcfR_to_tidy_conversion.Rd + Status: 404 + Message: Not Found + +Please write the doi as +\doi{10.18637/jss.v059.i10} +i.e. without the "doi.org/" prefix + +This issue was reproduced on WinBuilder, the suggested fix was applied, and the fix was validated by resubmitting to WinBuilder which no longer reported the issue. + ## Test environments @@ -12,15 +25,13 @@ R 4.3.2; Ubuntu 22.04.3 LTS R 4.4Mb libs 9.1Mb - * win-builder: - using R Under development (unstable) (2023-02-09 r83797 ucrt) - using platform: x86_64-w64-mingw32 (64-bit) - R was compiled by - gcc.exe (GCC) 12.2.0 - GNU Fortran (GCC) 12.2.0 - running under: Windows Server 2022 x64 (build 20348) - +* using R Under development (unstable) (2023-12-04 r85659 ucrt) +* using platform: x86_64-w64-mingw32 +* R was compiled by + gcc.exe (GCC) 12.3.0 + GNU Fortran (GCC) 12.3.0 +* running under: Windows Server 2022 x64 (build 20348) * GitHub Actions MacOS-latest (release) - macOS Monterey 12.7.1-R version 4.3.2 (2023-10-31) @@ -36,13 +47,8 @@ Windows Server 2012 R2 x64 (build 9600); R Under development (unstable) (2023-12 * rhub: None for this submission - ## revdepcheck results - -We checked 18 reverse dependencies (4 from CRAN + 14 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 0 new problems - * We failed to check 0 packages +None for this submission ## Thank you CRAN Core Team! diff --git a/man/vcfR_to_tidy_conversion.Rd b/man/vcfR_to_tidy_conversion.Rd index 389f501..78bca8a 100644 --- a/man/vcfR_to_tidy_conversion.Rd +++ b/man/vcfR_to_tidy_conversion.Rd @@ -112,7 +112,7 @@ optimized for operation on large data frames, and, though they can bog down with very large data sets, they provide a good framework for handling and filtering large variant data sets. For some background on the benefits of such "tidy" data frames, see -\doi{doi.org/10.18637/jss.v059.i10}. +\doi{10.18637/jss.v059.i10}. For some filtering operations, such as those where one wants to filter genotypes upon GT fields in combination with INFO fields, or more complex