Add docker operation mode #98

multimeric · 2024-06-18T07:51:35Z

Motivation: it's surprisingly difficult to get this to run, because there are some hidden dependencies and tricks required to get it working. Also, not everything is portable, as shown by #96. See also #95 for more motivation.

Changes

Add a Dockerfile
Add a conda environment definition (env.yaml)
Bump xslt to 1.4.5, since this compiles correctly using conda libraries
Document how to run this project using docker

Closes #95.

Testing
I have already tested this on https://github.com/carpentries-incubator/docker-introduction, which completed successfully. Some tweaks are needed however.

sstevens2 · 2024-07-10T17:46:37Z

@multimeric really appreciate your putting this together! And that you used it to convert my docker lesson! Must have felt a bit circular.

I'm trying to use this branch to convert my git lesson (with PRs/branches/conflicts) in the incubator to the workbench. I got the following error when I tried to build the image.

ERROR: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh R -e 'options(renv.config.pak.enabled = TRUE); renv::restore()'" did not complete successfully: exit code: 1

Any help you can provide?

multimeric · 2024-07-11T07:31:47Z

Happy to help. Can you list the steps you used, and the output from the build step?

sstevens2 · 2024-07-11T17:00:20Z

I cloned the lesson transition repo, then updated the submodule. Then ran the build command. Below is the full output from the build command.

