I tried to build the R package hyperSpec using Windows Vista. When I do so, I get the following error message:
warning in file.copy(pkgname, Tdir, recursive = TRUE)
Problem copying .\hyperSpec\data\barbiturates.rda to C:\Users\JenZIG\AppData\Local\Temp\RtmpOEIqBD\Rbuilde446d3a290d\hyperSpec\data\barbiturates.rda: Permission denied
It is all the same whether I use the command line with R CMD build or R Studio's Build Tools (RTools installed, all package dependencies installed).
To solve the problem, I tried to change the path for the temporary directory or to manually set the permissions for the folders but without success. I tried to execute everything as administrator but again no success.
I think, a similar problem was discussed here:
https://stat.ethz.ch/pipermail/r-devel/2013-April/066389.html
However, there is no solution provided for this problem.
In addition, I have the same problem when I try to build the package with Win7.
I had this problem. I had previously installed the package in question using the command line:
sudo R -e "install.packages('somepackage', repos='http://cran.rstudio.com/')"
Then when I tried building the somepackage package from source I got the permission denied message.
The solution was to run the following from the command line:
sudo R -e "remove.packages('somepackage')"
Then I was able to build and check somepackage from source.
EDIT
I see that the original question was specific to Windows. In that case I think you simply need to run a powershell window as administrator and use the following command:
Rscript.exe "remove.packages('somepackage')"
What worked for me was unloading the package, removing the package, restarting R Studio, and then reinstalling it.
(in R Studio on the right hand side of the interface there is a tab called "Packages" that lets you do all of these things)
Related
I am trying to install package SBCK from R build using Rscript build.R -c -v -i in windows command prompt following the steps given here. However, I ended up with package SBCK being not installed because of following error/warning InstallationWarning: package 'SBCK' is in use and will not be installed. I have no package with name SBCK installed on my system, so I do not understand why I am getting this warning message and thus not to be able to install the R package.
I know that similar question have been asked before here but solution there does not work in my case.
I am using R version 4.2.0 on Windows 10.
Once 'build.R' is run, "SBCK_0.5.0.tar.gz" is created in the 'SBCK-R' folder.
You can now install it via the package archive file option or pointing to that file in the install.packages command. I faced the same issue and this solved it.
I can't start rstudio from my linux terminal. It always shows me this message:
Unable to determine real path of R script /home/remi/anaconda3/bin/R (system error 2 (No such file or directory))
I have Kubuntu 18 and anaconda installed on it.
I had trouble with installing curl and other libraries that need curl.
Since it was maybe due to a problem of paths, I removed R and RStudio from my conda environment in order to work only on the R and RStudio installed in Kubuntu. Something must have gone wrong.
I have tried to remove and reinstall both R and RStudio but it didn't work.
Weirdly, I can launch RStudio from my application launcher and I was able to install all the libraries I needed.
I would like to be able to launch RStudio from the terminal without any problem.
Does someone know what the problem is ?
Thank you !
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'm trying to install Apache Zeppelin on my old computer that runs Ubuntu. So far, I'm able to install Zeppelin very easily by cloning the latest 0.6.0 snapshot release using
git clone https://github.com/apache/incubator-zeppelin.git
cd incubator-zeppelin
mvn clean package -DskipTests
but I want to have R on Zeppelin. Supposedly, the 0.6.0 snapshot has two R interpreters, but when I run the R tutorial (the pre-made note that uses %r), I get this list of errors.
I followed several guides to try and install R as an interpreter, but each one resulted in some kind of error. I tried this instructional:
http://www.r-bloggers.com/interactive-data-science-with-r-in-apache-zeppelin-notebook/, and got a build failure on "R Interpreter". The error message was
"dependency 'evaluate' is not available for package 'rzeppelin'
* removing '/home/rebecca/Zeppelin-With-R/R/lib/rzeppelin'"
and then a bit lower down
Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:exec (default) on project zeppelin-zrinterpreter: Command execution failed. Process exited with an error: 1
I also tried this Stack Overflow guide: Anyone tried to add R interpreter onto Apache Zeppelin?, and while I was able to run incubator-zeppelin, I received an error when I used either the %spark.r or %r interpreter tags, saying both "interpreter not found" and "prefix not found". Spark doesn't work either after following the first solution, getting the same error mentioned in the second solution (the jar file not being there), and then trying the second solution.
Does anyone have a guide for installing R onto the newest version of Zeppelin? I'm very flexible in the way I can install it. I can run other operating systems onto my computer, and I also have Virtual Box installed on my other computer, which is a mac.
There is currently a bug in the latest HEAD of zeppelin that was recently introduced and prevents the R interpreter from launching cleanly
Did anyone created a Zeppelin Jira Issue for that?
