Hello, I am wondering if there is a way to suppress ALL start up messages in loading packages. In other words, I have a lot of library calls, like so:

require(splines)
require(ggplot2)
require(dplyr)
require(tidyverse)
require(reshape2)
require(knitr)
require(MASS)
require(moanin)
require(topGO)

I would like for none of these to print messages about conflicts or the "Welcome to Bioconductor" message etc. BUT I don't want to put suppressPackageStartupMessages in front of every call (and remember to do it for every new library I might add in the future).

For context, this is not interactive code. This is code run on the command line (via a makefile) using Rscript and these messages really clog up my output. Moreover, I have a large pipeline of code, so I have a slew of such existing .R/.Rmd files to compile, so in addition to not wanting to have the messy code, I don't want to manually have to add suppressPackageStartupMessages manually to each call in each file. I'd rather add a single line of code at the top of each existing file.

Finally, I know that in Rmarkdown, I can set the option message=FALSE, so it doesn't show up in my compiled output. However, I am not only running .Rmd files. Furthermore, even for those that are .Rmd, I am running them via Rscript so that while those messages don't show up in the html compiled file, it does get output to the terminal (not sure why) hence making very cluttered output when I'm trying to review the output of my calls that I've piped to a log file.

Thanks so much for any suggestions!

Elizabeth Purdom

Hi Elizabeth,

You don't need to put suppressPackageStartupMessages in front of every call. Putting it once in front of all the calls should be enough:

suppressPackageStartupMessages({
library(splines)
library(ggplot2)
library(dplyr)
etc...
})

Also it's safer to use library() rather than require() as the latter will only issue a warning if a package is missing while the former will raise an error. Better to get a hard failure early rather than after several hours of computation ;-)

Cheers,

H.

How about

> startThat <- function(package) suppressPackageStartupMessages(require(package, character.only = TRUE))
> startThat("splines")
> startThat("ggplot2")