thr3ads.net - R SIG Debian - [R-sig-Debian] installing tydiverse on Linux Mint [Jan 2024]

If this information is useful, please help other people find it:
Share via:

Luben Dimov

2024-Jan-02 03:59 UTC

[R-sig-Debian] installing tydiverse on Linux Mint

Dear Dirk,

I am writing to ask for your help with installing tydiverse on Linux
Mint (Distro: Linux Mint 21.2 Victoria base: Ubuntu 22.04 jammy)...

I tried your instructions from
http://dirk.eddelbuettel.com/blog/code/r4/ but could not get it to
work:

download.file("https://github.com/eddelbuettel/r2u/raw/master/inst/scri
pts/add_cranapt_focal.sh",
              "add_cranapt_focal.sh")
Sys.chmod("add_cranapt_focal.sh", "0755")
system("./add_cranapt_focal.sh")
install.packages("tidyverse")
library(tidyverse)
install.packages("brms")
library(brms)


The problems seem to start after the the command:
system("./add_cranapt_focal.sh")

as follows:

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
> Sys.chmod("add_cranapt_focal.sh", "0755")
> system("./add_cranapt_focal.sh")[sudo] password:             
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
victoria-cran40/ Release' does not have a Release file.
Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d
instead (see apt-key(8)).
Executing: /tmp/apt-key-gpghome.BcNNAWMs7G/gpg.1.sh --keyserver
keyserver.ubuntu.com --recv-keys A1489FE2AB99A21A
gpg: key A1489FE2AB99A21A: public key "Dirk Eddelbuettel
<edd at debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key A6616109451BBBF2: "Linux Mint Repository Signing Key
<root at linuxmint.com>" not changed
gpg: key A6616109451BBBF2: 12 signatures not checked due to missing
keys
gpg: error writing keyring '/etc/apt/trusted.gpg.d/linuxmint-
keyring.gpg': Permission denied
gpg: error reading '[stdin]': Permission denied
gpg: import from '[stdin]' failed: Permission denied
gpg: Total number processed: 2
gpg:       skipped new keys: 1
gpg:              unchanged: 1
./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
Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d
instead (see apt-key(8)).
Executing: /tmp/apt-key-gpghome.lW5hTPHArp/gpg.1.sh --keyserver
keyserver.ubuntu.com --recv-keys 67C2D66C4B1D4339 51716619E084DAB9
gpg: key 51716619E084DAB9: "Michael Rutter <marutter at
gmail.com>" 1 new
signature
gpg: key 67C2D66C4B1D4339: public key "Launchpad PPA for Dirk
Eddelbuettel" imported
gpg: Total number processed: 2
gpg:               imported: 1
gpg:         new signatures: 1
cp: cannot create regular file
'/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc~': Permission denied
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu
victoria-cran40/ Release' does not have a Release file.
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
r-base-core is already the newest version (4.3.2-1.2204.0).
r-base-core set to manually installed.
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
./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
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
make is already the newest version (4.3-4.1build1).
python3-dbus is already the newest version (1.2.18-3build1).
python3-apt is already the newest version (2.4.0ubuntu2).
python3-gi is already the newest version (3.42.1-0ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Installing package into ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3?
(as ?lib? is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/bspm_0.5.5.tar.gz'
Content type 'application/x-gzip' length 26800 bytes (26 KB)
=================================================downloaded 26 KB

* installing *source* package ?bspm? ...
** package ?bspm? successfully unpacked and MD5 sums checked
** using staged installation
* NOT installing D-Bus service
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary
installation path
* DONE (bspm)

The downloaded source packages are in
	?/tmp/RtmphMoSrw/downloaded_packages?
./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> install.packages("tidyverse")Installing package into ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3?
(as ?lib? is unspecified)
also installing the dependencies ?systemfonts?, ?textshaping?, ?ragg?

trying URL 'https://cloud.r-
project.org/src/contrib/systemfonts_1.0.5.tar.gz'
Content type 'application/x-gzip' length 80638 bytes (78 KB)
=================================================downloaded 78 KB

trying URL 'https://cloud.r-
project.org/src/contrib/textshaping_0.3.7.tar.gz'
Content type 'application/x-gzip' length 35100 bytes (34 KB)
=================================================downloaded 34 KB

trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.7.tar.gz'
Content type 'application/x-gzip' length 425500 bytes (415 KB)
=================================================downloaded 415 KB

trying URL 'https://cloud.r-
project.org/src/contrib/tidyverse_2.0.0.tar.gz'
Content type 'application/x-gzip' length 704618 bytes (688 KB)
=================================================downloaded 688 KB

