Is it possible to use Rstudio and the library "dtw" on Linux Mint?
I have an error message: dependencies 'proxy' missing, which seems to need R>3.3 but it isn't disponible from the package manager (I'm on 3.2).
Thanks
You'll need to update R. You say you're on Mint so go here https://cran.r-project.org and choose download R for Linux then choose either Ubuntu or Debian depending on the version of mint you're running and follow the instructions on that page.
Related
I am trying to install two packages in R (3.3.2): devtools and git2r. They are depending on the existence of zlib. This comes with macOS Sierra (10.12.3) and it's version 1.2.8 by default.
When I'm trying to install these packages I get the error below.
I've been trying a lot of things.
directly installing via CRAN in RStudio: no effect.
trying to locate zlib on macOS: can't find zlib.
installing via R CMD INSTALL git2r: no effect.
I notice someone has a similar issue posted on GitHub: https://github.com/ropensci/git2r/issues. There is no solution yet.
Does anyone here have an idea?
Thanks!
Sander
ERROR MESSAGE BELOW
configure error in "/private/tmp/RtmpP6HZFx/R.INSTALLe73412909267/git2r"
configure error
The zlib library that is required to build git2r was not found.
Please install:
zlib1g-dev (package on e.g. Debian and Ubuntu)
zlib-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the zlib library is installed on your system but the git2r configuration is unable to find it, you can specify the include and lib path to zlib with:
"R CMD INSTALL --configure-args='--with-zlib-include=INCLUDE_PATH --with-zlib-lib=LIB_PATH' git2r"
See "config.log" for more details
ERROR: configuration failed for package "git2r"
*removing "/usr/local/lib/R/3.3/site-library/git2r"
UPDATE: the same issue persists on macOS X 10.12.5 in combination with R 3.4.0 - the latter I need for DESeq2.
Solution...Mmm. Not really. I simply uninstalled R and all the packages, and than I reinstalled everything again. I installed R and RStudio via homebrew, following the instructions here: https://rud.is/b/2015/10/22/installing-r-on-os-x-100-homebrew-edition/.
Oddly enough: all issues disappeared.
UPDATE #1: this solution does not - obviously - work for the combination R 3.4.0 and macOS X 10.12.5. We need a solution for this issue.
UPDATE #2: I have discovered what I believe was the issue: a wrong path to the xcode command line tools.
sudo xcode-select --reset did the trick and now xcode-select -p points to /Library/Developer/CommandLineTools. And which xcode-select points to /usr/bin/xcode-select. Googling I discovered that it is not needed to install Xcode through the App Store as it states on http://railsapps.github.io/xcode-command-line-tools.html:
"On earlier versions of macOS, it was more difficult to install Xcode Command Line Tools. It required a huge download of the full Xcode package from the Mac App Store or registration as an Apple developer for a smaller Command Line Tools package. Mac OS X Mavericks made installation of Xcode Command Line Tools much simpler.".
i was having the same problem. i have a note 8(samsung). just go to GitHub and install zlib from there.
I need some help with installing Shiny package on the following system:
Ubuntu 12.04 64 bits
R version 3.0.2 "Frisbee Sailing"
When I try to install a Shiny package by running:
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
I tried different repos or even by running install.packages('shiny') in R session as sudo, the package fails to install.
There's no errors, but rather a message that "The downloaded source packages are in '/tmp/....'
and when I try to use it (library(shiny)), I got an error that package was not found.
Now, I did not have same issue and everything worked fine on:
Ubuntu 12.04 64 bits
R version 3.0.1 "Good Sport".
Please, help me see what I am missing here.
The issues you are describing are caused by out-of-memory crashes. You are probably on a VPS like EC2 or something similar. If you are using the free micro instance on EC2 or the lowest package( 512mb ram) on digital ocean then you should enable swap (you should enable swap anyway). For EC2 see How do you add swap to an EC2 instance? . For digital ocean see https://www.digitalocean.com/community/articles/how-to-add-swap-on-ubuntu-12-04
Actually, I just tried to install a different library, ggplot2, and it is the same issue.
So, it is not related to Shiny package. All the libraries I tried to install just keep being saved to a /tmp folder as archived gz files. Not really sure why R does not install them.
So, eventually I just used R CMD INSTALL [path to the package .gz]
and it worked all right. I installed all 3 libraries in the following order: Rcpp, httpuv and the shiny. library(shiny) command now loads the library ok.
