So I have been following the instructions here and I can't seem to figure out why XGBoost will not install correctly for R. I ran the appropriate command in the R Console only to still get:
./dmlc-core/include/dmlc/omp.h:13:9: warning: Warning: OpenMP is not available,
project will be compiled into single-thread code. Use OpenMP-enabled compiler to get benefit of multi-threading. [-W#pragma-messages]
The command that I have been running in the R console is:
install.packages("drat", repos="https://cran.rstudio.com")
drat:::addRepo("dmlc")
install.packages("xgboost", repos="http://dmlc.ml/drat/", type = "source")
Does anyone have updated instructions on how to download XGBoost? I have gcc 7 by the way.
Install Homebrew.
Open a new terminal
brew install gcc --without-multilib
Related
I have been trying to install Rattle on my Os into my R using this instructions:
https://zhiyzuo.github.io/installation-rattle/
I get to Line 7 and input
~$ brew install --with-x11 cairo
and then get
Updating Homebrew...
Usage: brew install [options] formula|cask
Install a formula or cask. Additional options specific to a formula may be
appended to the command.
Unless HOMEBREW_NO_INSTALL_CLEANUP is set, brew cleanup will then be run for
the installed formulae or, every 30 days, for all formulae.
...
**Error: invalid option: --with-x11**'''
Ive tried to continue on installing Cairo without the "--with-x11" (as been suggested they no longer support that).
So I did just "brew install cairo" that worked.
I go to line 9 Now we can install gtk+ by:
~$ brew install --build-from-source --verbose gtk+
And I get:
**Error: gtk+ 2.24.32 did not build
Logs:
/Library/Logs/Homebrew/gtk+/00.options.out
/Library/Logs/Homebrew/gtk+/01.configure.cc
/Library/Logs/Homebrew/gtk+/config.log
/Library/Logs/Homebrew/gtk+/01.configure
READ THIS: https://docs.brew.sh/Troubleshooting'''
If this helps in the last part I see in the terminal things saying:
==> ./configure --disable-dependency-tracking --disable-silent-rules - -prefix=/usr/local/Cellar/gtk+/2.24.32_3 --disable-glibtest --enable-introspection=yes --with-gdktarget=x11 --enable-x11-backend
configure: WARNING: unrecognized options: --enable-x11-backend
and
configure: error: Package requirements (cairo-xlib >= 1.6) were not met:
No package 'cairo-xlib' found
Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.
Alternatively, you may set the environment variables CAIRO_BACKEND_CFLAGS
and CAIRO_BACKEND_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
Anyone have any suggestions for this ?
Thanks.
I used to work in R 3.4.0 version. Hovewer, this version doesn't support such packages as keras and tensorflow.
I was adviced to upgrade my R version to the newest one.
I downloaded the most recent R version 4.0.2 from the official site, then ran the following code:
install.packages("keras")
library(keras)
install_keras()
And got the following error:
Error in install_keras() :
You should call install_keras() only in a fresh R session that has not yet initialized Keras and TensorFlow (this is to avoid DLL in use errors during installation)
After this, when I tried to quit R session by q() , I faced the following error:
Error: option error has NULL value
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error: option error has NULL value
I've never faced such an error before. When I used old R version, I typed q() and then had to choose between y and n. No errors appeared.
I'm asking you to help to to solve this problem.
You need to create a new environment and then you can install R 4.+ in Anaconda. Follow these steps.
conda create --name r4-base
After activating r4-base run these commands
conda activate r4-base
conda install -c conda-forge r-base
conda install -c conda-forge/label/gcc7 r-base
Finally, you will notice r-basa version 4 will be installed.
Thereafter, you can install any supported packages. But with this only, you won't have the ability to use it in the Jupyter notebook. You need to install install.packages('IRkernel') and Jupyter notebook as well if you want to use it. Otherwise you are good to go with R-Studio.
For Jupyter Installation and RKernel.
conda install jupyter
Then open the R console. Write in R console
install.packages('IRkernel')
IRkernel::installspec()
Congrats! You can use Notebook for Python and R.
Find the location of R.exe on your computer. In my computer, this executable is at
C:\Program Files\R\R-3.4.3\bin
Open another Anaconda Prompt as Administrator and change directories to wherever R.exe is on your computer with cd file path. On my computer, it’s cd C:\Program Files\R\R-3.4.3\bin, but it might be different for you.
Then run R from within Anaconda Prompt in Admin mode with R.exe
You’ll notice that you’re in an R session. From here, run the following three commands into the terminal.
install.packages("devtools")
devtools::install_github("IRkernel/IRkernel")
IRkernel::installspec()
In order, they (1) install the devtools package which gets you the install_github() function, (2) install the IR Kernel from GitHub, and (3) tell Jupyter where to find the IR Kernel.
Open Jupyter notebook and enjoy your new R kernel!
Get more information here
#Rheatey Bash works perfectly. but i was facing python.exe this program cant start because api-ms-win-core-path-l1-1-0.dll python system error. this is a problem running on windows 7 but i resolved this issue by installing the kernel following https://richpauloo.github.io/2018-05-16-Installing-the-R-kernel-in-Jupyter-Lab/ and it works fine
Conda was used to install R in my centos 7 sysytem. conda install r
the version of installed r is r-3.4.1.
However, when I use r, there have a error output. "/usr/local/bin/miniconda3/lib64/R/bin/exec/R: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory"
Some tests have been used according to search by google use the keyword "libtinfow.so.6".
Only two information can be found. They have no help to me.
enter image description here
I had the same problem on a recent centos installation. But I think this has nothing to do with centos, but rather to misconfiguration related to different R packages version. To solve the problem, I just uninstall all the R related packages and gxx and gcc packages using "conda uninstall ". Than I installed R using "conda install -c r r", which force to install gcc and gxx within the same process.
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.
When installing GLPK from (from https://www.gnu.org/software/glpk), I get the following error:
libtool: install: /usr/bin/install -c .libs/libglpk.36.dylib /usr/local/lib/libglpk.36.dylib
install: /usr/local/lib/libglpk.36.dylib: Permission denied
I have tried installing to other locations successfully, but python does not find the package. I would like to run. Note: I am using Enghought Canopy to run Python on Mac OS X version 10.9.4.
You don't install a non-python package into Python. You install it on your system (not a python issue, maybe someone else will have a suggestion), and then install a python package which "wraps" it -- provides access to it in python. If you have already successfully installed GLPK, then you should simply be able to open a Canopy Terminal window from the Canopy Tools menu, and type:
pip install glpk
EDIT: It looks like this is the best place for examples of using it: http://www.tfinley.net/software/pyglpk/examples.html