fail to install Rmarkdown from terminal

[dprat]

Hi,

I saw several topics concerncing the installation of the package Rmarkdown but none of them answer my issue.
I need to install rmarkdown on a remote ubuntu machine from the terminal but it's not working and I don't know why, here the error:

install.packages("rmarkdown")

trying URL 'https://cran.biotools.fr/src/contrib/rmarkdown_2.4.tar.gz'

Content type 'application/x-gzip' length 3202546 bytes (3.1 MB)

==================================================

downloaded 3.1 MB

• installing source package ‘rmarkdown’ ...

** package ‘rmarkdown’ successfully unpacked and MD5 sums checked

** R

** inst

** byte-compile and prepare package for lazy loading

Error in rbind(info, getNamespaceInfo(env, "S3methods")) :

number of columns of matrices must match (see arg 2)

ERROR: lazy loading failed for package ‘rmarkdown’

• removing ‘/home/miniconda3/envs/py37/lib/R/library/rmarkdown’

The downloaded source packages are in

‘/tmp/Rtmpa99yBs/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

Warning message:

In install.packages("rmarkdown") :

installation of package ‘rmarkdown’ had non-zero exit status

Do you have any idea ?

I tried this solution but it didn't worked for me :

R-3.5.3 on WIN10 Pro - Error: package or namespace load failed for '...' in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

Thanks !

[technocrat]

Anaconda is a wonderful package manager for Python. For R, not so much. This forum is full of unresolved Anaconda installation of R package fails.

[cderv]

I see indeed you are using R from Anaconda. This can create undesired effect when it comes to packages installation.

Some hints:

• you can try another mirror: For example, try the public package manager : https://packagemanager.rstudio.com/
  As you are on ubuntu, you can also choose a binary version of the package
  look at : https://packagemanager.rstudio.com/client/#/repos/2/overview

• You can try to use anaconda own solution: https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/

• I just discovered this project around conda two: https://medium.com/@mari_meir/rhumba-a-faster-r-distribution-d619fb93043a
  Maybe it can help.

End at last, if you don't mind change it, you could use R without Anaconda and I guess you won't have this issue.

Hope it helps

[dprat]

So you're recommanding to not use R with Anaconda, interesting.
When installing Anaconda, it's setting himself by default for R, python, etc. by modifying the .bash_profile file.
I need to modify this then.
Problem is that I think when you are in a virtual environment conda looks for R version of the environment (if I'm correct).
Anyway thanks for your advice

[cderv]

@dprat

So you're recommanding to not use R with Anaconda, interesting.

I just know it works better and that there are some issue reported regarding R with Anaconda. But it should work. You can try the other methods of installation I posted.

If someone use R and do not benefit from feature linked to Anaconda or Conda, I would advice to use standard distribution of R without Anaconda stuff.