Outstanding `R CMD check` errors, warnings and relevant notes.

Arr. Here be the list, matey:

DESCRIPTION file looks fine. Not sure what's up here:

Package has a VignetteBuilder field but no prebuilt vignette index.

Easy:

The Title field should be in title case, current version then in title case:
‘R tools for inferring new IGHV alleles from Rep-Seq data’
‘R Tools for Inferring New IGHV Alleles from Rep-Seq Data’

See the .Rbuildignore file I put in the igtools wiki:

* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  vignettes/.build.timestamp
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

No spaces in filenames, I assume:

* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  tests/tigger benchmarking.R
These are not fully portable file names.

Also easy:

* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

Probably best to just add the alakazam dependency, rather than fix this:

* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getSegment.Rd':
  ‘str_extract’

See section 'Cross-references' in the 'Writing R Extensions' manual.

See how to document data objects in the alakazam/shm packages. For example, DNA_COLORS in SeqCore.R alakazam or HS5FModel in TargetModels.R in shm:

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘germline_ighv’ ‘sample_db’
Undocumented data sets:
  ‘germline_ighv’ ‘sample_db’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

Missing roygen comments:

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'createGermlines'
  ‘germline’
Documented arguments not in \usage in documentation object 'createGermlines':
  ‘sequence’

Undocumented arguments in documentation object 'detectNovelV'
  ‘quiet’

Undocumented arguments in documentation object 'findNovelAlleles'
  ‘germlines’
Documented arguments not in \usage in documentation object 'findNovelAlleles':
  ‘germline’

Documented arguments not in \usage in documentation object 'runTigger':
  ‘v_length_col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

Example doesn't work:

* checking examples ... ERROR
Running examples in ‘tigger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modifyChangeoDb
> ### Title: Standardize Sample Db data
> ### Aliases: modifyChangeoDb
> 
> ### ** Examples
> 
> data(sample_db)
> corrected_sample_db = modifySampleDb(sample_db, cols_to_add = c("V_GENE"))
Error: could not find function "modifySampleDb"
Execution halted

We'll need to remove the tests in the tests folder that aren't actually unit tests before submitting the CRAN:

* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' calls not declared from:
  ‘alakazam’ ‘shm’

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