Full output here

$ docker build . --tag lesson-transition
[+] Building 68.2s (11/12)                                                                                  docker:desktop-linux
 => [internal] load build definition from Dockerfile                                                                        0.0s
 => => transferring dockerfile: 678B                                                                                        0.0s
 => [internal] load metadata for docker.io/mambaorg/micromamba:1.5.8                                                        0.6s
 => [auth] mambaorg/micromamba:pull token for registry-1.docker.io                                                          0.0s
 => [internal] load .dockerignore                                                                                           0.0s
 => => transferring context: 2B                                                                                             0.0s
 => [1/7] FROM docker.io/mambaorg/micromamba:1.5.8@sha256:7644c62611ba0b661d7dbd905c1c66af9c8a9253cd0b483396500d95120f8415  0.0s
 => [internal] load build context                                                                                           0.4s
 => => transferring context: 41.39MB                                                                                        0.4s
 => CACHED [2/7] COPY --chown=mambauser:mambauser env.yaml /tmp/env.yaml                                                    0.0s
 => CACHED [3/7] RUN micromamba install -y -n base -f /tmp/env.yaml && micromamba clean --all --yes                         0.0s
 => [4/7] COPY --chown=mambauser:mambauser . lesson-transition                                                              0.2s
 => [5/7] WORKDIR lesson-transition                                                                                         0.0s
 => ERROR [6/7] RUN R -e 'options(renv.config.pak.enabled = TRUE); renv::restore()'                                        66.9s
------
 > [6/7] RUN R -e 'options(renv.config.pak.enabled = TRUE); renv::restore()':
0.350
0.350 R version 4.3.2 (2023-10-31) -- "Eye Holes"
0.350 Copyright (C) 2023 The R Foundation for Statistical Computing
0.350 Platform: aarch64-conda-linux-gnu (64-bit)
0.350
0.350 R is free software and comes with ABSOLUTELY NO WARRANTY.
0.350 You are welcome to redistribute it under certain conditions.
0.350 Type 'license()' or 'licence()' for distribution details.
0.350
0.350 R is a collaborative project with many contributors.
0.350 Type 'contributors()' for more information and
0.350 'citation()' on how to cite R or R packages in publications.
0.350
0.350 Type 'demo()' for some demos, 'help()' for on-line help, or
0.350 'help.start()' for an HTML browser interface to help.
0.350 Type 'q()' to quit R.
0.350
0.390 # Bootstrapping renv 1.0.3 ---------------------------------------------------
0.390 - Downloading renv ... OK
1.124 - Installing renv  ... OK
5.978
6.077 - Project '/tmp/lesson-transition' loaded. [renv 1.0.3]
6.080 - None of the packages recorded in the lockfile are currently installed.
6.102 > options(renv.config.pak.enabled = TRUE); renv::restore()
