Bioconductor Formatting

[jmitchell81]

06.18.24 Reviewer Comments

• I still don't see any set.seed() calls in the HTML vignettes. #126
• 2. You still have at least one occurence of domino2 in your doc. Please make sure to find and correct them all.
• It doesn't seem that you use standard markdown syntax in your .Rmd files. As a consequence there are many small cosmetic problems with the rendering of the HTML vignettes. See for example \underline{named} vector or {SingleCellExperiment} here #124
• 4. Four mysterious lines of code right below the title of the vignette and before any text. That's quite an unusual and pretty dry way to start a vignette! What is this code? What does it do? Why is it here? Does it work properly without explicitly loading any package first? What package(s)?
• For example, if I run these four lines of code in a fresh R session and try to display the dom object, I get hundreds of screens of output. This is unfortunate because domino objects actually have a show() method whose purpose is to prevent that. But that method is defined in the dominoSignal package and since the package is not loaded the method is not found. Or maybe it's because the package does not export the method, I'm not sure. In any case you need to export that method. #125
• Many of the examples in the man pages use a non-exported non-documented symbol (dominoSignal:::pbmc_dom_built_tiny). This is not good practice. You should only expose symbols that are exported and documented to the user. (edited) #123

BiocCheck Errors

• ERROR: Packages providing 2 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail. #35
• ERROR: No biocViews terms found #37
• ERROR: Package directory 'domino' must match Package: field (got 'domino2').
• ERROR: At least 80% of man pages documenting exported objects must have runnable examples #58
• ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags.
• vignette building fails for mac os #56
• persistent cache #70
• pick new tiny examples to use withtestdata.R
• recreate pbmc_domino_built.rds for the vignette #110

BiocCheck Warnings

• WARNING: The following files are over 5MB in size #44
• WARNING: Avoid T/F variables; If logical, use TRUE/FALSE #38
• WARNING: Add non-empty \value sections to the following man pages #42

BiocCheck Notes

• NOTE: Consider clarifying how 5 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). #40
• NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed #39
• NOTE: Update R version dependency from 3.6.2 to 4.2.0.
• NOTE: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph #45
• NOTE: 'sessionInfo' not found in vignette(s)
• NOTE: Avoid sapply(); use vapply()
• NOTE: Avoid 1:...; use seq_len() or seq_along()
• NOTE: Avoid 'cat' and 'print' outside of 'show' methods
• NOTE: Avoid the use of 'paste' in condition signals
• NOTE: Recommended function length <= 50 lines.There are 11 functions > 50 lines #54
• NOTE: Consider shorter lines; 601 lines (15%) are > 80 characters long
• NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs. #41
• NOTE: Consider multiples of 4 spaces for line indents; 1173 lines (29%) are not.
• NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel

shortening functions

frequently used internal functions

• gene ortholog conversion

create_rl_map_cellphonedb

• class checks for inputs
• internal function for replacing empty cells with "False"
• internal function Python -> R true/false syntax
• construction of rl_map without for loop
• set fixed columns for receptor and ligand descriptions
• [ ]

[jmitchell81]

00BiocCheck.log

BiocCheck() log from commit 0d16a1c as of 10/18/23

[kjkrishnan]

#125 - I'm pretty sure this is because for some reason show and print were tagged as internal instead of exported. I think I fixed it on the krishnan_rmd_fix_134 branch, but we should double check to be sure

[dimalvovs]

all done!