failed to install pkgdown
eitsupi opened this issue · comments
In the task of setting up r2u on a container, pkgdown download failed twice consecutively.
Any thoughts?
#18 25.50 E: Failed to fetch https://r2u.stat.illinois.edu/ubuntu/pool/dists/focal/main/r-cran-pkgdown_2.0.7-1.ca2004.1_all.deb Undetermined Error [IP: 192.17.190.167 443]
Strange. Can you rule out networking? "Works fine here" and illinois.edu is rather well connected in general.
With apologies for the meta chars inject by Emacs shell mode:
edd@rob:~$ docker run --rm -ti rocker/r2u:jammy
�]0;root@57261ac55d74: /�root@57261ac55d74:/# install.r pkgdown
install.r pkgdown
Get:1 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Get:2 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease [3626 B]
Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease
Get:3 https://r2u.stat.illinois.edu/ubuntu jammy Release [5713 B]
Get:4 https://r2u.stat.illinois.edu/ubuntu jammy Release.gpg [793 B]
Get:5 http://archive.ubuntu.com/ubuntu jammy InRelease [270 kB]
Get:6 https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ Packages [33.5 kB]
Get:7 https://r2u.stat.illinois.edu/ubuntu jammy/main all Packages [7265 kB]
Get:8 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [541 kB]
Get:9 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 Packages [2305 kB]
Get:10 http://security.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [36.3 kB]
Get:11 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [634 kB]
Get:12 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [939 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/universe amd64 Packages [17.5 MB]
Get:16 http://archive.ubuntu.com/ubuntu jammy/main amd64 Packages [1792 kB]
Get:17 http://archive.ubuntu.com/ubuntu jammy/multiverse amd64 Packages [266 kB]
Get:18 http://archive.ubuntu.com/ubuntu jammy/restricted amd64 Packages [164 kB]
Get:19 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [545 kB]
Get:20 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [922 kB]
Get:21 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [1191 kB]
Get:22 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [42.2 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 [25.5 kB]
Fetched 34.8 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-sys amd64 3.4.2-1.ca2204.1 [40.1 kB]
Get:2 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-askpass amd64 1.1-1.ca2204.1 [21.7 kB]
Get:3 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-base64enc amd64 0.1-3-1.ca2204.1 [26.9 kB]
Get:4 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-brio amd64 1.1.3-1.ca2204.1 [31.6 kB]
Get:5 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-rlang amd64 1.1.1-1.ca2204.1 [1488 kB]
Get:6 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-fastmap amd64 1.1.1-1.ca2204.1 [61.7 kB]
Get:7 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-cachem amd64 1.0.8-1.ca2204.1 [66.9 kB]
Get:8 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-digest amd64 0.6.31-1.ca2204.1 [184 kB]
Get:9 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libxml2 amd64 2.9.13+dfsg-1ubuntu0.3 [763 kB]
Get:10 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-ellipsis amd64 0.3.2-1.ca2204.1 [34.5 kB]
Get:11 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-htmltools amd64 0.5.5-1.ca2204.1 [340 kB]
Get:12 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-jquerylib all 0.1.4-1.ca2204.1 [298 kB]
Get:13 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-jsonlite amd64 1.8.5-1.ca2204.1 [629 kB]
Get:14 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-memoise all 2.0.1-1.ca2204.1 [47.6 kB]
Get:15 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-mime amd64 0.12-1.ca2204.1 [33.7 kB]
Get:16 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-fs amd64 1.6.2-1.ca2204.1 [272 kB]
Get:17 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-r6 all 2.5.1-1.ca2204.1 [83.2 kB]
Get:18 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-rappdirs amd64 0.3.3-1.ca2204.1 [44.9 kB]
Get:19 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-sass amd64 0.4.6-1.ca2204.1 [2237 kB]
Get:20 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-bslib all 0.5.0-1.ca2204.1 [4226 kB]
Get:21 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-ps amd64 1.7.5-1.ca2204.1 [300 kB]
Get:22 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-processx amd64 3.8.1-1.ca2204.1 [320 kB]
Get:23 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-callr all 3.7.3-1.ca2204.1 [404 kB]