6.322 # Downloading packages -------------------------------------------------------
6.323 - Downloading pak from r-lib ...                OK [8.3 Mb in 0.44s]
6.993 Successfully downloaded 1 package in 0.74 seconds.
6.993
6.994 The following package(s) will be installed:
6.994 - pak [0.7.2]
6.994 These packages will be installed into "/tmp/lesson-transition/renv/library/R-4.3/aarch64-conda-linux-gnu".
6.994
6.994 # Installing packages --------------------------------------------------------
7.096 - Installing pak ...                            OK [installed binary and cached in 0.92s]
8.022 Successfully installed 1 package in 1 second.
8.898 ! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
9.302
11.37 ✔ Updated metadata database: 3.83 MB in 9 files.
11.37
11.38 ℹ Updating metadata database
15.67 ✔ Updating metadata database ... done
15.67
20.49
20.49 → Will install 86 packages.
20.50 → Will download 45 CRAN packages (13.33 MB).
20.50 → Will download 41 packages with unknown size.
20.51 + askpass       1.2.0      [bld][cmp][dl] (6.04 kB)
20.51 + assertthat    0.2.1      [bld][dl] (12.74 kB)
20.51 + base64enc     0.1-3      [bld][cmp][dl] (7.83 kB)
20.51 + brio          1.1.4      [bld][cmp][dl]
20.51 + bslib         0.6.1      [bld][dl]
20.51 + cachem        1.0.8      [bld][cmp][dl]
20.51 + callr         3.7.3      [bld][dl]
20.51 + cli           3.6.2      [bld][cmp][dl]
20.51 + clipr         0.8.0      [bld][dl] (21.90 kB)
20.51 + commonmark    1.9.1      [bld][cmp][dl] (145.98 kB)
20.51 + cpp11         0.4.7      [bld][dl] (285.78 kB)
20.51 + crayon        1.5.2      [bld][dl]
20.51 + credentials   2.0.1      [bld][dl] (283.84 kB) + ✖ git
20.51 + curl          5.2.0      [bld][cmp][dl] + ✖ libcurl4-openssl-dev, ✖ libssl-dev
20.51 + desc          1.4.3      [bld][dl] (80.07 kB)
20.51 + digest        0.6.34     [bld][cmp][dl]
20.51 + docopt        0.7.1      [bld][dl] (29.46 kB)
20.51 + downlit       0.4.3      [bld][dl]
20.51 + dplyr         1.1.4      [bld][cmp][dl] (1.21 MB)
20.51 + ellipsis      0.3.2      [bld][cmp][dl] (8.07 kB)
20.51 + evaluate      0.23       [bld][dl]
20.51 + fansi         1.0.6      [bld][cmp][dl] (482.48 kB)
20.51 + fastmap       1.1.1      [bld][cmp][dl]
20.51 + fontawesome   0.5.2      [bld][dl] (1.28 MB)
20.51 + fs            1.6.3      [bld][cmp][dl] + ✖ make
20.51 + generics      0.1.3      [bld][dl] (172.20 kB)
20.51 + gert          2.0.1      [bld][cmp][dl] (122.72 kB) + ✖ libgit2-dev
20.51 + gh            1.4.0      [bld][dl]
20.51 + gitcreds      0.1.2      [bld][dl] (62.57 kB) + ✖ git
20.51 + glue          1.7.0      [bld][cmp][dl] (105.42 kB)
20.51 + here          1.0.1      [bld][dl] (32.95 kB)
20.51 + highr         0.10       [bld][dl]
20.51 + htmltools     0.5.7      [bld][cmp][dl]
20.51 + httpuv        1.6.14     [bld][cmp][dl] + ✖ make, ✖ zlib1g-dev
20.51 + httr          1.4.7      [bld][dl] (118.50 kB)
20.51 + httr2         1.0.0      [bld][dl]
20.51 + ini           0.3.1      [bld][dl] (3.49 kB)
20.51 + jquerylib     0.1.4      [bld][dl] (520.21 kB)
20.51 + jsonlite      1.8.8      [bld][cmp][dl] (1.05 MB)
20.51 + knitr         1.45       [bld][dl] + ✖ pandoc
20.51 + later         1.3.2      [bld][cmp][dl] (63.60 kB)
