I am trying to install R Shiny on Azure , Linux (centos 8.2.2004). Using the manual : https://linuxize.com/post/how-to-install-r-on-centos-7/
However I can not install packages. I receive error :
"ERROR: failed to lock directory ‘/usr/lib64/R/library’ for modifying Try removing ‘/usr/lib64/R/library/00LOCK-Rcpp’ ERROR: dependency ‘Rcpp’ is not available for package ‘later’
* removing ‘/usr/lib64/R/library/later’ ERROR: dependencies ‘Rcpp’, ‘later’ are not available for package ‘promises’
* removing ‘/usr/lib64/R/library/promises’ ERROR: dependencies ‘Rcpp’, ‘promises’, ‘later’ are not available for package ‘httpuv’
* removing ‘/usr/lib64/R/library/httpuv’ ERROR: dependencies ‘httpuv’, ‘later’, ‘promises’ are not available for package ‘shiny’
* removing ‘/usr/lib64/R/library/shiny’
The downloaded source packages are in
‘/tmp/RtmpGIfMqF/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages("shiny") : installation of package ‘Rcpp’ had non-zero exit status 2: In install.packages("shiny") : installation of package ‘later’ had non-zero exit status 3: In install.packages("shiny") : installation of package ‘promises’ had non-zero exit status 4: In install.packages("shiny") : installation of package ‘httpuv’ had non-zero exit status 5: In install.packages("shiny") : installation of package ‘shiny’ had non-zero exit status"
I have tried to fix the issue however , was able. If you have some ideas, please advice, thanks.
I solved the problem finally. There was necessary to delete the folder :
sudo rm -rf /usr/lib64/R/library/00LOCK-Rcpp
Then tried instal shiny package again and worked fine.
Related
I've been trying to run an LGCP in 'inlabru' that was taking forever so I've been set up with a Unix account to access an RStudio server. The trouble is now I am getting non-zero exit status installation errors for a few packages. Specifically 'rgdal' and 'inlabru'. I have tried (for 'rgdal') installing the dependencies and PROJ/GDAL without any success. The end of the error is:
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/rgdal’
Warning in install.packages :
installation of package ‘rgdal’ had non-zero exit status
ERROR: dependency ‘systemfonts’ is not available for package ‘svglite’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/svglite’
Warning in install.packages :
installation of package ‘svglite’ had non-zero exit status
ERROR: dependency ‘terra’ is not available for package ‘raster’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/raster’
Warning in install.packages :
installation of package ‘raster’ had non-zero exit status
ERROR: dependencies ‘s2’, ‘units’ are not available for package ‘sf’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/sf’
Warning in install.packages :
installation of package ‘sf’ had non-zero exit status
ERROR: dependency ‘raster’ is not available for package ‘leaflet’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/leaflet’
Warning in install.packages :
installation of package ‘leaflet’ had non-zero exit status
ERROR: dependencies ‘sf’, ‘svglite’ are not available for package ‘leafpop’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/leafpop’
Warning in install.packages :
installation of package ‘leafpop’ had non-zero exit status
ERROR: dependencies ‘raster’, ‘terra’ are not available for package ‘satellite’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/satellite’
Warning in install.packages :
installation of package ‘satellite’ had non-zero exit status
ERROR: dependencies ‘leaflet’, ‘raster’, ‘sf’ are not available for package ‘leafem’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/leafem’
Warning in install.packages :
installation of package ‘leafem’ had non-zero exit status
ERROR: dependencies ‘leafem’, ‘leaflet’, ‘leafpop’, ‘raster’, ‘satellite’, ‘sf’ are not available for package ‘mapview’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/mapview’
Warning in install.packages :
installation of package ‘mapview’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp57pHoc/downloaded_packages’
I am thinking it is the library that is failing the installation because it's a server, but I've tried changing .libPaths() to a folder on my drive with no success. I have also tried running
install.packages("rgdal", type="source", repos="http://R-Forge.R-project.org", configure.args=c('--with-gdal-config=/opt/local/bin/gdal-config'))
and get
configure: error: gdal-config not found - configure argument error.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/home/staff4/ebryce/R/x86_64-pc-linux-gnu-library/4.1/rgdal’
Warning in install.packages :
installation of package ‘rgdal’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp57pHoc/downloaded_packages’
Any help is greatly appreciated!
gdal (and friends) are not installed
sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev
I keep struggling installing shiny on a ubuntu 20.4 vm on EC2.
I followed this procedure.
Then I tried:
install.packages("shiny")
install.packages("shiny", dependencies = T)
install.packages("shiny", dependencies = T, INSTALL_opts ='--no-lock')
I also add 4GB of SWAP memory.
But no way...
Here are my outputs:
** R
** demo
** byte-compile and prepare package for lazy loading Error: package ‘promises’ was installed before R 4.0.0: please re-install it
Execution halted ERROR: lazy loading failed for package ‘httpuv’
removing ‘/usr/local/lib/R/site-library/httpuv’ ERROR: dependency ‘openssl’ is not available for package ‘httr’
removing ‘/usr/local/lib/R/site-library/httr’ ERROR: dependency ‘textshaping’ is not available for package ‘ragg’
removing ‘/usr/local/lib/R/site-library/ragg’ ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
removing ‘/usr/local/lib/R/site-library/shiny’ ERROR: dependency ‘httr’ is not available for package ‘webdriver’
removing ‘/usr/local/lib/R/site-library/webdriver’ ERROR: dependencies ‘httr’, ‘shiny’, ‘webdriver’, ‘httpuv’ are not available
for package ‘shinytest’
removing ‘/usr/local/lib/R/site-library/shinytest’
The downloaded source packages are in
‘/tmp/RtmpGvP9AB/downloaded_packages’ Warning messages: 1: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘openssl’ had non-zero exit status 2: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘textshaping’ had non-zero exit status 3: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘httpuv’ had non-zero exit status 4: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘httr’ had non-zero exit status 5: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘ragg’ had non-zero exit status 6: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘shiny’ had non-zero exit status 7: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘webdriver’ had non-zero exit status 8: In
install.packages("shiny", dependencies = TRUE) : installation of
package ‘shinytest’ had non-zero exit status
Each time I try to install a dependency "by hand", an other missing one, deeper nested, shows up.
