R SIG Debian - Jan 2024 - installing tydiverse on Linux Mint

Hello Luben,

As explained by Dirk, r2u is not tested with Mint, but since Mint is
based on Ubuntu and takes most of their packages from there, it may be
worth trying to get this working as if your Mint ("victoria")
installation really was Ubuntu ("jammy"). Most of the following comes
with no warranty; if you break it, you get both pieces:

On Mon, 01 Jan 2024 22:59:34 -0500
Luben Dimov <luben.dimov at gmail.com> wrote:
>
download.file("https://github.com/eddelbuettel/r2u/raw/master/inst/scri
> pts/add_cranapt_focal.sh",
>               "add_cranapt_focal.sh")
> trying URL
> 'https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranap
> t_focal.sh'
> Content type 'text/plain; charset=utf-8' length 1799 bytes
> =================================================> downloaded 1799 bytes
> (Distro: Linux Mint 21.2 Victoria base: Ubuntu 22.04 jammy)
I think you meant the Ubuntu 22.04 ("jammy")-compatible script:
https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranapt_jammy.sh
> > Sys.chmod("add_cranapt_focal.sh", "0755")
> > system("./add_cranapt_focal.sh")  
> [sudo] password:   
I've just read both scripts and I don't see them using sudo (the
comments say it has to be run as root). Have you edited the script?
> E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
> victoria-cran40/ Release' does not have a Release file.
You need to find this line in /etc/apt/sources.list* and replace
victoria-cran40 with jammy-cran40.
> gpg: error writing keyring '/etc/apt/trusted.gpg.d/linuxmint-
> keyring.gpg': Permission denied
> ./add_cranapt_focal.sh: line 16: /etc/apt/sources.list.d/cranapt.list:
> Permission denied
> ./add_cranapt_focal.sh: line 19: /etc/apt/sources.list.d/cran-r.list:
> Permission denied
> '/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc~': Permission denied
> ./add_cranapt_focal.sh: line 25: /etc/apt/preferences.d/99cranapt:
> Permission denied
> ./add_cranapt_focal.sh: line 26: /etc/apt/preferences.d/99cranapt:
> Permission denied
> ./add_cranapt_focal.sh: line 27: /etc/apt/preferences.d/99cranapt:
> Permission denied
> ./add_cranapt_focal.sh: line 28: /etc/apt/preferences.d/99cranapt:
> Permission denied
> Installing package into
> ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3? (as ?lib? is
> unspecified)
> ./add_cranapt_focal.sh: line 36: /usr/lib/R/etc/Rprofile.site:
> Permission denied
> ./add_cranapt_focal.sh: line 37: /usr/lib/R/etc/Rprofile.site:
> Permission denied
All these are due to the script running as your user, not the
administrator account. Please double-check that you have the
jammy-compatible script, not the focal-compatible script, and run it as
the superuser.
> --------------------------- [ANTICONF]
> --------------------------------
> Configuration failed to find the fontconfig freetype2 library. Try
> installing:
>  * deb: libfontconfig1-dev (Debian, Ubuntu, etc)
>  * rpm: fontconfig-devel (Fedora, EPEL)
>  * csw: fontconfig_dev (Solaris)
>  * brew: freetype (OSX)
> If fontconfig freetype2 is already installed, check that
'pkg-config'
> is in your
> PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.pc file. If
> pkg-config
> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
> -------------------------- [ERROR MESSAGE] ---------------------------
> <stdin>:1:10: fatal error: fontconfig/fontconfig.h: No such file or
> directory
> compilation terminated.
> --------------------------------------------------------------------
The configure script of the systemfonts package is telling you which
system packages you need to install before it is able to do its job.
Does it help to retry install.packages() after installing the
libfontconfig1-dev Mint package?

-- 
Best regards,
Ivan

Ivan,

On 2 January 2024 at 10:15, Ivan Krylov wrote:
| I've just read both scripts and I don't see them using sudo (the
| comments say it has to be run as root). Have you edited the script?

[...]
 
| You need to find this line in /etc/apt/sources.list* and replace
| victoria-cran40 with jammy-cran40.

[...]

| All these are due to the script running as your user, not the
| administrator account. Please double-check that you have the
| jammy-compatible script, not the focal-compatible script, and run it as
| the superuser.

Many thanks for carefully reading the log!

I wrote those r2u setup scripts (for focal and jammy) intending for folks to
_carefully_ do these steps one at a time, and checking for errors. That
wasn't the usage pattern here, apart from being on the wrong distro and
under
wrong permissions. Using Unix and Linux can take some learning and I am sure
Luben will benefit from your careful tips which are appreciated as always.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

Thank you for the suggestions Ivan. I tried but still couldn't install
tidyverse:

On Tue, 2024-01-02 at 10:15 +0300, Ivan Krylov wrote:
> 
> >
download.file("https://github.com/eddelbuettel/r2u/raw/master/inst/scri
> > pts/add_cranapt_focal.sh",
> > ????????????? "add_cranapt_focal.sh")
> > trying URL
> >
'https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranap
> > t_focal.sh'
> > Content type 'text/plain; charset=utf-8' length 1799 bytes
> > =================================================> > downloaded
1799 bytes
> 
> > (Distro: Linux Mint 21.2 Victoria base: Ubuntu 22.04 jammy)
> 
> I think you meant the Ubuntu 22.04 ("jammy")-compatible script:
>
https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranapt_jammy.
> sh
Following your suggestions, I first changed?"vicrtoria" to
"jammy" in the
sources.list.d:

Active apt repos in: /etc/apt/sources.list.d/cran.list
    1: deb [signed-by=/usr/share/keyrings/cran.gpg]
https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/

And then I tried running this in the Linux Mint terminal, with and without sudo:

download.file("https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranapt_jammy.sh
",
              "add_cranapt_jammy.sh")

and when I saw that the URL redirects, I tried the URL of where it sends you:

download.file("https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_jammy.sh
",
              "add_cranapt_jammy.sh")

(in the terminal the quote and comma are at the end of the line, not on a
separate line, btw).

but each time I get this error: 
bash: syntax error near unexpected token `('
bash: syntax error near unexpected token `)'

I also tried running them in the RStudio terminal but get a similar result:
bash: syntax error near unexpected token
`"https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranapt_jammy.sh",'
bash: syntax error near unexpected token `)'

and 

bash: syntax error near unexpected token
`"https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranapt_jammy.
sh",'
bash: syntax error near unexpected token `)'

What am I still doing wrong?