I would like to be able to install the rstan package from binaries (without compiling from source). This blog post by Dirk Eddelbuettel has some clear instructions that should enable me to do exactly that. However I get the following error message when I try and install RStan. Here are the commands I used.
docker run --rm -ti rocker/r-ubuntu:18.04 bash
apt-get update; apt-get dist-upgrade -y
apt-get install -y r-cran-rstan
This produces the following error message.
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-rstan : Depends: r-cran-v8 but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Installing the R tidyverse package using Dirk's instructions works fine. I am working on a Ubuntu OS within the Windows Subsystem for Linux (WSL-2).
These things can happen -- the best best is to then try
sudo apt install r-cran-v8
which reveals r-cran-node64 is required but not available.
I work much more with 20.04 than 18.04 so I don't what is going on here. I would recommend asking on the r-sig-debian list if anybody else has seen this.
PS And if you try 20.04 instead it works there.
Related
I am using the tutorial at
https://www.phusionpassenger.com/docs/tutorials/deploy_to_production/installations/oss/ownserver/ruby/nginx/
to install Passenger (6.0.4) for use with Nginx. I get to the point where I'm installing the 'libnginx-mod-http-passenger' package, and get the following...
deploy#rpi-tick1:~ $ sudo apt-get install -y libnginx-mod-http-passenger
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libnginx-mod-http-passenger
I am installing for Raspbian-stretch (Debian), and have set up /etc/apt/sources.list.d/passsenger.list as shown below (as instructed in the tutorial)
deploy#rpi-tick1:~ $ cat /etc/apt/sources.list.d/passenger.list
deb https://oss-binaries.phusionpassenger.com/apt/passenger stretch main
It appears that repository contains only 'passenger-doc' packages. Any help would be appreciated.
I just ran into this issue myself while testing out whether my passenger setup will work on an ARM based Ubuntu instance. I believe the cause is that package is available for amd64 but not ARM. I see that you are using Raspbian and Raspberry Pi's are ARM based systems.
I want to install jsoncpp
Instructions to reproduce:
Install both meson (which requires Python3) and ninja.
When I run sudo apt-get install meson ninja I get the following results:
$ sudo apt-get install meson ninja
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
meson : Depends: ninja-build but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
I am trying to install ninja which removes meson, and installing meson removes ninja, with the above error. Does anyone know what to do about this?
The correct Debian package for the ninja build system is ninja-build.
sudo apt-get install meson ninja-build
When I install a fcitx related package an error show that qtbase-abi-5-5-1 is needed but not installed.
wsx#wsx:~/Downloads$ sudo apt install ./fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb ./libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'fcitx-frontend-qt5-rstudio' instead of './fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
Note, selecting 'libfcitx-qt5-1-rstudio' instead of './libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
fcitx-frontend-qt5-rstudio : Depends: qtbase-abi-5-5-1 but it is not installable
E: Unable to correct problems, you have held broken packages.
I tried using command sodu apt install qtbase-abi-5 to find the package but failed. I then download the .deb package from https://ubuntu.pkgs.org/16.04/ubuntu-updates-main-amd64/libqt5core5a_5.5.1+dfsg-16ubuntu7.5_amd64.deb.html but it was not work, the page show that this .deb package provide the qtbase-abi-5 package. Interestingly, I can find few information about this error by google. Some info from Ask ubuntu forum say that it seems the qtbase-abi-5 is not included in libqt5core5a.
I don't know how to fix it. Can you give me some suggestion or some link which do can download qtbase-abi-5 ?
Thanks #GAD3R for your answer, I am sorry that it fails.
wsx#wsx:~$ sudo apt-cache search qtbase-abi
libqt5core5a - Qt 5 core module
wsx#wsx:~$ sudo apt install libqt5core5a
Reading package lists... Done
Building dependency tree
Reading state information... Done
libqt5core5a is already the newest version (5.9.1+dfsg-10ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
wsx#wsx:~$ sudo apt install ./Downloads/fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb ./Downloads/libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'fcitx-frontend-qt5-rstudio' instead of './Downloads/fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
Note, selecting 'libfcitx-qt5-1-rstudio' instead of './Downloads/libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
fcitx-frontend-qt5-rstudio : Depends: qtbase-abi-5-5-1 but it is not installable
E: Unable to correct problems, you have held broken packages.
