[R] problem installing RGBL library

[varin sacha]

Bert,

Thanks ! It works !

Best,







Le samedi 22 avril 2023 à 19:42:18 UTC+2, Bert Gunter <bgunter.4567 using gmail.com> a écrit : 





Is lvida.R in your working directory?
Try using the full path name to the file instead in source()

-- Bert

On Sat, Apr 22, 2023 at 9:38 AM varin sacha via R-help
<r-help using r-project.org> wrote:
>
> 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'
> >>
> >> ______________________________________________
> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
> >
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.