cran-comments.md

In tardipede/concatipede: Easy Concatenation of Fasta Sequences

Test environments

• local macOS 11.4, R 4.0.2
• 0 errors | 0 warnings | 0 notes
• rhub::check_for_cran(), platform Fedora Linux, R-devel

• 0 errors | 0 warnings | 2 notes ``` ❯ checking CRAN incoming feasibility ... NOTE Maintainer: ‘Matteo Vecchi [e-mail]’

  New submission

  Possibly mis-spelled words in DESCRIPTION: Fasta (2:30)

  ❯ checking examples ... NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed auto_match_seqs 7.495 0.181 1.9 ``` * rhub::check_for_cran(), platform Windows Server 2008 R2 SP1, R-devel, 32/64 bit - 0 errors | 0 warnings | 0 note

• rhub::check_for_cran(), platform macOS 10.13.6 High Sierra, R-release, brew (with spell-check turned off)

• 0 errors | 0 warnings | 1 notes ``` ❯ checking CRAN incoming feasibility ... NOTE Maintainer: ‘Matteo Vecchi [e-mail]’

  New submission ```

• rhub::check_for_cran(), platform Ubuntu Linux 20.04.1 LTS, R-release, GCC

• 0 errors | 0 warnings | 1 note ``` ❯ checking CRAN incoming feasibility ... NOTE Maintainer: ‘Matteo Vecchi [e-mail]’

  New submission

  Possibly mis-spelled words in DESCRIPTION: Fasta (2:30) ```

Comments

• r-hub checks return only minor notes.
• We addressed all the comments received after the first CRAN submission (see below) and bumped the package version number to 1.0.1.
• Details of changes to address comments after first CRAN submission:
• 1 Please write TRUE and FALSE instead of T and F. (Please don't use 'T' or 'F' as vector names.), e.g.: man/get_genbank_table.Rd: get_genbank_table( df = NULL, filename = NULL, writetable = F, out = "", excel.sheet = 1 ) man/rename_sequences.Rd: rename_sequences( fasta_files, df = NULL, filename = NULL, marker_names = NULL, out = NULL, format = "fasta", excel.sheet = 1, unalign = F, exclude ) DONE

• 2 Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar) Missing Rd-tags: example-files-shipped-with-the-package.Rd: \value pipe.Rd: \arguments, \value rename_sequences.Rd: \value DONE: : Added a \value tag for rename_sequences(). Improved the import of magrittr's pipe so that it is properly documented. Added a function concatipede_example() to document in a clean way the example files shipped with the package. There should be no missing Rd tags now.

• 3 ``` Please always make sure to reset to user's options(), working directory or par() after you changed it in examples and vignettes and demos. e.g.: oldpar <- par(mfrow = c(1,2)) ... par(oldpar)

  old <- options(digits = 3)
  ...
  options(old)
  
  oldwd <- getwd()
  ...
  setwd(oldwd)
  
  e.g.: tests and vignette
  ```
  

  DONE: : Double-checked that the initial working directory was restored at the end of the tests. Made sure that options(), working directory, and par() are restored in the vignette.

tardipede/concatipede documentation built on April 15, 2022, 6:25 p.m.