TRADEtools fails build check

[aguzzolb]

Hello @ajaynadig, @bdharris17, and @chriswzou. Thank you for developing this very useful package!

TRADEtools is not currently passing the build check. It is failing because of two things:

1. DESeq2, S4Vectors, stats4, and BiocGenerics are missing from the package DESCRIPTION file, but TRADEtools tries to load it in the vignette.

2. The data used in the examples is not included in the package and therefore cannot be loaded properly.

"1" could easily be fixed by adding DESeq2, S4Vectors, stats4, and BiocGenerics under suggested in the DESCRIPTION file.

"2" could be fixed in many ways, but here are two suggestions:

• Adding something like this to your example so that it can access the data. I pulled this code from your vignette, so it should work:

# Load GATA1 data
gata1_url <- "https://github.com/ajaynadig/TRADEtools/releases/download/0.99.0/GATA1_K562Essential_DESeq2output.Rdata"
gata1_file <- tempfile(fileext = ".Rdata")
download.file(gata1_url, gata1_file, mode = "wb")
load(gata1_file)
GATA1_K562_results <- results_pseudobulk

# Load MED12 data
med12_url <- "https://github.com/ajaynadig/TRADEtools/releases/download/0.99.0/MED12_K562Essential_DESeq2output.Rdata"
med12_file <- tempfile(fileext = ".Rdata")
download.file(med12_url, med12_file, mode = "wb")
load(med12_file)
MED12_K562_results <- results_pseudobulk

• Wrapping your example in \dontrun{ ... } so that the example is not run when performing checks.

Here are the logs I got from running the build checks:
TRADEtools_build_check.log

Cheers!