-
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
ok
ok
Hi @jwollbret
Thanks for getting back to me on this.
I'm sure you are subscribed to bioc-devel.
I will take a look at this today and get back to you. I think we should skip the SPB and just review the package behind the scenes and get the package converted from workflow to software.