cran-comments.md

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 <[email protected]>’
    
    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 <[email protected]>’
    
     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 <[email protected]>’
    
    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.