[R] problem installing RGBL library

[varin sacha]

The problem is that I am trying to run this R code :
https://github.com/dmalinsk/lv-ida/blob/master/example.R

 
So I run :

library(pcalg)
library(igraph)
library(RBGL)
source("lvida.R")


Here is what I get :

source("lvida.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'lvida.R': No such file or directory

So, I guess the problem is coming from the source not from the libraries? How to solve that problem?

Best,






Le samedi 22 avril 2023 à 18:30:48 UTC+2, Eric Berger <ericjberger using gmail.com> a écrit : 





looks fine.
what's the problem?

On Sat, Apr 22, 2023 at 7:27 PM varin sacha <varinsacha using yahoo.fr> wrote:
> Eric,
> 
> Here it is :
> 
> 
> library(RBGL)
> Loading required package: graph
> Loading required package: BiocGenerics
> 
> Attaching package: ‘BiocGenerics’
> 
> The following objects are masked from ‘package:igraph’:
> 
>   normalize, path, union
> 
> The following objects are masked from ‘package:stats’:
> 
>   IQR, mad, sd, var, xtabs
> 
> The following objects are masked from ‘package:base’:
> 
>   anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
>   mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max,
>   which.min
> 
> 
> Attaching package: ‘graph’
> 
> The following objects are masked from ‘package:igraph’:
> 
>   degree, edges, intersection
> 
> 
> Attaching package: ‘RBGL’
> 
> The following objects are masked from ‘package:igraph’:
> 
>   bfs, dfs, transitivity
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Le samedi 22 avril 2023 à 18:12:56 UTC+2, Eric Berger <ericjberger using gmail.com> a écrit : 
> 
> 
> 
> 
> 
> What happens with the command
>> library(RBGL)
> 
> 
> 
> On Sat, Apr 22, 2023 at 7:08 PM varin sacha via R-help <r-help using r-project.org> wrote:
>> Dear R-experts,
>> 
>> How to solve that problem?
>> 
>> My R version is 4.2.1
>> 
>> Here below trying to install RGBL library found here : https://bioconductor.org/packages/release/bioc/html/RBGL.html
>> 
>> So, I run this R code :
>> 
>> if (!require("BiocManager", quietly = TRUE))
>>     install.packages("BiocManager")
>> 
>> BiocManager::install("RBGL")
>> 
>> 
>> Here is what I get :
>> 
>>> if (!require("BiocManager", quietly = TRUE))
>> + install.packages("BiocManager")
>> Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.1 (2022-06-23)
>>>
>>> BiocManager::install("RBGL")
>> Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.1 (2022-06-23)
>> Warning message:
>> package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'RBGL'
>> 
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
> 
>