User: Robert K. Bradley

Reputation:
40
Status:
New User
Location:
United States
Twitter:
@bradleybio
Last seen:
3 months ago
Joined:
6 years, 2 months ago
Email:
r*******@fredhutch.org

Posts by Robert K. Bradley

<prev • 39 results • page 2 of 4 • next >
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Comment: C: possible bug resulting in warnings when reading tags with scanBam and ScanBamPar
... Martin, thank you for the quick response and fix. I updated Rsamtools per your instructions. I no longer gett the above warning message. However, I think that a new bug may have been introduced. I can read in the BAM version of the following SAM file without problems if I don't specify parameters: ...
written 13 months ago by Robert K. Bradley40
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possible bug resulting in warnings when reading tags with scanBam and ScanBamParam
... Hello, I'm getting a strange warning message when I attempt to read in tag information from BAM files with scanBam. I haven't seen this warning in the past. I don't get the warning message if I ignore tags. The BAM file appears to be read in despite the warnings. Please see the following example, i ...
rsamtools written 13 months ago by Robert K. Bradley40 • updated 13 months ago by Martin Morgan ♦♦ 23k
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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 15 months 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 15 months 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 15 months 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 15 months 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 15 months ago by Robert K. Bradley40 • updated 15 months ago by Martin Morgan ♦♦ 23k
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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 2.7 years 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 2.7 years ago by Robert K. Bradley40
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Comment: C: error with downloading AnnotationHub item AH134
... Wonderful. Thank you! ...
written 2.8 years ago by Robert K. Bradley40

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