MX Linux Forum

Posted: **Fri Jan 05, 2024 6:48 am**

Hello everyone,

I am trying to do some work in R but I am unable to install most packages because I can't seem to be able to get a recent enough version of R via the MX repos to be able to download extra R packages I need. Every time I try to download packages I bump into the problem of having some unmet dependencies that cannot be installed because higher versions are needed. Ultimately, I come to the problem of not having a recent enough version of r-base-core.

I tried installing the latest deb binary via Gdebi but I get the message that:

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r-base-core : Depends: libc6 (>= 2.35) but 2.31-13+deb11u7 is to be installed
               Depends: libicu72 (>= 72.1~rc-1~) but it is not installable
               Depends: libtiff6 (>= 4.0.3) but it is not installable

Strangely enough, when I try to find more recent version of the packages I am missing either via synaptic or via the MX package installer, I cannot find them. I enable the test repo in synaptic but I never see more recent versions becoming available, and looking for packages via the MX package installer in the MX Test Repo or the Debian Backports tab doesn't even show any results.

I guess I've come to the point where I just need to ask the MX community if we can get a more recent build of r-base-core to the MX repos. I am currently running MX-21.3_ahs_x64.

EDIT: I recently tried installing the deb for the latest version of libc6 (2.36_9), but Gdebi warned me that it would remove all of these packages:

https://imgur.com/MXwaRI5.png

So I aborted the installation. That seems like a sure way to break the system. Any help here would be much appreciated

Full system info:

