Questions tagged [r]

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

44 questions with no upvoted or accepted answers
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9
votes
1answer
7k views

Installing openssl on R

I'm trying to install openssl inside R, using install.packages('openssl'), but I'm getting an error message: * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and ...
4
votes
2answers
356 views

bash/cygwin broken after installing rtool?

Usually I can solve problems on my own (and Google). But recently I am baffled by this strange hiccup. Background: I use a chain of scripts for file-processing (in Windows, under Cygwin. Scripts ...
3
votes
0answers
146 views

Using ack to effectively search and RStudio project directory

I'm interested in running ack search on a RStudio project directory that mostly contains *.R script files but also some project files and often *.git files. Directory The project folder structure ...
2
votes
0answers
2k views

R configure file error: C compiler cannot create executables

I am trying to install R 3.3.1 on AIX 6.1 server. I am getting below error. checking whether the C compiler works... no configure: error: in `/opt/R-3.3.1': configure: error: C compiler cannot ...
2
votes
0answers
531 views

Running R script and global variable overriding with <<- from cron

I have a R script that works just fine when I run it from RStudio. However, once I schedule it through cron under user RStudio only with home directory (/home/rstudio), it halts at the very step I ...
2
votes
0answers
1k views

How to install rJava Package in Linux Mint

I already have installed R, and Java in Linux Mint, to install rJava I used this command, in Rstudio- install.packages("rJava") it starts installing, but eventually it returns some errors and ...
2
votes
0answers
258 views

Running R scripts on a Linux cluster

I have access to an IBM IDataplex Cluster with CentOS v.6.2. If I want to run the following R script on R: library(data.table) library(mgcv) library(reshape2) library(dplyr) library(tidyr) library(...
2
votes
0answers
159 views

GNU/R 'no audio drivers are available'

Error message as in title shows up in console when trying to execute play() function from audio package. I found plenty of references to this question, but link provided in the answer is dead. How to ...
2
votes
1answer
430 views

ess has disappeared from emacs

I frequently use emacs ess functions. Specifically, I use r-mode and run R in emacs. However, quite suddenly, emacs is no longer offering ess options. r-mode is no longer an option in emacs nor is R. ...
2
votes
1answer
790 views

Launch R code from within vim-r-plugin as separate window instead of inside tmux/screen?

I use the vim-r-plugin to write R code in vim. It is a nice plugin and I love that the plugin lets me run code directly from within vim. However, the R prompt is opened in a console which is ...
1
vote
1answer
212 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 ...
1
vote
0answers
17 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 ...
1
vote
0answers
20 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 ...
1
vote
0answers
408 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-...
1
vote
1answer
518 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 ...
1
vote
0answers
40 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 (...
1
vote
0answers
46 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 ...
1
vote
1answer
141 views

Merge two tables based on value in first column

I have 1 table like this (csv file): p1 p10 p16 p19 p25 p3 p5 p6 p8 p9 con1 567 0 3 0 18 17 8 4 6 7 con3 490 7 6 2 23 26 20 14 12 29 con4 737 1 4 1 ...
1
vote
0answers
23 views

Cropped plot labels in knitted PDF in Linux

Has anyone experienced having their plot labels cropped in knitted PDF's in Linux? This does not happen in my Windows machine. Here is a minimal r-markdown example to replicate this problem. --- ...
1
vote
0answers
468 views

R: how to install RCurl on Debian Linux 9 (stretch)?

I have tried all kind of libcurl apt packages and so forth. I need RCurl for h2o in Debian Stretch. How can I install RCurl in Debian? ** R ** data ** inst ** preparing package for lazy loading ** ...
1
vote
0answers
410 views

How to increase memory limit and number of cores that Rstudio uses on a cluster

I launched Rstudio using FastX on Rivanna cluster (CentOS Linux release 7.3.1611 (Core)): https://arcs.virginia.edu/rivanna The main goal for doing that was to significantly increase the speed of ...
1
vote
1answer
100 views

secure apt R pgp key no_pubkeys found

I already applied the solutions on these pages Why failing to get CRAN key for R backports? and https://cran.r-project.org/bin/linux/debian/#secure-apt for installing R on Debian Linux Jessie ...
1
vote
0answers
874 views

Arch Linux - Cronie is not working and nestat does not output logs?

