How to install RStudio (wrapper) packages declaratively?

Help
1

Hi :slight_smile:

The desired behavior

I want to install the tidyverse and snakecase declaratively in my configuration.nix file.

What I’ve tried

I tried reading the official documentation on how to add packages declaratively from CRan to RStudio. Unfortunately, I still don’t understand how to add packages. I tried searching other questions on this Discourse, but the questions either assume you understand where to type things in or they are building environments on the fly rather than installing declaratively.

I tried copying the code in the official documentation and pasting it right above my environment.systemPackages = with pkgs, where all of my programs are installed. The code snippet is this:

with pkgs;
let
  RStudio-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ ggplot2 dplyr xts ]; };
in ...

As you can see, I copied the code literally with the exception of changing r to rstudio. I also added RStudio-with-my-packages to my environment.systemPackages = with pkgs. However, when I try to rebuild, I get an error saying there’s an unexpected with in the code.

Background

Two days ago I reinstalled NixOS. I am on the 23.05 channel. Apart from my attempts at adding R packages, the only changes I have made to the configuration.nix is adding applications to the environment.systemPackages = with pkgs;, and adding mullvad-vpn and syncthing as services.

I have a hunch that I am not understanding the Nix language well enough to write my own code and that on its own would solve this problem. I tried skimming the Nix Pills to see if anything would address my predicament, but I couldn’t see it.

What do I need to understand to install R packages declaratively?
What do I need to do to install R packages declaratively?

1 Like
2

I’d recommend reading up on the language basics first: Nix language basics — nix.dev documentation

Essentially, let bindings have to precede an expression and be where an expression is allowed to be, as does with, just dumping it randomly in the code clearly doesn’t work. It’s hard to explain why syntax is wrong, that’s just not how the language works. Also doesn’t help that you’re sharing an expression that’s in an illegal place without sharing where the expression is - the problem isn’t visible in your example :wink:

Just to be clear, you’re doing everything to install R packages right, at a glance. You’re just not putting it in the right place, so just going through a full basic tutorial (not the nix pills, far too advanced) should clear that up. Your problem is likely that you don’t understand scoping, functions, and/or attrsets. And also how all of those are no different from NixOS modules.

The nix language tutorial does a much better job than I can do here, teaching to program in a discourse thread is impractical.

If you still struggle after that, come back with a more complete example, will be much easier to help then :slight_smile:

3

Thanks for the response.

I looked into the tutorial and think I understand what with, let, and in attempt to do.

However, I still don’t know how to the scoping and the expressions should translate into me trying to install the tidyverse and snakecase R packages.

I attempted to include R-with-my-packages in the scope of environment.systemPackages, but I still get a compilation error telling me there’s an unexpected let.

Here’s my configuration.nix:

# Edit this configuration file to define what should be installed on
# your system.  Help is available in the configuration.nix(5) man page
# and in the NixOS manual (accessible by running ‘nixos-help’).

{ config, pkgs, ... }:

{
  imports =
    [ # Include the results of the hardware scan.
      ./hardware-configuration.nix
    ];

  # Bootloader.
  boot.loader.systemd-boot.enable = true;
  boot.loader.efi.canTouchEfiVariables = true;

  networking.hostName = "nixos"; # Define your hostname.
  # networking.wireless.enable = true;  # Enables wireless support via wpa_supplicant.

  # Configure network proxy if necessary
  # networking.proxy.default = "http://user:password@proxy:port/";
  # networking.proxy.noProxy = "127.0.0.1,localhost,internal.domain";

  # Enable networking
  networking.networkmanager.enable = true;

  # Set your time zone.
  time.timeZone = "America/Guatemala";

  # Select internationalisation properties.
  i18n.defaultLocale = "en_US.UTF-8";

  i18n.extraLocaleSettings = {
    LC_ADDRESS = "es_GT.UTF-8";
    LC_IDENTIFICATION = "es_GT.UTF-8";
    LC_MEASUREMENT = "es_GT.UTF-8";
    LC_MONETARY = "es_GT.UTF-8";
    LC_NAME = "es_GT.UTF-8";
    LC_NUMERIC = "es_GT.UTF-8";
    LC_PAPER = "es_GT.UTF-8";
    LC_TELEPHONE = "es_GT.UTF-8";
    LC_TIME = "es_GT.UTF-8";
  };

  # Enable the X11 windowing system.
  services.xserver.enable = true;

  # Enable the GNOME Desktop Environment.
  services.xserver.displayManager.gdm.enable = true;
  services.xserver.desktopManager.gnome.enable = true;

