I am new in working with linux. I am trying to analyse sequencing data using dropEst pipeline https://github.com/hms-dbmi/dropEst#dropreport. I want to run the DropReport and for that I need to install dropEstR package.
I tried by :
devtools::install_github('hms-dbmi/dropEst/dropestr' , dependencies = T)
as they suggest and I get as an error:
bash: syntax error near unexpected token
`'hms-dbmi/dropEst/dropestr','
Do you have any idea what should I do differently?
I think you are using the "wrong" shell. You have to use R/RStudio, when you want to use the devtools package. From CRAN:
Title Tools to Make Developing R Packages Easier
I just tried you command in RStudio but installation fails in the end:
ERROR: dependency 'Rcpp' is not available for package 'dropestr'
* removing 'C:/R/R-3.4.2/library/dropestr'
Installation failed: Command failed (1)
You have to run such script on RStudio for R. Import your project here and run it.
You can download it from enter link description here
Happy Coding.
Related
Downloaded package from below URL.
Attempted to install using below command; response shown.
library(dalton.rqi,lib.loc='/home/X/Desktop/')
Error: package ‘dalton.rqi’ was built before R 3.0.0: please re-install it
https://my.clevelandclinic.org/departments/anesthesiology/depts/outcomes-research/risk-quantification
It appears this is a compiled package that maybe I don't have the source for? Is there a way to force install of the package? I'm unable to install using Rstudio GUI in its current form as a zip. Tried repackaging to tar.gz has Rstudio was looking for and also had a non-zero exit status error.
Any ideas?
I'm afraid this can't be achieved directly. The error message says it well: to use a package in R it needs to be built on an R version matching yours.
I can suggest two ways to move forward:
Contact the authors, ask for the R sources (it is somewhat surprising they did not make them available in the first place), and build the package yourself.
Downgrade your R version as far back as needed to match the one this pre-built package used.
I was trying to install the package RINDSEL but I am unable to install it and I keep getting the following error:
Error in install.packages : cannot open the connection
I downloaded the package from:
rindsel_1.0_2.zip | Integrated Breeding Platform
and loaded it from the directory. Other packages from the directory can be installed but just not this one.
Is the package corrupt or could there be any other error?
I would really be grateful for any help. Thanks in advance
Rename the zip file RinSel Software into Rindsel. That's the name specified in the discription file.
Then, you can install the package in R with the command
install.packages("C:/path/to/Rindsel.zip",repos=NULL,type="win.binary")
That works fine... at first (!!!).
Problem with the Rindsel package is. It is quite old. It was build with R 2.13.1. Therefore, if you want to load the library which would be the next step to use the package in R you will get the error:
Problems building package (Error: "package has been build before R-3.0.0")
My suggestion: Contact the authors of the package and ask them if they can either provide the source file that you can build the package by yourself or if they can bundle the Rindsel package with a newer R version.
(Or you could try to hunt down an old R version and see if you can get the thing running with an old R... However, I would not seriously suggest to do that. It would probably result in conflicting dependencies with the other required packages...)
EDIT 15-02-2018: OP asked if one can build an R package with sources that are presumeably the Rindsel source files.
Yes, basically, you could do that. You would have to make a your own description and namespace file and put the source file in the R folder than invoke the command in R to build it....
But it's not neccessary with the script files provided by the link the OP posted.
OP, just run the scripts in R! It's quite easy.
Download the zip-file and extract it on your machine.
Go to that directory. The R command would be
setwd('path/to/your/directory')
Than run the R script, e.g, the KNIndex.r. It's simple:
source('KNIndex.r')
Then the script will run and produce some output / prompts.
For future readers,
I was able to fix the error by running RStudio with administrative privileges to get the command to work.
