User: balin
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Posts by balin
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... Here's my experimentation (modified from ?UniProt.ws::UniProt.ws):
library(UniProt.ws)
system.time(up <- UniProt.ws(taxId=9606))
user system elapsed
0.278 0.057 47.151
... this is insanely long.
Additionally (also from the main example):
res <- select(up,
keys = c("226 ...
written 5 months ago by
balin • 0
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... The current UnipProt.ws appears disfunctional in my hands. When running through the example of UniProt.ws::UniProt.ws connecting to the db is excruciatingly slow and the final exemplary lookup fails.
My own use case also does not work.
Is the package functioning for anybody? Is it abandoned? Are t ...
written 5 months ago by
balin • 0
• updated
5 months ago by
James W. MacDonald ♦ 49k
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... On Wed, 2018-05-16 at 13:22 +0000, Martin Morgan [bioc] wrote:
> Activity on a post you are following on support.bioconductor.org
> User Martin Morgan wrote Comment: R 3.5.0/Bioconductor version 3.6:
> OS-dependent behavior divergence for list concatenation of
> SummarizedExperiment:
> ...
written 11 months ago by
balin • 0
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... I don't ... loads without a hitch.
...
written 11 months ago by
balin • 0
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...
> BiocInstaller::biocLite('BiocUpgrade')
Error: Bioconductor version 3.6 cannot be upgraded with R version 3.5.0
...
written 11 months ago by
balin • 0
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...
> BiocInstaller::biocValid()
[1] TRUE
...
written 11 months ago by
balin • 0
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... @Martin Morgan
1) I have not down anything out of the ordinary (other than maintaining my dev environment in switchr) - is switchr known to generate this kind of R/bioc mismatch?
2) isn't it strange that the apparently mismatched R/bioc combination does the concatenation just fine, but your matche ...
written 11 months ago by
balin • 0
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... Weirder by the minute ... here's my (again error free) reproduction including sessionInfo() ...
I note a difference in SummarizedExperiment version (above 1.10., me 1.8), which BiocInstaller::biocLite(checkBuild=T) does not change ... where does that difference come from?
> nrows <- 200; ncols ...
written 11 months ago by
balin • 0
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... Consider the following code:
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GenomicRanges::GRanges(rep(c("chr1", "chr2"), c(50, 150)),
IRanges::IRanges(floor(runif(200, 1e5, 1e6)), width=100),
strand=sample(c("+", ...
written 11 months ago by
balin • 0
• updated
11 months ago by
James W. MacDonald ♦ 49k
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