Could someone help me with this, please ?
Not sure if you were able to solve your issues. Recently I also faced similar issues in trying to install Shiny server and related packages in EC2. I researched a bit and came across a Rstudio server AMI (Amazon Machine Image)- https://www.louisaslett.com/RStudio_AMI/, maintained by Louis Aslett. You can choose the AMI from the nearest region and once the instance is up and running, you can directly start using R-studio or Shiny. I find it very helpful.
To install openssl R package, you'll also need system-wide installation of the samename package. You could try something like sudo apt-get install openssl. Search the internet for dependencies of other packages.
I am attempting to install the R package "codebook" on OSX. I receive the following error message. I receive similar error messages when I try to independently install these dependencies. Is there a way that I install via the terminal or otherwise install these dependencies?
My apologies if this is not enough information in order to provide guidance. Please let me know and I would be happy to provide additional context. I am using RStudio Version 1.0.136
Thank you
ERROR: compilation failed for package ‘RcppEigen’
installation of package ‘RcppEigen’ had non-zero exit status
ERROR: dependencies ‘lavaan’, ‘OpenMx’, ‘semTools’ are not available for package ‘MBESS’
installation of package ‘MBESS’ had non-zero exit status
ERROR: dependency ‘igraph’ is not available for package ‘DiagrammeR’
installation of package ‘DiagrammeR’ had non-zero exit status
ERROR: dependency ‘RcppEigen’ is not available for package ‘lme4’
installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘DiagrammeR’ is not available for package ‘data.tree’
installation of package ‘data.tree’ had non-zero exit status
ERROR: dependencies ‘car’, ‘data.tree’, ‘DiagrammeR’, ‘lavaan’, ‘lme4’, ‘MBESS’ are not
available for package ‘userfriendlyscience’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/userfriendlyscience’
Warning in install.packages :
installation of package ‘userfriendlyscience’ had non-zero exit status
ERROR: dependency ‘userfriendlyscience’ is not available for package ‘codebook’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/codebook’
I'm trying to install ggplot2 on my campus' Rstudio server. Unfortunately I receive the classic "installation of package 'ggplot2' had non-zero exit status." I've looked through the many threads of users who've had the same problem with other packages, but haven't found any workable solutions.
I've tried using install.packages("ggplot2", dependencies = TRUE), which hasn't worked.
Also, I'm running the most recent version of OSX on a MacBook Pro.
This is the error message I receive:
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/mnt/trafficstop/jrleary/R/x86_64-redhat-linux-gnu-library/3.5/vctrs’
Warning in install.packages :
installation of package ‘vctrs’ had non-zero exit status
ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
* removing ‘/mnt/trafficstop/jrleary/R/x86_64-redhat-linux-gnu-library/3.5/pillar’
Warning in install.packages :
installation of package ‘pillar’ had non-zero exit status
ERROR: dependency ‘pillar’ is not available for package ‘tibble’
* removing ‘/mnt/trafficstop/jrleary/R/x86_64-redhat-linux-gnu-library/3.5/tibble’
Warning in install.packages :
installation of package ‘tibble’ had non-zero exit status
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
* removing ‘/mnt/trafficstop/jrleary/R/x86_64-redhat-linux-gnu-library/3.5/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
I'm on Ubuntu 12.04.5 and have R v.3.1.3 installed.
I'm using the command
install.packages("ggvis")
And that yields
ERROR: dependency ‘mime’ is not available for package ‘shiny’
* removing ‘/home/milia/R/x86_64-pc-linux-gnu-library/3.1/shiny’
ERROR: dependency ‘shiny’ is not available for package ‘ggvis’
* removing ‘/home/milia/R/x86_64-pc-linux-gnu-library/3.1/ggvis’
The downloaded source packages are in
‘/tmp/Rtmp6Cz9En/downloaded_packages’
Warning messages:
1: In install.packages("ggvis") :
installation of package ‘shiny’ had non-zero exit status
2: In install.packages("ggvis") :
installation of package ‘ggvis’ had non-zero exit status
So I figured I had to install shiny first. So I typed
install.packages("shiny")
Which gave:
ERROR: dependency ‘mime’ is not available for package ‘shiny’
* removing ‘/home/milia/R/x86_64-pc-linux-gnu-library/3.1/shiny’
The downloaded source packages are in
‘/tmp/Rtmp6Cz9En/downloaded_packages’
Warning message:
In install.packages("shiny") :
installation of package ‘shiny’ had non-zero exit status
So I thought installing mime.
Did as usual
install.packages("mime")
Which gave
Warning message:
In install.packages("mime") :
installation of package ‘mime’ had non-zero exit status
I'm not sure what to do next, and the similar problems in stack with a non-zero exit status didn't help much.
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