.BioconductorQualitative.yml

Bioconductor:
    package:
      Multi platform build/check:
        Usage: https://builder.r-hub.io/
        Status: OK
      argument values:
        Usage: Don’t trust users to provide correct argument values
        Status: OK
      Choose good package name:
        Status: OK
      Make sure that your package idea is actually new:
        Status: OK
    CodingStyle:
      Indentation:
        Usage: Use 4 spaces for indenting. No tabs.
        Status: OK
      LineLength:
        Usage: No lines longer than 80 characters.
        Status:
        NOTE:
            1: seem impossible to format to 80, even using limits of 70 char, and this using formatR or orther r stylers (e.g., tidyverse-style)
      Variable:
        Name:
          Usage:
            1: Use camelCaps  initial lowercase, then alternate case between words.
            Status:
              Note: REVIEW NEEDED
      Function:
        Name:
          Usage:
            1: Use camelCaps initial lower case, then alternate case between words.
            2: DoNotUse Do not use ‘.’ (in the S3 class system, some(x) where x is class A will dispatch to some.A).
            3: Prefix Prefix non-exported functions with a ‘.’.
            Status:
              NOTE: OK
      Class:
        Name:
          Usage:
            Use CamelCaps: initial upper case, then alternate case between words.
            Status: OK
      File:
        RCode:
          Name:
            Usage:
              Prefix: Use the prefix ‘methods-‘ for S4 class methods, e.g., ‘methods-coverage.R’. Generic definitions can be listed in a single file, ‘AllGenerics.R’, and class definitions in ‘AllClasses.R’.
              Extension: Filename extension for R code should be ‘.R’.
              Status:
                NOTE: OK
        man:
          Name:
            Usage:
              Extension: Filename extension for man pages should be ‘.Rd’.
              Status:
                NOTE: OK
      Comments:
        Usage:
          Marker: Use “##” to start full-line comments
          Indentation: Indent at the same level as surrounding code.
        Status:
          NOTE: OK
      UseOfSpace:
        Usage:
          AfterComma: Always use space after a comma. This a, b, c.
          AroundEqualOperator: No space around “=” when using named arguments to functions. This somefunc(a=1, b=2)
          AroundBinaryOperator: Space around all binary operators a == b.
          Status: OK
      Namespaces:
        Usage: Import all symbols used from packages other than “base”. Except for default packages (base, graphics, stats, etc.) or when overly tedious, fully enumerate imports.
        Export: Export all symbols useful to end users. Fully enumerate exports.
      End-User messages:
        Usage:
          messages: message() communicates diagnostic messages (e.g., progress during lengthy computations) during code evaluation.
          Warnings: warning() communicates unusual situations handled by your code.
          stop: stop() indicates an error condition.
          print: cat() or print() are used only when displaying an object to the user, e.g., in a show method.
      Test coverage:
        Usage:
        Status: OK
    build:
      Command: R build .
      Status: OK
    check:
      Guidelines: http://r-pkgs.had.co.nz/check.html
      Command: R CMD check SOMNiBUS_*.tar.gz
      Checks:
        Global Status:
          ERROR: 1
          WARNING: 1
          NOTE: 2
          Metadata:
            Status: OK
          Package structure:
            Status: OK
          Description:
            Status: OK
          Namespace:
            Status: OK
          R code:
            Status:
              NOTE:
                1: "Unexported objects imported by ':::' calls"
                2: "Undefined global functions or variables"
          Data: OK
          Documentation:
            Status: OK
          Demos:
          Compiled code:
          Tests:
          Vignettes:
    BiocCheck:
      Guidelines: http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#bioccheck
      Checks:
        Global Status:
          ERROR: 2
          WARNING: 0
          NOTE: 7
        Dependency Checks:
          Status:
            NOTE:
              1: Consider clarifying how 1 object(s) are initialized. Maybe it is part of a data set loaded with data(), or perhaps part of       an object referenced in with() or within().
        Deprecated Package Checks:
          Status:
        Remotes Usage Check:
          Status:
        Version Checks:
          Status:
        Package and File Size Check:
          Status:
        biocViews Checks:
          Status:
        Build System Compatibility Checks:
          Status:
        NAMESPACE checks:
          Status:
        Vignette Checks:
          Status:
        Checking Install or Update Package Calls in R code:
          Status:
        Coding Practices Checks:
          Status:
            NOTE:
              1: Avoid '<<-' if possible (found in 1 files)
              2: Avoid sapply(); use vapply()
        Function length checking:
          Status:
            NOTE:
              1: Recommended function length <= 50 lines.
        man page checking:
          Status:
            ERROR:
              1: Consider shorter lines; 198 lines (12%) are > 80 charactersAt least 80% of man pages documenting exported objects must have runnable examples. The following pages do not (BSMethEMUpdate.Rd, BSMethSim.Rd)
        NEWS checks:
          Status:
        Unit Test Checks:
          Status:
        Formatting checks:
          Status:
            NOTE:
              1: Consider shorter lines; 198 lines (12%) are > 80 characters
              2: Consider multiples of 4 spaces for line indents, 116
        Duplication checks:
          Status:
        bioc-devel Subscription Check:
          Status:
            ERROR:
        Support Site Registration Check:
          Status:
            ERROR: