Not able to install packages MicrosoftML and mrsdeploy in R studio - r

I am trying to deploy R code onto server. But for I think we need to install both MicrosoftML and mrsdeploy. But I get an error while trying to download:
install.packages("MicrosoftML")
Installing package into ‘C:/Users/vinay/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘MicrosoftML’ is not available (for R version 3.5.2)
install.packages("mrsdeploy")
Installing package into ‘C:/Users/vinay/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘mrsdeploy’ is not available (for R version 3.5.2)

As the above error suggest you that the packages MicrosoftML and mrsdeploy are not available in R version 3.5.2, so you will have to use the R version in which these packages are present/compatible.
You can refer to this issue:
https://github.com/MicrosoftDocs/feedback/issues/352
For MicrosoftML refer to this:
https://learn.microsoft.com/en-gb/machine-learning-server/r/concept-what-is-the-microsoftml-package

You need to make an R Client deployment to have the ability to use the RevoScaleR, MicrosoftML, and mrsdeploy packages. Specifically for R version 3.5.2 and Ubuntu 14.04 - 16.04, please follow the following steps:
# Install as root or sudo
sudo su
# If your system does not have the https apt transport option, add it now
apt-get install apt-transport-https
# Set the package repository location containing the R Client distribution.
# On Ubuntu 14.04.
# wget http://packages.microsoft.com/config/ubuntu/14.04/prod/packages-microsoft-prod.deb
# On Ubuntu 16.04.
wget http://packages.microsoft.com/config/ubuntu/16.04/packages-microsoft-prod.deb
# Register the repo.
dpkg -i packages-microsoft-prod.deb
# Check for microsoft-prod.list configuration file to verify registration.
ls -la /etc/apt/sources.list.d/
# Update packages on your system
apt-get update
# Install the 3.5.2 packages
# Alternative for 3.4.1: apt-get install microsoft-r-client-packages-3.4.1
# Alternative for 3.4.3: apt-get install microsoft-r-client-packages-3.4.3
apt-get install microsoft-r-client-packages-3.5.2
# List the packages
ls /opt/microsoft/rclient/
Then download one of:
Ubuntu 14.04:
wget https://packages.microsoft.com/ubuntu/14.04/prod/pool/main/m/microsoft-r-client-packages-3.5.2/microsoft-r-client-packages-3.5.2.deb
Ubuntu 16.04:
wget https://packages.microsoft.com/ubuntu/16.04/prod/pool/main/m/microsoft-r-client-packages-3.5.2/microsoft-r-client-packages-3.5.2.deb
Install the packages with:
dpkg -i *.deb
If you use RStudio you can on Linux add R_LIBS_SITE=/opt/microsoft/rclient/3.5.2/libraries/RServer on bottom of the file /opt/microsoft/rclient/3.5.2/runtime/R/etc/Renviron
Both packages mrsdeploy and MicrosoftML will be now available from RStudio as you can check with:
library(mrsdeploy)
library(MicrosoftML)
For instructions like the above for newer R versions please check this Microsoft Docs page.

Related

installation of package ‘devtools’ had non-zero exit status - R packge or R studio

R version 3.4.4. Ubuntu 18.04.5 LTS.
install.packages('devtools')
The output shows missing "gert", "usethis".
Then I tried to install the failed packages "gert".
install.packages('gert', repos='https://cran.rstudio.com/')
Output is an error of missing "libgit2-dev".
Next, I went to install "libgit2-dev", and failed all the time.
The reason of failure of installing "libgit2" is, one shall install the "git2r" instead. (Reference: https://github.com/libgit2/libgit2 and https://github.com/ropensci/git2r)
** Solve the "gert" below:**
install.packages('git2r') # https://github.com/ropensci/git2r\
install.packages('gert')\
below refers to: https://github.com/r-lib/gert the installation hints.
On Linux you need to install libgit2:
Debian: libgit2-dev
Fedora / CentOS: libgit2-devel
For Ubuntu Trusty and Xenial, you can use libgit2 backports from
this ppa:
sudo add-apt-repository ppa:cran/libgit2
sudo apt-get update
sudo apt-get install libgit2-dev
DONE!
After that, the package "usethis" can be installed normally.
install.packages('usethis')
DONE!
In the end, the "devtools" can also be installed normally.
install.packages('devtools')\
The error of "non-zero status" does not show up.
library(devtools)
Loading required package: usethis
Extend story:
the package tidyverse can be intalled successfully after the devtools problem got solved.
Happy end.

Installation of igraph package of R in ubuntu

I am using the following command for the installation of igraph package of R in ubuntu : install.packages("igraph")
But I am getting an error saying:
Warning: unable to access index for repository
http://ftp.iitm.ac.in/cran/src/contrib: cannot open URL
'http://ftp.iitm.ac.in/cran/src/contrib/PACKAGES' Warning messages:
package ‘igraph’ is not available (for R version 3.3.2)
Can someone please guide regarding this problem, where I am going wrong in this...
You probably want a binary package anyway, and I recently re-explained how to do this:
The easiest way is something like this (and I am showing only the commands, not the output while I do this in a Docker instance of Ubuntu 16.04, and I am doing this in Docker where the account is root; otherwise add sudo in front)
apt-get update # refresh
apt-get install software-properties-common
add-apt-repository -y "ppa:marutter/rrutter"
add-apt-repository -y "ppa:marutter/c2d4u"
apt-get update # now with new repos
apt-get install r-cran-igraph
and it will just work with all its dependencies. You didn't tell us what Ubuntu version you have. What I showed works eg in Ubuntu 16.04; for much older releases you need a different package for the add-apt-repository command.
I suspect either the server is down or your network is down or you need to go via a proxy.
I can duplicate this message by setting an unobtainable CRAN mirror with:
> options(repos="http://example.com/")
> install.packages("foo")
Installing package into ‘/nobackup/rowlings/RLibrary/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://example.com/src/contrib:
cannot open URL 'http://example.com/src/contrib/PACKAGES'
Warning message:
package ‘foo’ is not available (for R version 3.2.3)
So either try again and maybe the server is up, or check your local network is okay, or try another CRAN mirror, or check with your local network admins to see if you need to set a proxy server.
you have to install build-essential first
sudo apt-get install build-essential
also on Ubuntu and Debian Linux the lixml2 and libxml2-dev packages are needed to install to R.
if that does not work check the webpage of the package for extra documentation