* installing *source* package ?systemfonts? ...
** package ?systemfonts? successfully unpacked and MD5 sums checked
** using staged installation
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGSUsing PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [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.
--------------------------------------------------------------------
ERROR: configuration failed for package ?systemfonts?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/systemfonts?
ERROR: dependency ?systemfonts? is not available for package
?textshaping?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/textshaping?
ERROR: dependencies ?systemfonts?, ?textshaping? are not available for
package ?ragg?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/ragg?
ERROR: dependency ?ragg? is not available for package ?tidyverse?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/tidyverse?

The downloaded source packages are in
	?/tmp/RtmpCt4Y9p/downloaded_packages?
Warning messages:
1: In install.packages("tidyverse") :
  installation of package ?systemfonts? had non-zero exit status
2: In install.packages("tidyverse") :
  installation of package ?textshaping? had non-zero exit status
3: In install.packages("tidyverse") :
  installation of package ?ragg? had non-zero exit status
4: In install.packages("tidyverse") :
  installation of package ?tidyverse? had non-zero exit status







Btw, I did first try getting tidyverse through
install.packages("tidyverse") but couldn't (which is why I tried
your
method):
> install.packages("tidyverse")Installing package into ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3?
(as ?lib? is unspecified)
also installing the dependencies ?systemfonts?, ?textshaping?, ?ragg?

trying URL 'https://cloud.r-
project.org/src/contrib/systemfonts_1.0.5.tar.gz'
Content type 'application/x-gzip' length 80638 bytes (78 KB)
=================================================downloaded 78 KB

trying URL 'https://cloud.r-
project.org/src/contrib/textshaping_0.3.7.tar.gz'
Content type 'application/x-gzip' length 35100 bytes (34 KB)
=================================================downloaded 34 KB

trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.7.tar.gz'
Content type 'application/x-gzip' length 425500 bytes (415 KB)
=================================================downloaded 415 KB

trying URL 'https://cloud.r-
project.org/src/contrib/tidyverse_2.0.0.tar.gz'
Content type 'application/x-gzip' length 704618 bytes (688 KB)
=================================================downloaded 688 KB

* installing *source* package ?systemfonts? ...
** package ?systemfonts? successfully unpacked and MD5 sums checked
** using staged installation
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGSUsing PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [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.
--------------------------------------------------------------------
ERROR: configuration failed for package ?systemfonts?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/systemfonts?
Warning in install.packages :
  installation of package ?systemfonts? had non-zero exit status
ERROR: dependency ?systemfonts? is not available for package
?textshaping?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/textshaping?
Warning in install.packages :
  installation of package ?textshaping? had non-zero exit status
ERROR: dependencies ?systemfonts?, ?textshaping? are not available for
package ?ragg?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/ragg?
Warning in install.packages :
  installation of package ?ragg? had non-zero exit status
ERROR: dependency ?ragg? is not available for package ?tidyverse?
* removing ?/home/luben/R/x86_64-pc-linux-gnu-library/4.3/tidyverse?
Warning in install.packages :
  installation of package ?tidyverse? had non-zero exit status

The downloaded source packages are in
	?/tmp/RtmpBTgwsS/downloaded_packages?

Dirk Eddelbuettel

2024-Jan-02 04:14 UTC

head link

[R-sig-Debian] installing tydiverse on Linux Mint

Luben,

r2u instructions are at the site; there are two scripts for Ubuntu focal and
jammy. I tested those repeatedly. Many people used them.

We also support Docker installationsl; the docker images are also rebuilt
frequently. r2u is also used around the clock on CI, likely most often 'from
scratch' on more base-level Ubuntu installations.

I never used Linux Mint. If this differs, you will have to work out how to
cover any and all edges you encounter. I never claimed r2u was for Mint.

r2y has delivered well over ten millions binary packages since we started
this, and is running likely thousands of automated jobs each way.  On the
supported platforms, i.e. mostly Ubuntu jammy.

Cheers, Dirk

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

Ivan Krylov

2024-Jan-02 07:15 UTC

head link

[R-sig-Debian] 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

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

[R-sig-Debian] installing tydiverse on Linux Mint

[R-sig-Debian] installing tydiverse on Linux Mint

[R-sig-Debian] installing tydiverse on Linux Mint