  # Configure keymap in X11
  services.xserver = {
    layout = "us";
    xkbVariant = "";
  };

  # Enable CUPS to print documents.
  services.printing.enable = true;

  # Enable sound with pipewire.
  sound.enable = true;
  hardware.pulseaudio.enable = false;
  security.rtkit.enable = true;
  services.pipewire = {
    enable = true;
    alsa.enable = true;
    alsa.support32Bit = true;
    pulse.enable = true;
    # If you want to use JACK applications, uncomment this
    #jack.enable = true;

    # use the example session manager (no others are packaged yet so this is enabled by default,
    # no need to redefine it in your config for now)
    #media-session.enable = true;
  };

  # Enable touchpad support (enabled default in most desktopManager).
  # services.xserver.libinput.enable = true;

  # Define a user account. Don't forget to set a password with ‘passwd’.
  users.users.agua = {
    isNormalUser = true;
    description = "Agua";
    extraGroups = [ "networkmanager" "wheel" ];
    packages = with pkgs; [
      firefox
      thunderbird
    ];
  };

  # Enable automatic login for the user.
  services.xserver.displayManager.autoLogin.enable = true;
  services.xserver.displayManager.autoLogin.user = "agua";

  # Workaround for GNOME autologin: https://github.com/NixOS/nixpkgs/issues/103746#issuecomment-945091229
  systemd.services."getty@tty1".enable = false;
  systemd.services."autovt@tty1".enable = false;

  # Allow unfree packages
  nixpkgs.config.allowUnfree = true;


  # List packages installed in system profile. To search, run:
  # $ nix search wget
  let
    R-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ snakecase ]; };
  in
  environment.systemPackages = with pkgs; [
    neovim # Do not forget to add an editor to edit configuration.nix! The Nano editor is also installed by default.
    rstudioWrapper
    R-with-my-packages
    mullvad-vpn
    brave
    vlc
    zotero
    libreoffice
    keepassxc
    element-desktop
    signal-desktop
    freetube
    calibre
    anki
    marktext
    gparted
    czkawka
    dupeguru
    git
    meld
    cryptomator
    transmission-gtk
    mullvad-browser
    zettlr
    gimp-with-plugins
    unetbootin
    tutanota-desktop
    appimage-run
    joplin-desktop
    airshipper
    yt-dlp
    anki-bin
    gnome.gnome-tweaks
    wget
    vscodium-fhs
  ];

  # Some programs need SUID wrappers, can be configured further or are
  # started in user sessions.
  # programs.mtr.enable = true;
  # programs.gnupg.agent = {
  #   enable = true;
  #   enableSSHSupport = true;
  # };

  # List services that you want to enable:

  # Enable the OpenSSH daemon.
  # services.openssh.enable = true;

  # Open ports in the firewall.
  # networking.firewall.allowedTCPPorts = [ ... ];
  # networking.firewall.allowedUDPPorts = [ ... ];
  # Or disable the firewall altogether.
  # networking.firewall.enable = false;

  # Mullvad option/service
  services.mullvad-vpn.enable = true;

  # Syncthing option/service
  services = {
    syncthing = {
      enable = true;
      user = "agua";
      dataDir = "/home/agua/Documents";
      configDir = "/home/agua/Documents/.config/syncthing";
      overrideDevices = true;
      overrideFolders = true;
      devices = {
        "fairphone" = { id = "HAJMXNK-RMI6GLJ-ZDYCK6S-SMGCDTU-3EU55A3-OVD6LTY-NTQIG7I-RO3VTQL"; };
      };
    };
  };

  # This value determines the NixOS release from which the default
  # settings for stateful data, like file locations and database versions
  # on your system were taken. It‘s perfectly fine and recommended to leave
  # this value at the release version of the first install of this system.
  # Before changing this value read the documentation for this option
  # (e.g. man configuration.nix or on https://nixos.org/nixos/options.html).
  system.stateVersion = "23.05"; # Did you read the comment?

}

What am I missing? How could I fix it?

4

That’s close, what you want is environment.systemPackages = with pkgs; let ... in [ ... ];. Let bindings return an expression after substituting variables that are bound. Here you want to bind R-with-my-packages and use it in the list.

1 Like
5

Thank you. I changed my configuration.nix to this:

# Edit this configuration file to define what should be installed on
# your system.  Help is available in the configuration.nix(5) man page
# and in the NixOS manual (accessible by running ‘nixos-help’).

