I am trying to install the "GISTools" R package in my R Jupyter notebook in IBM's Data Science Experience (DSX) with the following command:
install.packages("GISTools", depend = T)
however, I get the following error message: Installing package into
‘/gpfs/global_fs01/sym_shared/YPProdSpark/user/s17c-9f3318fc11f06c-d37a4b9405b6/R/libs’
(as ‘lib’ is unspecified)
also installing the dependency ‘rgeos’
Warning message in install.packages("GISTools", depend = T):
“installation of package ‘rgeos’ had non-zero exit status”Warning message in install.packages("GISTools", depend = T):
“installation of package ‘GISTools’ had non-zero exit status”
When I try library(GISTools) command, I get the following error message:
Error in library(GISTools): there is no package called ‘GISTools’
Traceback:
1. library(GISTools)
2. stop(txt, domain = NA)
I have looked at the following links in particular (and several other threads on Stack Overflow) but have not been able to resolve my issue:
Cannot install R packages in Jupyter Notebook
conda - How to install R packages that are not available in "R-essentials"?
Please can someone help?
Thanks,
V
GISTools have dependency on R package rgeos.
Now installing rgeos need you to have GEOS installed.
https://cran.r-project.org/web/packages/rgeos/rgeos.pdf
I attempted to install GEOS on DSX, it seems that GEOS need sudo permissions to install which are not available on DSX as a user.
https://duntuk.com/how-install-geos-centos
"make[7]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/include/geos/algorithm/locate" || /bin/mkdir -p "/usr/local/include/geos/algorithm/locate"
/bin/mkdir: cannot create directory ‘/usr/local/include/geos’: Permission denied
make[7]: *** [install-geosHEADERS] Error 1"
You will need to rely on DSX Team to first install GEOS package installed and then you can install rgeos.
Please raise uservoice to get that installed so that you can install rgeos and then GISTools.
https://datascix.uservoice.com/
Hope that helps!!!
Thanks,
Charles.
Related
hi i am trying to install package for experiment designs like this
install.packages("daewr", dependencies = T)
but it returns the following
configure: error: GNU MP not found, or not 4.1.4 or up, see http://gmplib.org
ERROR: configuration failed for package ‘gmp’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/gmp’
Warning in install.packages :
installation of package ‘gmp’ had non-zero exit status
ERROR: dependency ‘gmp’ is not available for package ‘partitions’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/partitions’
Warning in install.packages :
installation of package ‘partitions’ had non-zero exit status
ERROR: dependency ‘partitions’ is not available for package ‘DoE.base’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/DoE.base’
Warning in install.packages :
installation of package ‘DoE.base’ had non-zero exit status
ERROR: dependency ‘DoE.base’ is not available for package ‘FrF2’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/FrF2’
Warning in install.packages :
installation of package ‘FrF2’ had non-zero exit status
ERROR: dependency ‘FrF2’ is not available for package ‘daewr’
* removing ‘/home/yeferson/R/x86_64-pc-linux-gnu-library/4.0/daewr’
Warning in install.packages :
installation of package ‘daewr’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpB1bSe0/downloaded_packages’
so i decided to download the file from https://cran.r-project.org/web/packages/daewr/index.html
after trying to install it returns me
also installing the dependencies ‘gmp’, ‘partitions’, ‘DoE.base’, ‘FrF2.catlg128’
I try to install the first one but it asks for a Bessel package and it still gives me problems
I solved it by installing dependency one by one, many answer you install the dependencies but they do not say how I will explain them for the new ones in linux and in R to install the daerw package with the aforementioned problems, install the following in the linux console
sudo apt-get install libgsl-dev
with that install libraries now I can open R and install
install.packages('gsl')
then I opened the linux console again and installed
sudo apt-get install libgmp-dev
I go back to R and install
install.packages("gmp", dependencies = T)
now I can install the package without problems
install.packages("daewr", dependencies = T)
library(daewr)
I hope that any comment is welcome.
I am receiving a non-zero exit status when trying to install ggpubr in my R Jupyter Notebook. I was having this same issue about 2 weeks ago when trying to install gglot2, which I kept fumbling around including changing the CRAN and the package eventually installed.
I think there may be an issue at installing the dependencies in Jupyter notebook. I went back to the previous notebook where I installed ggplot2 and tried to run that code to see whether ggplot2 would reinstall--it doesn't and now that also returns non-zero exit status. I don't understand why I was once able to eventually install ggplot2 and I no longer can and I cannot install ggpubr either.
Note I've been able to install both ggplot2 and ggpubr in R, so I think this may be a Jupyter Notebook issue. I am an absolute beginner with coding, so any help with this and advice is much appreciated!!