Get:24 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-cli amd64 3.6.1-1.ca2204.1 [1223 kB]
Get:25 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-cpp11 all 0.4.3-1.ca2204.1 [225 kB]
Get:26 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-curl amd64 5.0.1-1.ca2204.1 [434 kB]
Get:27 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-rprojroot all 2.0.3-1.ca2204.1 [97.3 kB]
Get:28 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-desc all 1.4.2-1.ca2204.1 [318 kB]
Get:29 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-evaluate all 0.21-1.ca2204.1 [81.0 kB]
Get:30 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-fansi amd64 1.0.4-1.ca2204.1 [296 kB]
Get:31 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-glue amd64 1.6.2-1.ca2204.1 [143 kB]
Get:32 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-lifecycle all 1.0.3-1.ca2204.1 [112 kB]
Get:33 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-vctrs amd64 0.6.3-1.ca2204.1 [1213 kB]
Get:34 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-withr all 2.5.0-1.ca2204.1 [222 kB]
Get:35 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-yaml amd64 2.3.7-1.ca2204.1 [106 kB]
Get:36 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-downlit all 0.4.2-1.ca2204.1 [111 kB]
Get:37 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-fontawesome all 0.5.1-1.ca2204.1 [1304 kB]
Get:38 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-xfun amd64 0.39-1.ca2204.1 [402 kB]
Get:39 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-highr all 0.10-1.ca2204.1 [39.3 kB]
Get:40 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-openssl amd64 2.0.6-1.ca2204.1 [640 kB]
Get:41 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-httr all 1.4.6-1.ca2204.1 [471 kB]
Get:42 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-knitr all 1.43-1.ca2204.1 [1264 kB]
Get:43 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-magrittr amd64 2.0.3-1.ca2204.1 [199 kB]
Get:44 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-utf8 amd64 1.2.3-1.ca2204.1 [134 kB]
Get:45 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pillar all 1.9.0-1.ca2204.1 [596 kB]
Get:46 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pkgconfig all 2.0.3-1.ca2204.1 [18.9 kB]
Get:47 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-purrr amd64 1.0.1-1.ca2204.1 [472 kB]
Get:48 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-systemfonts amd64 1.0.4-1.ca2204.1 [237 kB]
Get:49 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-textshaping amd64 0.3.6-1.ca2204.1 [98.2 kB]
Get:50 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-ragg amd64 1.2.5-1.ca2204.2 [407 kB]
Get:51 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-stringi amd64 1.7.12-1.ca2204.1 [872 kB]
Get:52 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-stringr all 1.5.0-1.ca2204.1 [281 kB]
Get:53 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-tinytex all 0.45-1.ca2204.1 [133 kB]
Get:54 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-rmarkdown all 2.22-1.ca2204.1 [2004 kB]
Get:55 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-tibble amd64 3.2.1-1.ca2204.1 [603 kB]
Get:56 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-whisker all 0.4.1-1.ca2204.1 [62.4 kB]
Get:57 https://r2u.stat.illinois.edu/ubuntu jammy/main amd64 r-cran-xml2 amd64 1.3.4-1.ca2204.1 [218 kB]
Get:58 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-pkgdown all 2.0.7-1.ca2204.1 [706 kB]
Fetched 27.7 MB in 0s (0 B/s)
Selecting previously unselected package libxml2:amd64.
(Reading database ... 18437 files and directories currently installed.)
Preparing to unpack .../00-libxml2_2.9.13+dfsg-1ubuntu0.3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.13+dfsg-1ubuntu0.3) ...
Selecting previously unselected package r-cran-sys.
Preparing to unpack .../01-r-cran-sys_3.4.2-1.ca2204.1_amd64.deb ...
Unpacking r-cran-sys (3.4.2-1.ca2204.1) ...
Selecting previously unselected package r-cran-askpass.
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Unpacking r-cran-askpass (1.1-1.ca2204.1) ...
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Unpacking r-cran-rlang (1.1.1-1.ca2204.1) ...
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Unpacking r-cran-fastmap (1.1.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-cachem.
Preparing to unpack .../07-r-cran-cachem_1.0.8-1.ca2204.1_amd64.deb ...
Unpacking r-cran-cachem (1.0.8-1.ca2204.1) ...
Selecting previously unselected package r-cran-digest.
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Unpacking r-cran-digest (0.6.31-1.ca2204.1) ...
