Questions tagged [r]
R is a programming language and software environment, mostly used for statistical computing and graphics.
171
questions
-1
votes
1
answer
90
views
nix-shell default.nix: How to install rPackages.data_table with the zlib dependency?
I have a multi-user installation of nix on ubuntu 22.04. I'm trying to develop an R package that depends on data.table, but am unable to install data.table with zlib headers so that I can use the ...
0
votes
1
answer
67
views
Saving the output from individual shell scripts
I have a bash script that loops over iterations. How do i save the output from the individual scripts in the bash file according to the iteration?
#Working directory
cd /lustre/nobackup/WUR/ABGC/...
- 1
0
votes
1
answer
19
views
Getting year of Postixct format
"Thu Apr 21 11:15:00.375 2022" how to get the year of this expression?
Followings are tested.
1- as.POSIXct(strptime("Thu Apr 21 11:15:00.375 2022", format='%c'),origin='1970-01-01'...
- 3
0
votes
0
answers
152
views
configure: error: libcurl >= 7.28.0 library and headers are required with support for https at HPC
I met an issue when I tried to configure for R installation in HPC. I'm trying to install R-4.1.0 and 4.3.0; both show similar issue.
configure: error: libcurl >= 7.28.0 library and headers are ...
0
votes
0
answers
70
views
VS Code Won't Recognize R Installation
I installed R via the commands at this website. Running R in terminal works properly; running which R returns /usr/bin/R. VS code cannot find R despite the path for rterm and rpath being given ...
0
votes
1
answer
24
views
No precompiled R binaries for centOS?
I need to install R on my centOS linux server, preferably just by downloading the precompiled binaries on https://cran.r-project.org/, but I don't see an option for centOS. Does anyone know where ...
- 101
0
votes
0
answers
8
views
Within-cell operations in matching R data frames
I have two matching data frames in R, one has strings separated by underscores and the other has matching counts for the strings also separated by underscores. Here are some excerpts:
strings_df:
...
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0
votes
0
answers
31
views
R script does not save its output
I am trying to run a maximum likelihood phylogenetic tree with the following R script in linux:
#! usr/bin/Rscript
library(dada2)
library(phangorn)
library(DECIPHER)
penseqs <- readRDS("...
2
votes
0
answers
81
views
Rscript behaving badly
This works:
TMPDIR="/tmp/___"
export TMPDIR
mkdir -p "$TMPDIR"
script="$TMPDIR"/myscript
cat <<'EOF' > "$script" ...
- 33.8k
0
votes
0
answers
111
views
On running xdg-settings get default-we-browser, I get the following message "unknown desktop environment"
I am running an R script that tries to open a link on the linux server.
But on running the script, I get the following error
xdg-open: no method available for opening 'https://unix.stackexchange.com/'
...
0
votes
0
answers
41
views
object of type 'closure' is not subsettable error in R
Here's my code
tapply(data$/AverageCoverage, eccle$locus, summary)
I'm not sure how to fix this
2
votes
0
answers
72
views
Line plot on replicated data in R
I am trying to do a line plot using ggplot on my replicated data. There are five data sets and each data has five replicates as a1, a2, a3, a4, a5. Similarly for data b, I have b1, b2, b3, b4 and b5. ...
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0
votes
1
answer
115
views
crontab not running rscript
I have this single program that doesn't run from cron (RScript). I've tried running an sh script and calling it from that. Calling it by its full path and the likes. But it won't run. Running it ...
2
votes
0
answers
266
views
Unable to install "tidyverse" in R or Rstudio without running into errors and/or non-zero exit status
I've been having troubles with installing the tidyverse package in Rstudio and more recently when reinstalling R. I'll post my most recent error message when reinstalling R below after system info.
My ...
0
votes
1
answer
166
views
Installing DAAG library in R
I have Linux Mint. What is wrong with the installation of DAAG package in the R programming language, please?
> install.packages("DAAG")
It gives an error:
Installing package into ‘/...
- 15
1
vote
1
answer
167
views
How do I update R CRAN packages when updating from Debian buster to bullseye?
I need to update a server, which has the R statistics system installed from the CRAN repo, from Debian 10 (buster) to Debian 11 (bullseye).
The "repo line" for the buster CRAN repo is stored ...
- 359
1
vote
2
answers
567
views
Where is my shiny server
I am new to linux.
I try to deploy a shiny server locally on my windows machine with ubuntu WSL.
I successfully installed ubuntu WSL on my windows machine and I can start ubuntu.