Using macOS Mojave 10.14.6
install.packages("ggpubr")
also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’
Warning message in install.packages("ggpubr"): “installation of package ‘nloptr’ had non-zero exit status”
Warning message in install.packages("ggpubr"): “installation of package ‘lme4’ had non-zero exit status”
Warning message in install.packages("ggpubr"): “installation of package ‘pbkrtest’ had non-zero exit status”
Warning message in install.packages("ggpubr"): “installation of package ‘car’ had non-zero exit status”
Warning message in install.packages("ggpubr"): “installation of package ‘rstatix’ had non-zero exit status”
Warning message in install.packages("ggpubr"): “installation of package ‘ggpubr’ had non-zero exit status”
Updating HTML index of packages in '.Library' Making 'packages.html'
...done
I kept getting the non-zero exit status when trying to install packages with Jupyter notebook with R kernel and was failing because of multiple dependencies when wanting to install a package. I am not an expert in any of these so please forgive me if I make an error in explaining or if it is a non-issue for you but please feel free to comment to clear things out. I just want to share my success story so hopefully it can help someone else:
I am working on a MacBook Pro. Here are the information I get when I run R.version() on my jupyter notebook with R kernel:
$platform 'x86_64-conda_cos6-linux-gnu'
$arch 'x86_64'
$os 'linux-gnu'
$system 'x86_64, linux-gnu'
$language 'R'
$version.string 'R version 3.6.1 (2019-07-05)'
These are the steps to take to fix the issue:
Go to https://anaconda.org/
Search the package name that you are trying to install
Copy the one line that is given to install the package, it should be something like:
Conda install -c r r-caret
#conda install -c r r-package_name
NOTE: sometimes during installing packages, you’re asked whether or not you want to continue, so add --y at the end of the above statement to continue, so something like this
Conda install -c r r-caret --y (I will always add it just to be on the safe side)
Click on the new launcher (+ icon) to create a new notebook with PySpark (once opened it has .ipynp extension)
On the first cell paste the copied line from step 3 and run
Once done, restart the kernel on the current notebook
Restart the kernel on your other notebook with R kernel
Run library (package_name) on your notebook with R kernel (e.x. library(caret))
I have been trying over the weekend to install mosaic, car and some other packages on an R kernel (3.4.2) in Jupyter Notebook running Ubuntu 16.04. I have tried install.packages('car', '/home/jayaramdas/anaconda3/lib/R/library/', repos='http://cran.us.r-project.org'): it returns:
also installing the dependency ‘pbkrtest’
Warning message in install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
“installation of package ‘pbkrtest’ had non-zero exit status”Warning message in install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
“installation of package ‘car’ had non-zero exit status”
I've tried installing it in the original R package and I get this:
Warning messages:
1: In install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
installation of package ‘pbkrtest’ had non-zero exit status
2: In install.packages("car", "/home/jayaramdas/anaconda3/lib/R/library/", :
installation of package ‘car’ had non-zero exit status
I tried using Rstudio to install it, but it won't let me write the file. I also tried downloading the zip file for Ubuntu and it still gave the 'non-zero exiterror. Is this a usual problem that people have withcar` and other R packages? I am just trying to figure how to add some packages to my jupyter notebook.
You are on Ubuntu. You want to use a package manager (conda).
May I suggest you use the native one?
sudo apt-get install r-cran-car
will install car and all its dependencies. If not, file an Ubuntu bug report.
Similarly, you can get many more packages from Ubuntu: apt-cache search 'r-cran-*'. And once you consider the Rutter PPAs you have a large part of CRAN prebuilt.
I've installed geos, proj-4.8.0 and gdal-1.9.2, yet, after installing the R package rgeos, rgdal fails to install.
Here is a look at my home directory:
. . . and the error I get running install.packages("rgdal", type="source"):
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/mainstorage/michaeld/R/x86_64-redhat-linux-gnu-library/3.1/rgdal/libs/rgdal.so':
libgdal.so.1: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/mainstorage/michaeld/R/x86_64-redhat-linux-gnu-library/3.1/rgdal’
The downloaded source packages are in
‘/tmp/Rtmpt51iFG/downloaded_packages’
Warning message:
In install.packages("rgdal", type = "source") :
installation of package ‘rgdal’ had non-zero exit status
I infer that this error has something to do with a dependent library. . . but that is all I gather.
I should mention that running sudo yum install libgdal1 libgdal1-dev libgeos libgeos-dev as suggested here yields the following:
No package libgdal1 available.
No package libgdal1-dev available.
Package geos-3.4.2-1.3.amzn1.x86_64 already installed and latest version
No package libgeos-dev available.
So, perhaps the better question is how do I install these dev packages?
Thanks for any direction.