If that does not fix it, you might wish to try
Installing "r tools" if that is not installed already. That can be downloaded from
https://cran.r-project.org/bin/windows/Rtools/
Download a relevant package that you are trying to install (e.g., tidyverse_1.3.0.zip) from https://cran.rstudio.com/
and install that from local path
It can also be installed directly from the web using install.packages("https://cran.rstudio.com/bin/windows/contrib/4.0/tidyverse_1.3.0.zip")
I had the same problem. R was not able to extract and compile the package files to the default installation directory for some system-specific reasons (not R related).
I was able to fix this by specifying the installation directory of the package lib using:
install.packages("your package", lib = 'path/to your/required/installation/directory')
You can then load the package by specifying the lib.loc option while loading it:
library('your package', lib.loc='path/to your/required/installation/directory')
A better solution:
Create a new environment variable (if you are using windows) R_LIBS_USER with the following directory path/to your/required/installation/directory.
This will change the default installation directory of the packages and make it easier to load and install them without specifying the location everytime.
I am trying to create clustered box plots in R. Everything about my code seems on track, but when I try to run it I get the error warning
"Error in loadNamespace(name) : there is no package called ‘digest’.
When I try to download the package digest in the R package Installer I get a bunch of errors stating that the download of digest failed.
How do I get the digest package, OR is there a way to do clustered box plots without this? Thanks!
I had the same problem with install.packages("digest") on OS10.11.6 (running with the defaults). But it worked by specifying the repos:
install.packages('digest', repos='http://cran.us.r-project.org')
I had a similar error message recently and managed to solve the problem by downloading the tar.gz file directly from the CRAN Repository (see https://cran.r-project.org/web/packages/digest/index.html and download "digest_0.6.15.tar.gz") and then you can install it in RStudio (Tools -> Install Packages -> Install from Package/Archive File).
Please be patient with me as I'm a total noob, but I'm really trying to learn.
I'm trying to make a choropleth map for my country, and found an R package on Github that handles it excellently. However, I'm working on a university computer and I don't have write privileges on any drive but M://, so whenever the package tries to install on C:// it obviously throws an error. This hasn't been a problem since I can just specify a libpath as an argument on install.packages, but devtools::install_github does not seem to have such an argument.
I tried using
with_libpaths(new = "M:\R\win-library\3.2", install_github('diegovalle/mxmaps'))
But I got an error message saying
with_libpaths' is deprecated. Use 'withr::with_libpaths' instead.
I take this to mean that I need to install the "withr" package in order to use that? However, I keep getting errors when trying to install that package. First, I got
Warning in install.packages : installation of package ‘withr’ had
non-zero exit status
because of the not having access to C:// issue. I usually bypass this by installing directly from the binaries, but when I try that it tells me
"Warning in install.packages : package ‘withr’ is not available (for R
version 3.2.2)".
Other than updating my version of R (which will be a nighmare since I don't have installation privileges on this machine), how else can I either install withr or find another way to specify the directory to install the package from github?
I would suggest you to go with latest version of 3.4.All above mentioned packages are available under latest version.
Two ways to set local library paths (at least on Linux running R 3.5.3):
(1) At the beginning of your script, set the the .libPaths option to your local library path, i.e.: .libPaths("M:\R\win-library\3.2")
(2) Add to your .Renviron file a line that specifies your local library path: i.e.: R_LIBS="M:\R\win-library\3.2"
Note: For (1) You will need to manually run every time you start a new R session, whereas (2) will be set automatically when R starts.
I try to install the package RSelenium:
devtools::install_github("ropensci/RSelenium")
This gives me following error:
Downloading GitHub repo ropensci/RSelenium#master
from URL https://api.github.com/repos/ropensci/RSelenium/zipball/master
Installing RSelenium
Error: Found continuation line starting ' <!DOCTYPE html PUB ...' at begin of record.
Some research thaught me that I can simple install it using
install.packages("RSelenium, type="Source").
This indeed successfully installs the package, but gives trouble when using the function getPageSource() as mentioned here.
EDIT: I'd also like to add that before the package installed successfully, but at one point it suddenly kept on failing.