Dear msa maintainer, hi Ulrich,

For keeping my log files clean, I like to load a library like this:

library(mylibrary, warn.conflicts = FALSE)

This results in no output for most of my packages.

msa, however, does not support this usage. When I do (here I go even further to silence the output):

library(msa, warn.conflicts = FALSE, quietly = TRUE, verbose = FALSE)

I get:

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid


Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

I can imagine some of these un-suppressable output is caused by upstream, but maybe not. Also, this may be a consequence of an earlier question by me regarding being able to call a package's functions by using the scope operator.

I hope you'll help getting my log files clean :+1:

Cheers, Richel Bilderbeek