Can anyone run following commands successfully?
$ wget http://ikuya.info/tmp/fcitx-qt5-rstudio-qt542.tar.gz
$ tar xf fcitx-qt5-rstudio-qt542.tar.gz
$ sudo apt install ./fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb ./libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb
The package libqt5core5a provide qtbase-abi-5-5-1.
apt-cache search qtbase-abi
libqt5core5a - Qt 5 core module
To install the qtbase-abi-5-5-1 , run the following command :
sudo apt update
sudo apt upgrade
sudo apt dist-upgrade
sudo apt install libqt5core5a
I am learning to use RSelenium in an EC2 instance, and I found this handy guide on doing so - https://rpubs.com/grahamplace/rselenium-ec2 - however the guide focuses on an Ubuntu instance and I am using an Amazon Linux Instance. In order to install RSelenium, the guide says I must externally (outside of R but ssh'd into my EC2 instance) install the packages xml (XML i think, case sensitive) and RCurl. The guide's relevant lines of code are:
sudo apt-get install r-cran-xml
sudo apt-get install r-cran-RCurl
however, since I'm in an Amazon Linux instance, I tried:
sudo yum install r-cran-xml
sudo yum install r-cran-RCurl
for which I get the following error:
No package r-cran-RCurl available.
Error: Nothing to do
Note: I was successful in installing R on my machine (my instance), and I am able to simply type R to launch R in the EC2 instance.
Note2: install.packages('XML') and install.packages('RCurl') with R launched do not work either.
Any help appreciated with this, thanks!
the amazon linux R package has a different name:
sudo yum install -y R
then you tried (in R) install.packages(c('XML','RCurl')), but the installation failed.
as you discovered and describe in the comment below, you needed to install an additional amazon linux package, libxml2-devel, in order to install.packages('XML') successfully.
this is what I get when I run sudo yum install -y R
No package R available.
Error: Nothing to do
R is available in Amazon Linux Extra topic "R3.4"
To use, run
sudo amazon-linux-extras install R3.4
Learn more at
https://aws.amazon.com/amazon-linux-2/faqs/#Amazon_Linux_Extras
I'm a newbie to Linux and try to install the latest R version on my Raspberry.
My Raspberry runs on Wheezy 7.8.
I followed instructions on CRAN, so I
added
deb http://cran.rstudio.com/bin/linux/debian wheezy-cran3/
to /etc/apt/sources.list
ran apt-get update which was successful and gave me only a "signature error" for the public key as pointed out on the CRAN-site
ran apt-get install r-base
But the result of the last command is
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 3.1.2-1~wheezycran3.0) but it is not going to be installed
Depends: r-recommended (= 3.1.2-1~wheezycran3.0) but it is not going to be installed
Recommends: r-base-html but it is not going to be installed
Recommends: r-doc-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
I tried to install R-2.15 before and then run the above commands. R-2.15 could be installed successfuly, but I'd need R-3* really.
I did browse the web, but couldn't find any useful hints for my specific problem, so I appreciate any support you could give me.
Thanks!
If it is of any use:
apt-cache policy r-base gives
r-base:
Installed: (none)
Candidate: 3.1.2-1~wheezycran3.0
Version table:
3.1.2-1~wheezycran3.0 0
500 http://cran.rstudio.com/bin/linux/debian/ wheezy-cran3/ Packages
3.1.0-1~wheezycran3.0 0
500 http://cran.rstudio.com/bin/linux/debian/ wheezy-cran3/ Packages
2.15.1-4 0
500 http://mirrordirector.raspbian.org/raspbian/ wheezy/main armhf Packages
apt-cache policy r-base-core gives
r-base-core:
Installed: (none)
Candidate: 2.15.1-4
Version table:
2.15.1-4 0
500 http://mirrordirector.raspbian.org/raspbian/ wheezy/main armhf Packages
uname -a gives
Linux raspberrypi 3.18.5+ #744 PREEMPT Fri Jan 30 18:19:07 GMT 2015 armv6l GNU/Linux
I had the same situation and decided to install that from the source code instead of install R from the repository(apt-get command).