For me it is working on Zeppelin branch-0.6
build Zeppelin with r profile: -DskipTests -Prthis will...
create a directory 'R' in git repo root
copy the 'zeppelin-rinterpreter*.jar' into git_repo_root/interpreter/spark
build Zeppelin with build distro profile: e.g. -DskipTests -Pbuild-distr -Pspark-1.6 -Phadoop-2.6
use zeppelin-distribution/target/zeppelin*.tar.gz for installation
ensure both 1.1 and 1.2 are present in your zeppelin installation
The error you're getting is that you need to have the R package evaluate installed. You can install this simply by launching R and typing install.packages('evaluate').
That said, your excerpt mentions the directory Zeppelin-with-R. That's my repo, which is the R interpreter in the form when it was accepted into Zeppelin. That is version 0.5.6, not 0.6.0. There is currently a bug in the latest HEAD of zeppelin that was recently introduced and prevents the R interpreter from launching cleanly. Your best bet for now is to use the one from my repo and install clean, without trying to pull-in from Zeppelin HEAD.
I'm pretty new to R so apologies for a stupid question. I'm trying to get rcpp running but I'm stuck in an endless loop of R asking me to re-install RTools.
I broadly followed the code in this blog post, although first time off I installed everything by hand & I've subsequently re-installed everything a few times over. I'm running Windows 7, R version 3.1.2, R Studio Version 0.98.1091 (not that this should matter much) and RTools 3.1.
An edited highlight of what my console looks like is as follows:
> library(installr)
Welcome to installr version 0.15.3...
> install.Rtools()
Loading required package: devtools
No need to install Rtools - You've got the relevant version of Rtools installed
> find_rtools()
[1] TRUE
> library(Rcpp)
> evalCpp("1+1")
Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput, :
Error 65535 occurred building shared library.
At which point a dialog box pops up saying:
Install Build Tools
Compiling C/C++ code for R requires installation of additional build tools.
Do you want to install the additional tools now?
And then I get directed to download and re-install RTools 3.1 from cran all over again.
I've seen that this can be an issue with the PATH variable but I've tried various things including:
Nothing (extra) in the PATH variable
Including both references to R (C:\Program Files\R\R-3.1.2\bin\x64) and RTools (C:\RBuildTools\3.1\bin;C:\RBuildTools\3.1\gcc-4.6.3\bin;) in the PATH. Once with RTools first, once with R first
Including just a reference to RTools in the PATH as the initial install file directed me to do.
Any ideas on things to try would be gratefully accepted!
EDIT
Following Dirk's comment it looks like I might have a problem with how RTools is installed. I've followed the instructions from several blogs / tutorials on how to install RTools; all to no avail (yet!)
This GitHub page gives some instructions on how install and check that the installation has worked. I've followed all the checks (see below for copy of the console) and it looks like I have a working install of RTools, but when I try to run evalCPP() again I get the same error as before directing me to install RTools.
> Sys.getenv('PATH')
[1] "C:\\Program Files\\R\\R-3.1.2\\bin\\x64;C:\\RTools\\bin;C:\\RTools\\gcc-4.6.3\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\Enterprise Vault\\EVClient\\;C:\\Program Files (x86)\\Microsoft SQL Server\\100\\Tools\\Binn\\VSShell\\Common7\\IDE\\;C:\\Program Files (x86)\\Microsoft SQL Server\\100\\Tools\\Binn\\;C:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Binn\\;C:\\Program Files (x86)\\Microsoft SQL Server\\100\\DTS\\Binn\\;C:\\Program Files (x86)\\Microsoft Visual Studio 9.0\\Common7\\IDE\\PrivateAssemblies\\;C:\\Program Files\\Microsoft SQL Server\\110\\Tools\\Binn\\;C:\\Program Files\\Microsoft\\Web Platform Installer\\;C:\\Program Files (x86)\\Microsoft SDKs\\TypeScript\\1.0\\;C:\\Program Files\\Microsoft SQL Server\\100\\DTS\\Binn\\"
Warning message:
printing of extremely long output is truncated
> system('g++ -v')
Using built-in specs.
