Some packages fail to install
USMortality opened this issue · comments
Some packages, e.g. ggplot2 fail to install:
Minimal example:
FROM eddelbuettel/r2u:22.04
RUN sudo apt-get -y install r-cran-ggplot2output:
docker build . -t cronicle -f ./Dockerfile --platform linux/amd64 13:42:32
[+] Building 11.0s (5/5) FINISHED
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 1.10kB 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/eddelbuettel/r2u:22.04 0.2s
=> CACHED [1/2] FROM docker.io/eddelbuettel/r2u:22.04@sha256:1d3a92aab5abad11787cd6b6c9479960db9f4e56dcc7f837768da2e3f3c4dfe2 0.0s
=> ERROR [2/2] RUN sudo apt-get -y install r-cran-ggplot2 10.7s
------
> [2/2] RUN sudo apt-get -y install r-cran-ggplot2:
#5 0.638 Reading package lists...
#5 5.752 Building dependency tree...
#5 6.551 Reading state information...
#5 7.202 The following additional packages will be installed:
#5 7.202 r-cran-cli r-cran-colorspace r-cran-digest r-cran-fansi r-cran-farver
#5 7.202 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle
#5 7.202 r-cran-magrittr r-cran-munsell r-cran-pillar r-cran-pkgconfig r-cran-r6
#5 7.202 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8
#5 7.203 r-cran-vctrs r-cran-viridislite r-cran-withr
#5 7.206 Suggested packages:
#5 7.206 r-cran-callr r-cran-covr r-cran-htmltools r-cran-htmlwidgets r-cran-knitr
#5 7.206 r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
#5 7.206 r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-kernlab
#5 7.206 r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr
#5 7.206 r-cran-png r-cran-jpeg r-cran-rcartocolor r-cran-scico r-cran-viridis
#5 7.206 r-cran-wesanderson r-cran-tinytest r-cran-simplermarkdown r-cran-unitizer
#5 7.206 r-cran-ragg r-cran-ggplot2movies r-cran-hexbin r-cran-hmisc r-cran-interp
#5 7.206 r-cran-mapproj r-cran-maps r-cran-maptools r-cran-multcomp r-cran-profvis
#5 7.206 r-cran-quantreg r-cran-rgeos r-cran-sf r-cran-svglite r-cran-vdiffr
#5 7.206 r-cran-xml2 r-cran-crayon r-cran-dbi r-cran-forcats r-cran-microbenchmark
#5 7.206 r-cran-r.utils r-cran-rprintf r-cran-rsqlite r-cran-stringr r-cran-waldo
#5 7.206 r-cran-magick r-cran-lintr r-cran-tidyverse r-cran-bit64 r-cran-debugme
#5 7.206 r-cran-diagrammer r-cran-formattable r-cran-lubridate r-cran-nanotime
#5 7.206 r-cran-nycflights13 r-cran-palmerpenguins r-cran-stringi r-cran-units
#5 7.206 r-cran-disposables r-cran-pryr r-cran-fs r-cran-usethis r-cran-dichromat
#5 7.206 r-cran-hms r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate r-cran-mockr
#5 7.206 r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-generics
#5 7.206 r-cran-pkgdown r-cran-zeallot
#5 7.588 The following NEW packages will be installed:
#5 7.588 r-cran-cli r-cran-colorspace r-cran-digest r-cran-fansi r-cran-farver
#5 7.589 r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling
#5 7.589 r-cran-lifecycle r-cran-magrittr r-cran-munsell r-cran-pillar
#5 7.589 r-cran-pkgconfig r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales
#5 7.590 r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr
#5 7.971 0 upgraded, 24 newly installed, 0 to remove and 14 not upgraded.
#5 7.971 Need to get 18.5 MB of archives.
#5 7.971 After this operation, 29.1 MB of additional disk space will be used.