20.51 + lifecycle     1.0.4      [bld][dl] (107.66 kB)
20.51 + magrittr      2.0.3      [bld][cmp][dl] (267.07 kB)
20.51 + memoise       2.0.1      [bld][dl] (17.85 kB)
20.51 + mime          0.12       [bld][cmp][dl] (12.56 kB)
20.51 + openssl       2.1.1      [bld][cmp][dl] + ✖ libssl-dev
20.51 + pandoc        0.2.0      [bld][dl] (42.68 kB)
20.51 + pegboard      0.7.6      [bld][cmp][dl] (GitHub: ad2542f)
20.51 + pillar        1.9.0      [bld][dl] (444.53 kB)
20.51 + pkgconfig     2.0.3      [bld][dl] (6.08 kB)
20.51 + pkgdown       2.0.7      [bld][dl] + ✖ pandoc
20.51 + processx      3.8.3      [bld][cmp][dl]
20.51 + promises      1.2.1      [bld][cmp][dl]
20.51 + ps            1.7.6      [bld][cmp][dl]
20.51 + purrr         1.0.2      [bld][cmp][dl] (220.87 kB)
20.51 + R6            2.5.1      [bld][dl] (63.42 kB)
20.51 + ragg          1.2.7      [bld][cmp][dl] + ✖ libfreetype6-dev, ✖ libjpeg-dev, ✖ libpng-dev, ✖ libtiff-dev
20.51 + rappdirs      0.3.3      [bld][cmp][dl] (12.29 kB)
20.51 + Rcpp          1.0.12     [bld][cmp][dl] (3.43 MB)
20.51 + rlang         1.1.3      [bld][cmp][dl]
20.51 + rmarkdown     2.25       [bld][dl] + ✖ pandoc
20.51 + rprojroot     2.0.4      [bld][dl] (59.95 kB)
20.51 + rstudioapi    0.15.0     [bld][dl]
20.51 + sandpaper     0.16.5     [bld][cmp][dl] (GitHub: 82d0ee3) + ✖ pandoc
20.51 + sass          0.4.8      [bld][cmp][dl] + ✖ make
20.51 + servr         0.29       [bld][dl]
20.51 + stringi       1.8.3      [bld][cmp][dl] + ✖ libicu-dev
20.51 + stringr       1.5.1      [bld][dl] (176.60 kB)
20.51 + sys           3.4.2      [bld][cmp][dl] (20.17 kB)
20.51 + systemfonts   1.0.5      [bld][cmp][dl] + ✖ libfontconfig1-dev, ✖ libfreetype6-dev
20.51 + textshaping   0.3.7      [bld][cmp][dl] + ✖ libfreetype6-dev, ✖ libfribidi-dev, ✖ libharfbuzz-dev
20.51 + tibble        3.2.1      [bld][cmp][dl] (565.98 kB)
20.51 + tidyselect    1.2.0      [bld][dl]
20.51 + tinkr         0.2.0.9000 [bld][cmp][dl] (GitHub: 8a57235)
20.51 + tinytex       0.49       [bld][dl]
20.51 + usethis       2.2.2      [bld][dl]
20.51 + utf8          1.2.4      [bld][cmp][dl] (241.08 kB)
20.51 + varnish       1.0.3      [bld][cmp][dl] (GitHub: 1f1e219)
20.51 + vctrs         0.6.5      [bld][cmp][dl] (969.07 kB)
20.51 + whisker       0.4.1      [bld][dl] (28.59 kB)
20.51 + withr         3.0.0      [bld][dl] (107.68 kB)
20.51 + xfun          0.42       [bld][cmp][dl]
20.51 + xml2          1.3.6      [bld][cmp][dl] (294.71 kB) + ✖ libxml2-dev
20.51 + xslt          1.4.5      [bld][cmp][dl] (17.79 kB) + ✖ libxslt-dev
20.51 + yaml          2.3.8      [bld][cmp][dl]
20.51 + zip           2.3.1      [bld][cmp][dl] (111.28 kB)
20.52 ✖ Missing 17 system packages. You'll probably need to install them manually:
20.52 + git                   - credentials, gitcreds
20.52 + libcurl4-openssl-dev  - curl
20.52 + libfontconfig1-dev    - systemfonts
20.52 + libfreetype6-dev      - systemfonts, textshaping, ragg
20.52 + libfribidi-dev        - textshaping
20.52 + libgit2-dev           - gert
20.52 + libharfbuzz-dev       - textshaping
20.52 + libicu-dev            - stringi
20.52 + libjpeg-dev           - ragg
20.52 + libpng-dev            - ragg