{ config, pkgs, ... }:

{
  imports =
    [ # Include the results of the hardware scan.
      ./hardware-configuration.nix
    ];

  # Bootloader.
  boot.loader.systemd-boot.enable = true;
  boot.loader.efi.canTouchEfiVariables = true;

  networking.hostName = "nixos"; # Define your hostname.
  # networking.wireless.enable = true;  # Enables wireless support via wpa_supplicant.

  # Configure network proxy if necessary
  # networking.proxy.default = "http://user:password@proxy:port/";
  # networking.proxy.noProxy = "127.0.0.1,localhost,internal.domain";

  # Enable networking
  networking.networkmanager.enable = true;

  # Set your time zone.
  time.timeZone = "America/Guatemala";

  # Select internationalisation properties.
  i18n.defaultLocale = "en_US.UTF-8";

  i18n.extraLocaleSettings = {
    LC_ADDRESS = "es_GT.UTF-8";
    LC_IDENTIFICATION = "es_GT.UTF-8";
    LC_MEASUREMENT = "es_GT.UTF-8";
    LC_MONETARY = "es_GT.UTF-8";
    LC_NAME = "es_GT.UTF-8";
    LC_NUMERIC = "es_GT.UTF-8";
    LC_PAPER = "es_GT.UTF-8";
    LC_TELEPHONE = "es_GT.UTF-8";
    LC_TIME = "es_GT.UTF-8";
  };

  # Enable the X11 windowing system.
  services.xserver.enable = true;

  # Enable the GNOME Desktop Environment.
  services.xserver.displayManager.gdm.enable = true;
  services.xserver.desktopManager.gnome.enable = true;

  # Configure keymap in X11
  services.xserver = {
    layout = "us";
    xkbVariant = "";
  };

  # Enable CUPS to print documents.
  services.printing.enable = true;

  # Enable sound with pipewire.
  sound.enable = true;
  hardware.pulseaudio.enable = false;
  security.rtkit.enable = true;
  services.pipewire = {
    enable = true;
    alsa.enable = true;
    alsa.support32Bit = true;
    pulse.enable = true;
    # If you want to use JACK applications, uncomment this
    #jack.enable = true;

    # use the example session manager (no others are packaged yet so this is enabled by default,
    # no need to redefine it in your config for now)
    #media-session.enable = true;
  };

  # Enable touchpad support (enabled default in most desktopManager).
  # services.xserver.libinput.enable = true;

  # Define a user account. Don't forget to set a password with ‘passwd’.
  users.users.agua = {
    isNormalUser = true;
    description = "Agua";
    extraGroups = [ "networkmanager" "wheel" ];
    packages = with pkgs; [
      firefox
      thunderbird
    ];
  };

  # Enable automatic login for the user.
  services.xserver.displayManager.autoLogin.enable = true;
  services.xserver.displayManager.autoLogin.user = "agua";

  # Workaround for GNOME autologin: https://github.com/NixOS/nixpkgs/issues/103746#issuecomment-945091229
  systemd.services."getty@tty1".enable = false;
  systemd.services."autovt@tty1".enable = false;

  # Allow unfree packages
  nixpkgs.config.allowUnfree = true;


  # List packages installed in system profile. To search, run:
  # $ nix search wget
#  let
#    R-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ snakecase ]; };
#  in
  environment.systemPackages = with pkgs;
  let
    RStudio-with-my-packages = rstudioWrapper.override{
      packages = with rPackages; [ tidyverse snakecase ]; };
  in
  [
    neovim # Do not forget to add an editor to edit configuration.nix! The Nano editor is also installed by default.
    rstudioWrapper
    RStudio-with-my-packages
    mullvad-vpn
    brave
    vlc
    zotero
    libreoffice
    keepassxc
    element-desktop
    signal-desktop
    freetube
    calibre
    anki
    marktext
    gparted
    czkawka
    dupeguru
    git
    meld
    cryptomator
    transmission-gtk
    mullvad-browser
    zettlr
    gimp-with-plugins
    unetbootin
    tutanota-desktop
    appimage-run
    joplin-desktop
    airshipper
    yt-dlp
    anki-bin
    gnome.gnome-tweaks
    wget
    vscodium-fhs
  ];

  # Some programs need SUID wrappers, can be configured further or are
  # started in user sessions.
  # programs.mtr.enable = true;
  # programs.gnupg.agent = {
  #   enable = true;
  #   enableSSHSupport = true;
  # };