Code: Select all

System:    Kernel: 5.18.0-4mx-amd64 [5.18.16-1~mx21+1] x86_64 bits: 64 compiler: gcc v: 10.2.1 
           parameters: BOOT_IMAGE=/boot/vmlinuz-5.18.0-4mx-amd64 root=UUID=<filter> ro quiet splash 
           Desktop: Xfce 4.18.1 tk: Gtk 3.24.24 info: xfce4-panel wm: xfwm 4.18.0 vt: 7 
           dm: LightDM 1.26.0 Distro: MX-21.3_ahs_x64 Wildflower September 18  2022 
           base: Debian GNU/Linux 11 (bullseye) 
Machine:   Type: Desktop Mobo: Acer model: Aspire C27-1655 v: 1.0 serial: <filter> 
           UEFI: American Megatrends v: R01-A3 date: 11/03/2021 
CPU:       Info: Quad Core model: 11th Gen Intel Core i7-1165G7 bits: 64 type: MT MCP 
           arch: Tiger Lake family: 6 model-id: 8C (140) stepping: 1 microcode: B4 cache: 
           L2: 12 MiB 
           flags: avx avx2 lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx bogomips: 44851 
           Speed: 1550 MHz min/max: 400/4700 MHz Core speeds (MHz): 1: 1550 2: 1213 3: 1202 
           4: 1225 5: 1201 6: 1243 7: 1181 8: 1198 
           Vulnerabilities: Type: itlb_multihit status: Not affected 
           Type: l1tf status: Not affected 
           Type: mds status: Not affected 
           Type: meltdown status: Not affected 
           Type: mmio_stale_data status: Not affected 
           Type: retbleed status: Not affected 
           Type: spec_store_bypass mitigation: Speculative Store Bypass disabled via prctl 
           Type: spectre_v1 mitigation: usercopy/swapgs barriers and __user pointer sanitization 
           Type: spectre_v2 
           mitigation: Enhanced IBRS, IBPB: conditional, RSB filling, PBRSB-eIBRS: SW sequence 
           Type: srbds status: Not affected 
           Type: tsx_async_abort status: Not affected 
Graphics:  Device-1: Intel TigerLake-LP GT2 [Iris Xe Graphics] vendor: Acer Incorporated ALI 
           driver: i915 v: kernel bus-ID: 0000:00:02.0 chip-ID: 8086:9a49 class-ID: 0300 
           Device-2: Realtek USB2.0 camera type: USB driver: uvcvideo bus-ID: 3-5:3 
           chip-ID: 0bda:5830 class-ID: 0e02 
           Display: x11 server: X.Org 1.20.14 compositor: xfwm4 v: 4.18.0 driver: 
           loaded: modesetting unloaded: fbdev,vesa display-ID: :0.0 screens: 1 
           Screen-1: 0 s-res: 1920x1080 s-dpi: 96 s-size: 508x285mm (20.0x11.2") 
           s-diag: 582mm (22.9") 
           Monitor-1: eDP-1 res: 1920x1080 hz: 30 dpi: 94 size: 519x324mm (20.4x12.8") 
           diag: 612mm (24.1") 
           OpenGL: renderer: Mesa Intel Xe Graphics (TGL GT2) v: 4.6 Mesa 22.0.5 
           direct render: Yes 
Audio:     Device-1: Intel Tiger Lake-LP Smart Sound Audio vendor: Acer Incorporated ALI 
           driver: sof-audio-pci-intel-tgl alternate: snd_hda_intel,snd_sof_pci_intel_tgl 
           bus-ID: 0000:00:1f.3 chip-ID: 8086:a0c8 class-ID: 0401 
           Sound Server-1: ALSA v: k5.18.0-4mx-amd64 running: yes 
           Sound Server-2: PulseAudio v: 14.2 running: yes 
Network:   Device-1: Intel Wi-Fi 6 AX201 driver: iwlwifi v: kernel modules: wl port: 4000 
           bus-ID: 0000:00:14.3 chip-ID: 8086:a0f0 class-ID: 0280 
           IF: wlan0 state: up mac: <filter> 
           Device-2: Realtek RTL8111/8168/8411 PCI Express Gigabit Ethernet driver: r8169 
           v: kernel port: 3000 bus-ID: 0000:03:00.0 chip-ID: 10ec:8168 class-ID: 0200 
           IF: eth0 state: down mac: <filter> 
Bluetooth: Device-1: Intel type: USB driver: btusb v: 0.8 bus-ID: 3-10:4 chip-ID: 8087:0026 
           class-ID: e001 
           Report: hciconfig ID: hci0 rfk-id: 1 state: up address: <filter> bt-v: 3.0 lmp-v: 5.2 
           sub-v: 2014 hci-v: 5.2 rev: 2014 
           Info: acl-mtu: 1021:4 sco-mtu: 96:6 link-policy: rswitch sniff link-mode: slave accept 
           service-classes: rendering, capturing, object transfer, audio 
RAID:      Hardware-1: Intel Volume Management Device NVMe RAID Controller driver: vmd v: 0.6 
           port: 4000 bus-ID: 0000:00:0e.0 chip-ID: 8086.9a0b rev: class-ID: 0104 
Drives:    Local Storage: total: 953.87 GiB used: 79.53 GiB (8.3%) 
           SMART Message: Unable to run smartctl. Root privileges required. 
           ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Western Digital 
           model: PC SN530 SDBPNPZ-1T00-1114 size: 953.87 GiB block-size: physical: 512 B 
           logical: 512 B speed: 31.6 Gb/s lanes: 4 type: SSD serial: <filter> rev: 21113000 
           temp: 57.9 C scheme: GPT 
Partition: ID-1: / raw-size: 945.61 GiB size: 929.7 GiB (98.32%) used: 79.53 GiB (8.6%) fs: ext4 
           dev: /dev/nvme0n1p2 maj-min: 259:2 
           ID-2: /boot/efi raw-size: 256 MiB size: 252 MiB (98.46%) used: 274 KiB (0.1%) fs: vfat 
           dev: /dev/nvme0n1p1 maj-min: 259:1 
Swap:      Kernel: swappiness: 15 (default 60) cache-pressure: 100 (default) 
           ID-1: swap-1 type: partition size: 8 GiB used: 0 KiB (0.0%) priority: -2 
           dev: /dev/nvme0n1p3 maj-min: 259:3 
Sensors:   System Temperatures: cpu: 27.8 C mobo: N/A 
           Fan Speeds (RPM): N/A 
Repos:     Packages: note: see --pkg apt: 2805 lib: 1327 flatpak: 0 
           No active apt repos in: /etc/apt/sources.list 
           Active apt repos in: /etc/apt/sources.list.d/debian-stable-updates.list 
           1: deb http://deb.debian.org/debian/ bullseye-updates main contrib non-free
           Active apt repos in: /etc/apt/sources.list.d/debian.list 
           1: deb http://deb.debian.org/debian/ bullseye main contrib non-free
           2: deb http://security.debian.org/debian-security/ bullseye-security main contrib non-free
           Active apt repos in: /etc/apt/sources.list.d/dropbox.list 
           1: deb [arch=i386,amd64] http://linux.dropbox.com/debian/ sid main
           Active apt repos in: /etc/apt/sources.list.d/mx.list 
           1: deb http://nl.mxrepo.com/mx/repo/ bullseye main non-free
           2: deb http://nl.mxrepo.com/mx/testrepo/ bullseye test
           3: deb http://nl.mxrepo.com/mx/repo/ bullseye ahs
           Active apt repos in: /etc/apt/sources.list.d/teams.list 
           1: deb [arch=amd64] https://packages.microsoft.com/repos/ms-teams/ stable main
           Active apt repos in: /etc/apt/sources.list.d/zotero.list 
           1: deb [signed-by=/usr/share/keyrings/zotero-archive-keyring.gpg by-hash=force] https://zotero.retorque.re/file/apt-package-archive/ ./
Info:      Processes: 284 Uptime: 1d 3h 21m wakeups: 1 Memory: 15.38 GiB used: 6.89 GiB (44.8%) 
           Init: SysVinit v: 2.96 runlevel: 5 default: 5 tool: systemctl Compilers: gcc: 10.2.1 
           alt: 10 Client: shell wrapper v: 5.1.4-release inxi: 3.3.06 
Boot Mode: UEFI

