User: balin

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balin0
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Posts by balin

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Comment: C: UniProt.ws non-functional or abandoned?
... 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 7 months ago by balin0
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UniProt.ws non-functional or abandoned?
... 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 ...
uniprot.ws uniprot uniprot accessions written 7 months ago by balin0 • updated 7 months ago by James W. MacDonald50k
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Comment: C: R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list conc
... 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 13 months ago by balin0
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Comment: C: R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list conc
... I don't ... loads without a hitch. ...
written 13 months ago by balin0
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Comment: C: R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list conc
... > BiocInstaller::biocLite('BiocUpgrade') Error: Bioconductor version 3.6 cannot be upgraded with R version 3.5.0 ...
written 13 months ago by balin0
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Comment: C: R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list conc
... > BiocInstaller::biocValid() [1] TRUE ...
written 13 months ago by balin0
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Comment: C: R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list conc
... @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 13 months ago by balin0
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Comment: C: R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list conc
... 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 13 months ago by balin0
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R 3.5.0/Bioconductor version 3.6: OS-dependent behavior divergence for list concatenation of SummarizedExperiment
... 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("+", ...
bug summarizedexperiment 3.5.0 written 13 months ago by balin0 • updated 13 months ago by James W. MacDonald50k

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