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Story #16264
closed
Handle R SDK dependencies better
Added by Peter Amstutz almost 5 years ago. Updated about 4 years ago.
Status:
Resolved
Priority:
Normal
Assigned To:
Category:
SDKs
Target version:
Start date:
Due date:
% Done:
100%
Estimated time:
(Total: 0.00 h)
Story points:
-
Release:
Release relationship:
Auto
Description
Our build was broken for a while because Rcpp (a transitive dependency of a package we depend on) had a new release that is broken on R 3.3.
We were running our tests on Debian 9, which ships with R 3.3.
A fix was committed to upstream Rcpp, so the problem resolved itself, but we should have a more stable strategy for R dependencies.
Recompiling R dependencies every time is also very expensive.
Options¶
Use Debian packages¶
When we did the R SDK originally (about two years ago) most of the packages we needed were not in Debian. Since then, it appears they have been added to Debian 10, and are also available in a Debian 9 backport:
https://packages.debian.org/search?keywords=r-cran-devtools&searchon=names&suite=all§ion=all
Of course this requires targeting Debian for the test builds, but we do that already. To get the maximum benefit it also requires that all the R packages we need are in Debian.
Pinned install¶
R doesn't have anything like a Gemfile.lock or "pip freeze". However someone has created a tool that computes an install plan so each package is installed at exactly each version we want.
This works on any R install. The drawback is that we still end up compiling the whole world every time.
Files
| 20200925-doc-gen-timing.png (91.4 KB) 20200925-doc-gen-timing.png | Ward Vandewege, 09/25/2020 06:26 PM |
Updated by Peter Amstutz almost 5 years ago
- Related to Bug #16267: arvbox build uses arvados-server install added
Updated by Peter Amstutz almost 5 years ago
Currently I think the solution is for #16053 to include installing the appropriate R packages from Debian 10.
Updated by Peter Amstutz almost 5 years ago
- Related to Story #16053: [boot] subcommand to install/update dev and runtime dependencies added
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-04-08 Sprint to 2020-04-22
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-04-22 to 2020-05-06 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-05-06 Sprint to 2020-05-20 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-05-20 Sprint to 2020-06-03 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-06-03 Sprint to 2020-06-17 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-06-17 Sprint to 2020-07-01 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-07-01 Sprint to 2020-07-15
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-07-15 to 2020-08-12 Sprint
Updated by Peter Amstutz over 4 years ago
- Related to Bug #16586: ArvadosR: Dependency package(s) 'XML' not available. added
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-08-12 Sprint to 2020-08-26 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-08-26 Sprint to 2020-09-09 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-09-09 Sprint to 2020-09-23 Sprint
Updated by Peter Amstutz over 4 years ago
- Target version changed from 2020-09-23 Sprint to 2020-10-07 Sprint
Updated by Peter Amstutz about 4 years ago
Now that all the test infrastructure (including arvbox) is on Debian 10, we can install the following packages for development and everything works great:
r-cran-devtools r-cran-knitr r-cran-markdown r-cran-roxygen2 r-cran-xml
Updated by Ward Vandewege about 4 years ago
- Status changed from New to In Progress
Updated by Ward Vandewege about 4 years ago
Peter Amstutz wrote:
Now that all the test infrastructure (including arvbox) is on Debian 10, we can install the following packages for development and everything works great:
r-cran-devtools r-cran-knitr r-cran-markdown r-cran-roxygen2 r-cran-xml
I've added those packages to the dependencies that are installed by `arvados-server install -type test`.
A quick test in arvbox showed a large reduction in the time needed to build the R documentation, I recorded 6.41s for the old way (from flock release to done), and 1:23s with this patch.
Ready for review at 4adf06fe21ff6aa9c08afee2268871c85394b217 on branch 16264-add-r-dependencies.
This is the log for the R doc generation with the patch applied:
2020-09-24_19:36:24.30744 + [[ ! -f /usr/src/arvados/doc/no-sdk ]]
2020-09-24_19:36:24.30746 + cd /usr/src/arvados/sdk/R
2020-09-24_19:36:24.30748 + R --quiet --vanilla --file=install_deps.R
2020-09-24_19:36:24.47131 > # Copyright (C) The Arvados Authors. All rights reserved.
