I have spent a lot of time trying to solve this, but still no luck. I am trying to get Rgraphviz to work with R 2.14.1 on a Max OS X Lion
These are the steps I took in order to install and use Rgraphviz on Mac OS X Lion:
Installed graphviz via: sudo port install graphviz
Checked that the installation was successful : pkg-config --modversion libgvc
Result: 2.28.0 <- That means its OK
Under R 2.14.1
source("http://www.bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
Whenever I try to use the library I get the following error
Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.5.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so
Check that (1) graphviz is installed on your system; (2) the installed version of
graphviz matches '2.26.3'; this is the version used to build this Rgraphviz
package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin'
directory is in the system 'PATH' variable. See additional instructions in the
'README' file of the Rgraphviz 'source' distribution, available at
Some things I notice
The graphviz suggested in the "help" file is 2.26.3 and the graphviz installed by Mac Ports is 2.28.0, but as it is a newer version I don't think this makes a difference, and besides I can not find v 2.26.3
Suggestion number (3) seems to be the key, but I can't find/don't have a bin directory under graphbiz
Also when I run a locate Rgraphviz.so there are no results.
Any clue towards a solution will be much appreciated,
Thanks a lot!
Thanks for the final answer, the installation seems to work for me! (I still have to check that the package runs properly). Just a quick observation: Graphviz was installed in /usr/local on my machine so that the above command had to be entered as follows:
sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.32.0.tar.gz
One more fail point. If you used Fink to install graphviz, you may still, like me, encounter separate build errors even after you use the configure arguments to point to graphviz, which now look like:
R CMD INSTALL --configure-args='--with-graphviz=/sw' Rgraphviz_1.34.0.tar.gz
The installation will fail during build errors for LL_funcs.c because it is looking for libraries that do not install unless you ALSO install graphviz-dev. You will see this:
In file included from LL_funcs.c:1:
common.h:31:17: error: gvc.h: No such file or directory
common.h:32:22: error: gvplugin.h: No such file or directory
common.h:35:20: error: gvcext.h: No such file or directory
common.h:39:20: error: gvcjob.h: No such file or directory
followed by many more build errors of course. Just be sure to
fink install graphviz-dev
Related
I have a general question about how to effectively load any kind of external package into R. I have found that many sources detailing this information are simply insufficient, but I will leave out mentioning those respective URLs. I have successfully loaded external packages into R before, but I am having difficulties loading the fgui package.
In my specific case, I cannot load the library fgui into R Studio. First I download directly from CRAN with the command:
install.packages("fgui", lib="~/Documents/R_dir")
This works fine for me. My working directory is set to ~/Documents/R_dir
The next command I use is:
library("fgui", lib.loc="~/Documents/R_dir")
The error I get is:
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
Error: package or namespace load failed for ‘fgui’
I have examined the thread "Error when trying to load library(ggplot2) in R" but it did not answer my question.
Please help me with any suggestions to get the package fgui to work properly in R Studio and feel free to address the more general issue of effectively loading external packages into R.
tcltk is not a typical package. It's probably already installed on your system and it cannot be installed using the usual install.packages procedure because it is not on CRAN (just like the base packages that come with R, like stats, etc.). Also, tcltk2 is not the same as tcltk; that is a package that expands upon (and depends on) the functionality of tcltk.
So, start with this:
> capabilities("tcltk")
tcltk
TRUE
If that comes back FALSE it means that your R was not built with tcltk support. You don't say what OS you're using, so it's a little bit difficult to help you.
That said, if you're on Linux, you need to rebuild R with tcltk support. This should be relatively straightforward. Basically, make sure Tcl and tk are available on your system in a standard location (something like sudo apt-get install tcl8.5-dev tk8.5-dev) and then rebuild R per usual procedures.
If you're on Mac OS, you're encountering the same error that John Fox describes here in relation to Rcmdr. In short, it's probably one of two things:
A file permission issue related to the directory where you have Tcl installed. To quote Fox: "You can verify the source of this problem by issuing the following command at the R command prompt:
system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
# ls: /usr/local/lib: Permission denied
# ls: /usr/local/lib/libtcl*: Permission denied
# drwx------ 8 root wheel 272 Sep 24 10:21 /usr/local
If the output of the system command looks like the above, you should go to Terminal and do the following: sudo chmod -R a+rX /usr/local and enter your password to change directory permissions.
You have an out-dated version of X-Windows. Try running Mac OS Software Update.