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Unpacking r-cran-ellipsis (0.3.2-1.ca2204.1) ...
Selecting previously unselected package r-cran-htmltools.
Preparing to unpack .../10-r-cran-htmltools_0.5.5-1.ca2204.1_amd64.deb ...
Unpacking r-cran-htmltools (0.5.5-1.ca2204.1) ...
Selecting previously unselected package r-cran-jquerylib.
Preparing to unpack .../11-r-cran-jquerylib_0.1.4-1.ca2204.1_all.deb ...
Unpacking r-cran-jquerylib (0.1.4-1.ca2204.1) ...
Selecting previously unselected package r-cran-jsonlite.
Preparing to unpack .../12-r-cran-jsonlite_1.8.5-1.ca2204.1_amd64.deb ...
Unpacking r-cran-jsonlite (1.8.5-1.ca2204.1) ...
Selecting previously unselected package r-cran-memoise.
Preparing to unpack .../13-r-cran-memoise_2.0.1-1.ca2204.1_all.deb ...
Unpacking r-cran-memoise (2.0.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-mime.
Preparing to unpack .../14-r-cran-mime_0.12-1.ca2204.1_amd64.deb ...
Unpacking r-cran-mime (0.12-1.ca2204.1) ...
Selecting previously unselected package r-cran-fs.
Preparing to unpack .../15-r-cran-fs_1.6.2-1.ca2204.1_amd64.deb ...
Unpacking r-cran-fs (1.6.2-1.ca2204.1) ...
Selecting previously unselected package r-cran-r6.
Preparing to unpack .../16-r-cran-r6_2.5.1-1.ca2204.1_all.deb ...
Unpacking r-cran-r6 (2.5.1-1.ca2204.1) ...
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Preparing to unpack .../17-r-cran-rappdirs_0.3.3-1.ca2204.1_amd64.deb ...
Unpacking r-cran-rappdirs (0.3.3-1.ca2204.1) ...
Selecting previously unselected package r-cran-sass.
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Unpacking r-cran-sass (0.4.6-1.ca2204.1) ...
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Selecting previously unselected package r-cran-ps.
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Unpacking r-cran-ps (1.7.5-1.ca2204.1) ...
Selecting previously unselected package r-cran-processx.
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Unpacking r-cran-processx (3.8.1-1.ca2204.1) ...
Selecting previously unselected package r-cran-callr.
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Selecting previously unselected package r-cran-httr.
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Selecting previously unselected package r-cran-knitr.
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Unpacking r-cran-pillar (1.9.0-1.ca2204.1) ...
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Unpacking r-cran-pkgconfig (2.0.3-1.ca2204.1) ...
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Unpacking r-cran-purrr (1.0.1-1.ca2204.1) ...
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Setting up r-cran-fansi (1.0.4-1.ca2204.1) ...
Setting up r-cran-glue (1.6.2-1.ca2204.1) ...
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Setting up r-cran-jsonlite (1.8.5-1.ca2204.1) ...
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Setting up r-cran-utf8 (1.2.3-1.ca2204.1) ...
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Setting up r-cran-cpp11 (0.4.3-1.ca2204.1) ...
Setting up r-cran-ps (1.7.5-1.ca2204.1) ...
Setting up r-cran-tinytex (0.45-1.ca2204.1) ...
Setting up r-cran-knitr (1.43-1.ca2204.1) ...
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Setting up r-cran-cachem (1.0.8-1.ca2204.1) ...
Setting up r-cran-r6 (2.5.1-1.ca2204.1) ...
Setting up r-cran-magrittr (2.0.3-1.ca2204.1) ...
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Setting up r-cran-pkgdown (2.0.7-1.ca2204.1) ...
Processing triggers for libc-bin (2.35-0ubuntu3.1) ...
�]0;root@57261ac55d74: /�root@57261ac55d74:/# R
R
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(pkgdown)
library(pkgdown)
> Thank you for your quick response!
Comparing with your log I realized that the error I saw was on focal, but on my side I was able to install pkgdown successfully. I will retry again as it seems to be a strange network error.