20.52 + libssl-dev            - curl, openssl
20.52 + libtiff-dev           - ragg
20.52 + libxml2-dev           - xml2
20.52 + libxslt-dev           - xslt
20.52 + make                  - fs, httpuv, sass
20.52 + pandoc                - sandpaper, knitr, pkgdown, rmarkdown
20.52 + zlib1g-dev            - httpuv
20.66 ℹ Getting 45 pkgs (13.33 MB) and 41 pkgs with unknown sizes
21.46 ✔ Got brio 1.1.4 (source) (13.08 kB)
21.51 ✔ Got downlit 0.4.3 (source) (36.89 kB)
21.54 ✔ Got systemfonts 1.0.5 (source) (80.64 kB)
21.57 ✔ Got textshaping 0.3.7 (source) (35.10 kB)
21.63 ✔ Got htmltools 0.5.7 (source) (134.68 kB)
21.64 ✔ Got yaml 2.3.8 (source) (94.76 kB)
21.67 ✔ Got digest 0.6.34 (source) (178.16 kB)
21.69 ✔ Got askpass 1.2.0 (source) (6.04 kB)
21.71 ✔ Got base64enc 0.1-3 (source) (7.83 kB)
21.72 ✔ Got httr2 1.0.0 (source) (212.03 kB)
21.74 ✔ Got sys 3.4.2 (source) (20.32 kB)
21.74 ✔ Got assertthat 0.2.1 (source) (12.61 kB)
21.75 ✔ Got evaluate 0.23 (source) (28.35 kB)
21.76 ✔ Got R6 2.5.1 (source) (64.11 kB)
21.77 ✔ Got gh 1.4.0 (source) (41.21 kB)
21.79 ✔ Got xslt 1.4.5 (source) (17.98 kB)
21.81 ✔ Got callr 3.7.3 (source) (97.81 kB)
21.87 ✔ Got crayon 1.5.2 (source) (40.57 kB)
21.90 ✔ Got zip 2.3.1 (source) (111.44 kB)
21.93 ✔ Got pandoc 0.2.0 (source) (42.76 kB)
21.94 ✔ Got ps 1.7.6 (source) (129.49 kB)
21.95 ✔ Got here 1.0.1 (source) (32.91 kB)
22.00 ✔ Got xml2 1.3.6 (source) (294.72 kB)
22.02 ✔ Got ragg 1.2.7 (source) (425.50 kB)
22.06 ✔ Got httr 1.4.7 (source) (118.57 kB)
22.11 ✔ Got fansi 1.0.6 (source) (482.60 kB)
22.26 ✔ Got lifecycle 1.0.4 (source) (108.36 kB)
22.30 ✔ Got openssl 2.1.1 (source) (1.21 MB)
22.32 ✔ Got pkgconfig 2.0.3 (source) (6.10 kB)
22.35 ✔ Got curl 5.2.0 (source) (715.88 kB)
22.45 ✔ Got rlang 1.1.3 (source) (763.76 kB)
22.45 ✔ Got tidyselect 1.2.0 (source) (101.50 kB)
22.50 ✔ Got dplyr 1.1.4 (source) (1.21 MB)
22.52 ✔ Got docopt 0.7.1 (source) (29.57 kB)
22.53 ✔ Got credentials 2.0.1 (source) (283.00 kB)
22.57 ✔ Got pillar 1.9.0 (source) (441.98 kB)
22.63 ✔ Got jquerylib 0.1.4 (source) (520.37 kB)
22.79 ✔ Got vctrs 0.6.5 (source) (967.95 kB)
22.80 ✔ Got tinkr 0.2.0.9000 (source) (169.22 kB)
23.05 ✔ Got pkgdown 2.0.7 (source) (871.47 kB)
23.11 ✔ Got servr 0.29 (source) (23.05 kB)
23.12 ✔ Got ellipsis 0.3.2 (source) (8.30 kB)
23.24 ✔ Got promises 1.2.1 (source) (3.15 MB)
23.34 ✔ Got Rcpp 1.0.12 (source) (3.43 MB)
23.40 ✔ Got glue 1.7.0 (source) (105.90 kB)
23.40 ✔ Got withr 3.0.0 (source) (108.37 kB)
23.46 ✔ Got gitcreds 0.1.2 (source) (62.81 kB)
23.47 ✔ Got utf8 1.2.4 (source) (239.71 kB)
23.51 ✔ Got commonmark 1.9.1 (source) (146.41 kB)
23.53 ✔ Got memoise 2.0.1 (source) (17.88 kB)
23.54 ✔ Got magrittr 2.0.3 (source) (267.20 kB)
23.59 ✔ Got later 1.3.2 (source) (62.18 kB)
23.63 ✔ Got rprojroot 2.0.4 (source) (61.64 kB)
23.65 ✔ Got cpp11 0.4.7 (source) (285.35 kB)
23.67 ✔ Got cli 3.6.2 (source) (569.77 kB)
23.69 ✔ Got httpuv 1.6.14 (source) (1.88 MB)
23.71 ✔ Got highr 0.10 (source) (15.08 kB)
23.75 ✔ Got tibble 3.2.1 (source) (565.72 kB)
23.77 ✔ Got purrr 1.0.2 (source) (218.46 kB)
23.78 ✔ Got clipr 0.8.0 (source) (21.95 kB)
23.82 ✔ Got desc 1.4.3 (source) (80.47 kB)
23.82 ✔ Got whisker 0.4.1 (source) (28.69 kB)