  # List services that you want to enable:

  # Enable the OpenSSH daemon.
  # services.openssh.enable = true;

  # Open ports in the firewall.
  # networking.firewall.allowedTCPPorts = [ ... ];
  # networking.firewall.allowedUDPPorts = [ ... ];
  # Or disable the firewall altogether.
  # networking.firewall.enable = false;

  # Mullvad option/service
  services.mullvad-vpn.enable = true;

  # Syncthing option/service
  services = {
    syncthing = {
      enable = true;
      user = "agua";
      dataDir = "/home/agua/Documents";
      configDir = "/home/agua/Documents/.config/syncthing";
      overrideDevices = true;
      overrideFolders = true;
      devices = {
        "fairphone" = { id = "HAJMXNK-RMI6GLJ-ZDYCK6S-SMGCDTU-3EU55A3-OVD6LTY-NTQIG7I-RO3VTQL"; };
      };
    };
  };

  # This value determines the NixOS release from which the default
  # settings for stateful data, like file locations and database versions
  # on your system were taken. It‘s perfectly fine and recommended to leave
  # this value at the release version of the first install of this system.
  # Before changing this value read the documentation for this option
  # (e.g. man configuration.nix or on https://nixos.org/nixos/options.html).
  system.stateVersion = "23.05"; # Did you read the comment?

}

With that configuration.nix, I managed to sudo nixos-rebuild switch successfully.

Unfortunately, if I open RStudio I do not see my R packages. I am not sure whether they should immediately appear or whether I should do something within RStudio.

If, after doing the previous changes, I run within RStudio install.packages("tidyverse") and install.packages("snakecase"), some of the dependencies are installed and can be used in RStudio. However, not all packages are installed.

If I then run install.packages("tidyverse") again, RStudio tries to install the packages that weren’t successfully installed before. This could help you see what RStudio is not successfully installing:

> install.packages("tidyverse")
Installing package into ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘gargle’, ‘curl’, ‘ids’, ‘openssl’, ‘systemfonts’, ‘textshaping’, ‘googledrive’, ‘googlesheets4’, ‘haven’, ‘httr’, ‘ragg’, ‘rvest’, ‘xml2’

trying URL 'https://cran.rstudio.com/src/contrib/gargle_1.5.1.tar.gz'
Content type 'application/x-gzip' length 626790 bytes (612 KB)
==================================================
downloaded 612 KB

trying URL 'https://cran.rstudio.com/src/contrib/curl_5.0.1.tar.gz'
Content type 'application/x-gzip' length 714177 bytes (697 KB)
==================================================
downloaded 697 KB

trying URL 'https://cran.rstudio.com/src/contrib/ids_1.0.1.tar.gz'
Content type 'application/x-gzip' length 91213 bytes (89 KB)
==================================================
downloaded 89 KB

trying URL 'https://cran.rstudio.com/src/contrib/openssl_2.0.6.tar.gz'
Content type 'application/x-gzip' length 1206602 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/systemfonts_1.0.4.tar.gz'
Content type 'application/x-gzip' length 81757 bytes (79 KB)
==================================================
downloaded 79 KB

trying URL 'https://cran.rstudio.com/src/contrib/textshaping_0.3.6.tar.gz'
Content type 'application/x-gzip' length 35722 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'https://cran.rstudio.com/src/contrib/googledrive_2.1.1.tar.gz'
Content type 'application/x-gzip' length 1609266 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/googlesheets4_1.1.1.tar.gz'
Content type 'application/x-gzip' length 232584 bytes (227 KB)
==================================================
downloaded 227 KB

trying URL 'https://cran.rstudio.com/src/contrib/haven_2.5.3.tar.gz'
Content type 'application/x-gzip' length 313303 bytes (305 KB)
==================================================
downloaded 305 KB

trying URL 'https://cran.rstudio.com/src/contrib/httr_1.4.6.tar.gz'
Content type 'application/x-gzip' length 157621 bytes (153 KB)
==================================================
downloaded 153 KB

trying URL 'https://cran.rstudio.com/src/contrib/ragg_1.2.5.tar.gz'
Content type 'application/x-gzip' length 427859 bytes (417 KB)
==================================================
downloaded 417 KB

trying URL 'https://cran.rstudio.com/src/contrib/rvest_1.0.3.tar.gz'
Content type 'application/x-gzip' length 94659 bytes (92 KB)
==================================================
downloaded 92 KB

trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.3.5.tar.gz'
Content type 'application/x-gzip' length 272664 bytes (266 KB)
==================================================
downloaded 266 KB