I come here so far:
...
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0
votes
1
answer
32
views
Install DESeq2 on Archlinux
I tried running the recommended installation instructions:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("...
- 101
1
vote
0
answers
286
views
Load AppArmor profile inside Docker container
I would like to load another AppArmor profile inside a Docker container. The docker container itself uses the docker-default profile. The other profile is supposed to enforce the docker-default ...
- 71
2
votes
1
answer
910
views
Installing R from R project repo (Debian 10): key issue
I wanted to install R from the R Project repository on Debian 10. The following packages are required:
sudo apt install dirmngr -- install-recommends
sudo apt install software-properties-common apt-...
- 61
1
vote
1
answer
835
views
How to update R on Linux mint
I am not able to update R version 3.* on 4.*
What I have done according to this page:
I checked /etc/apt/sources.list
#deb cdrom:[Linux Mint 19.2 Tina - Release amd64 20190729]/ bionic contrib main ...
- 15
0
votes
1
answer
52
views
Installation R Debian - errors
I am trying to download R on my virtual machine, but for some reasons I get the following error:
~$ sudo apt install r-base
Reading package lists... Done
Building dependency tree
Reading state ...
- 1
0
votes
1
answer
103
views
To update R to v4 I deleted v3 but cannot install now
I had R version 3.. and needed to install v4 to do that first I tried to update R but did not work.
As this post suggests I deleted R packages. When I tried to delete folders which are output of R -e '...
- 103
0
votes
1
answer
133
views
Cannot install R packages on a UNIX system
I'm trying to install R packages (including ggplot2) on a UNIX system but receive the following error messages:
c++ -m64 -std=c++11 -I"/usr/local/lib64/R/include" -DNDEBUG -Itestthat -I/usr/...
- 349
0
votes
2
answers
244
views
Bash script for reading multiple files
I have multiple R scripts to read (up to 3 i.e. tr1.R, tr2.R, tr3.R).
The bash script for reading a single script is given below
#!/bin/bash
#PBS -l nodes=1:ppn=10,walltime=00:05:00
#PBS -M
#PBS -m e
...
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1
vote
1
answer
1k
views
How can I submit multiple R job at once?
I have a R-script which runs multiple files say file=1 to 50.
I usually submit repeated jobs say 5 times with 10 files each time by changing the number in R-script.
So, how can I submit the 5-job at ...
- 21
5
votes
1
answer
766
views
How to install R 4.0.* on Raspbian GNU/Linux 10 (buster)?
I believe I have followed the instructions on the relevant CRAN site to update R to the newest version (currently R 4.0.5) but with no luck.
I'm running
$ cat /etc/os-release
PRETTY_NAME="...
- 173
6
votes
5
answers
10k
views
Local installation of pcre2 not detected while installing R 4.0.4 from source
I am trying to do a build and local install of R 4.0.4 on Red Hat Linux 6.8. There were several unmet dependencies which I resolved by doing local installations (following the procedure in this). ...
- 161
2
votes
1
answer
3k
views
libcairo undefined symbol: FT_Get_Var_Design_Coordinates error when calling R from compiled MATLAB application on Centos7
I'm posting this question to document the solution to a problem which had me stuck for several weeks for which no answer was found on StackExchange or discussion boards. (Answer forthcoming)
I'm ...
0
votes
1
answer
155
views
Unable to Update R on Linux Mint 18
I originally posted this on the Stack Overflow site. I understand that it is inappropriate to ask the same question on multiple sites, but they were unable to help and I was told to come here.
I am ...
- 115
1
vote
1
answer
587
views
Cannot install 'stringi' R package -- C compiler problem?
> install.packages("stringi")
[...]
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for ...
- 1,111
5
votes
1
answer
11k
views
The repository 'https://cloud.r-project.org/bin/linux/ubuntu bionic Release' does not have a Release file
My computer has Linux Mint 19.1 Tessa with R version 3.6.3. I am trying to do sudo apt-get update and I am having this error:
Err:21 https://cloud.r-project.org/bin/linux/ubuntu bionic Release ...
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2
votes
1
answer
1k
views
How to solve "Error: (converted from warning) Setting LC_CTYPE failed, using "C"?
I am trying to install a library in R and I have a this message
Error: (converted from warning) Setting LC_CTYPE failed, using "C"
What I saw is some solutions but for mac User, like this ...
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0
votes
0
answers
44
views
How to ask a question in R when running the R script in linux?
