[R-sig-Debian] installing tydiverse on Linux Mint
Luben Dimov
|uben@d|mov @end|ng |rom gm@||@com
Tue Jan 2 04:59:34 CET 2024
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 using debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key A6616109451BBBF2: "Linux Mint Repository Signing Key
<root using 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 using 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_CFLAGS=
Using 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_CFLAGS=
Using 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’
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