#5 7.971 Get:1 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-cli amd64 3.4.1-1.ca2204.1 [1,162 kB]
#5 8.249 Get:2 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-colorspace amd64 2.0-3-1.ca2204.1 [2,499 kB]
#5 8.757 Get:3 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-digest amd64 0.6.30-1.ca2204.1 [184 kB]
#5 8.789 Get:4 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-fansi amd64 1.0.3-1.ca2204.1 [295 kB]
#5 8.844 Get:5 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-farver amd64 2.1.1-1.ca2204.1 [1,420 kB]
#5 9.092 Get:6 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-glue amd64 1.6.2-1.ca2204.1 [143 kB]
#5 9.118 Get:7 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-gtable all 0.3.1-1.ca2204.1 [154 kB]
#5 9.145 Get:8 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-isoband amd64 0.2.6-1.ca2204.1 [1,821 kB]
#5 9.463 Get:9 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-rlang amd64 1.0.6-1.ca2204.1 [1,449 kB]
#5 9.715 Get:10 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-labeling all 0.4.2-1.ca2204.1 [61.0 kB]
#5 9.727 Get:11 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-lifecycle all 1.0.3-1.ca2204.1 [112 kB]
#5 9.750 Get:12 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-munsell all 0.5.0-1.ca2204.1 [231 kB]
#5 9.790 Get:13 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-r6 all 2.5.1-1.ca2204.1 [83.2 kB]
#5 9.809 Get:14 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-rcolorbrewer all 1.1-3-1.ca2204.1 [54.0 kB]
#5 9.820 Get:15 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-viridislite all 0.4.1-1.ca2204.1 [1,296 kB]
#5 10.04 Get:16 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-scales all 1.2.1-1.ca2204.1 [587 kB]
#5 10.15 Get:17 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-magrittr amd64 2.0.3-1.ca2204.1 [199 kB]
#5 10.18 Get:18 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-utf8 amd64 1.2.2-1.ca2204.1 [135 kB]
#5 10.21 Get:19 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-vctrs amd64 0.5.0-1.ca2204.1 [1,191 kB]
#5 10.41 Get:20 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pillar all 1.8.1-1.ca2204.1 [619 kB]
#5 10.51 Get:21 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pkgconfig all 2.0.3-1.ca2204.1 [18.9 kB]
#5 10.51 Get:22 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-tibble amd64 3.1.8-1.ca2204.1 [640 kB]
#5 10.61 Get:23 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-withr all 2.5.0-1.ca2204.1 [222 kB]
#5 10.65 Err:24 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-ggplot2 all 3.3.6-1.ca2204.1
#5 10.65 404 Not Found [IP: 192.17.190.167 443]
#5 10.67 Fetched 14.6 MB in 3s (4,796 kB/s)
#5 10.67 E: Failed to fetch https://r2u.stat.illinois.edu/ubuntu/pool/dists/jammy/main/r-cran-ggplot2_3.3.6-1.ca2204.1_all.deb 404 Not Found [IP: 192.17.190.167 443]
#5 10.67 E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
------
executor failed running [/bin/sh -c sudo apt-get -y install r-cran-ggplot2]: exit code: 100
Please try again with a step of apt update in between. This is used numerous times each day in automated fashion (i.e. GitHub Actions) as well as manually. If you use the available bspm interface it is even easier:
edd@rob:~$ docker run --rm -ti eddelbuettel/r2u:22.04 bash
root@a44b714feef1:/# install.r ggplot2
Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease
Get:1 https://r2u.stat.illinois.edu/ubuntu jammy Release [5713 B]
Get:2 https://r2u.stat.illinois.edu/ubuntu jammy Release.gpg [793 B]
Hit http://archive.ubuntu.com/ubuntu jammy InRelease
Get:3 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Get:4 https://r2u.stat.illinois.edu/ubuntu jammy/main all Packages [6760 kB]
Get:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [114 kB]
Get:6 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 Packages [2179 kB]
Get:7 https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu jammy InRelease [18.1 kB]
Get:8 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [584 kB]
Get:9 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [99.8 kB]
Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [946 kB]
Get:11 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [764 kB]
Get:12 https://ppa.launchpadcontent.net/edd/misc/ubuntu jammy InRelease [18.1 kB]
Get:13 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [486 kB]
Get:14 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [568 kB]
Get:15 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [8097 B]