Moderator: image changed to link, please read the forum rules

Posted: **Fri Jan 05, 2024 7:18 am**

I think you're probably going to need to upgrade to/install separately/run Live MX-23. If you do a websearch on "debian r-base-core" you can see the various versions available:

bullseye: 4.0.4-1
bookworm (MX-23): 4.2.2.20221110-2
trixie: 4.3.2-1
sid: 4.3.2-1

It's possible that once on a bookworm base MX could backport the trixie version (I'll take a look today).

Posted: **Fri Jan 05, 2024 7:30 am**

Thanks for the quick reply Jerry3904. I actually managed to install the particular package I was missing. How, I don't know, because R kept telling me the installation was unsuccessful, but after an R restart I loaded the package with some errors, but still usable.

Still I have troubles with other packages. Particularly those needed to run HTML compilations from R.

Is it possible to upgrade to MX23 without reinstalling? I am running MX on a very recent computer and installing it was a pain (I got lucky that someone in Acer Costumer support also happened to be a Linux enthusiast and guided me through the changes that I needed to do in the BIOS) so I would like to avoid reinstalling because this is my work computer and I can't afford to loose functionality for more than a couple of hours.

Otherwise I think I can wait until the trixie version is backported.

Thanks again for the support.

Posted: **Fri Jan 05, 2024 12:39 pm**

Currently. the MX 21 test repo has a somewhat newer 4.1.2.

Posted: **Fri Jan 05, 2024 12:45 pm**

I enable the test repo in synaptic but I never see more recent versions becoming available

We set up the test repo that way on purpose, so they won't be seen as automatic upgrades. They will still appear in Synaptic if you check the "versions". I would guess that you already have the test repo 4.1.2 installed, anyway.

Posted: **Fri Jan 05, 2024 2:25 pm**

4.3.2 does backport successfully on MX 23 and MX 21. Now trying MX 19 packages.

Posted: **Fri Jan 05, 2024 4:39 pm**

That's good news, @Stevo -- thanks.