Install shiny on remote Debian machine with R version 3.1.1

I am trying to host an shiny app on an remote Debian machine. Yet, i have encountered an R version issue when installing shiny package. I will basically walk through the steps that I took in the process:
After SSH into the VM, I install and update the r-base:
sudo apt-get update
sudo apt-get install r-base
sudo apt-get install r-base-dev
The latest version I can get for R is 3.1.1. Then, I was trying to install "shiny" package as root by the following command:
sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
Then, I was getting the error message like:
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://cran.rstudio.com/src/contrib
Warning message:
package ‘shiny’ is not available (for R version 3.1.1)
Is there any work-around on this issue? Such as starch the apt-get to install the latest R version rather than 3.1.1? Or possibly install shiny from a Github repo? Please help! Thanks!
You should be able to get the R package yourself, rather than using apt-get. This way you can choose which release to install. For example:
wget http://cran.rstudio.com/src/base/R-3/R-3.2.2.tar.gz
tar zxvf R-3.2.2.tar.gz; cd R-3.2.2/
./configure; make;
sudo make install
Then you can get shiny through the terminal as well, rather than within R:
wget https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz
sudo R CMD INSTALL shiny_0.13.2.tar.gz
credit to Huiong Tian, from whom I learned this a while back:
http://withr.me/install-shiny-server-on-raspberry-pi/

unable to install rvest package

I need to install rvest package for R version 3.1.2 (2014-10-31)
I get these errors:
checking whether the C++ compiler supports the long long type... no
*** stringi cannot be built. Upgrade your C++ compiler's settings
ERROR: configuration failed for package ‘stringi’
* removing ‘/usr/local/lib64/R/library/stringi’
ERROR: dependency ‘stringi’ is not available for package ‘stringr’
* removing ‘/usr/local/lib64/R/library/stringr’
ERROR: dependency ‘stringr’ is not available for package ‘httr’
* removing ‘/usr/local/lib64/R/library/httr’
ERROR: dependency ‘stringr’ is not available for package ‘selectr’
* removing ‘/usr/local/lib64/R/library/selectr’
ERROR: dependencies ‘httr’, ‘selectr’ are not available for package ‘rvest’
* removing ‘/usr/local/lib64/R/library/rvest’
Any ideas on how I could install R package rvest?
My system is Ubuntu 14.04 with R:3.2.3, and I had the same problem.
Then I checked err meg and tried to install library of libcurl4-openssl-dev and libxml2-dev:
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libxml2-dev
After installed, install.packages("rvest") was successful.
I needed dependencies such as Rcurl, XML, rvest, xml2, when I was trying to install tidyverse, DESeq2, RUVSeq in Rstudio Version 1.1.456 on a fresh installed Ubuntu 18.04. Anyway, there were a bunch of missing dependencies. This answer might fit better as a comment for Ubuntu 18.04, but I don't have that many reputation. So just trying to make a summary of solutions works for Ubuntu 18.04 here.
In the terminal, run:
sudo apt-get install libcurl4-openssl-dev libssl-dev
sudo apt-get install libxml2-dev
Then within Rstudio,
install.packages("xml2")
install.packages("rvest")
install.packages("tidyverse") # might need other dependencies installed in Rstudio
Got tidyverse!
In the terminal:
sudo apt-get install libmysqlclient-dev ## for RMySQL
Then within the Rstudio
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite('RUVSeq') ## might have messages as following
installation path not writeable, unable to update packages: cluster, foreign, MASS, Matrix, mgcv, nlme, survival
In the terminal:
sudo R ## give R the root permission
## in the R session within the terminal
pks <- c('cluster', 'foreign', 'MASS', 'Matrix', 'mgcv', 'nlme', 'survival')
install.packages(pks)
q()
That's my own experience. Hope this one has a good Generalizability.
I was able to build the stringi package as this:
install.packages('stringi', configure.args='--disable-cxx11')
My answer is definitely late to this question. Nevertheless, somebody may find it useful.
I run into the same problem so I run this command on the shell:
sudo apt-get upgrade pkg-config
It worked for me.

‘seewave' install error “'sndfile.h' file not found” (for R 3.2.0 under OSX Yosemite)

When updating to R 3.2.0 I had to reinstall seewave.
I managed to install the required packages fftw, tuneR, rgl, and rpanel.
But, when trying to compile seewave I got the message:
stft.c:3:11: fatal error: 'sndfile.h' file not found
On linux it is sufficient to install libsndfile library, for example with
sudo apt-get install libsndfile1-dev
On OS X just do:
brew install libsndfile
Pisca46 - Installing via 'brew install libsndfile' helped.
On CentOS, the package has a different name :
sudo yum install libsndfile-devel
I also had to install the fftw-devel yum package

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