User: Kyle Johnsen

gravatar for Kyle Johnsen
Kyle Johnsen20
Reputation:
20
Status:
New User
Location:
United States/Brigham Young University
Last seen:
2 months, 3 weeks ago
Joined:
2 years, 8 months ago
Email:
j************@gmail.com

Posts by Kyle Johnsen

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How can I create a GmapGenome that doesn't start at index 1?
... Ok. That won't exactly work for what I wanted to do, since I wanted to have the BAM files and genome all ready to plug into a pipeline of which variant calling is only a part, but thank you for the response! ...
written 3 months ago by Kyle Johnsen20
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Comment: C: How can I create a GmapGenome that doesn't start at index 1?
... Ok, in my case, I want to call variants in this region, but the BAM files are in genomic coordinates. If I understand right, `mapToTranscripts()` would help if I had the BAM files in transcript coordinates, called variants, and then converted to genomic coordinates. Is that right, and if so, is that ...
written 3 months ago by Kyle Johnsen20
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How can I create a GmapGenome that doesn't start at index 1?
... Let me explain: I want to use a small "reference genome" of only a gene, for use in examples. But I need it to still have the coordinates that correspond to the actual genome coordinates. But when I create a `GmapGenome` using this truncated fasta, it begins at index 1, which prevents me from using ...
gmapr written 3 months ago by Kyle Johnsen20
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Answer: A: Strange problem in example check of package
... After some investigation, I discovered that my examples that interacted with graphics did cause the problem. I edited those parts out of the examples (I missed one place when I tried this the first time) and it worked. I guess this is a problem with R itself--my function calls graphics.off() to clea ...
written 7 months ago by Kyle Johnsen20
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Strange problem in example check of package
... I'm not sure what's going on. The examples in my documentation seem to run okay, then I get a weird error at the end apparently outside of my code. I thought something about the example itself could have been messing things up, but as you can see, the error persists even with a commented-out example ...
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Answer: A: Can't access devel version of ExperimentHub in Travis CI
... Installing bioc-devel in the before_script using BiocManager::install(version='devel', ask=FALSE) fixed it. Thank you Lori! ...
written 7 months ago by Kyle Johnsen20
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Comment: C: Can't access devel version of ExperimentHub in Travis CI
... I tried it (using the r_github_packages option on the .travis.yml), and again BiocManager::install(version='devel') fails. If you look at the package versions, the most recent version of BiocManager is definitely there (v1.30.2.9003). Travis build: https://travis-ci.org/kjohnsen/MMAPPR2/jobs/43639 ...
written 7 months ago by Kyle Johnsen20
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Comment: C: Can't access devel version of ExperimentHub in Travis CI
... I restarted the build above after deleting all caches on Travis, thinking that could make a difference, and didn't realize the old log would be overwritten. So it's re-running right now. As for using BiocManager, I already tried it, and install(version='devel') failed inexplicably. Here are the bui ...
written 7 months ago by Kyle Johnsen20
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Comment: C: Can't access devel version of ExperimentHub in Travis CI
... Yes, I have...here's a more recent log where I ran possibleDates() and confirmed that only release snapshots are available: https://api.travis-ci.org/v3/job/436206153/log.txt ...
written 7 months ago by Kyle Johnsen20
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Comment: C: Can't access devel version of ExperimentHub in Travis CI
... Yes, here's the link to the repository (the problem is on the refactor-data branch): https://github.com/kjohnsen/MMAPPR2/tree/refactor-data And here's a link to the failing build: https://travis-ci.org/kjohnsen/MMAPPR2/builds/433856348 ...
written 7 months ago by Kyle Johnsen20

Latest awards to Kyle Johnsen

Scholar 8 months ago, created an answer that has been accepted. For A: Can't access devel version of ExperimentHub in Travis CI
Scholar 8 months ago, created an answer that has been accepted. For A: Strange problem in example check of package

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