Story #16264

Handle R SDK dependencies better

Added by Peter Amstutz over 1 year ago. Updated about 1 year 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 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&section=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.

https://www.ccdatalab.org/blog/2019/8/9/pinning-transitive-r-dependencies-for-fun-and-reproducible-builds

This works on any R install. The drawback is that we still end up compiling the whole world every time.

20200925-doc-gen-timing.png (91.4 KB) 20200925-doc-gen-timing.png Ward Vandewege, 09/25/2020 06:26 PM

Subtasks

Task #16879: ReviewNewPeter Amstutz


Related issues

Related to Arvados - Bug #16267: arvbox build uses arvados-server installResolved09/24/2020

Related to Arvados - Story #16053: [boot] subcommand to install/update dev and runtime dependenciesResolved03/31/2020

Related to Arvados - Bug #16586: ArvadosR: Dependency package(s) 'XML' not available.Resolved

Associated revisions

Revision 27992e62
Added by Ward Vandewege about 1 year ago

Merge branch '16264-add-r-dependencies' into master

closes #16264

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

History

#1 Updated by Peter Amstutz over 1 year ago

  • Description updated (diff)

#2 Updated by Peter Amstutz over 1 year ago

  • Related to Bug #16267: arvbox build uses arvados-server install added

#3 Updated by Peter Amstutz over 1 year ago

Currently I think the solution is for #16053 to include installing the appropriate R packages from Debian 10.

#4 Updated by Peter Amstutz over 1 year ago

  • Related to Story #16053: [boot] subcommand to install/update dev and runtime dependencies added

#5 Updated by Peter Amstutz over 1 year ago

  • Category set to SDKs

#6 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-04-08 Sprint to 2020-04-22

#7 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-04-22 to 2020-05-06 Sprint

#8 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-05-06 Sprint to 2020-05-20 Sprint

#9 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-05-20 Sprint to 2020-06-03 Sprint

#10 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-06-03 Sprint to 2020-06-17 Sprint

#11 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-06-17 Sprint to 2020-07-01 Sprint

#12 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-07-01 Sprint to 2020-07-15

#13 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-07-15 to 2020-08-12 Sprint

#14 Updated by Peter Amstutz over 1 year ago

  • Related to Bug #16586: ArvadosR: Dependency package(s) 'XML' not available. added

#15 Updated by Peter Amstutz over 1 year ago

  • Description updated (diff)

#16 Updated by Peter Amstutz over 1 year ago

  • Target version changed from 2020-08-12 Sprint to 2020-08-26 Sprint

#17 Updated by Peter Amstutz about 1 year ago

  • Target version changed from 2020-08-26 Sprint to 2020-09-09 Sprint

#18 Updated by Peter Amstutz about 1 year ago

  • Target version changed from 2020-09-09 Sprint to 2020-09-23 Sprint

#19 Updated by Peter Amstutz about 1 year ago

  • Target version changed from 2020-09-23 Sprint to 2020-10-07 Sprint

#20 Updated by Peter Amstutz about 1 year 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

#21 Updated by Peter Amstutz about 1 year ago

  • Assigned To set to Ward Vandewege

#22 Updated by Ward Vandewege about 1 year ago

  • Status changed from New to In Progress

#23 Updated by Ward Vandewege about 1 year 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_19:36:30.59411 ^M  |                                                                            ^M  |.........................................................             |  82%
2020-09-24_19:36:30.59411   ordinary text without R code
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2020-09-24_19:36:30.59412 ^M  |                                                                            ^M  |..........................................................            |  83%
2020-09-24_19:36:30.59412 label: unnamed-chunk-37
2020-09-24_19:36:30.59413 ^M  |                                                                            ^M  |...........................................................           |  84%
2020-09-24_19:36:30.59413   ordinary text without R code
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2020-09-24_19:36:30.59413 ^M  |                                                                            ^M  |............................................................          |  85%
2020-09-24_19:36:30.59414 label: unnamed-chunk-38
2020-09-24_19:36:30.59414 ^M  |                                                                            ^M  |.............................................................         |  87%
2020-09-24_19:36:30.59414   ordinary text without R code
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2020-09-24_19:36:30.59414 ^M  |                                                                            ^M  |.............................................................         |  88%
2020-09-24_19:36:30.59415 label: unnamed-chunk-39
2020-09-24_19:36:30.59415 ^M  |                                                                            ^M  |..............................................................        |  89%
2020-09-24_19:36:30.59415   ordinary text without R code
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2020-09-24_19:36:30.59416 ^M  |                                                                            ^M  |...............................................................       |  90%
2020-09-24_19:36:30.59416 label: unnamed-chunk-40
2020-09-24_19:36:30.59417 ^M  |                                                                            ^M  |................................................................      |  91%
2020-09-24_19:36:30.59417   ordinary text without R code
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2020-09-24_19:36:30.59417 ^M  |                                                                            ^M  |................................................................      |  92%
2020-09-24_19:36:30.59418 label: unnamed-chunk-41
2020-09-24_19:36:30.59418 ^M  |                                                                            ^M  |.................................................................     |  93%
2020-09-24_19:36:30.59418   ordinary text without R code
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2020-09-24_19:36:30.59419 ^M  |                                                                            ^M  |..................................................................    |  94%
2020-09-24_19:36:30.59419 label: unnamed-chunk-42
2020-09-24_19:36:30.59419 ^M  |                                                                            ^M  |...................................................................   |  96%
2020-09-24_19:36:30.59420   ordinary text without R code
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2020-09-24_19:36:30.59420 ^M  |                                                                            ^M  |....................................................................  |  97%
2020-09-24_19:36:30.59421 label: unnamed-chunk-43
2020-09-24_19:36:30.59421 ^M  |                                                                            ^M  |....................................................................  |  98%
2020-09-24_19:36:30.59421   ordinary text without R code
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2020-09-24_19:36:30.59422 ^M  |                                                                            ^M  |..................................................................... |  99%
2020-09-24_19:36:30.59422 label: unnamed-chunk-44 (with options)
2020-09-24_19:36:30.59422 List of 1
2020-09-24_19:36:30.59422  $ engine: chr "bash" 
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2020-09-24_19:36:30.59423 ^M  |                                                                            ^M  |......................................................................| 100%
2020-09-24_19:36:30.59423   ordinary text without R code
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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

#24 Updated by Peter Amstutz about 1 year ago

LGTM.

#25 Updated by Peter Amstutz about 1 year ago

Please update the jenkins test image as well

#26 Updated by Ward Vandewege about 1 year ago

  • % Done changed from 0 to 100
  • Status changed from In Progress to Resolved

#27 Updated by Ward Vandewege about 1 year ago

After rebuilding the compute image on Jenkins:

#28 Updated by Peter Amstutz about 1 year ago

  • Release set to 25

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