COLLECT_GCC=C:\RTools\GCC-46~1.3\bin\G__~1.EXE
COLLECT_LTO_WRAPPER=c:/rtools/gcc-46~1.3/bin/../libexec/gcc/i686-w64-mingw32/4.6.3/lto-wrapper.exe
Target: i686-w64-mingw32
Configured with: /data/gannet/ripley/Sources/mingw-test3/src/gcc/configure --host=i686-w64-mingw32 --build=x86_64-linux-gnu --target=i686-w64-mingw32 --with-sysroot=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/mingw32 --prefix=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/mingw32 --with-gmp=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --with-mpfr=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --with-mpc=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --disable-shared --enable-static --enable-targets=all --enable-languages=c,c++,fortran --enable-libgomp --enable-sjlj-exceptions --enable-fully-dynamic-string --disable-nls --disable-werror --enable-checking=release --disable-win32-registry --disable-rpath --disable-werror CFLAGS='-O2 -mtune=core2 -fomit-frame-pointer' LDFLAGS=
Thread model: win32
gcc version 4.6.3 20111208 (prerelease) (GCC)
> system('where make')
C:\Rtools\bin\make.exe
I've also had a look at Appendix D of R Installation and Admin. I can't see anything in here I've not already tried except for section D.4 which implies I might need to rebuild rcpp from source using my installed RTools. I don't have time to do this right away but will give it a try unless people say this route is not worth my time.
EDIT v2
So I tried building rcpp from source ... and that didn't work either. I downloaded both the package source and windows binaries from the CRAN Rcpp package page. In the R console I now get:
> install.packages(pkgs = "C:/Rcpp_0.11.4.tar.gz", repos = NULL, contriburl = NULL, type = "source", verbose = TRUE)
Installing package into ‘C:/Users/james.macadie/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
system (cmd0): C:/PROGRA~1/R/R-31~1.2/bin/x64/R CMD INSTALL
Warning in install.packages :
package ‘C:/Rcpp_0.11.4.tar.gz’ is not available (for R version 3.1.2)
I guess my active questions now boil down to:
Reading the whole of the post above can anyone tell me how to fix things so it just works? Or, failing that...
What tests can I run to check I really do have Rtools installed correctly? Everything I have found on the internet suggests I do: system('where make') etc. However, the evidence of being unable to run evalCpp or other rccp functions suggests I don't.
What am I doing wrong when building from source? Should I try the command line option?
EDIT v3
Running evalCpp with showOutput= TRUE and verbose = TRUE I think I've tracked the error back to R CMD SHLIB not working. I followed this blog, which shows how to work with the command line R directly. However when I get to the line R CMD SHLIB sequence_examples.c the execution just skips straight to the next command line without doing anything, generating any files in the directory or throwing any errors. I tried running the --help options at the command line but get the same sort of error:
C:\Users\james.macadie> R --help
Or: R CMD command args
where 'command' is one of:
INSTALL Install add-on packages
REMOVE Remove add-on packages
SHLIB Make a DLL for use with dynload
BATCH Run R in batch mode
build Build add-on packages
check Check add-on packages
Rprof Post process R profiling files
Rdconv Convert Rd format to various other formats
Rdiff difference R output files
Rd2pdf Convert Rd format to PDF
Rd2txt Convert Rd format to pretty text
Stangle Extract S/R code from vignette
Sweave Process vignette documentation
config Obtain configuration information about R
open Open a file via Windows file associations
texify Process a latex file
Use
R CMD command --help
for usage information for each command.
C:\Users\james.macadie> R CMD SHLIB --help
C:\Users\james.macadie>
N.B. for people reading the earlier code samples higher up this post I have changed a few things since those code snapshots:
I've installed R directly into C:\R. It used to be in C:\Program Files\R\ but as has been suggested file paths with spaces in can cause problems
I'm referencing Rtools under C:\Rtools\ and not C:\RBuildTools\
Thanks for any suggestions, as ever
Had the same endless loop issue when trying to install Twitter's BreakoutDetection (which is also written in cpp)
fixed by executing the following
Sys.setenv(PATH="%PATH%;C:/Rtools/gcc-4.6.3/bin;c:/Rtools/bin")
and then answering "no" when presented with the following prompt:
"Install Build Tools Compiling C/C++ code for R requires installation of additional build tools. Do you want to install the additional tools now?"
Didn't try these actions independently so not sure if either on their own would have fixed the issue
I found that ensuring all of these were in my path fixed it. I did this with RStudio closed; I didn't reboot after.
C:\Program Files\R\R-3.1.3\bin\x64
C:\Program Files\R\R-3.1.3\bin
C:\RBuildTools\3.2\bin
C:\RBuildTools\3.2\gcc-4.6.3\bin64
C:\RBuildTools\3.2\gcc-4.6.3\bin
C:\RBuildTools\3.2\gcc-4.6.3\i686-w64-mingw32\bin
These are on my Win7-64bit computer. YMMV, and I'm mostly posting this to ensure others see it if they are having the same issue.
In the end it was something a bit left-field. Inspired by the following post, I had a look at the ComSpec environment variable. Not quite sure how, but I had it set to "cmd.exe".
Removing the double quotes, so it said cmd.exe, and then rebooting fixed everything.
Thanks to all who've tried to help.
I experienced the same problem, I fixed this problem by adding Rtools dir into env variables:
Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")