Article describing how to handle (and suppress) package startup messages

[PeteHaitch]

I almost always want to wrap library() in suppressPackageStartupMessages() for my reprexes, but I always forget the first time around :( This is particularly true for Bioconductor packages, which tend to be very noisy because many depend on BiocGenerics (which masks a bunch of base function with equivalent S4 generics and reports this fact). For example, here I load the widely used SummarizedExperiment Bioconductor package:

library(SummarizedExperiment)
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> 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,
#>     colMeans, colnames, colSums, dirname, do.call, duplicated,
#>     eval, evalq, Filter, Find, get, grep, grepl, intersect,
#>     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
#>     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
#>     Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
#>     table, tapply, union, unique, unsplit, which, which.max,
#>     which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:base':
#> 
#>     expand.grid
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: DelayedArray
#> Loading required package: matrixStats
#> 
#> Attaching package: 'matrixStats'
#> The following objects are masked from 'package:Biobase':
#> 
#>     anyMissing, rowMedians
#> Loading required package: BiocParallel
#> 
#> Attaching package: 'DelayedArray'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
#> The following objects are masked from 'package:base':
#> 
#>     aperm, apply

Created on 2018-03-28 by the reprex package (v0.2.0).

Session info

devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                                             
#>  version  R Under development (unstable) (2018-03-05 r74359)
#>  system   x86_64, darwin15.6.0                              
#>  ui       X11                                               
#>  language (EN)                                              
#>  collate  en_AU.UTF-8                                       
#>  tz       America/New_York                                  
#>  date     2018-03-28
#> Packages -----------------------------------------------------------------
#>  package              * version   date       source        
#>  backports              1.1.2     2017-12-13 CRAN (R 3.5.0)
#>  base                 * 3.5.0     2018-03-06 local         
#>  Biobase              * 2.39.2    2018-01-25 Bioconductor  
#>  BiocGenerics         * 0.25.3    2018-02-09 Bioconductor  
#>  BiocParallel         * 1.13.3    2018-03-23 Bioconductor  
#>  bitops                 1.0-6     2013-08-17 CRAN (R 3.5.0)
#>  compiler               3.5.0     2018-03-06 local         
#>  datasets             * 3.5.0     2018-03-06 local         
#>  DelayedArray         * 0.5.22    2018-03-02 Bioconductor  
#>  devtools               1.13.5    2018-02-18 CRAN (R 3.5.0)
#>  digest                 0.6.15    2018-01-28 CRAN (R 3.5.0)
#>  evaluate               0.10.1    2017-06-24 CRAN (R 3.5.0)
#>  GenomeInfoDb         * 1.15.5    2018-02-04 Bioconductor  
#>  GenomeInfoDbData       1.1.0     2017-12-16 Bioconductor  
#>  GenomicRanges        * 1.31.23   2018-03-28 Bioconductor  
#>  graphics             * 3.5.0     2018-03-06 local         
#>  grDevices            * 3.5.0     2018-03-06 local         
#>  grid                   3.5.0     2018-03-06 local         
#>  htmltools              0.3.6     2017-04-28 CRAN (R 3.5.0)
#>  IRanges              * 2.13.28   2018-02-24 Bioconductor  
#>  knitr                  1.20      2018-02-20 CRAN (R 3.5.0)
#>  lattice                0.20-35   2017-03-25 CRAN (R 3.5.0)
#>  magrittr               1.5       2014-11-22 CRAN (R 3.5.0)
#>  Matrix                 1.2-12    2017-11-20 CRAN (R 3.5.0)
#>  matrixStats          * 0.53.1    2018-02-11 CRAN (R 3.5.0)
#>  memoise                1.1.0     2017-04-21 CRAN (R 3.5.0)
#>  methods              * 3.5.0     2018-03-06 local         
#>  parallel             * 3.5.0     2018-03-06 local         
#>  Rcpp                   0.12.16   2018-03-13 CRAN (R 3.5.0)
#>  RCurl                  1.95-4.10 2018-01-04 CRAN (R 3.5.0)
#>  rmarkdown              1.9       2018-03-01 CRAN (R 3.5.0)
#>  rprojroot              1.3-2     2018-01-03 CRAN (R 3.5.0)
#>  S4Vectors            * 0.17.38   2018-03-28 Bioconductor  
#>  stats                * 3.5.0     2018-03-06 local         
#>  stats4               * 3.5.0     2018-03-06 local         
#>  stringi                1.1.7     2018-03-12 CRAN (R 3.5.0)
#>  stringr                1.3.0     2018-02-19 CRAN (R 3.5.0)
#>  SummarizedExperiment * 1.9.16    2018-03-28 Bioconductor  
#>  tools                  3.5.0     2018-03-06 local         
#>  utils                * 3.5.0     2018-03-06 local         
#>  withr                  2.1.2     2018-03-15 CRAN (R 3.5.0)
#>  XVector                0.19.9    2018-02-28 Bioconductor  
#>  yaml                   2.1.18    2018-03-08 CRAN (R 3.5.0)
#>  zlibbioc               1.25.0    2017-10-31 Bioconductor

