I am currently trying to install packages on R. On the startup, I get the normal R message with
"Error: object 'getw' not found"
When I use the install.packages function, I get the same error at the end of the installation, one for each package I tried to install.
However, when I start R with R --no-init-file I can install packages normally.
I have been fishing around with Rprofile and other initialization settings of R. I have also done clean installs of R, and the message still appears.
Does anyone have an idea about how to remove this error? Also, this machine is running Ubuntu 14.04 Trust Tahr.
This sounds like something is wrong with the .Rprofile file. There can be more than one such file. At the beginning of an R session, R first searches for such a file in the working directory, then in the home directory.
You may also want to check if the environment variable R_PROFILE_USER is set (In an R shell, this can be checked with Sys.getenv("R_PROFILE_USER")). If yes, look at the .Rprofile file in that directory to see if there is any suspicious entry.
If all fails, make a copy of the .Rprofile file in your home directory and (if applicable) in your working directory with a different name. Then delete the file and try the installation again. If this succeeds you can afterwards restore the old .Rprofile file(s) by using the copy/copies that you made before.
I had the same error. In my case, this was due to a previous partially failed uninstall of the package I was trying to install. Manually removing the partially uninstalled version of the package then allowed intall.packages to succeed.
Full details:
I had run devtools::install_github(...) which prompted about newer versions of some required packages being available. I opted to install these updated versions in response to the prompt. One of these packages (Rcpp) failed to be installed with an error about being unable to remove the older version of that package (presumably due to the file being in use/locked somehow).
When I tried to install a newer version of Rcpp from install.packages, I got the above error.
After investigating various things, I eventually ran .libPaths() which output the location my packages are installed. I went to this folder, found the Rcpp subfolder, which was mostly empty except one file (Rcpp.dll) - presumably the file that failed to be deleted before. I deleted this file manually and deleted the Rcpp folder.
I then retried install.packages(...) which now succeeded.
Related
For many R packages I try to install (on my Windows 10 machine), I get a warning:
> install.packages('rstan')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
I thought this was just an erroneous error message since the installation seemed to proceed anyway, but recently I tried to install a package (rstan) and found it completely nonfunctional. My hunch is that since rstan relies completely on compiling code with rcpp, maybe I only got away with the previous packages because I wasn't using the functions in them that relied on Rtools.
I reinstalled Rtools 4.0, and devtools::find_rtools() returns TRUE. But when I run Sys.getenv()['PATH'] there is no Rtools on the path. There isn't a place in the installation process to tell it I want Rtools on the path either, so these instructions don't help - the menus they refer to don't exist for me. So I thought this might be an issue where the new Rtools 4.0 doesn't put itself on the system path. But the problem persisted even after I directly edited the Windows path environment variables (both system and user versions) to include the path given to me by pkgbuild::rtools_path() (C:\rtools40\usr\bin, a path which both exists and appears to be correct).
This doesn't seem to be the same problem as Rtools 4.0 (Rstudio falsely claims it was deleted), since there are no claims Rtools was deleted. It's also not the same as Rtools not being detected by R as far as I can tell: I'm not leaving any features out of my Rtools installation - I'm not even getting the option to in my install wizard.
Would appreciate any advice or recommendations.
Rtools40 requires that you add its bin directory to your PATH variable. The full instructions are here.
You can update your ~/.Renviron file with any of the following methods:
You can do that manually by opening ~/.Renviron and putting the following in it:
PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"
You can also use R (Gui or RStudio or Shell) with the following:
writeLines(
'PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"',
con = file("~/.Renviron", open = "a")
)
Both of these methods require a restart of R.
I am trying to copy R packages from a directory on one linux server and install them on another. I started out by writing a script that would loop through a list of all the R packages I needed and install them. This worked for a majority of packages, but, since I am forced to utilize R 3.0.3, a significant number of packages are unavailable for this version of R. Meaning that R was trying to install the most recent versions of these specific packages.
