"quiet" mode for AnnotationHub?
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@robert-k-bradley-5997
Last seen 2.5 years ago
United States

Hello,

I'm wondering whether there is a "quiet" mode for AnnotationHub, in which it would only print serious warnings or errors. Currently it displays snapshot and cache information whenever accessed. An example follows.

I'm interested in such a "quiet" mode because I regularly access AnnotationHub objects over and over within a pipeline, and so my logging information becomes clogged with these messages.

Thank you,

Rob

> hub = AnnotationHub()
snapshotDate(): 2016-10-11

> dna = hub[["AH134"]]
require(“Rsamtools”)
loading from cache ‘/Users/rbradley//.AnnotationHub/134’
    ‘/Users/rbradley//.AnnotationHub/14095’

> getOption ("verbose")
[1] FALSE

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.2

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  grDevices utils     datasets  stats     graphics  methods   base     

other attached packages:
[1] Rsamtools_1.26.1     Biostrings_2.42.1    XVector_0.14.0       GenomicRanges_1.26.1 GenomeInfoDb_1.10.1  IRanges_2.8.1        S4Vectors_0.12.1     AnnotationHub_2.6.4
[9] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8                   AnnotationDbi_1.36.0          zlibbioc_1.20.0               BiocParallel_1.8.1            xtable_1.8-2                 
 [6] R6_2.2.0                      httr_1.2.1                    tools_3.3.2                   Biobase_2.34.0                DBI_0.5-1                    
[11] htmltools_0.3.5               yaml_2.1.14                   digest_0.6.10                 interactiveDisplayBase_1.12.0 shiny_0.14.2                 
[16] bitops_1.0-6                  curl_2.3                      memoise_1.0.0                 RSQLite_1.1-1                 mime_0.5                     
[21] compiler_3.3.2                BiocInstaller_1.24.0          httpuv_1.3.3                 
AnnotationHub • 714 views
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@schifferl
Last seen 4 days ago
Boston University, Boston, MA

If you were to put your AnnotationHub calls inside an invisible that would hide the messages. For example,

invisible(AnnotationHub())
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Additionally, there is another function to remove messages from output:

suppressMessages(AnnotationHub()[["AH134"]])
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Entering edit mode
@robert-k-bradley-5997
Last seen 2.5 years ago
United States

Thank you for the quick response. invisible doesn't seem to accomplish what I want, but suppressMessages does. Thanks for the simple fix suggestion.

Best,

Rob

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