After installing Mavericks on my Mac, I'm not able to run Rattle anymore.
Because of compatibility issues between RStudio and 10.9 (http://www.r-bloggers.com/rstudio-and-os-x-10-9-mavericks/), I installed v 0.98.433 of RStudio and R 3.0.2
Tried to launch Rattle the normal way: none.
I tried in a different way:
I manually launched xQuartz to install GTK+
via R-Studio I installed RGtg2 and Cairo
Installed Rattle, launched it and I got 1 sec message from Rattle, before it disappeared, crashing R session.
I then tried going back to R 2.15.3 (using RSwitch), doing same procedure.
Rattle starts with no ricognizable character and a bunch of related error messages on the RStudio console, from Pango.
Problem is it is looking for a directory .../pango/1.6.0 that does not exist (I have /1.8.0).
Is there any one who came out with a working combination of R/RStudio/Rattle on Mavericks?
I have a course I'm going to teach on data mining next semester and I introduced Rattle as the core tool, but I need it running.
Going back to previous Mac OS is not an option, because students may have the latest version.
Any help would be highly appreciated
I believe that the problem is with the GTK2 and Cairo modules. After building a few packages from source, rattle works for me...
I have had difficulties with Cairo/GTK2 since Mountain Lion. I got crashes using Simon's binary packages for these. Note that I updated my system to Mavericks, so I have not tried this on a clean install... I also have Homebrew installed for building programs from source. I use the ATT binary installer for R (thanks, Simon) for most packages but build a few packages from source. There were some hiccups and I spent a lot of time searching with Google. Here is what I did:
One needs XCode and the Xcode command line tools installed. After you install XCode, you need to run
sudo xcode-select --install
to install the command line tools. Then install Homebrew according to directions from the web site... Install gtk+ and cairo with their dependencies with:
brew install gtk+ cairo
And wait quite a while for everything to build....
The first problem I had is that I couldn't build any R packages from source because of this error:
make: llvm-gcc-4.2: No such file or directory
Google to the rescue...
I needed to change two lines in Makeconf in /Library/Frameworks/R.framework/Resources/etc to
CC=clang
CXX=clang++
Note: the R Mac Tools page now says this should be:
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
Then download the source packages for RGtk2, Cairo, and cairoDevice. I do all the work in my ~/bld directory with:
cd ~/bld
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Versions/Current/Resources/lib/pkgconfig:$PKG_CONFIG_PATH
R CMD install RGtk2_2.20.25.tar.gz
R CMD install Cairo_1.5-2.tar.gz
R CMD install cairoDevice_2.19.tar.gz
Hope this helps.
I have been trying to install bigmemory on my R installation.
My OS is windows 7 64 bit and I have tried it on R V2.15.1,2.15.2 and 3.0.1 64 bit but I cant get it to work.
I have tried several options
download the current source and run the command in R v3.0.1
install.packages("D:/Downloads/bigmemory_4.4.3.tar.gz", repos =
NULL, type="source")
but this gives an error "ERROR: Unix-only
package"
download older sources and run a similar commands, in the various
installations of R V2 V3 etc,
This gives me an error "ERROR:
configuration failed for package 'bigmemory'"
Any ideas? I am actually trying to install bigrf but bigmemory seems to be a dependency. Is there any workaround for this?
Many thanks
Seems the github version installs OK on Windows:
install.packages(c("BH","biglm"))
library(devtools)
devtools::install_github('kaneplusplus/bigmemory')
library(bigmemory)
the package authors told me they are fixing the CRAN one to work on Windows again too.
Going to the CRAN page here, shows you that you have to compile the sources on windows. Google how to do it or look at official document : here
Of course if package A depends on B you have to install B before A yourself.
EDIT: actually it says OS_type : unix
I'm trying to build the R package bigmemory for Windows 8 x64. However, when running R CMD INSTALL --build bigmemory_4.4.3.tar.gz, I receive the error ERROR: Unix-only package. I do not know why this is happening, but my guess is that it has something to do with the configure file of the package. I'm using R 3.0.1, 64 bit.
See this link, Windows support has been suspended. It's not your R-version, if you want to make use of it you'll have to use cygwin or install a Linux partition. You can also try the package ff.
The bigmemory NEWS, says "Windows support is temporarily suspended due to issues with the Boost headers." for the most current version of bigmemory.
The package you mention in the comments doesn't depend on a specific version of bigmemory, so you could try to build one of the older versions of bigmemory from the archive.