User: Robert K. Bradley

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

Posts by Robert K. Bradley

<prev • 31 results • page 1 of 4 • next >
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Comment: C: possible bug resulting in warnings when reading tags with scanBam and ScanBamPar
... Thank you! It's working without problems for me now. ...
written 11 weeks ago by Robert K. Bradley40
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Comment: C: possible bug resulting in warnings when reading tags with scanBam and ScanBamPar
... My sessionInfo is below (I couldn't include it in the above response due to the character limit): > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS attached base packages: [1] stats4 parallel grid grDevices utils ...
written 11 weeks ago by Robert K. Bradley40
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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 11 weeks 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 11 weeks ago by Robert K. Bradley40 • updated 11 weeks ago by Martin Morgan ♦♦ 22k
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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 4 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 4 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 4 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 4 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 4 months ago by Robert K. Bradley40 • updated 4 months ago by Martin Morgan ♦♦ 22k
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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 21 months ago by Robert K. Bradley40

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