I am trying to find a solution that does not involve me having to go through each package, find the version we are running on the old server, then going to CRAN and downloading the archived .tar.gz file.
Ideally, I would like to loop through the directory of R packages, make them all into .tar.gz files, move those files to the new server, and install them like that. However, I ran into the following issue when I tried to "build" one these packages.
R CMD build car
Read 1 item
* checking for file ‘car/DESCRIPTION’ ... OK
* preparing ‘car’:
* checking DESCRIPTION meta-information ... OK
Warning in file(con, "r") :
cannot open file 'man': No such file or directory
Error in file(con, "r") : cannot open the connection
ERROR
computing Rd index failed
I tried another using devtools::build('abind'), but this also failed with the same errors above.
Should I change my approach or is there something missing with what I am doing? Any help on this would be appreciated.
Your general approach won't work: tar.gz files contain the source for a package, but not all of it is installed when you install a package, so you can't recreate the tar.gz file from the installed files.
What might work if you didn't want to work with such an ancient version of R is to use Microsoft's CRAN "time machine" (https://mran.microsoft.com/timemachine), but I think it only goes back to R 3.2.3.
Copying the library might work, but binaries of those files are probably linked to system library files at particular locations, so I wouldn't trust it to be reliable.
I think your best option would be to update R to the current release (or maybe 3.5.3, the last patch release of the previous series), then just install current versions of the packages you want.
If this is impossible for some reason, then you're likely to have no choice but installing versions matching the ones you had installed. At least you can find versions automatically: the installed.packages() function returns a matrix with package name in column "Package" and its version in column "Version". Run that on the old system, then build them on the new system using the remotes::install_version() function (which claims to work on R back to 3.0.0, but I bet it hasn't been tested there lately).
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.
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'm new to R. Trying to install the package UsingR but running into problems:
library(UsingR,lib="C:\[whereitwent]")
Loading required package: HistData
Error: package ‘HistData’ could not be loaded
In addition: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called ‘HistData’
Now when I did the install.packages("UsingR", lib="C:\[whereitwent]") bit, there was a weird part:
Warning: unable to move temporary installation ‘C:[where it went]\library\file7946ce71334\acepack’ to ‘C:\[whereitwent]\R-Portable\App\R-Portable\library\acepack’ package ‘HistData’ successfully unpacked and MD5 sums checked
I was having this same problem yesterday except instead of "there is no package called 'HistData' it was telling me there is no package called 'Formula'. I uninstalled and reinstalled R Portable this morning, tried again, and this is the result. My professor did this exact thing on her computer right in front of me yesterday and everything worked fine. I've tried this on two computers myself and it's the same issue both places. I've tried googling this but can't find anything substantive, and frankly I'm not really even sure how to google this exact issue. Can anyone help me identify the problem?
Note: "[whereitwent]" is my edit here so I'm not showing off my whole thing including my name. Everything else is copied and pasted exactly as is.
If you just want to be able to install packages, this will set library path:
.libPaths('C:/[path]')
you might need to escape the slashes, I'm sorry I don't use windows. You can add this to a file .Rprofile in your home folder and you won't have to do it again.
Alternatively (or in concert) you may want to look at the packrat package which will install packages with the project you're working on
This error is related to permissions issues, run R or RStudio as administrator (assuming you're on windows) and re-install the package.
If you are unable to run as administrator you usually will not be able to write to the C:\Program Files directory on a corporate computer. All you need to do is change the directory to which the package is installing to a folder to which you have read write permissions. For example, on my computer:
install.packages("gdata", lib = "C:/Users/mkemp6/Desktop/Rscrap", repos = "http://dirichlet.mat.puc.cl/")
To view permissions on a specific folder, right click the folder, select the "Security" tab and and highlight your username.
The same problem was solved by updating R to 3.1.3
I was experiencing similar issue on my Ubuntu machine. I solved it by running R as a "sudo" user and then install the packages from CRAN.