Created on 2018-03-28 by the reprex package (v0.2.0).

Yeeesh ...

I see reprex() has a tidyverse_quiet argument and that there was some discussion of the more general case in #70. Would you be amenable to revisiting this issue? I'd be happy to lead a PR.

Thanks for a very useful package!

[jennybc]

Hmm, yes, in my life the tidyverse package was the worst offender, so I took the easy way out there!

I am open to solving this more generally. Will you make another comment here, laying out the best options from #70 and I'll tag some others in to advise?

[cderv]

To share my experience, for all the messages about masked functions, I often use in my reprex the warn.conflicts = FALSE argument in library calls. For example, library(dplyr, warn.conflicts = FALSE) at the beginning of the reprex.

Moreover, there is also a quietly that I did not use for now. I do not know if any of this is enough for this bioconductor 📦 . I think it could suppress some of the messages and is kind of lighter than suppressPackageStartupMessages.

One solution could be to modify library calls to add those arguments if desired. The advantage I find is that this modification is not some magical suppression by reprex, but just the automatic activation of some already existing option. By magical, I imply not visible in code, in such way that if anyone copy the reprex, the messages would be there (even if not shown in the reprex code). I find it clearer if messages are deactivated explicitly.

[PeteHaitch]

@jennybc: Great, thanks. I'll do that

@cderv: Thanks for your thoughts. I'd not considered using arguments to library(). However, it appears that warn.conflicts = FALSE only warns of conflicts from the package argument, not its dependencies. E.g., library(BiocGenerics, warn.conflicts = FALSE) does not warn, but library(SummarizedExperiment, warn.conflicts = FALSE) emits warnings from BiocGenerics (an 'Import' of SummarizedExperiment https://github.com/Bioconductor/SummarizedExperiment/blob/master/DESCRIPTION#L16)

[cderv]

However, it appears that warn.conflicts = FALSE only warns of conflicts from the package argument, not its dependencies.

@PeteHaitch , Good to know! thanks for trying. library(SummarizedExperiment, warn.conflicts = FALSE, quietly = TRUE) does the same ?

[PeteHaitch]

Good to know! thanks for trying. library(SummarizedExperiment, warn.conflicts = FALSE, quietly = TRUE) does the same ?

It still produces a lot of output, and at a quick glance I can't tell what (if anything) is different from when quietly = FALSE. Will keep digging

[jennybc]

I have found quietly to be rather disappointing in the past @PeteHaitch. I don't think it's going to help us here.

[cderv]

Sorry for misleading here with quietly try - no need to dig further I think. Personally, warn.conflicts = FALSE is useful, quietly not so much - I observed in the past the same unclear behavior.

The proposition in previous issue of adding a #+ message = FALSE chunk option is an easy one so suppress only library calls. However, I fear that it also would suppress some messages useful for debugging in the reprex.

The other solution to call knit inside a suppressPackageStartupMessages call could solve it too without the drawbacks. I find this solution not so difficult to implement I think.

[jennybc]

I don't really see an attractive way to fix this in reprex.

I suggest an article showing the things a user can do to suppress these messages, so we can all link to it or re-read it when we need a refresher.