Admin: Valerie Obenchain

gravatar for Valerie Obenchain
Valerie Obenchain ♦♦ 6.1k
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Posts by Valerie Obenchain

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Comment: C: VariantAnnotation Installation Failure
... I'm not an RStudio expert but yes, I would think restarting R within RStudio should delete the tmp/. If you restarted R and still got the error it sounds like a problem on our end with the caching. I'll look into this further. Valerie ...
written 23 days ago by Valerie Obenchain ♦♦ 6.1k
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Answer: A: VariantAnnotation Installation Failure
... Hi Andrew, The issue you're seeing is related to a stale PACKAGES file. This file lists package versions - if it's stale then the version will not match that in the repository (e.g., trying to retrieve VariantAnnotation 1.22.0 when the package had moved on to 1.22.1 or greater). There are a couple ...
written 24 days ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: Bioconductor 3.5 is released
... Updated the post with a few changes to  the 'Deprecated and Defunct Packages'. section. Valerie ...
written 8 weeks ago by Valerie Obenchain ♦♦ 6.1k
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News: Bioconductor 3.5 is released
... April 25, 2017 Bioconductors: We are pleased to announce Bioconductor 3.5, consisting of 1383 software packages, 316 experiment data packages, and 911 annotation packages. There are 88 new software packages, and many updates and improvements to existing packages; Bioconductor 3.5 is compatible wi ...
news bioconductor release written 8 weeks ago by Valerie Obenchain ♦♦ 6.1k • updated 7 weeks ago by Hervé Pagès ♦♦ 12k
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Comment: C: What are out-of-bound ranges? Is it necessary to get rid of them?
... Please tag your message with the package name, ChIPpeakAnno, so the author is aware of the question. ...
written 9 weeks ago by Valerie Obenchain ♦♦ 6.1k • updated 9 weeks ago by Martin Morgan ♦♦ 20k
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Comment: C: AnnotationHub-cant extract database
... The problem is with the version of AnnotationHub - it's 2 (soon to be 3 ) releases old. The current release is version 2.6.5 seen here: http://www.bioconductor.org/checkResults/release/bioc-LATEST/ The old 2.4.2 version does not have the correct logic implemented for the OrgDb objects. The data in ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Answer: A: AnnotationHub-cant extract database
... Hi, Your sessionInfo() looks good. I see you're using the current release (Bioconductor 3.4) and have the current version of AnnotationHub loaded. Bioconductor 3.4 was released in October 2016 that is why when you load AnnotationHub the default snapshot date is 2016-10-11: > hub = AnnotationHub ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: AnnotationHub-cant extract database
... Cut and paste error? Not sure what happened but it would be good to see the output of sessionInfo() from your coworker. ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: AnnotationHub-cant extract database
... We need to see the output of sessionInfo() for both you and your coworker. This will show the R/Bioconductor package versions you're using. For example, here is mine - > sessionInfo() R Under development (unstable) (2017-03-15 r72352) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Fedora ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: AnnotationHub-cant extract database
... Please show the exact commands you and your coworker are running and include the output from sessionInfo(). It does not matter if you are on windows, linux or mac; what will matter is the version of R/Bioconductor you are using. Valerie ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.1k

Latest awards to Valerie Obenchain

Scholar 24 days ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 8 weeks ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 10 weeks ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 3 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 4 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 14 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 14 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 14 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 14 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 14 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 14 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 14 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 14 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Scholar 14 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: AnnotationHub: two broad peaks from same url are not the same
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 14 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 15 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Guru 15 months ago, received more than 100 upvotes.

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