2020-09-24_19:36:24.47134 > #
2020-09-24_19:36:24.47134 > # SPDX-License-Identifier: Apache-2.0
2020-09-24_19:36:24.47134 >
2020-09-24_19:36:24.47134 > options(repos=structure(c(CRAN="http://cran.wustl.edu/")))
2020-09-24_19:36:24.47136 > if (!requireNamespace("devtools")) {
2020-09-24_19:36:24.47138 + install.packages("devtools")
2020-09-24_19:36:24.47139 + }
2020-09-24_19:36:24.47272 Loading required namespace: devtools
2020-09-24_19:36:25.04066 > if (!requireNamespace("roxygen2")) {
2020-09-24_19:36:25.04069 + install.packages("roxygen2")
2020-09-24_19:36:25.04069 + }
2020-09-24_19:36:25.04086 Loading required namespace: roxygen2
2020-09-24_19:36:25.21787 > if (!requireNamespace("knitr")) {
2020-09-24_19:36:25.21789 + install.packages("knitr")
2020-09-24_19:36:25.21790 + }
2020-09-24_19:36:25.21790 > if (!requireNamespace("markdown")) {
2020-09-24_19:36:25.21790 + install.packages("markdown")
2020-09-24_19:36:25.21791 + }
2020-09-24_19:36:25.21806 Loading required namespace: markdown
2020-09-24_19:36:25.22394 > if (!requireNamespace("XML")) {
2020-09-24_19:36:25.22396 + # XML 3.99-0.4 depends on R >= 4.0.0, but we run tests on debian
2020-09-24_19:36:25.22397 + # stable (10) with R 3.5.2 so we install an older version from
2020-09-24_19:36:25.22397 + # source.
2020-09-24_19:36:25.22397 + install.packages("https://cran.r-project.org/src/contrib/Archive/XML/XML_3.99-0.3.tar.gz", repos=NULL, type="source")
2020-09-24_19:36:25.22399 + }
2020-09-24_19:36:25.22412 Loading required namespace: XML
2020-09-24_19:36:25.39980 >
2020-09-24_19:36:25.39982 > devtools::install_dev_deps()
2020-09-24_19:36:27.53800
2020-09-24_19:36:29.26694
2020-09-24_19:36:29.26708 >
2020-09-24_19:36:29.29854 + test '' = --only-deps
2020-09-24_19:36:29.29856 + cd /usr/src/arvados/doc
2020-09-24_19:36:29.29864 + bundle exec rake generate baseurl=http://172.17.0.2:8001 arvados_api_host=172.17.0.2:8000 arvados_workbench_host=http://172.17.0.2
2020-09-24_19:36:29.78374 zenweb-fix-body.rb:4: warning: already initialized constant ZenwebTextile::VERSION
2020-09-24_19:36:29.78379 zenweb-textile.rb:8: warning: previous definition of VERSION was here
2020-09-24_19:36:29.78400 rm -rf sdk/python/arvados
2020-09-24_19:36:29.78410 rm -rf sdk/R
2020-09-24_19:36:29.78947 rm -rf sdk/java-v2/javadoc
2020-09-24_19:36:29.79626 rm -rf
2020-09-24_19:36:29.79634 rm -rf .site
2020-09-24_19:36:29.82145 ^[[0;91;49mWarning: pdoc3 not found, Python documentation will not be generated^[[0m
2020-09-24_19:36:29.83433 cp css/R.css sdk/R/arvados
2020-09-24_19:36:29.83434 tgt
2020-09-24_19:36:29.83434 /usr/src/arvados/doc
2020-09-24_19:36:30.59352 Loading required package: knitr
2020-09-24_19:36:30.59354 Loading required package: markdown
2020-09-24_19:36:30.59354
2020-09-24_19:36:30.59354
2020-09-24_19:36:30.59354 processing file: README.Rmd
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2020-09-24_19:36:30.59424 output file: /usr/src/arvados/doc/sdk/R/README.md
2020-09-24_19:36:30.59424
2020-09-24_19:36:30.59425 [1] "/usr/src/arvados/doc/sdk/R/README.md"
2020-09-24_19:37:42.36398 Starting a Gradle Daemon, 1 incompatible and 2 stopped Daemons could not be reused, use --status for details
Updated by Peter Amstutz about 4 years ago
Please update the jenkins test image as well
Updated by Ward Vandewege about 4 years ago
- Status changed from In Progress to Resolved
- % Done changed from 0 to 100
Applied in changeset arvados|27992e62e71eb2ad4297c4eb3f4e787c4b000b90.
Updated by Ward Vandewege about 4 years ago
After rebuilding the compute image on Jenkins:
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