nturaga/BgeeCall_review.md

## BgeeCall_review.md

      
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              BgeeCall_review.md
            
          
    BgeeCall review

BiocCheck


Basic run of BiocCheck('BgeeCall') on the package
  * ERROR: Packages providing 1 object(s) used in this package should
  be imported in the NAMESPACE file, otherwise packages importing
  this package may fail.

  package::object in function()
  graphics::mtext in plot_distributions()


File size too big, software packages need to be 5MB in size or
less. Please check "BFG cleaner".
  * Checking individual file sizes...
  	* WARNING: The following files are over 5MB in size:
  '.git/objects/pack/pack-94ca9deb2be0a9e6fc630aa9c82ad98cb3dfbb24.pack'


Other issues,


* Checking for valid maintainer...
    * WARNING: Use Authors@R (preferred) or Author/Maintainer fields
      not both.
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import BgeeDB in NAMESPACE as well as DESCRIPTION.
* Checking vignette directory...
    This is a software package
    * WARNING: Vignette[s] still using 'VignetteIndexEntry{Vignette
      Title}' Update the following files from using template values:
        bgeecall-manual.Rmd


Coding practice issues,

* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        retrieveFromCommunity.R (line 27, column 27)
        retrieveFromCommunity.R (line 44, column 31)
		
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to the following man
      pages which document exported objects:
      create_kallisto_index.Rd, generate_calls_workflow.Rd,

Please run BiocCheck('BgeeCall') on the package and make the
appropriate changes. Install the package BiocCheck and run the
function. We cannot make the change without fixing the issues given
above.
You end up getting,
Summary:
ERROR count: 1
WARNING count: 5
NOTE count: 8

R CMD build

ok
R CMD INSTALL

ok