Re: [R] problem installing RGBL library
Bert,
Thanks ! It works !
Best,
Le samedi 22 avril 2023 à 19:42:18 UTC+2, Bert Gunter
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
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
> a écrit :
>
>
>
>
>
> looks fine.
> what's the problem?
>
> On Sat, Apr 22, 2023 at 7:27 PM varin sacha 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
> > a écrit :
> >
> >
> >
> >
> >
> > What happens with the command
> >> library(RBGL)
> >
> >
> >
> > On Sat, Apr 22, 2023 at 7:08 PM varin sacha via R-help
> > 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@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@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@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.
Re: [R] problem installing RGBL library
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
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
> a écrit :
>
>
>
>
>
> looks fine.
> what's the problem?
>
> On Sat, Apr 22, 2023 at 7:27 PM varin sacha 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
> > a écrit :
> >
> >
> >
> >
> >
> > What happens with the command
> >> library(RBGL)
> >
> >
> >
> > On Sat, Apr 22, 2023 at 7:08 PM varin sacha via R-help
> > 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@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@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@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.
Re: [R] problem installing RGBL library
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 a
écrit :
looks fine.
what's the problem?
On Sat, Apr 22, 2023 at 7:27 PM varin sacha 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
> a écrit :
>
>
>
>
>
> What happens with the command
>> library(RBGL)
>
>
>
> On Sat, Apr 22, 2023 at 7:08 PM varin sacha via R-help
> 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@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@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.
Re: [R] problem installing RGBL library
looks fine.
what's the problem?
On Sat, Apr 22, 2023 at 7:27 PM varin sacha 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 <
> ericjber...@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@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@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.
> >
>
>
[[alternative HTML version deleted]]
__
R-help@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.
Re: [R] problem installing RGBL library
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 a
écrit :
What happens with the command
> library(RBGL)
On Sat, Apr 22, 2023 at 7:08 PM varin sacha via R-help
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@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@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.
Re: [R] problem installing RGBL library
What happens with the command
> library(RBGL)
On Sat, Apr 22, 2023 at 7:08 PM varin sacha via R-help
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@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.
>
[[alternative HTML version deleted]]
__
R-help@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] problem installing RGBL library
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@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.