23.85 ✔ Got gert 2.0.1 (source) (123.48 kB)
23.87 ✔ Got processx 3.8.3 (source) (163.68 kB)
23.89 ✔ Got generics 0.1.3 (source) (173.58 kB)
23.91 ✔ Got fastmap 1.1.1 (source) (46.41 kB)
23.93 ✔ Got stringr 1.5.1 (source) (177.06 kB)
23.96 ✔ Got rappdirs 0.3.3 (source) (12.20 kB)
23.97 ✔ Got ini 0.3.1 (source) (3.48 kB)
23.98 ✔ Got mime 0.12 (source) (12.60 kB)
24.04 ✔ Got rstudioapi 0.15.0 (source) (115.69 kB)
24.09 ✔ Got sass 0.4.8 (source) (3.03 MB)
24.10 ✔ Got cachem 1.0.8 (source) (26.51 kB)
24.11 ✔ Got tinytex 0.49 (source) (34.20 kB)
24.18 ✔ Got jsonlite 1.8.8 (source) (1.05 MB)
24.25 ✔ Got usethis 2.2.2 (source) (371.06 kB)
24.29 ✔ Got fs 1.6.3 (source) (1.19 MB)
24.33 ✔ Got xfun 0.42 (source) (142.60 kB)
24.39 ✔ Got fontawesome 0.5.2 (source) (1.27 MB)
24.48 ✔ Got knitr 1.45 (source) (898.76 kB)
24.58 ✔ Got rmarkdown 2.25 (source) (2.19 MB)
24.69 ✔ Got bslib 0.6.1 (source) (6.06 MB)
24.77 ✔ Got pegboard 0.7.6 (source) (607.12 kB)
24.97 ✔ Got sandpaper 0.16.5 (source) (963.54 kB)
25.07 ✔ Got varnish 1.0.3 (source) (2.51 MB)
25.34 ✔ Got stringi 1.8.3 (source) (11.92 MB)
25.40 ℹ Packaging varnish 1.0.3
25.41 ℹ Building brio 1.1.4
25.70 ℹ Building digest 0.6.34
25.75 ℹ Building xfun 0.42
25.90 ℹ Building fastmap 1.1.1
25.97 ℹ Building fs 1.6.3
26.26 ℹ Building curl 5.2.0
26.35 ℹ Building yaml 2.3.8
27.18 ✔ Packaged varnish 1.0.3 (1.8s)
27.23 ℹ Building varnish 1.0.3
27.58 ✔ Built brio 1.1.4 (1.9s)
27.65 ℹ Building rlang 1.1.3
28.57 ✔ Built varnish 1.0.3 (1.2s)
28.59 ℹ Building cli 3.6.2
28.94 ✔ Built xfun 0.42 (3s)
28.98 ℹ Building rstudioapi 0.15.0
29.37 ✔ Built fastmap 1.1.1 (3.4s)
29.38 ℹ Building assertthat 0.2.1
30.47 ✔ Built assertthat 0.2.1 (1s)
30.50 ℹ Building sys 3.4.2
30.82 ✔ Built rstudioapi 0.15.0 (1.7s)
30.85 ℹ Building base64enc 0.1-3
31.00 ✔ Built curl 5.2.0 (4.6s)
31.02 ℹ Building R6 2.5.1
31.83 ✔ Built digest 0.6.34 (6s)
31.85 ✔ Built sys 3.4.2 (1.3s)
31.86 ℹ Building Rcpp 1.0.12
32.42 ✔ Built base64enc 0.1-3 (1.5s)
32.45 ✔ Built R6 2.5.1 (1.3s)
32.46 ℹ Building fansi 1.0.6
32.55 ℹ Building generics 0.1.3
32.72 ℹ Building glue 1.7.0
33.35 ✔ Built yaml 2.3.8 (6.9s)
33.37 ℹ Building magrittr 2.0.3
33.71 ✔ Built generics 0.1.3 (1.1s)
33.73 ℹ Building pkgconfig 2.0.3
34.73 ✔ Built glue 1.7.0 (1.9s)
34.79 ℹ Building utf8 1.2.4
34.93 ✔ Built pkgconfig 2.0.3 (1.1s)
35.00 ℹ Building withr 3.0.0
35.14 ✔ Built magrittr 2.0.3 (1.6s)
35.16 ℹ Building clipr 0.8.0
36.26 ✔ Built clipr 0.8.0 (1s)
36.29 ℹ Building commonmark 1.9.1
36.76 ✔ Built withr 3.0.0 (1.6s)
36.77 ℹ Building cpp11 0.4.7
38.08 ✔ Built fansi 1.0.6 (5.5s)
38.09 ℹ Building gitcreds 0.1.2
38.16 ✔ Built cpp11 0.4.7 (1.3s)
38.17 ℹ Building ini 0.3.1
39.20 ✔ Built utf8 1.2.4 (4.2s)
39.24 ℹ Building jsonlite 1.8.8
39.47 ✔ Built ini 0.3.1 (1.2s)
39.48 ℹ Building mime 0.12
39.57 ✔ Built gitcreds 0.1.2 (1.4s)
39.58 ℹ Building rappdirs 0.3.3
40.68 ✔ Built mime 0.12 (1.2s)
40.72 ℹ Building rprojroot 2.0.4
40.98 ✔ Built rappdirs 0.3.3 (1.3s)
41.00 ℹ Building whisker 0.4.1
41.08 ✔ Built cli 3.6.2 (12.1s)
41.11 ℹ Building zip 2.3.1
42.09 ✔ Built rprojroot 2.0.4 (1.3s)
42.10 ℹ Building evaluate 0.23
42.29 ✔ Built whisker 0.4.1 (1.2s)
42.31 ℹ Building crayon 1.5.2
