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Questions tagged [r]

R is a programming language and software environment, mostly used for statistical computing and graphics.

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Fetch data from a large file based on time and date recursively

Fetch data based on date(column 1) and time (column 2). Each date has time in column 2. Based on each date in column1 two files are to be generated which will have all the fields based on time 6:00 to ...
Gavin's user avatar
  • 91
2 votes
1 answer
245 views

SSH session termination on script error when sourcing multiple sub-scripts

I'm facing an issue with SSH on a server. Running individual scripts (source s01.sh, etc.) works fine, with errors displayed in the console. However, when using a master script to source these scripts,...
jay.sf's user avatar
  • 227
0 votes
1 answer
256 views

How to have R 4.1 on Debian 11? Debian 11 won't update

Debian 11 only updates to R 4.0.4. I have packages that require at least R 4.1.0 to be installed. I already tried adding the official R repository to the source list as the official website tells to ...
BsAxUbx5KoQDEpCAqSffwGy554PSah's user avatar
0 votes
0 answers
247 views

Error in readRDS("file.rds") : error reading from connection Execution halted

I am unable to read an rds file into R via my remote server. I am able to read it into R on Rstudio, but it will not work when using my remote server. It was working previously, but R on the server ...
Warsame's user avatar
0 votes
1 answer
103 views

R Packages won't install via ansible (ALMA Linux 8)

Problem I would like to use ansible to provision a virtual box. This box will need to do multiple things, but it needs to have R installed as well as some specific packages that aren't included in ...
Hugh Warden's user avatar
0 votes
1 answer
814 views

error: libcurl >= 7.28.0 library and headers are required with support for https

I'm sorry for having written such a long question, but given how many times similar questions have been asked, I felt like I had to give a lot more context. In my system, I get. . . checking for curl-...
Sweet Shell O'Mine's user avatar
-1 votes
1 answer
159 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 ...
basesorbytes's user avatar
0 votes
1 answer
97 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/...
Mabel's user avatar
  • 1
0 votes
1 answer
26 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'...
Fkiran's user avatar
  • 3
0 votes
1 answer
52 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 ...
roulette01's user avatar
2 votes
0 answers
119 views

Rscript behaving badly

This works: TMPDIR="/tmp/___" export TMPDIR mkdir -p "$TMPDIR" script="$TMPDIR"/myscript cat <<'EOF' > "$script" ...
Ole Tange's user avatar
  • 35.8k
1 vote
0 answers
203 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/' ...
Narayan Shubha's user avatar
2 votes
0 answers
92 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. ...
Gavin's user avatar
  • 91
0 votes
1 answer
173 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 ...
BlackNinja's user avatar
2 votes
0 answers
367 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 ...
notsotidyverse's user avatar
0 votes
1 answer
315 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 ‘/...
Carly's user avatar
  • 15
1 vote
1 answer
257 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 ...
dave559's user avatar
  • 389
1 vote
2 answers
835 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: ...
TarJae's user avatar
  • 113
0 votes
1 answer
34 views

Install DESeq2 on Archlinux

I tried running the recommended installation instructions: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("...
Galen's user avatar
  • 101
1 vote
0 answers
500 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 ...
user's user avatar
  • 71
2 votes
1 answer
1k 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-...
maxechstack's user avatar
1 vote
1 answer
1k 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 ...
Carly's user avatar
  • 15
0 votes
1 answer
58 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 ...
Miriam_G's user avatar
0 votes
1 answer
115 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 '...
alkanstein's user avatar
0 votes
1 answer
177 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/...
Bob's user avatar
  • 349
0 votes
2 answers
340 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 ...
b_takhel's user avatar
1 vote
1 answer
2k 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 ...
b_takhel's user avatar
5 votes
1 answer
850 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="...
jay.sf's user avatar
  • 227
6 votes
5 answers
14k 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). ...
Dronacharya's user avatar
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 ...
Zachary Klamer's user avatar
0 votes
1 answer
164 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 ...
E Tam's user avatar
  • 127
1 vote
1 answer
712 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 ...
adatum's user avatar
  • 1,161
5 votes
1 answer
12k 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 ...
user435322's user avatar
2 votes
1 answer
2k 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 ...
coding's user avatar
  • 121
0 votes
0 answers
47 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 ...
zara's user avatar
  • 1,333
1 vote
0 answers
23 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 ...
nateroe's user avatar
  • 111
6 votes
1 answer
3k 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 ...
n0542344's user avatar
  • 406
1 vote
0 answers
63 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 ...
Amadou Kone's user avatar
1 vote
0 answers
787 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-...
biologistor's user avatar
1 vote
1 answer
51 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 ...
GigaZaur's user avatar
1 vote
0 answers
236 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 ...
Praveen Kumar-M's user avatar
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 = ...
user979974's user avatar
0 votes
0 answers
32 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 ...
1toneboy's user avatar
  • 441
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 ...
user15181's user avatar
0 votes
1 answer
137 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 ...
Peligrochon's user avatar
5 votes
3 answers
7k 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')...
nevrome's user avatar
  • 213
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 ...
Eleonora's user avatar
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-...
guest's user avatar
  • 1
0 votes
1 answer
110 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 ...
Alkesh Mahajan's user avatar
0 votes
1 answer
1k 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 ...
Yaseen Ahammed's user avatar