Here is the command I run on my Raspberry Pi 2.
I could install and run R(3.1.2) sucessfully.
It might not be complete answer for you because I might already installed the library like gcc you did not have before. If you encounter the other issue, please let me know. I would like to solve it.
Just as a side note on this topic, because sudo make install process took a long time(maybe over a hour. I'm not sure because I feel asleep before I knew it...), I recommend you to do this when you have enough or before going to sleep like me.
wget http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz
mkdir R_HOME
mv R-3.1.2.tar.gz R_HOME/
cd R_HOME/
tar zxvf R-3.1.2.tar.gz
cd R-3.1.2/
sudo apt-get install gfortran libreadline6-dev libx11-dev libxt-dev
./configure
make
sudo make install
R
The cause of your problem is likely that the cran repository provides armel versions of the packages, and not armhf (which is the expected architecture for your RPI). If this is right, then you have two solutions:
The first work-around could be to download the armel version of the packages and then force their installation despite the architecture mismatch. It is supposed to work according to the Debian wiki, although you may experience performance issues:
The CPU in the Raspberry Pi implements the ARMv6 ISA (with VFP2) and
is thus incompatible with the Debian armhf port baseline of ARMv7+VFP3
and ARM hardware-floating-point ports for other distributions, which
all have the same baseline. It is compatible with Debian armel
(armv4t, soft(emulated) FP), but floating-point tasks will be slow
when running the Debian armel port.
To do that, you can try to reinstall the packages by specifying the armel architecture, for example:
apt-get install r-base:armel
If it doesn't work this way, you can otherwise download the packages from http://cran.r-project.org/bin/linux/debian/wheezy-cran3/ and install them manually using a commandline like:
dpkg --install --force-architecture xxxx_armel.deb yyyy_armel.deb zzzz_armel.deb
The other solution would be to compile R from its source.
I solved my initial question by upgrading Wheezy to Jessie. I am not an expert, but Jessie seems to be the current testing version of Debian, while Wheezy is the stable release - see here.
For upgrading, I followed the instructions here, or here, or here. Note: Upgrading takes quite a while and during the process you're required to answer some questions.
A word of caution though: Jessie is still testing and some people recommend not to use it yet, for a discussion see e.g. here.
I did set it up completely from a new completely new image, and it works well.
After having upgraded to Jessie I installed R-3.1.1. using
sudo apt-get install r-base
And I'd like to thank all those who have answered my question and given alternative ways of solving the problem above.
I'm able to install R-3.1.2 into raspbian using answer from teramonagi. I confirm it can install successfully on Raspberry Pi model B/B+.
However, before you can actually use R (install packages and run some R scripts), you have to increase the swap file size for Raspberry Pi due to lack of RAM (This service works very similar to page file in window, it kicks in when RAM usage is high). You can configure it by edit one of the config file by enter command below in LX terminal.
sudo nano /etc/dphys-swapfile
CONF_SWAPSIZE=100 #(change 100 to 512 or 1024, up to you, save the file)
sudo /etc/init.d/dphys-swapfile stop
sudo /etc/init.d/dphys-swapfile start #(restart swap file service with new swap file size)
Take note though, some users argued that increase swap file size can actually ruin your SD card. So apply this change at your own risk. I've been running my Pi with this configuration for my R automation for 1 month now. No issue so far.
Hope this helps.
Edit: If you are using model B/B+, i recommend to configure swap file size first then compile R.
That's what I've done to update my r-base on wheezy:
HOW TO UPDATE r-base 2.15 to 3.x ON DEBIAN WHEEZY
add these lines at the end of "/etc/apt/sources.list"
deb http://cran.revolutionanalytics.com/bin/linux/debian wheezy-cran3/
deb-src http://cran.revolutionanalytics.com/bin/linux/debian wheezy-cran3/
add the missing publich key of cran
gpg --keyserver pgpkeys.mit.edu --recv-key 06F90DE5381BA480
gpg -a --export 06F90DE5381BA480 | sudo apt-key add -
update and upgrade
apt-get update
aptitude -t wheezy-cran3 install r-base r-base-dev