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

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
--------------------------- [ANTICONF] --------------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.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: curl/curl.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
--------------------------- [ANTICONF] --------------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.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] ---------------------------
tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory
    1 | #include <openssl/opensslv.h>
      |          ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
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/agua/R/x86_64-pc-linux-gnu-library/4.2/systemfonts’
Warning in install.packages :
  installation of package ‘systemfonts’ had non-zero exit status
* installing *source* package ‘haven’ ...
** package ‘haven’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-lz
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the zlib library. Try installing:
 * deb: zlib1g-dev (Debian, Ubuntu, etc)
 * rpm: zlib-devel (Fedora, EPEL)
 * csw: libz_dev (Solaris)
 * brew: zlib (OSX)
If zlib is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a zlib.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: zlib.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘haven’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/haven’
Warning in install.packages :
  installation of package ‘haven’ had non-zero exit status
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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: configuration failed for package ‘xml2’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/xml2’
Warning in install.packages :
  installation of package ‘xml2’ had non-zero exit status
ERROR: dependency ‘openssl’ is not available for package ‘ids’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/ids’
Warning in install.packages :
  installation of package ‘ids’ had non-zero exit status
ERROR: dependency ‘systemfonts’ is not available for package ‘textshaping’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/textshaping’
Warning in install.packages :
  installation of package ‘textshaping’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
ERROR: dependencies ‘httr’, ‘openssl’ are not available for package ‘gargle’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/gargle’
Warning in install.packages :
  installation of package ‘gargle’ had non-zero exit status
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/ragg’
Warning in install.packages :
  installation of package ‘ragg’ had non-zero exit status
ERROR: dependencies ‘httr’, ‘xml2’ are not available for package ‘rvest’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/rvest’
Warning in install.packages :
  installation of package ‘rvest’ had non-zero exit status
ERROR: dependencies ‘gargle’, ‘httr’ are not available for package ‘googledrive’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/googledrive’
Warning in install.packages :
  installation of package ‘googledrive’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘gargle’, ‘googledrive’, ‘httr’, ‘ids’ are not available for package ‘googlesheets4’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/googlesheets4’
Warning in install.packages :
  installation of package ‘googlesheets4’ had non-zero exit status
ERROR: dependencies ‘googledrive’, ‘googlesheets4’, ‘haven’, ‘httr’, ‘ragg’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/agua/R/x86_64-pc-linux-gnu-library/4.2/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmp37wQRn/downloaded_packages’

Additionally, if I try to install those dependencies manually, I get the very same errors that are displayed above. In other words, if within RStudio I run install.packages("xml2"), I get the same error as above.

What could be causing my problem? What can I do about it?

6

Unfortunately, if I open RStudio I do not see my R packages. I am not sure whether they should immediately appear or whether I should do something within RStudio.

They will just be available. Your problem is you have also installed a bare rstudioWrapper into your system packages and due to ordering it’s taking precedence in your path, so you’re launching an rstudio without any packages. If you remove it then you will call the right wrapper by default.

On installing packages imperatively using install.packages: you can of course do this and they will install into your home directory by default, however you will have to provide any dependencies the packages require. Your commands failed when it tried to install the curl dependency, because you do not have curl.dev in your environment. Since you’re already got the declarative version, I suggest you stick to that rather than trying to install packages imperatively, otherwise you’ll end up needing a lot of things in your environment.

1 Like
7

Amazing! It worked!

For future NixOS and RStudio users, here’s what I ended up with in the environment.systemPackages =… part of my configuration.nix file (of course, your personal packages will vary depending on what you work with):

  # List packages installed in system profile. To search, run:
  # $ nix search wget
#  let
#    R-with-my-packages = rstudioWrapper.override{ packages = with rPackages; [ snakecase ]; };
#  in
  environment.systemPackages = with pkgs;
  let
    RStudio-with-my-packages = rstudioWrapper.override{
      packages = with rPackages; [ tidyverse snakecase ]; };
  in
  [
    neovim # Do not forget to add an editor to edit configuration.nix! The Nano editor is also installed by default.
    RStudio-with-my-packages
    other-programs-you-want-to-install
  ];

Thank you, @jbedo and @TLATER. I marked this as the solution so that the final result appears at the top, but as to credit, you two got me closer to the answer! I hope this way of marking a solution is okay. Otherwise please let me know :slight_smile:

1 Like