broken dependencies?
bbolker opened this issue · comments
With the usual apologies if this is the wrong venue for this question ...
I just installed the latest r-base-core via apt-get upgrade (on Pop!_OS 22.04 LTS, which is an Ubuntu derivative):
apt list r-base-core
r-base-core/jammy-cran40,now 4.3.1-3.2204.0 amd64 [residual-config]
Many packages were removed. When I try to reinstall them I get (for example):
$ sudo apt-get install r-cran-tibble
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
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 resolve the situation:
The following packages have unmet dependencies:
r-base-core : Breaks: r-cran-tibble (< 3.2.1+dfsg-2~) but 3.2.1-1.ca2204.1 is to be installed
E: Unable to correct problems, you have held broken packages.
When I install via bspm I get:
> install.packages("tibble")
Error: dbus: Call failed: Could not activate remote peer: unit failed.
When I disable bspm I am able to install tibble as usual, at the price of the usual giant compilation of lots of packages ...
Happy to provide any additional information/diagnostics that would be useful ...
Yes, a colleague alerted me to this earlier. It is (a long and sad story) but mostly due to Debian upstream having imposed the Breaks: in r-base-core (that is essentially a 100% 'inside Debian baseball' story where my hand was forced; I don't really want to get into it).
The corollarry is that the Ubuntu backport binaries we all use at CRAN have the same Breaks:
Breaks: r-cran-cairo (<< 1.6-0-4~), r-cran-fnn (<< 1.1.3.2-1~), r-cran-intervals (<< 0.15.3-1~), r-cran-magick (<< 2.7.4+dfsg-2~), r-cran-maldiquant (<< 1.22.1-1~), r-cran-ps (<< 1.7.5-1~), r-cran-ragg (<< 1.2.5-3~), r-cran-svglite (<< 2.1.1-3~), r-cran-tibble (<< 3.2.1+dfsg-2~), r-cran-tikzdevice (<< 0.12.4-3~), r-cran-vdiffr (<< 1.0.5-3~)
And that breaks tibble.
Now, the good news is you are two hours behind my colleague ... and I just fixed it (by rebuilding the affected packages with a higher version number so now they should install).
My first test worked. Details below. So I think we can close this. But big thanks for the (first public) report.
edd@rob:~$ dkrrr rocker/r2u:jammy # dkrrr is local alias of mine
root@5953df94b8cb:/# install.r tibble
Get:1 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease
Get:2 https://r2u.stat.illinois.edu/ubuntu jammy Release [5713 B]
Get:3 https://r2u.stat.illinois.edu/ubuntu jammy Release.gpg [793 B]
Get:4 http://archive.ubuntu.com/ubuntu jammy InRelease [270 kB]
Get:5 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [723 kB]
Get:6 https://r2u.stat.illinois.edu/ubuntu jammy/main all Packages [7322 kB]
Get:7 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [725 kB]
Get:8 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [952 kB]
Get:9 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 Packages [2321 kB]
Get:10 http://security.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [44.0 kB]
Get:11 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease [3626 B]
Get:12 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ Packages [40.9 kB]
Get:13 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [119 kB]
Get:14 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [108 kB]
Get:15 http://archive.ubuntu.com/ubuntu jammy/restricted amd64 Packages [164 kB]
Get:16 http://archive.ubuntu.com/ubuntu jammy/universe amd64 Packages [17.5 MB]
Get:17 http://archive.ubuntu.com/ubuntu jammy/main amd64 Packages [1792 kB]
Get:18 http://archive.ubuntu.com/ubuntu jammy/multiverse amd64 Packages [266 kB]
Get:19 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [749 kB]
Get:20 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1208 kB]
Get:21 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [49.8 kB]
Get:22 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [1017 kB]
Get:23 http://archive.ubuntu.com/ubuntu jammy-backports/main amd64 Packages [49.4 kB]
Get:24 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [25.6 kB]
Fetched 35.5 MB in 0s (0 B/s)
Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Get:1 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-cli amd64 3.6.1-1.ca2204.1 [1223 kB]
Get:2 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-fansi amd64 1.0.4-1.ca2204.1 [296 kB]
Get:3 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-glue amd64 1.6.2-1.ca2204.1 [143 kB]
Get:4 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-rlang amd64 1.1.1-1.ca2204.1 [1488 kB]
Get:5 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-lifecycle all 1.0.3-1.ca2204.1 [112 kB]
Get:6 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-magrittr amd64 2.0.3-1.ca2204.1 [199 kB]
Get:7 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-utf8 amd64 1.2.3-1.ca2204.1 [134 kB]
Get:8 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-vctrs amd64 0.6.3-1.ca2204.1 [1213 kB]
Get:9 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pillar all 1.9.0-1.ca2204.1 [596 kB]
Get:10 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pkgconfig all 2.0.3-1.ca2204.1 [18.9 kB]
Get:11 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3.ca2204.1 [603 kB]
Fetched 6027 kB in 0s (0 B/s)
Selecting previously unselected package r-cran-cli.
