User: Robert K. Bradley

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40
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New User
Location:
United States
Twitter:
@bradleybio
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1 month, 1 week ago
Joined:
5 years ago
Email:
r*******@fredhutch.org

Posts by Robert K. Bradley

<prev • 27 results • page 1 of 3 • next >
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Comment: C: initialization of AnnotationHub() in version 2.12.0 is problematically verbose
... I tried uninstalling both yaml and AnnotationHub and then reinstalling AnnotationHub. I'm not encountering problems now! I don't know what the origin of the problem was, but it seems to be fixed. Thank you again for your quick responses and help! Best wishes, Rob > library (AnnotationHub) Lo ...
written 5 weeks ago by Robert K. Bradley40
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Comment: C: initialization of AnnotationHub() in version 2.12.0 is problematically verbose
... Thank you for the suggestion. I tried the above yaml commands, but didn't encounter a problem: > yaml <- httr::content(httr::GET("http://bioconductor.org/config.yaml"), encoding="UTF-8", as="text") > obj <- yaml::yaml.load(yaml)   ...
written 5 weeks ago by Robert K. Bradley40
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Comment: C: initialization of AnnotationHub() in version 2.12.0 is problematically verbose
... Hi Martin, Thank you for the quick reply! I didn't manually install yaml, although I presume that it was installed/updated when I recently upgraded to R 3.5.0. It would be great if you would be willing to please reach out to the yaml maintainer. I tried updating yaml manually via biocLite() and di ...
written 5 weeks ago by Robert K. Bradley40
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Comment: C: initialization of AnnotationHub() in version 2.12.0 is problematically verbose
... My inquiry above is related to, but distinct from, my previous question regarding a "quiet" mode for AnnotationHub: https://support.bioconductor.org/p/90640/#90645 As you can see from the response to my question above, suppressMessages() or invisible() was sufficient to prevent the messages. The m ...
written 5 weeks ago by Robert K. Bradley40
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initialization of AnnotationHub() in version 2.12.0 is problematically verbose
... After updating to R 3.5.0 and Bioconductor 3.7, I discovered that initializing an AnnotationHub object (version 2.12.0) is problematically verbose. I tried wiping the cached annotationhub.sqlite3 and index.rds, but that didn't fix the problem. The verbosity cannot be suppressed by suppressMessages() ...
annotationhub written 5 weeks ago by Robert K. Bradley40 • updated 5 weeks ago by Martin Morgan ♦♦ 21k
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Answer: A: "quiet" mode for AnnotationHub?
... 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 ...
written 18 months ago by Robert K. Bradley40
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"quiet" mode for AnnotationHub?
... 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 AnnotationHu ...
annotationhub written 18 months ago by Robert K. Bradley40
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Comment: C: error with downloading AnnotationHub item AH134
... Wonderful. Thank you! ...
written 19 months ago by Robert K. Bradley40
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Comment: C: error with downloading AnnotationHub item AH134
... Hi Valerie, Thank you for looking into this so quickly. I'd like to use the version 69 file if possible in order to ensure continuity with previous analyses that we've conducted using that version. (I know that the assembly should presumably be stable w.r.t. the version, but just to be sure I'll st ...
written 20 months ago by Robert K. Bradley40
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error with downloading AnnotationHub item AH134
... Hello, Downloading the AnnotationHub object AH134 (the hg19 genome) does not currently work, even though the source URL for that object exists and can be manually downloaded. Here is a reproducible code example: > library (AnnotationHub) Loading required package: BiocGenerics Loading required ...
annotationhub written 20 months ago by Robert K. Bradley40 • updated 20 months ago by Valerie Obenchain ♦♦ 6.5k

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