Posted: **Fri Jan 05, 2024 5:40 pm**

Many thanks Stevo. I do indeed have the 4.1.2 version from the test repo installed. There's no rush since I won't be using the work computer until Monday. Still, I know I'll need a more recent version of R at some point so your work is much appreciated

Posted: **Fri Jan 05, 2024 9:24 pm**

Just sent up[ 4.3.2 packages for MX 19, 21, and 23 test repos. I bet it would even build on Debian 9 if we still supported it.

Posted: **Mon Jan 08, 2024 3:00 am**

Many thanks Stevo!

Posted: **Tue Jan 09, 2024 12:28 am**

Did you manage to install and get any use from 4.3.2 yet, and does it resolve those issues in your first post?

Thanks in advance...

Posted: **Tue Jan 09, 2024 3:03 am**

I'm having some trouble updating. I tried via the MX Package installed and I was able to install r-base-core 4.3.2, but not r-base. Although I clicked on 'install dependencies', it kept giving me errors that the package could not be installed because other packages depended on it.

I then tried synaptic, but if I enable the test repos I cannot reload. I have some custom repos (Zotero and Skype) that are giving me errors and preventing the packages from reloading.

Is there anything I'm doing wrong here?

EDIT: Something else I also noticed is that after selecting r-recommended from the MX package installed (in the repos tab) it says that 0 bytes of archives will be downloaded and 167 MB will be released. That doesn't seem right, right?

Posted: **Tue Jan 09, 2024 8:53 am**

Can you get it to work if those two third-party repos are disabled temporarily?

FWIW, I just installed r-base, r-base-core, and the recommends with MXPI without a hitch.

Code: Select all

2024-01-09  05:45:51  install  r-recommended                                                all    <none>                                4.3.2-1~mx23+1
2024-01-09  05:45:51  install  r-base-html                                                  all    <none>                                4.3.2-1~mx23+1
2024-01-09  05:45:51  install  r-base                                                       all    <none>                                4.3.2-1~mx23+1
2024-01-09  05:45:50  install  r-cran-survival                                              amd64  <none>                                3.5-3-1
2024-01-09  05:45:50  install  r-cran-spatial                                               amd64  <none>                                7.3-16-1
2024-01-09  05:45:50  install  r-cran-rpart                                                 amd64  <none>                                4.1.19-1
2024-01-09  05:45:50  install  r-cran-nnet                                                  amd64  <none>                                7.3-18-1
2024-01-09  05:45:50  install  r-cran-nlme                                                  amd64  <none>                                3.1.162-1
2024-01-09  05:45:50  install  r-cran-mgcv                                                  amd64  <none>                                1.8-41-1
2024-01-09  05:45:49  install  r-cran-matrix                                                amd64  <none>                                1.5-3-1
2024-01-09  05:45:49  install  r-cran-lattice                                               amd64  <none>                                0.20-45-3
2024-01-09  05:45:49  install  r-cran-kernsmooth                                            amd64  <none>                                2.23-20-1
2024-01-09  05:45:49  install  r-cran-foreign                                               amd64  <none>                                0.8.84-1
2024-01-09  05:45:49  install  r-cran-codetools                                             all    <none>                                0.2-19-1
2024-01-09  05:45:49  install  r-cran-cluster                                               amd64  <none>                                2.1.4-1
2024-01-09  05:45:48  install  r-cran-mass                                                  amd64  <none>                                7.3-58.2-1
2024-01-09  05:45:48  install  r-cran-class                                                 amd64  <none>                                7.3-21-1
2024-01-09  05:45:48  install  r-cran-boot                                                  all    <none>                                1.3-28.1-1
2024-01-09  05:45:47  install  r-base-core                                                  amd64  <none>                                4.3.2-1~mx23+1

Posted: **Tue Jan 09, 2024 9:05 am**

I disabled the zotero repo and was able to reload the packages in synaptic successfully.