❯ docker run --rm -it rocker/r2u:focal bash
Unable to find image 'rocker/r2u:focal' locally
focal: Pulling from rocker/r2u
eaead16dc43b: Already exists
a0cc6007e3cb: Already exists
1db444ab1a65: Already exists
Digest: sha256:a85b915c674e71681d2eba31bd6114ac8cf490b182a0e67f276a98717eaec5b6
Status: Downloaded newer image for rocker/r2u:focal
root@fd3d1d31839f:/# install.r pkgdown
Get:1 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease [3622 B]
Ign https://r2u.stat.illinois.edu/ubuntu focal InRelease
Get:2 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
Get:3 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ Packages [78.0 kB]
Get:4 https://r2u.stat.illinois.edu/ubuntu focal Release [5713 B]
Get:5 https://r2u.stat.illinois.edu/ubuntu focal Release.gpg [793 B]
Get:6 https://r2u.stat.illinois.edu/ubuntu focal/main all Packages [7296 kB]
Get:7 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]
Get:9 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]
Get:10 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
Get:11 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [2416 kB]
Get:12 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB]
Get:13 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]
Get:14 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [1064 kB]
Get:15 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1275 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [31.2 kB]
Get:17 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2820 kB]
Get:18 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1360 kB]
Get:19 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [3299 kB]
Get:20 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [28.5 kB]
Get:21 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [2554 kB]
Get:22 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]
Get:23 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [28.6 kB]
Get:24 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 Packages [2317 kB]
Fetched 36.8 MB in 6s (142 kB/s)
Install system packages as root...
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading package lists... Done
Building dependency tree
Reading state information... Done
Get:1 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libxml2 amd64 2.9.10+dfsg-5ubuntu0.20.04.6 [640 kB]
Get:2 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-sys amd64 3.4.2-1.ca2004.1 [39.0 kB]
Get:3 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-askpass amd64 1.1-1.ca2004.1 [21.3 kB]
Get:4 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-base64enc amd64 0.1-3-1.ca2004.1 [26.4 kB]
Get:5 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-brio amd64 1.1.3-1.ca2004.1 [30.9 kB]
Get:6 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-rlang amd64 1.1.1-1.ca2004.1 [1487 kB]
Get:7 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-fastmap amd64 1.1.1-1.ca2004.1 [60.3 kB]
Get:8 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-cachem amd64 1.0.8-1.ca2004.1 [66.8 kB]
Get:9 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-digest amd64 0.6.31-1.ca2004.1 [177 kB]
Get:10 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-ellipsis amd64 0.3.2-1.ca2004.1 [34.2 kB]
Get:11 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-htmltools amd64 0.5.5-1.ca2004.1 [341 kB]
Get:12 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-jquerylib all 0.1.4-1.ca2004.1 [283 kB]
Get:13 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-jsonlite amd64 1.8.5-1.ca2004.1 [615 kB]
Get:14 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-memoise all 2.0.1-1.ca2004.1 [47.4 kB]
Get:15 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-mime amd64 0.12-1.ca2004.1 [33.6 kB]
Get:16 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-fs amd64 1.6.2-1.ca2004.1 [261 kB]
Get:17 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-r6 all 2.5.1-1.ca2004.1 [82.7 kB]
Get:18 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-rappdirs amd64 0.3.3-1.ca2004.1 [44.9 kB]
Get:19 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-sass amd64 0.4.6-1.ca2004.1 [2147 kB]
Get:20 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-bslib all 0.5.0-1.ca2004.1 [4225 kB]
Get:21 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-ps amd64 1.7.5-1.ca2004.1 [294 kB]
Get:22 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-processx amd64 3.8.1-1.ca2004.1 [320 kB]
Get:23 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-callr all 3.7.3-1.ca2004.1 [403 kB]
Get:24 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-cli amd64 3.6.1-1.ca2004.1 [1219 kB]
Get:25 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-cpp11 all 0.4.3-1.ca2004.1 [214 kB]
Get:26 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-curl amd64 5.0.1-1.ca2004.1 [415 kB]