I wrote a code in R which has 2 variables in it: rep & x
the code is written in a way that I should go inside the script to change the values for X and rep variables depends on the input data. I ...
- 1,313
1
vote
0
answers
22
views
How to pass code to attached screen
I am running an R script using a Linux Workstation. I am new to Linux - thanks for your patience!
I first ran screen before running my R script, Rscript myRscript.R
After checking in on my script ...
- 111
6
votes
1
answer
2k
views
Vim-based alternative for Emacs tramp-mode
I'm currently using vim (actually neovim) as my IDE for writing and executing GNU R-code (using the Nvim-R-plugin, see also https://github.com/jalvesaq/Nvim-R, which serves as my REPL), which works ...
- 376
1
vote
0
answers
51
views
View multiline code chunks when browsing command history
I do datascience an use R frequently. The way that probably 99% of R users interact with R is RStudio, an IDE with a lot of great features. I'm increasingly working in the cloud, so Im trying to ...
- 155
1
vote
0
answers
776
views
Updating of R 3.5.3 to 4.0.2 on Ubuntu 18.04 LTS (bionic)
I have been trying to move from this version for a while, however all attempts have failed.
The steps I am following:
sudo apt-get remove r-base r-base-dev
sudo add-apt-repository 'deb https://cloud.r-...
- 11
1
vote
1
answer
41
views
R Version in screen different than expected
Invoking R in a new terminal session loads R version 4.0.0, but if I go into a screen and invoke R, version 3.4.3 is loaded. How can I set the version of R invoked in screen to always be the version ...
- 33
1
vote
0
answers
203
views
What are the equivalent data objects in Bash in comparison to R?
R was the first programming language I learned. It is always a pleasure to learn a new language associated with the first language.
Here comes my question. What are the equivalent data objects in ...
- 584
0
votes
3
answers
4k
views
Linux Centos 7 unable to install png and EBImage package on R
I am fighting to install png and EBImage R package on my linux centos 7 machine. I have always this error message:
Error: package or namespace load failed for ‘png’ in dyn.load(file, DLLpath = ...
- 185
0
votes
0
answers
27
views
Using R on terminal also using apt-offline also purging programmes
So I did something stupid, but deliberately.
So I've been using Linux (specifically MX Linux) for a few months, and I'm trying to learn it all in depth. Since coming from Windows 7 I like everything ...
- 103
1
vote
1
answer
2k
views
working directory in gnuplot
How do I specify the working directory for gnuplot in interactive mode?
If I want to call a script with "call 'label_loop.gnu'" and do not want to put the script file in the gnuplot installation ...
- 11
0
votes
1
answer
136
views
Fail to install R on linux Mint 19
I am struggling to install R, I am failing over and over again...
At first I just wanted to upgrade from 3.4.4 to 3.4.6 and it failed all the time so I decided to uninstall R completely and install it ...
5
votes
3
answers
5k
views
Downloading from a public server: SSL certificate problem: unable to get local issuer certificate
I want to download a file (https://discovery.ucl.ac.uk/1575442/1/Palmisanoetal.zip) from a public server via the R command
temp <- tempfile()
utils::download.file(db_url, temp, method = 'curl')...
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0
votes
1
answer
4k
views
Troubles with the installation of R on Ubuntu 18.04
I have this version of Ubuntu
Distributor ID: Ubuntu
Description: Ubuntu 18.04.3 LTS
Release: 18.04
Codename: bionic
on my computer in a dual boot with Windows.
I have tried to install R ...
0
votes
1
answer
2k
views
How one can install pdftools to RStudio on Ubuntu?
Does anyone knows how to install pdftools to RStudio 1.2.5019 that runs on Ubuntu 18.04.3 LTS? I tried:
> install.packages("pdftools")
Installing package into ‘/home/jaakko/R/x86_64-pc-linux-gnu-...
- 1
0
votes
1
answer
104
views
Install R on rhel 6
Am getting below error when I do ./configure -with-x=no
checking whether zlib support suffices... configure: error: zlib library and headers are required
Installation Steps which I follow
sudo ...
- 101
0
votes
1
answer
950
views
R packages won't install on conda R environment
I am trying to install an R package to an R environment created through conda on an HPC Server where I am doing some bioinformatics. I tried to run the usual R command (which works and install the ...
1
vote
3
answers
478
views
Sum occurrences of string for each row of a matrix using awk
I have a very long data frame (~11 million x 130) for which is sparsely filled with percentages (0.00 - 100.00, float).
The entries that are missing are labeled "NA", like so:
cat1 NA NA ...
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