Search
Question: "quiet" mode for AnnotationHub?
0
gravatar for Robert K. Bradley
11 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 11 months ago • written 11 months ago by Robert K. Bradley40
0
gravatar for Lucas Schiffer
11 months ago by
CUNY School of Public Health, New York, NY
Lucas Schiffer160 wrote:

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

invisible(AnnotationHub())
ADD COMMENTlink written 11 months ago by Lucas Schiffer160

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

suppressMessages(AnnotationHub()[["AH134"]])
ADD REPLYlink written 11 months ago by Lucas Schiffer160
0
gravatar for Robert K. Bradley
11 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 11 months ago by Robert K. Bradley40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 141 users visited in the last hour