Get:27 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-rprojroot all 2.0.3-1.ca2004.1 [96.0 kB]
Get:28 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-desc all 1.4.2-1.ca2004.1 [316 kB]
Get:29 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-evaluate all 0.21-1.ca2004.1 [81.0 kB]
Get:30 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-fansi amd64 1.0.4-1.ca2004.1 [292 kB]
Get:31 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-glue amd64 1.6.2-1.ca2004.1 [142 kB]
Get:32 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-lifecycle all 1.0.3-1.ca2004.1 [111 kB]
Get:33 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-vctrs amd64 0.6.3-1.ca2004.1 [1190 kB]
Get:34 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-withr all 2.5.0-1.ca2004.1 [220 kB]
Get:35 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-yaml amd64 2.3.7-1.ca2004.1 [100.0 kB]
Get:36 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-downlit all 0.4.2-1.ca2004.1 [112 kB]
Get:37 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-fontawesome all 0.5.1-1.ca2004.1 [1275 kB]
Get:38 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-xfun amd64 0.39-1.ca2004.1 [402 kB]
Get:39 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-highr all 0.10-1.ca2004.1 [38.9 kB]
Get:40 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-openssl amd64 2.0.6-1.ca2004.1 [607 kB]
Get:41 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-httr all 1.4.6-1.ca2004.1 [463 kB]
Get:42 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-knitr all 1.43-1.ca2004.1 [1241 kB]
Get:43 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-magrittr amd64 2.0.3-1.ca2004.1 [195 kB]
Get:44 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-utf8 amd64 1.2.3-1.ca2004.1 [124 kB]
Get:45 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-pillar all 1.9.0-1.ca2004.1 [581 kB]
Get:46 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-pkgconfig all 2.0.3-1.ca2004.1 [18.5 kB]
Get:47 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-purrr amd64 1.0.1-1.ca2004.1 [466 kB]
Get:48 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-systemfonts amd64 1.0.4-1.ca2004.1 [235 kB]
Get:49 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-textshaping amd64 0.3.6-1.ca2004.1 [101 kB]
Get:50 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-ragg amd64 1.2.5-1.ca2004.2 [398 kB]
Get:51 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-stringi amd64 1.7.12-1.ca2004.1 [849 kB]
Get:52 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-stringr all 1.5.0-1.ca2004.1 [282 kB]
Get:53 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-tinytex all 0.45-1.ca2004.1 [134 kB]
Get:54 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-rmarkdown all 2.22-1.ca2004.1 [1924 kB]
Get:55 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-tibble amd64 3.2.1-1.ca2004.1 [590 kB]
Get:56 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-whisker all 0.4.1-1.ca2004.1 [62.1 kB]
Get:57 https://r2u.stat.illinois.edu/ubuntu focal/main amd64 r-cran-xml2 amd64 1.3.4-1.ca2004.1 [211 kB]
Get:58 https://r2u.stat.illinois.edu/ubuntu focal/main all r-cran-pkgdown all 2.0.7-1.ca2004.1 [702 kB]
Fetched 27.1 MB in 6s (932 kB/s)
Selecting previously unselected package libxml2:amd64.
(Reading database ... 17869 files and directories currently installed.)
Preparing to unpack .../00-libxml2_2.9.10+dfsg-5ubuntu0.20.04.6_amd64.deb ...
Unpacking libxml2:amd64 (2.9.10+dfsg-5ubuntu0.20.04.6) ...
Selecting previously unselected package r-cran-sys.
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Unpacking r-cran-sys (3.4.2-1.ca2004.1) ...
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Processing triggers for libc-bin (2.31-0ubuntu9.9) ...r2u is really 'just apt'. I have no idea what devcontainers do to it so there may be something else going on.
(My fave anecdote of the 'what the heck' type is that "here" under recent Ubuntu (22.10 still for the server/desktop) that when I update r2u (generally weekday-daily, depending on their builds) then I get sporadic short 'cannot resolve' outs in Chrome (!!) while my (R-based, simple) code (in the r2u package) to update r2u runs. "That shouldn't happen either." Oh well. I think I generally set DNS up to two distinct server but maybe I failed to do so last time I upgrade my internet setup (moving to the so awesome fiber ... .)
I have no idea what devcontainers do to it so there may be something else going on.
It's simply a shell script calling the apt command, so there shouldn't be any difference there; there may be something wrong with GitHub's infrastructure.
Anyway it failed twice, but on the third re-run it worked fine.
Sorry for the trouble.
"Stuff happens" and that's what the issues are for! I am really you are finding r2u useful and are battle-testing it / building on top of it.