Silence messages about masked functions

Question

I'm trying to silence messages that explain that certain functions were masked by other packages. I have tried different combinations, but none delivered what I need.

The chunk I have is:

<<loadpkgs, echo=FALSE, warning=FALSE, message=FALSE>>=
suppressPackageStartupMessages(library(doMC))
suppressPackageStartupMessages(library(aroma.affymetrix))
suppressPackageStartupMessages(library(crlmm))
suppressPackageStartupMessages(library(snpStats))
suppressPackageStartupMessages(library(pd.genomewidesnp.6))
suppressPackageStartupMessages(library(GenomicRanges))
suppressPackageStartupMessages(library(ggbio))
@ 

But the output (which I hoped to be none) is (on the resulting PDF):

## Loading required package:  foreach
## foreach:  simple, scalable parallel programming from Revolution Analytics
## Use Revolution R for scalability, fault tolerance and more.
## http://www.revolutionanalytics.com
## Loading required package:  iterators
## Loading required package:  parallel
## Loading required package:  R.utils
## Loading required package:  R.oo
## Loading required package:  R.methodsS3
## R.methodsS3 v1.5.2 (2013-10-06) successfully loaded.  See ?R.methodsS3 for help.
## R.oo v1.15.8 (2013-10-10) successfully loaded.  See ?R.oo for help.
##
## Attaching package:  ’R.oo’
##
## The following objects are masked from ’package:methods’:
##
##    getClasses, getMethods

Any thoughts on how to solve this?

Answer 1

Setting the parameter warn.conflicts=FALSE in library() as in

library(dplyr, warn.conflicts=FALSE)

should do the trick. This is particularly useful with parallel computing when potentially hundreds or more cores are loading the library.

Answer 2

To get rid of the "Loading ..." messages use quietly=TRUE in the library call (and continue to use the suppressPackageStartupMessages):

suppressPackageStartupMessages(library(gdata, quietly=TRUE))

If you want to make this more compact, perhaps:

pkgs <-c('gdata', 'doMC', 'aroma.affymetrix', 'crlmm', 'snpStats', 
         'pd.genomewidesnp.6', 'GenomicRanges','ggbio')
for(p in pkgs) suppressPackageStartupMessages(library(p, quietly=TRUE, 
                                                      character.only=TRUE))

Might be safer to do some sort of test if you are going to suppress the "loading messages".

for(p in pkgs) suppressPackageStartupMessages( stopifnot( 
                                               library(p, quietly=TRUE, 
                                                        logical.return=TRUE, 
                                                        character.only=TRUE)))