I added a cronjob via crontab -e which is to be executed every minute. I enabled and started cronie on systemctl. Set editor $ export EDITOR=vim Add cront tasks $ crontab -e * * * * * Rscript /...
1
vote
1answer
256 views

Why is my R graphics device not refreshing and gets drawn so slowly through VNC?

The plotting speed of the graphics device is extremely slow when I use a VNC connection. The rest of the connection works perfectly fine so I cannot blame the network, it is specifically R devices ...
1
vote
1answer
501 views

Error : .onLoad failed in loadNamespace() for 'cairoDevice' on a Linux Machine

After spending 1 hour searching for the solution I am posting this here. Does any one know how to install cairoDevice,package on R, Linux Server. R CMD INSTALL cairoDevice_2.19.tar.gz * installing ...
0
votes
0answers
23 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). ...
0
votes
0answers
49 views

Structure needs cleaning error in R

Working in 64bit CentOS 7 Wanted to install MetaIntegrator package in RStudio which requires R > 3.6 So upgraded R using command sudo yum update R Restarted RStudio and attempted installation of ...
0
votes
0answers
25 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 ...
0
votes
0answers
29 views

Cron Job is running outside of defined schedule

I have a question and am relatively new to scheduling Cronjobs in R Studio. I have an R script that I would like to run every Monday - Friday, every 1 minute, and between the hours of 9 - 16 (9 am to ...
0
votes
0answers
30 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 ...
0
votes
0answers
9 views

Black and white georeferenced raster image to true color raster image

Is it possible to convert a black and white photo to True color (colored) preserving the geolocation in imagemagick or magick library in R?
0
votes
0answers
22 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 ...
0
votes
1answer
106 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 ...
0
votes
0answers
23 views

How to looping over a column and if pattern matches, count related characters in other columns using R?

I have a data frame with 1000 rows and 21 columns which the first column is miRNA gene names and other columns show each nucleotide in each position: What I want is to make a loop over the first ...
0
votes
1answer
2k 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
0answers
56 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 ...
0
votes
0answers
120 views

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 ...
0
votes
1answer
618 views

Can't find r-base package

I'm using Debian 9.1 and tried to install the r-base using the command sudo apt-get install r-base But it says that it can't find the r-base package.
0
votes
1answer
9k views

Loop over a data frame comparing elements of the firts and second row

I want to loop over a dataframe, I want to compare one of the elements of the actual row and the next row. for example, I have a data frame that looks like this: V1 V2 V3 ...
0
votes
1answer
44 views

Unable to type character “n” in ubuntu command line interfaces (R, mysql, python,…)

I am having a maddening problem which I hope someone has seen. I am working on ubuntu, remotely over putty. In the shell console, either bash or tcsh, everything is fine. Everything is also fine ...
0
votes
1answer
989 views

Install R package in Unix

I'm trying to install a package in R in Unix I used the following : install.packages("rminer", repos="http://cran.r-project.org", lib="~/R/libs/") I get the following error ERROR: compilation ...
0
votes
0answers
434 views

connection refused from server to local host

I have an R script on a remote server. The script needs my local display in order to generate plots. me@local$ ssh -Y me@remote_ip me@remote$ echo $DISPLAY localhost:52.0 $ Rscript myscript.R ...
-1
votes
3answers
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 ...
-2
votes
4answers
181 views

Filter specific numbers from multiple files

I have multiple files (apx. 150) that look like this: reconstructed_hap_4_Local_nt_haplo_freq_60.3 ...