I am not able to install Rcpp and many other packages (e.g. devtools) as a requirement for the opm-package.
Ubuntu 18.04, R Version: 3.5.1, gcc version 7.3.0
Can anybody give suggestions to fix this issue?
EDIT: I managed now to install rcpp via apt-get; I used the below suggested repos and R 3.5.1. Now I am stuck with installing Ckmeans (Package maintainer contacted).
EDIT_2: The author sent me a new version of Ckmeans, but the problem persists. To sum up: unable to install ckmeans; Ubuntu 18.04, R 3.5.1, repos c2d4u3.5, cran repos.
update: I removed the R-bionic ppa and reinstalled R (3.5.0) with r-base-dev. I managed to tackle down nearly all the dependencies for opm, if not within R, so at least with the ubuntu-r-cran-packages (from the abovely mentioned repos); only one dependency is missing (OPM-Script): Ckmeans. I tried to install from source with 5 different versions, but so far without success.
After today's System-update I was able to install Ckmeans.1d.dp_4.2.2 and opm_1.3.72 without any problem.
Related
cannot install phytools
tried with devtools
library(devtools)
install_github("liamrevell/phytools")
and
install.packages("phytools")
I keep getting the same error
ERROR: dependency ‘mnormt’ is not available for package ‘phytools’
and I cannot install mnormt because
package ‘mnormt’ is not available (for R version 3.6.3)
gfortran is already installed in my system
GNU Fortran (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
any help is highly appreciated,
thanks
On Ubuntu Linux I cannot get R to update to the latest version (>4.0 at the time of writing), so, like Dirk suggests I have to install an older version of the package, one compatible with the version of R I am running.
My R version is 3.6.3, released feb 2020
I go to the mnormt page and click on "old sources" https://cran.r-project.org/src/contrib/Archive/mnormt/
I see that version 1.5-6 is the most recent release which is prior to my version of R
Following these pages: "Installing older versions of packages" https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages I copy the relevant url into this code and run it in R
packageurl <- "https://cran.r-project.org/src/contrib/Archive/mnormt/mnormt_1.5-6.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
Which fixes my problem installing mnormt and also allows packages which depend on it to be installed in the standard way (as far as I tested it)
The current version of mnormt depends on a the current version of R; you chose to remain a version behind.
So just install the previous version of mnormt, for example via
cd /tmp
wget https://cran.r-project.org/src/contrib/Archive/mnormt/mnormt_1.5-7.tar.gz
R CMD INSTALL mnormt_1.5-7.tar.gz
Prefix that last INSTALL command with sudo, or change the permission/group membership of /usr/local/lib/R/site-library, if R tells you it cannot write there.
Once mnormt is installed, proceed with the installation of phytools.
Try to add the tag version to install command, for example: devtools::install_github('cran/mnormt#R-3.0.3')
Check what version you need and replace the tag after the '#'.
I installed the 'forecast' package in a Databricks environment a few days back. It was working fine until this morning when I restarted the cluster. Now, I can't install the package anymore. Could someone help with this?
Have already tried upgrading the current R version (3.5.2) to the latest (3.6.0). That would require upgrading the current Ubuntu version too, which I don't think is possible, since that is the version Databricks is linked to. If there's a way to upgrade the Ubuntu version as well, do let me know.
Here's a screenshot of the error:
FROM THE SCREENSHOT, The 'quadprog' latest version 1.5-5 supports only >= R-3.6 version as yours is R-3.5.2, I would suggest you to download old binaries from CRAN for quadprog and install (refer Install previous versions of R on ubuntu)
After installing quadprog, go for the other packages installation. If same error persists, please repeat above step for that packages too :)
If you are trying this operation through R Console, you can use
packageurl <- "https://cran.r-project.org/src/contrib/Archive/quadprog/quadprog_1.5-4.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
I recently upgraded Ubuntu 16.04 to 18.04 and started having problems concerning rvest and xml2 in my R installation.
I'm trying to install package kableExtra but i keep getting errors even though I have dependencies installed. install.packages("kableExtra") spits this:
Searching SO it came to my knowledge that I need dependencies libxml2-dev for xml2. What happens is that I already have it installed.
Some other important packages like tidyverse complains about those same dependencies. I usually solve things like this searching here and google, but this time it is not working. I need some serious help here.
I'll appreciate any tip.
I ran into this page with issues installing kableExtra on Ubuntu 20.04. This post helped.
sudo apt install libfontconfig1-dev
Two part question:
1) Like the person who asked this question (rgdal won't install on AWS RStudio AMI), I'm running into problems installing the rgdal package on R running on Ubuntu 16.04. The package wants GDAL 1.11.4 or later, and Synaptic Package manager is only offering GDAL 1.11.3.
The solution offered on the above question is to install an older version of rgdal from the archive. On the other hand, the answer given to this older question (Trouble getting latest version of GDAL on ubuntu running R) is to install a more recent version of GDAL from ubuntu-unstable.
Do both of these approaches work?
2) What are the steps required for each approach (or the approach that works if they don't both work)?
What finally worked for me was trying to install an earlier version (v1.2-20) of rgdal that was compatible with gdal 1.11.3.
I was able to identify the correct version of rgdal using the documentation page here:
https://www.rdocumentation.org/packages/rgdal/versions/1.2-20
Then I used the devtools package to install the correct version:
require(devtools)
install_version("rgdal", version="1.2-20")
This page has helpful information on installation of earlier versions of R packages:
https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
I attempted installing more recent versions of gdal both from source and with my package manager but continued to get various errors when I got to the step of trying to install rgdal.
What I don't know is why I kept getting errors when trying to work with gdal upgrades.
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.