It may also be solvable by creating a symbolic link as described in this answer.
This should never come up on Windows, unless you built R from source without tcl/tk support.
On Arch Linux, tk is a separate package from tcl and both need to be installed:
sudo pacman -S tcl tk
This is given that the output from capabilities("tcltk") with R is TRUE (which means your R is compiled with tcltk support as noted previously in the answers here, this should be the case if you installed it from the arch repos).
The official installation instructions for R say:
Note: the use of X11 (including tcltk) requires XQuartz to be
installed since it is no longer part of OS X. Always re-install
XQuartz when upgrading your OS X to a new major version.
So: Simply (re)install XQuartz if you want to use the tcltk package in R.
delete the X11 file on location : /opt
delete the X11 on application unitiltiy
reinstall X11 again
Problem solved...
For Mac-OS users:
I struggled with this problem recently and found that R-3.1.2 has a bug, which assumes that otool is installed when it is not.
R-3.0.0 (and later) ships with Tck/Tk 8.6.0, so you shouldn't need to install that.
Simply upgrading to a more recent version of R (3.4.2) fixed the problem for me.
I had the same issue and went down a rabbit hole before discovering a simple fix. If you install R from bianry it will include tcltk by default. Just run the installer with the default installation. You can get the .dmg here: https://cran.r-project.org/bin/macosx/
Easiest answer for Mac users:
1- Install tcl-tk using brew:
brew install tcl-tk
2- Run the following code:
ln -s /usr/local/Cellar/tcl-tk/$version/lib/libtcl8.6.dylib /usr/local/lib/libtcl8.6.dylib
ln -s /usr/local/Cellar/tcl-tk/$version/lib/libtk8.6.dylib /usr/local/lib/libtk8.6.dylib
Problem solved!
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've been using R and Rscript on my Linux CentOS 7 system and everything worked fine for years.
Today I tried to install a package, clusterSim, but my R environment does not seem to work anymore. Here's the error I get:
install.packages("clusterSim");
--- Please select a CRAN mirror for use in this session --- Warning: failed to download mirrors file (internet routines cannot be loaded);
using local file '/home/davide/miniconda3/lib/R/doc/CRAN_mirrors.csv'
Error: .onLoad failed in loadNamespace() for 'tcltk', details: call:
fun(libname, pkgname) error: Can't find a usable init.tcl in the
following directories:
/opt/anaconda1anaconda2anaconda3/lib/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.18/library
./tcl8.5.18/library
This probably means that Tcl wasn't installed properly.
I tried to install tcl, and I got this message:
sudo yum -y install tcl
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile * base:
centos.mirror.rafal.ca * epel: mirror.math.princeton.edu * extras:
mirror2.evolution-host.com * ius: mirror.team-cymru.org *
nux-dextop: li.nux.ro * updates: centos.mirror.iweb.ca Package
1:tcl-8.5.13-8.el7.x86_64 already installed and latest version Nothing
to do
Any idea on how to solve this problem? Thanks
Something related to this is already reported as a bug but is closed off as partially corrected.
Have you tried this ?
install.packages("clusterSim", repos='http://cran.us.r-project.org')
Check out this for more !!!
Thanks to some friends on GitHub, I was able to solve this problem.
The problem is that now I have multiple versions of R on my laptop:
/usr/bin/R: the standard version I would like to use;
~/miniconda3/bin/R: the version installed by Miniconda that is causing me all the troubles.
First of all I had to understand what version is used by default by my system. I can do it with the which R command, that returned ~/miniconda3/bin/R
Then I realized I could have solve the problem by telling the system to stop using that R Miniconda version, and to employ the /usr/bin/R version instead.
I did this by editing the ~/.bashrc file. In the $PATH, my favourite R version path must be written before the Miniconda one.
Therefore my ~/.bashrc file now is something like this:
PATH=/usr/local/bin:$PATH
PATH=/usr/bin:$PATH
...
export PATH="$PATH:/home/davide/miniconda3/bin"
That's it; I hope this helps!
To me it looks like you are using R installed by conda. Do you also get this issue when you open R with /usr/bin/R in your terminal, because I believe which R will point to you conda repository.
See How to install R-packages not in the conda repositories? for extra info.
I solved this problem by using one of the following two approaches:
Prior to install a package I choose my CRAN mirror manually
chooseCRANmirror(graphics=F)
Prior to install I turn off the graphical menu
options("menu.graphics"=F)
Make sure conda in after /usr/bin in you PATH, check your ~/.bashrc
Does anyone have a link to clear instructions on how to install and configure the necessary latex packages to build R packages on a mac?