You probably need to update the dynamic library cache, using ldconfig as superuser.
Alternatively, rather than building the packages from source, you can enable the Extra Packages for Enterprise Linux (EPEL) repository.
On one computer running R 2.15.2 I have installed packages from a .zip file (these packages happened to be ggplot2 and data.table, but I don't think the specific package is my issue.) Everything works fine. I took these packages to a computer without an internet connection and installed them. This other computer is running R 3.0.1. The packages seemed to install without a problem (using R's "install package(s) from local zip file" option). When I call the packages with the library(), I get the following error:
Error: package '<insert name of newly installed package here>' was build before 3.0.0: please-re-install it
Can anyone explain potential causes for this error to be thrown? Are there particular directories that the .zip packages must be in for a proper install? If R is installed on a separate partition from where the .zip packages were loaded, could this cause the error?
I'm at a loss, any pointers are greatly appreciated. This is a difficult one to reproduce; if you need any other version/system parameters to understand the problem, please don't hesitate to ask.
I found this solution while look at GitHub ggplot2 issue #796
update.packages(checkBuilt = TRUE, ask = FALSE)
It will update all the packages that need to be reinstalled.
Running install.packages("codetools") can fix this issue for R 3.0.2, if you have the same problem like me:
installing to /home/user/R/x86_64-pc-linux-gnu-library/3.0/Rcpp/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘**codetools**’ was built before R 3.0.0: please re-install it
Error : unable to load R code in package ‘Rcpp’
ERROR: lazy loading failed for package ‘Rcpp’
I installed shiny according https://github.com/rstudio/shiny-server/wiki/Ubuntu-step-by-step-install-instructions
and got the same error at the step
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
Warning messages:
1: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘Rcpp’ had non-zero exit status
2: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘httpuv’ had non-zero exit status
3: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘shiny’ had non-zero exit status
I tried the answer by Richard Lee by starting R
R
and got the error
Warning in install.packages("shiny") :
'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to use a personal library instead? (y/n) n
Error in install.packages("shiny") : unable to install packages
obviously no write permission, so
sudo R
Now I tried again
install.packages("shiny")
and got a number of errors
Error : package ‘codetools’ was built before R 3.0.0: please re-install it
Error : package ‘RJSONIO’ was built before R 3.0.0: please re-install it
Error : package ‘caTools’ was built before R 3.0.0: please re-install it
Error : package ‘bitops’ was built before R 3.0.0: please re-install it
Error : package ‘digest’ was built before R 3.0.0: please re-install it
Error : package ‘xtable’ was built before R 3.0.0: please re-install it
Each time I got an error, I re-installed the requested package
install.packages("codetools")
install.packages("RJSONIO")
etc.
and eventually, I was able to install Rccp, httpuv, and even shiny.
Now it works!!
Also see
Shiny package installation on R version 3.0.2 "Frisbee Sailing"
I am using rkward on precise
I had a similar error using rkward. Specifically this one:
'lib = "/usr/local/lib/R/site-library"' is not writable
I temporarily changed the permissions for this directory so that rkward could run this from its console:
update.packages(checkBuilt = TRUE, ask = FALSE)
all to fix this:
Error: package '' was build before 3.0.0: please-re-install it
so that (sigh...) I could fix 'default' configuration for audio on precise. I couldn't use play() etc. in rkward.
That just needed phonon-backend-gtstreamer
I tried to install swirl on R(v3.1.0) on ubuntu 12.04LTS:
sudo R
install.packages("swirl")
But faced a similar error:
Error : package ‘codetools’ was built before R 3.0.0: please re-install it
Error : unable to load R code in package ‘httr’
ERROR: lazy loading failed for package ‘httr’
* removing ‘/usr/local/lib/R/site-library/httr’
ERROR: dependencies ‘testthat’, ‘httr’ are not available for package ‘swirl’
* removing ‘/usr/local/lib/R/site-library/swirl’
Doing following helped me:
install.packages('codetools')
install.packages("swirl")
library("swirl")
swirl()
| Welcome to swirl! Please sign in. If you've been here before, use the same
| name as you did then. If you are new, call yourself something unique.
What shall I call you?
I hope the same may help fix your installation issue.
Here is the work-around that I used:
I installed the latest version of R on an internet-capable computer. I then loaded the my required packages (Packages->install packages->select mirror->select package...
After R is finished installing, it displays a message of where the temporary .zip package is located. I navigated to this location, grabbed the temp package, and burnt it to a cd.
In this way, I could get the newer package build onto a computer without internet access. I would still be interested to know if there is an easy way to rebuild a package downloaded on an early R version to make it compatible with the latest version (without needed an internet connection).
Thanks for pointing me in the right direction #JoshuaUlrich