(Reading database ... 18447 files and directories currently installed.)
Preparing to unpack .../00-r-cran-cli_3.6.1-1.ca2204.1_amd64.deb ...
Unpacking r-cran-cli (3.6.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-fansi.
Preparing to unpack .../01-r-cran-fansi_1.0.4-1.ca2204.1_amd64.deb ...
Unpacking r-cran-fansi (1.0.4-1.ca2204.1) ...
Selecting previously unselected package r-cran-glue.
Preparing to unpack .../02-r-cran-glue_1.6.2-1.ca2204.1_amd64.deb ...
Unpacking r-cran-glue (1.6.2-1.ca2204.1) ...
Selecting previously unselected package r-cran-rlang.
Preparing to unpack .../03-r-cran-rlang_1.1.1-1.ca2204.1_amd64.deb ...
Unpacking r-cran-rlang (1.1.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-lifecycle.
Preparing to unpack .../04-r-cran-lifecycle_1.0.3-1.ca2204.1_all.deb ...
Unpacking r-cran-lifecycle (1.0.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-magrittr.
Preparing to unpack .../05-r-cran-magrittr_2.0.3-1.ca2204.1_amd64.deb ...
Unpacking r-cran-magrittr (2.0.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-utf8.
Preparing to unpack .../06-r-cran-utf8_1.2.3-1.ca2204.1_amd64.deb ...
Unpacking r-cran-utf8 (1.2.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-vctrs.
Preparing to unpack .../07-r-cran-vctrs_0.6.3-1.ca2204.1_amd64.deb ...
Unpacking r-cran-vctrs (0.6.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-pillar.
Preparing to unpack .../08-r-cran-pillar_1.9.0-1.ca2204.1_all.deb ...
Unpacking r-cran-pillar (1.9.0-1.ca2204.1) ...
Selecting previously unselected package r-cran-pkgconfig.
Preparing to unpack .../09-r-cran-pkgconfig_2.0.3-1.ca2204.1_all.deb ...
Unpacking r-cran-pkgconfig (2.0.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-tibble.
Preparing to unpack .../10-r-cran-tibble_3.2.1+dfsg-3.ca2204.1_amd64.deb ...
Unpacking r-cran-tibble (3.2.1+dfsg-3.ca2204.1) ...
Setting up r-cran-rlang (1.1.1-1.ca2204.1) ...
Setting up r-cran-fansi (1.0.4-1.ca2204.1) ...
Setting up r-cran-glue (1.6.2-1.ca2204.1) ...
Setting up r-cran-cli (3.6.1-1.ca2204.1) ...
Setting up r-cran-lifecycle (1.0.3-1.ca2204.1) ...
Setting up r-cran-pkgconfig (2.0.3-1.ca2204.1) ...
Setting up r-cran-utf8 (1.2.3-1.ca2204.1) ...
Setting up r-cran-magrittr (2.0.3-1.ca2204.1) ...
Setting up r-cran-vctrs (0.6.3-1.ca2204.1) ...
Setting up r-cran-pillar (1.9.0-1.ca2204.1) ...
Setting up r-cran-tibble (3.2.1+dfsg-3.ca2204.1) ...
root@5953df94b8cb:/#
I love open-source software/infrastructure when someone else does the work.
sudo apt-get update
cat removed_packages.txt | xargs sudo apt-get install -y
got me back to functioning. Thank you!
(I'll let you close this if you want, or keep it open for higher visibility if anyone else is looking for it ...)
Close is ok because the state of the world, at least for this tiny corner, is back to some semblance of normalcy.
People who search will find it under closed. All good!
Glad you're getting use out of r2u on your pop!_os box.
To recap, it really is an issue from 'upstream' Debian which the courtesy Ubuntu backport (that many of use via CRAN) carries over -- and which creates a bit of an issue with the r2u repo.
Now taken care of.