I have some scripts for building and checking R packages on a mac server. They seemed to work fine, but after upgrading to R 3.1.3, many of the packages started failing with
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'networkVignette.tex' failed.
Messages:
sh: /usr/local/bin/texi2dvi: No such file or directory
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
I found a thread which seemed to suggest I need a more recent version texinfo (5.2) than what is installed by default. And apparently I've I've got the wrong version installed in the wrong location?
which texi2pdf
/sw/bin/texi2pdf
texi2pdf --version
texi2pdf (GNU Texinfo 5.1) 5234
(same version is reported when running system('texi2pdf --version') in R )
This thread gives a link to a texinfo 5.2 source collection:
http://r.789695.n4.nabble.com/R-CMD-build-looking-for-texi2dvi-in-the-wrong-place-R-devel-td4701706.html
But I'm not familiar with installing executable from a tar.gz file on a mac. The R mac help pages I found suggest installing MacTex, which I tried but that didn't seem to help.
** Update: ** additional discussion of related problems on R-SIG-mac mailing list:
https://groups.google.com/forum/#!topic/r-sig-mac/xjyuFdl5Ezk
Update:
Here is where I'm currently at:
I removed my /sw directory to uninstall fink and all of its packages (couldn't figure out how to upgrade it)
installed homebrew
brew install texinfo installs version 5.2 the package,
but generates the message This formula is keg-only, which means it was not symlinked into /usr/local and actually installs in in /usr/local/Cellar/texinfo/5.2/bin which means it is not on the path and R won't find it.
manually symlink each of the texi2pdf, texi2dvi , etc as vincent suggests (this is because R has the /usr/local/bin location as default in the tools::texi2dvi function?
edited the /etc/paths file on the system to add /usr/local/bin so that finds the brew installed 5.2 version before it finds it before the osx system supplied version 4.6 version. This may not be necessary because R has it hardcoded?
All of this gets rid of the "can't find texi* errors", and gives me a bunch of latex errors (which I don't see on unix and windows builds) so I'm still kind of stuck.
This seems very hackish, so there must be a cleaner way? But it sounds like stuff with tex and mac is very sketchy at the moment? https://tex.stackexchange.com/questions/208181/why-did-my-tex-related-gui-program-stop-working-in-mac-os-x-yosemite
This worked for me on Mavericks and on Yosemite:
ln -s /usr/bin/texi2dvi /usr/local/bin/texi2dvi
ln -s /usr/bin/texi2pdf /usr/local/bin/texi2pdf
On my Lion system both the command which texi2pdf at a Terminal/bash prompt and from a R.app GUI prompt tell me that I have that program in:
system("which texi2pdf")
#/opt/local/bin/texi2pdf
That is a location typical for MacPorts installation. I think the /usr/local/bin/ is what the binary R version "expects". I'm not really that UNIX savvy, but I think the you can modify the PATH environment variable so that R will be able to find your installation. (Whether it will be compatible I cannot say since so much detail is missing from your question.) My Tex installation is MacTex, which I got from https://www.tug.org/mactex/. I admit to having a cobbled-together system:
system("echo $PATH")
# /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin
That gets set at the beginning of an R session because this is the first line in my .Rprofile-(invisible)file:
Sys.setenv(PATH="/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin")
I think /sw/bin/ installations signify a fink install, which I have had very little success with. Simon Urbanek suggests not using any package installers, but then leaves the rest of us UNIX weenies very little in the way of worked examples of how to install that various external packages that underpin the many interesting and oh-so-useful R packages. So I feel your pain, but I'm not running for President.
So I suppose you could try this at your R console before again attempting one of the earlier unsuccessful installs:
Sys.setenv(PATH=paste( Sys.getenv()$PATH, # should be the character string of the $PATH
"/sw/bin/", sep=":")
)
Wish I could offer guarantees, but if it breaks the only guarantee is that you get to keep all the pieces.
I ran into a similar error message using Mavericks 10.9.5 (factory configured) and R 3.1.
It turns out that I didn't have pdfLaTex. I went to this page: http://tug.org/mactex/ and downloaded the MacTex installation package. It's big (>2GB) but after I installed it, my R package build problems went away.
Hope this might be helpful to anyone else who runs into this error message.
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/")