-
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
Hello Nitesh,
I fixed some BiocCheck issues.
I still have one WARNING because my .pack file is bigger than 5Mo (it is actually 5.8Mo). It was already the case during the last review of my package. Is it ok for you if I keep it like that? I used bfg to remove all blob files bigger than 5Mo.
Remaining NOTES are :
[1] "Recommended function length <= 50 lines."
=> I have one big function of 120 lines. and 10 function between 50 and 76 lines. Not sure it is better to split them in different functions. Please tell me if you want me to work on this.
[2] "Consider adding runnable examples to the following man pages which document exported objects:"
=> The package is dependant of kallisto and these functions can not be run without kallisto. As it is not allowed to install kallisto by default user can choose to install it using a function but then I can not test 2 functions using kallisto (I added examples with dontrun{} tags)
[3] "Usage of dontrun{} / donttest{} found in man page examples."
=> correspond to examples of functions dependant of kallisto
[4] "Consider shorter lines; 235 lines (4%) are > 80 characters long."
=> I try to avoid long lines. These lines should not be longer than 100 characters
[5] "Consider multiples of 4 spaces for line indents, 61 lines(1%) are not."
=> do I need to take care of these lines?
[6] "Cannot determine whether maintainer is subscribed to the bioc-devel mailing\nlist (requires admin credentials). Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"
=> I am subscribed to the bioc-devel mailing list.
Hope my modifications/comments helped for the review process.
and... Merry Christmas :-D