Get:16 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [903 kB]
Get:17 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [7277 B]
Get:18 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy InRelease [17.5 kB]
Get:19 https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu jammy/main amd64 Packages [974 kB]
Get:20 https://ppa.launchpadcontent.net/edd/misc/ubuntu jammy/main amd64 Packages [5250 B]
Get:21 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main amd64 Packages [7604 B]
Fetched 14.6 MB in 0s (0 B/s)
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 3.4.1-1.ca2204.1 [1162 kB]
Get:2 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-colorspace amd64 2.0-3-1.ca2204.1 [2499 kB]
Get:3 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-fansi amd64 1.0.3-1.ca2204.1 [295 kB]
Get:4 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-farver amd64 2.1.1-1.ca2204.1 [1420 kB]
Get:5 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-glue amd64 1.6.2-1.ca2204.1 [143 kB]
Get:6 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-gtable all 0.3.1-1.ca2204.1 [154 kB]
Get:7 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-isoband amd64 0.2.6-1.ca2204.1 [1821 kB]
Get:8 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-rlang amd64 1.0.6-1.ca2204.1 [1449 kB]
Get:9 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-lifecycle all 1.0.3-1.ca2204.1 [112 kB]
Get:10 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-labeling all 0.4.2-1.ca2204.1 [61.0 kB]
Get:11 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-munsell all 0.5.0-1.ca2204.1 [231 kB]
Get:12 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-r6 all 2.5.1-1.ca2204.1 [83.2 kB]
Get:13 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-rcolorbrewer all 1.1-3-1.ca2204.1 [54.0 kB]
Get:14 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-viridislite all 0.4.1-1.ca2204.1 [1296 kB]
Get:15 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-scales all 1.2.1-1.ca2204.1 [587 kB]
Get:16 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-magrittr amd64 2.0.3-1.ca2204.1 [199 kB]
Get:17 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-utf8 amd64 1.2.2-1.ca2204.1 [135 kB]
Get:18 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-vctrs amd64 0.5.0-1.ca2204.1 [1191 kB]
Get:19 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pillar all 1.8.1-1.ca2204.1 [619 kB]
Get:20 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pkgconfig all 2.0.3-1.ca2204.1 [18.9 kB]
Get:21 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-tibble amd64 3.1.8-1.ca2204.1 [640 kB]
Get:22 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-withr all 2.5.0-1.ca2204.1 [222 kB]
Get:23 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-ggplot2 all 3.4.0-1.ca2204.1 [4051 kB]
Fetched 18.4 MB in 0s (0 B/s)
Selecting previously unselected package r-cran-cli.
(Reading database ... 21782 files and directories currently installed.)
Preparing to unpack .../00-r-cran-cli_3.4.1-1.ca2204.1_amd64.deb ...
Unpacking r-cran-cli (3.4.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-colorspace.
Preparing to unpack .../01-r-cran-colorspace_2.0-3-1.ca2204.1_amd64.deb ...
Unpacking r-cran-colorspace (2.0-3-1.ca2204.1) ...
Selecting previously unselected package r-cran-fansi.
Preparing to unpack .../02-r-cran-fansi_1.0.3-1.ca2204.1_amd64.deb ...
Unpacking r-cran-fansi (1.0.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-farver.
Preparing to unpack .../03-r-cran-farver_2.1.1-1.ca2204.1_amd64.deb ...
Unpacking r-cran-farver (2.1.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-glue.
Preparing to unpack .../04-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-gtable.
Preparing to unpack .../05-r-cran-gtable_0.3.1-1.ca2204.1_all.deb ...
Unpacking r-cran-gtable (0.3.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-isoband.
Preparing to unpack .../06-r-cran-isoband_0.2.6-1.ca2204.1_amd64.deb ...
Unpacking r-cran-isoband (0.2.6-1.ca2204.1) ...
Selecting previously unselected package r-cran-rlang.
Preparing to unpack .../07-r-cran-rlang_1.0.6-1.ca2204.1_amd64.deb ...
Unpacking r-cran-rlang (1.0.6-1.ca2204.1) ...
Selecting previously unselected package r-cran-lifecycle.
Preparing to unpack .../08-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-labeling.
Preparing to unpack .../09-r-cran-labeling_0.4.2-1.ca2204.1_all.deb ...
Unpacking r-cran-labeling (0.4.2-1.ca2204.1) ...
Selecting previously unselected package r-cran-munsell.
Preparing to unpack .../10-r-cran-munsell_0.5.0-1.ca2204.1_all.deb ...