43.21 ✔ Built evaluate 0.23 (1.1s)
43.22 ℹ Building ps 1.7.6
43.45 ✔ Built rlang 1.1.3 (15.5s)
43.47 ℹ Building docopt 0.7.1
44.40 ✔ Built crayon 1.5.2 (2s)
44.41 ℹ Building stringi 1.8.3
45.08 ✔ Built jsonlite 1.8.8 (5.7s)
45.18 ✔ Installed brio 1.1.4  (28ms)
45.27 ✔ Installed varnish 1.0.3 (github::carpentries/varnish@1f1e219) (69ms)
45.33 ✔ Installed digest 0.6.34  (34ms)
45.40 ✔ Installed xfun 0.42  (26ms)
45.41 ℹ Building highr 0.10
45.46 ✔ Built docopt 0.7.1 (1.9s)
45.48 ℹ Building tinytex 0.49
46.73 ✔ Built highr 0.10 (1.3s)
46.90 ✔ Installed fastmap 1.1.1  (137ms)
46.93 ✔ Installed highr 0.10  (18ms)
47.04 ✔ Installed curl 5.2.0  (63ms)
47.10 ✔ Installed yaml 2.3.8  (23ms)
47.17 ✔ Installed rlang 1.1.3  (34ms)
47.18 ℹ Building cachem 1.0.8
47.23 ✔ Built tinytex 0.49 (1.7s)
47.24 ℹ Building ellipsis 0.3.2
48.60 ✔ Built ps 1.7.6 (5.3s)
48.68 ✔ Installed tinytex 0.49  (21ms)
48.74 ✔ Built cachem 1.0.8 (1.5s)
48.77 ✔ Built ellipsis 0.3.2 (1.5s)
48.80 ✔ Installed cli 3.6.2  (86ms)
48.80 ℹ Building xml2 1.3.6
48.91 ✔ Installed cachem 1.0.8  (129ms)
48.92 ℹ Building memoise 2.0.1
49.07 ✔ Installed rstudioapi 0.15.0  (23ms)
49.10 ✔ Built commonmark 1.9.1 (12.8s)
49.14 ✔ Installed assertthat 0.2.1  (38ms)
49.23 ✔ Installed sys 3.4.2  (104ms)
49.23 ℹ Building askpass 1.2.0
49.34 ✔ Installed base64enc 0.1-3  (113ms)
49.39 ✔ Installed R6 2.5.1  (28ms)
49.40 ℹ Building desc 1.4.3
51.24 ✔ Built askpass 1.2.0 (2s)
51.27 ✔ Built memoise 2.0.1 (2.3s)
51.33 ✔ Installed askpass 1.2.0  (55ms)
51.33 ℹ Building openssl 2.1.1
51.59 ✔ Built desc 1.4.3 (2s)
51.62 ✔ Installed fansi 1.0.6  (323ms)
51.67 ✔ Installed generics 0.1.3  (24ms)
51.70 ✔ Installed glue 1.7.0  (50ms)
51.71 ℹ Building lifecycle 1.0.4
51.84 ✔ Installed magrittr 2.0.3  (135ms)
52.91 ✔ Installed pkgconfig 2.0.3  (1.1s)
52.97 ✔ Installed utf8 1.2.4  (25ms)
53.00 ✔ Built zip 2.3.1 (11.8s)
53.06 ✔ Installed withr 3.0.0  (70ms)
53.12 ✔ Installed clipr 0.8.0  (66ms)
53.17 ✔ Installed commonmark 1.9.1  (89ms)
53.20 ✔ Installed cpp11 0.4.7  (53ms)
53.22 ✔ Installed desc 1.4.3  (36ms)
53.23 ℹ Building systemfonts 1.0.5
53.30 ✔ Built lifecycle 1.0.4 (1.5s)
53.36 ✔ Installed lifecycle 1.0.4  (34ms)
53.37 ℹ Building vctrs 0.6.5
53.61 ✔ Installed gitcreds 0.1.2  (269ms)
53.66 ✔ Installed ini 0.3.1  (28ms)
53.75 ✔ Installed jsonlite 1.8.8  (37ms)
53.80 ✔ Installed memoise 2.0.1  (19ms)
53.84 ✔ Installed mime 0.12  (18ms)
53.88 ✔ Installed rappdirs 0.3.3  (18ms)
53.92 ✔ Installed rprojroot 2.0.4  (21ms)
53.97 ℹ Building here 1.0.1
54.98 ✔ Built here 1.0.1 (962ms)
55.03 ✔ Installed whisker 0.4.1  (18ms)
55.13 ✔ Installed zip 2.3.1  (70ms)
55.18 ✔ Installed here 1.0.1  (27ms)
55.23 ✔ Installed ellipsis 0.3.2  (21ms)
55.24 ℹ Building htmltools 0.5.7
56.71 ✔ Built xml2 1.3.6 (7.8s)
56.77 ✔ Installed xml2 1.3.6  (32ms)
56.82 ✔ Installed evaluate 0.23  (36ms)
56.82 ℹ Building knitr 1.45
57.96 ✔ Built openssl 2.1.1 (6.4s)
58.04 ✔ Installed openssl 2.1.1  (52ms)
58.05 ℹ Building credentials 2.0.1
58.41 ✔ Built fs 1.6.3 (32.1s)
58.43 ℹ Building httr 1.4.7
58.52 ✔ Built htmltools 0.5.7 (3.2s)
58.68 ✔ Installed htmltools 0.5.7  (58ms)
58.69 ℹ Building fontawesome 0.5.2
59.63 ✔ Built credentials 2.0.1 (1.5s)
59.66 ℹ Building jquerylib 0.1.4
