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kkdey / Logolas

R package for Enrichment Depletion Logos (EDLogos) and String Logos
https://kkdey.github.io/Logolas-pages
GNU General Public License v3.0
27 stars 1 forks source link

Excessive warnings produced without REBayes installed. #15

Open Neato-Nick opened 5 years ago

Neato-Nick commented 5 years ago

Hi,

when using this package without REBayes installed, using type = "EDLogo" produces the warning "Due to absence of package REBayes, switching to EM algorithm." This warning is helpful, but is produced hundreds of times upon execution. Is it possible to make this warning only display once after logomaker is run? It fills up the console otherwise.

library(Logolas)
data("seqlogo_example")
logomaker(seqlogo_example, type = "EDLogo")
#> using a background with equal probability for all symbols
#> The input is a positional weight matrix
#>                 (entries are probabilities)
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> Due to absence of package REBayes, switching to EM algorithm
#> color_type not provided, so switching to per_row option for
#>             color_type
#> using a background with equal probability for all symbols
#> frame width not provided, taken to be 1
#> frame width not provided, taken to be 1

Created on 2018-12-17 by the reprex package (v0.2.1)

pcarbo commented 5 years ago

@kkdey Maybe you need to switch to mixsqp (which is now on CRAN)!

kkdey commented 5 years ago

Just an update: @pcarbo and others are working to incorporate the change to the ashr package, the call to which creates the warnings messages....Will update this space as soon as it gets fixed.

Till that time, you can use one simple hack to get rid of these warning messages by using the suppressWarnings() wrap on the logomakerfunction call.

Thanks.