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Question: "quiet" mode for AnnotationHub?
0
gravatar for Robert K. Bradley
18 months ago by
United States
Robert K. Bradley40 wrote:

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                 
ADD COMMENTlink modified 18 months ago • written 18 months ago by Robert K. Bradley40
0
gravatar for Lucas Schiffer
18 months ago by
CUNY School of Public Health, New York, NY
Lucas Schiffer220 wrote:

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

invisible(AnnotationHub())
ADD COMMENTlink written 18 months ago by Lucas Schiffer220

Additionally, there is another function to remove messages from output:

suppressMessages(AnnotationHub()[["AH134"]])
ADD REPLYlink written 18 months ago by Lucas Schiffer220
0
gravatar for Robert K. Bradley
18 months ago by
United States
Robert K. Bradley40 wrote:

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

ADD COMMENTlink written 18 months ago by Robert K. Bradley40
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