61.02 ✔ Built fontawesome 0.5.2 (2.2s)
61.08 ✔ Installed fs 1.6.3  (35ms)
61.10 ℹ Building pandoc 0.2.0
61.19 ✔ Built jquerylib 0.1.4 (1.4s)
61.23 ℹ Building sass 0.4.8
62.32 ✔ Built httr 1.4.7 (3.8s)
62.37 ✔ Installed credentials 2.0.1  (25ms)
62.39 ℹ Building gert 2.0.1
62.87 ✔ Built Rcpp 1.0.12 (30.4s)
62.90 ✔ Built knitr 1.45 (5.8s)
62.91 ✔ Built pandoc 0.2.0 (1.7s)
62.96 ✔ Installed Rcpp 1.0.12  (72ms)
62.97 ℹ Building later 1.3.2
63.07 ✔ Installed knitr 1.45  (130ms)
63.15 ✔ Installed fontawesome 0.5.2  (146ms)
63.16 ℹ Building xslt 1.4.5
63.20 ✖ Failed to build gert 2.0.1 (697ms)
66.72 Error:
66.72 ! error in pak subprocess
66.72 Caused by error in `stop_task_build(state, worker)`:
66.72 ! Failed to build source package gert.
66.72 ---
66.72 Backtrace:
66.72 1. renv::restore()
66.72 2. renv:::renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclu…
66.72 3. pak$pkg_install(remotes)
66.72 4. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
66.72 5. err$throw(res$error)
66.72 ---
66.72 Subprocess backtrace:
66.72  1. base::withCallingHandlers(cli_message = function(msg) { …
66.72  2. get("pkg_install_do_plan", asNamespace("pak"))(...)
66.72  3. proposal$install()
66.72  4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
66.72  5. base::withCallingHandlers({ …
66.72  6. pkgdepends:::handle_events(state, events)
66.72  7. pkgdepends:::handle_event(state, i)
66.72  8. pkgdepends:::stop_task(state, worker)
66.72  9. pkgdepends:::stop_task_build(state, worker)
66.72 10. base::throw(pkg_error("Failed to build source package {.pkg {pkg}}.", …
66.72 11. | base::signalCondition(cond)
66.72 12. global (function (e) …
66.73 Traceback (most recent calls last):
66.73 6: renv::restore()
66.73 5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude,
66.73        project = project)
66.73 4: pak$pkg_install(remotes)
66.73 3: remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...),
66.73        list(proposal = NULL))
66.73 2: err$throw(res$error)
66.73 1: base::stop(cond)
66.73 Execution halted
------
Dockerfile:10
--------------------
   8 |     COPY --chown=$MAMBA_USER:$MAMBA_USER . lesson-transition
   9 |     WORKDIR lesson-transition
  10 | >>> RUN R -e 'options(renv.config.pak.enabled = TRUE); renv::restore()'
  11 |
  12 |     # This disables the interactive parts of the script
--------------------
ERROR: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh R -e 'options(renv.config.pak.enabled = TRUE); renv::restore()'" did not complete successfully: exit code: 1

multimeric · 2024-07-12T05:40:33Z

My best guess is that your docker is compiling it for ARM (the aarch64 I can see in the logs). This must cause the system dependencies to not install correctly, and therefore the dependent R packages such as gert also fail.

If you add --platform linux/amd64 to the docker build command, does it do anything differently?

multimeric added 6 commits June 18, 2024 16:31

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Add docker operation mode #98

Add docker operation mode #98

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Add docker operation mode #98

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