i think this is an interesting analysisi have not viewed talk but it
seems to me this could be a nice r journal paperquerying jim h on fate
of itdepends seems in orderthe topic is central to robustness of
ecosystem so i hope some tools can come out of this
On Wed, Feb 12, 2020 at 12:13
Martin, Vince, Sean,
thank you very much for your comments and suggestions, i've looked at
the package 'itdepends' from Jim Hester, this was a great suggestion. i
actually found a talk he gave about it on rstudioconf2019, here:
https://resources.rstudio.com/rstudio-conf-2019/it-depends-a-dial
There are some good ideas here that would provide enhancement to
BiocPkgTools. I don't have the bandwidth to incorporate right now, but
filing issues or a pull request with a skeleton would be helpful to keep
track.
Sean
On Sun, Feb 9, 2020 at 7:31 AM Vincent Carey
wrote:
> On Sat, Feb 8, 2020
On Sat, Feb 8, 2020 at 12:02 PM Martin Morgan
wrote:
> I find it quite interesting to identify formal strategies for removing
> dependencies, but also a little outside my domain of expertise. This code
>
It would be nice to collect the ideas in this thread into some
recommendations. The themes
I find it quite interesting to identify formal strategies for removing
dependencies, but also a little outside my domain of expertise. This code
library(tools)
library(dplyr)
## non-base packages the user requires for GenomicScores
deps <- package_dependencies("GenomicScores", db, recursive=TRUE
true, i was just searching for the shortest path, we can search for all
simple (i.e., without repeating "vertices") paths and there are up to
five routes from "GenomicScores" to "Matrix"
igraph::all_simple_paths(igraph::igraph.from.graphNEL(g),
from="GenomicScores", to="Matrix", mode="out")
[
Excellent! I think there are other, independent, paths between your immediate
dependents...
RBGL::sp.between(g, start="DT", finish="Matrix", detail=TRUE)[[1]]$path_detail
[1] "DT""crosstalk" "ggplot2" "mgcv" "Matrix"
??
Martin
On 2/6/20, 10:47 AM, "Robert Castelo" wrote:
hi Martin,
thanks for hint!! i wasn't aware of 'tools::package_dependencies()',
adding a bit of graph sorcery i get the result i was looking for:
repos <- BiocManager::repositories()[c(1,5)]
repos
BioCsoft
"https://bioconductor.org/packages/3.11/bioc";
The first thing is to get the correct repositories
repos = BiocManager::repositories()
(maybe trim the experiment and annotation repos from this). I also tried
pkgDepTools::makeDepGraph() but it took so long that I moved on... it has an
option 'keep.builtin' which might include Matrix.
There
hi,
when i load the package 'GenomicScores' in a clean session i see thorugh
the 'sessionInfo()' that the package 'Matrix' is listed under "loaded
via a namespace (and not attached)".
i'd like to know what is the dependency that 'GenomicsScores' has that
ends up requiring the package 'Matrix
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