However, trying to install r-base and r-recommended via MXPI didn't work:

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Hit:1 http://deb.debian.org/debian buster-updates InRelease
Hit:2 http://nl.mxrepo.com/mx/repo buster InRelease
Get:3 http://nl.mxrepo.com/mx/testrepo buster InRelease [6,806 B]
Hit:4 http://deb.debian.org/debian buster InRelease
Hit:5 http://deb.debian.org/debian-security buster/updates InRelease
Get:6 https://packages.microsoft.com/repos/ms-teams stable InRelease [5,931 B]
Hit:7 https://desktop-download.mendeley.com/download/apt stable InRelease
Get:8 http://nl.mxrepo.com/mx/testrepo buster/test amd64 Packages [1,239 kB]
Ign:9 http://linux.dropbox.com/debian buster InRelease
Hit:10 http://linux.dropbox.com/debian buster Release
Fetched 1,252 kB in 1s (926 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-recommended : Depends: r-cran-boot (>= 1.2.19) but it is not going to be installed
                 Depends: r-cran-class but it is not going to be installed
                 Depends: r-cran-cluster (>= 1.9.6-2) but it is not going to be installed
                 Depends: r-cran-codetools but it is not going to be installed
                 Depends: r-cran-foreign (>= 0.7-2) but it is not going to be installed
                 Depends: r-cran-kernsmooth (>= 2.2.14) but it is not going to be installed
                 Depends: r-cran-lattice (>= 0.10.11) but it is not going to be installed
                 Depends: r-cran-mass but it is not going to be installed
                 Depends: r-cran-matrix but it is not going to be installed
                 Depends: r-cran-mgcv (>= 1.1.5) but it is not going to be installed
                 Depends: r-cran-nlme (>= 3.1.52) but it is not going to be installed
                 Depends: r-cran-nnet but it is not going to be installed
                 Depends: r-cran-rpart (>= 3.1.20) but it is not going to be installed
                 Depends: r-cran-spatial but it is not going to be installed
                 Depends: r-cran-survival (>= 2.13.2-1) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Hit:1 http://nl.mxrepo.com/mx/repo buster InRelease
Hit:2 http://deb.debian.org/debian buster-updates InRelease
Hit:3 http://deb.debian.org/debian buster InRelease
Hit:4 http://deb.debian.org/debian-security buster/updates InRelease
Get:5 https://packages.microsoft.com/repos/ms-teams stable InRelease [5,931 B]
Hit:6 https://desktop-download.mendeley.com/download/apt stable InRelease
Ign:7 http://linux.dropbox.com/debian buster InRelease
Hit:8 http://linux.dropbox.com/debian buster Release
Fetched 5,931 B in 1s (5,920 B/s)

Reading package lists...

Posted: **Tue Jan 09, 2024 9:08 am**

I just tried, after enabling the test repositories via synaptic and successfully reloading packages, to install r-base, but after reloading the packages, I still see version 3.5.2-1 and not the latest version.

And if I only try to install r-base via MXPI I do see the latest version, but installation fails because it tell me it depends in r-recommended

Posted: **Tue Jan 09, 2024 10:26 pm**

Your QSI in the first few posts says MX 21.3, but the above show MX 19 (buster) repos.

Posted: **Wed Jan 10, 2024 2:34 am**

Oh xxxxxxx, yes. Sorry. I am constantly switching between computers and I since I use R in both of them I completely forgot that the original post was about my 21.3 computer. I seemed to remember you mentioned in one post that it could also work for 19, so I guess I considered the changes to apply to both. Sorry about that!

Yes: In MX 21.3 the installation went smoothly. Thanks!

Posted: **Thu Jan 11, 2024 2:37 am**

OK, so just the MX 19 version needs to lose the dependency on r-recommended, though I hope that doesn't make it almost useless.

Posted: **Thu Jan 11, 2024 3:01 am**

though I hope that doesn't make it almost useless.

I am afraid that would be the case. The packages in r-recommended are... strongly recommended. They are pretty much essential to work with R.

Still, I am able to use r in my MX 19 computer right now, so there's no rush to get the latest version working on the MX19 repos.

Many thanks for all the work!

MX Linux Forum

Request for a more recent version of R (r-base-core)

Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)

Re: Request for a more recent version of R (r-base-core)