Unpacking r-cran-munsell (0.5.0-1.ca2204.1) ...
Selecting previously unselected package r-cran-r6.
Preparing to unpack .../11-r-cran-r6_2.5.1-1.ca2204.1_all.deb ...
Unpacking r-cran-r6 (2.5.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-rcolorbrewer.
Preparing to unpack .../12-r-cran-rcolorbrewer_1.1-3-1.ca2204.1_all.deb ...
Unpacking r-cran-rcolorbrewer (1.1-3-1.ca2204.1) ...
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Preparing to unpack .../13-r-cran-viridislite_0.4.1-1.ca2204.1_all.deb ...
Unpacking r-cran-viridislite (0.4.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-scales.
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Unpacking r-cran-scales (1.2.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-magrittr.
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Unpacking r-cran-magrittr (2.0.3-1.ca2204.1) ...
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Unpacking r-cran-utf8 (1.2.2-1.ca2204.1) ...
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Unpacking r-cran-vctrs (0.5.0-1.ca2204.1) ...
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Unpacking r-cran-pillar (1.8.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-pkgconfig.
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Unpacking r-cran-pkgconfig (2.0.3-1.ca2204.1) ...
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Preparing to unpack .../20-r-cran-tibble_3.1.8-1.ca2204.1_amd64.deb ...
Unpacking r-cran-tibble (3.1.8-1.ca2204.1) ...
Selecting previously unselected package r-cran-withr.
Preparing to unpack .../21-r-cran-withr_2.5.0-1.ca2204.1_all.deb ...
Unpacking r-cran-withr (2.5.0-1.ca2204.1) ...
Selecting previously unselected package r-cran-ggplot2.
Preparing to unpack .../22-r-cran-ggplot2_3.4.0-1.ca2204.1_all.deb ...
Unpacking r-cran-ggplot2 (3.4.0-1.ca2204.1) ...
Setting up r-cran-rlang (1.0.6-1.ca2204.1) ...
Setting up r-cran-withr (2.5.0-1.ca2204.1) ...
Setting up r-cran-fansi (1.0.3-1.ca2204.1) ...
Setting up r-cran-glue (1.6.2-1.ca2204.1) ...
Setting up r-cran-cli (3.4.1-1.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 (1.2.2-1.ca2204.1) ...
Setting up r-cran-colorspace (2.0-3-1.ca2204.1) ...
Setting up r-cran-rcolorbrewer (1.1-3-1.ca2204.1) ...
Setting up r-cran-isoband (0.2.6-1.ca2204.1) ...
Setting up r-cran-gtable (0.3.1-1.ca2204.1) ...
Setting up r-cran-labeling (0.4.2-1.ca2204.1) ...
Setting up r-cran-farver (2.1.1-1.ca2204.1) ...
Setting up r-cran-viridislite (0.4.1-1.ca2204.1) ...
Setting up r-cran-r6 (2.5.1-1.ca2204.1) ...
Setting up r-cran-magrittr (2.0.3-1.ca2204.1) ...
Setting up r-cran-vctrs (0.5.0-1.ca2204.1) ...
Setting up r-cran-pillar (1.8.1-1.ca2204.1) ...
Setting up r-cran-munsell (0.5.0-1.ca2204.1) ...
Setting up r-cran-tibble (3.1.8-1.ca2204.1) ...
Setting up r-cran-scales (1.2.1-1.ca2204.1) ...
Setting up r-cran-ggplot2 (3.4.0-1.ca2204.1) ...
root@a44b714feef1:/# You can do the same with apt and installing r-cran-ggplot2 but you really need to make sure your apt indices are current and bspm does that for you. If you want to be old school do
$ docker run --rm -ti eddelbuettel/r2u:22.04 bash
# apt update
# apt install r-cran-ggplot2which will work the same way.
Thank you. That worked!
It's standard Debian / apt behavior -- it's makes the actual download and install (of possibly several packages) faster but it does require the preceding update step.
Yeah, I got it all working now. Thanks for making this package. Love blazing fast installs!
Yes, indeed.
And failsafe as it should never give you surprises of missing (system) libraries, plus via the apt integration will never uninstall / update system libraries we have dependencies on from R. It really works well -- so I am trying to spread the word.