Questions tagged [r]

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

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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 ...
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1 answer
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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 ‘/...
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1 answer
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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 ...
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  • 339
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2 answers
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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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Install DESeq2 on Archlinux

I tried running the recommended installation instructions: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("...
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0 answers
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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 ...
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2 votes
1 answer
428 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-...
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1 vote
1 answer
277 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 ...
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Rstudio GLIBCXX_3.4.26 dependency

I have installed the R package metaboliteIDmapping using: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("...
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1 answer
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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 ...
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1 answer
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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 '...
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1 answer
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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/...
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2 answers
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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
594 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 ...
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5 votes
1 answer
555 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="...
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3 votes
5 answers
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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). ...
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2 votes
1 answer
2k 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 ...
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1 answer
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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 ...
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1 answer
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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 ...
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3 votes
1 answer
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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
835 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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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 ...
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1 vote
0 answers
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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 ...
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5 votes
1 answer
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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 ...
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1 vote
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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 ...
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1 vote
0 answers
675 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-...
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1 vote
1 answer
33 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 ...
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0 answers
70 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 ...
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0 votes
3 answers
3k 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 = ...
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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 ...
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1 vote
1 answer
1k 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 ...
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1 answer
128 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 ...
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4 votes
3 answers
4k 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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1 answer
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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 ...
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1 answer
1k 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-...
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1 answer
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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 ...
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1 answer
303 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 ...
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1 vote
2 answers
312 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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-1 votes
1 answer
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What is the best way to get the latest version of R? [closed]

A lot of instructions that I find on here give instructions about how to install the latest version of R that either deliver an out of date version, or are very OS-dependent. I just bought a System76 ...
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15 votes
4 answers
33k views

Installing/updating R 3.6 on Ubuntu 18.04

I've recently acquired a machine with Ubuntu 18.04 on it. I installed R simply with: sudo apt-get install r-base And when I call $ R in console, it starts up with: R version 3.4.4 (2018-03-15) -- "...
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  • 339
1 vote
0 answers
44 views

R packages keep asking for update

The following R packages keep asking for updates, each and everyday, even after I update everything! r-cran-kernsmooth r-cran-mgcv r-cran-nnet r-cran-spatial Here they are on the list of OS Updates (...
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0 votes
2 answers
99 views

merge 1st column and 2nd column; 3rd and 4th column and so on with a separator

I have a text file with 61000 columns and 173 rows. I would like to merge data on every 2 columns i.e., columns 1 and 2 should be merged, 3 and 4 should be merged, 5 and 6 should be merged and so on. ...
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2 answers
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How to create a new column based on the values from multiple columns which are matching a particular string?

I have data frame which looks like this: df=data.frame( eye_problemsdisorders_f6148_0_1=c("A","C","D",NA,"D","A","C",NA,"B","A"), eye_problemsdisorders_f6148_0_2=c("B","C",NA,"A","C","B",NA,NA,"A"...
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0 votes
0 answers
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Install R package 'xml2' without root access

I would like to install xml2 R package (devtools package requires xml2) on a Red Hat server but I don't have root access, is it possible to install an R package without having root access? Thank you ...
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1 vote
0 answers
69 views

Old version of of R Cannot Find Packages on RHEL 7

I am working on a Redhat 7 linux server and utilizing an extremely old version of R (3.0.3 to be exact). I had to install this version of R from a source file. I properly configured the Renviron file ...
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0 votes
1 answer
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Add a part of value from file1 to column in file 2 if there is a match

I have 2 csv files: file (1 column)1: Prokaryote,Caudovirales,Myoviridae Prokaryote,Caudovirales,Podoviridae Prokaryote,Caudovirales,Siphoviridae Prokaryote,Ligamenvirales,Lipothrixviridae ...
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8 votes
1 answer
28k views

error while loading shared libraries; file too short

I am working on a CentOS 7 workstation. I had installed Rstudio and it was working fine until recently. But now, if I try to launch it at http://localhost:8787/ I get an error that says Unable to ...
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0 votes
1 answer
130 views

Extract data based on second column [closed]

Now I have a file format like ACTG,CD1,234 BGTY,CD2,561 CFRT,CD3,27 DGTY,CD4,45 EYTG,CD5,23 FJUI,CD1,78 GYHJ,CD2,89 HYHG,CD3,107 IUHJHU,CD4,55 JMJGT,CD5,77 I want my output file like: CD1,ACTG,234 ...
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1 vote
1 answer
142 views

Uninstall R from Docker image

I have tried: sudo apt-get remove r-base sudo apt-get remove r-base-core delete everything in .libPaths() The thing is, I'm using a Docker container which came with R installed in it. ...
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-1 votes
3 answers
2k views

How to calculate mean of each 3 columns in data frame?

I have a data frame like this: > head(dat_sg2) DwoC_2318_norm.1 DwoC_2318_norm.2 DwoC_2318_norm.3 DwoC_3395_norm.1 DwoC_3395_norm.2 DwoC_3395_norm.3 DwoC_6154_norm.1 ...
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