Admin: Valerie Obenchain
Valerie Obenchain ♦♦ 6.1k
- Reputation:
- 6,110
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 1 week, 6 days ago
- Joined:
- 6 years, 9 months ago
- Email:
- v****************@roswellpark.org
Posts by Valerie Obenchain
<prev
• 773 results •
page 1 of 78 •
next >
0
votes
1
answers
65
views
1
answers
... 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
0
votes
1
answers
65
views
1
answers
... 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
0
votes
0
answers
256
views
0
answers
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
8
votes
0
answers
256
views
0
answers
... 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 ...
written 8 weeks ago by
Valerie Obenchain ♦♦ 6.1k
• updated 7 weeks ago by
Hervé Pagès ♦♦ 12k
0
votes
1
answers
131
views
1
answers
... 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
0
votes
2
answers
152
views
2
answers
... 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
0
votes
2
answers
152
views
2
answers
... 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
0
votes
2
answers
152
views
2
answers
... 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
0
votes
2
answers
152
views
2
answers
... 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
0
votes
2
answers
152
views
2
answers
... 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
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
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.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 133 users visited in the last hour