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The most complete R development and data science platform.

Home Page: https://rsuite.io

License: Apache License 2.0

R 100.00%

rsuite rsuitecli r development deployment rstats

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rsuite's Issues

RSuite archived on CRAN

I'm the maintainer of the CRAN Task View on Reproducible Research. RSuite was recently removed from the task view because it was archived on CRAN (there's a strict policy that task views can't contain archived packages).

https://cran.r-project.org/package=RSuite

Apparently there was an error running an example on Solaris (I can relate to how frustrating Solaris errors are).

https://cran-archive.r-project.org/web/checks/2021/2021-05-16_check_results_RSuite.html

I know you've put a lot of work into RSuite, so if you get it back on CRAN, please open an issue at https://github.com/jdblischak/reproducible-research-ctv so that I can add it back to the task view. Thanks!

Support for R 4.0

I know that with R 4.0 came significant changes to how packages are handled.
Will RSuite support R 4.0 and above?

"--sh" does not work as expected in "rsuite docker ..." commands

Describe the bug

--sh only accepts the first string in its values if you have more than one strings.

To Reproduce

$ rsuite docker img --rver=3.5 -p debian --version 0.0.1 --sh="apt-get install libpq-dev"

Expected behavior

apt-get install libpq-dev is executed before the docker image gets built.

Logs

$ rsuite docker img --rver=3.5 -p debian --version 0.0.1 --sh="apt-get install libpq-dev"
ERROR: "install" is not a valid option, or does not support an argument

Environment

OS: macOS 10.14.4
RSuite/RSuiteCLI version: 0.36.252
R version: 3.6.0 (2019-04-26) -- "Planting of a Tree"

Additional context

I did some research on the optparse R library. It seems to be an incomplete copy of Python's optparse library, which has been deprecated for long. And as per this SO said in the last answer:

Optparse is not able to handle these situations (multiple strings). You can only use nargs to specify particular amount of valiables, but there is nothing like "one or more". You need to hack it or use different library (e.g. argparse or other).

I also checked the workarounds mentioned in other answers, but unfortunately, none of them worked:

wrapping apt-get install libpq-dev with double or single quotes
escaping the spaces like apt-get\ install\ libpq-dev
nargs, which is not even a thing in R's clone of optparse (docs here)

Then I happened to find that argparse actually exists in the R world, and is even maintained by the author who wrote R's optparse. Surprisingly, it depends on Python:

The package has a Python dependency.

That sounds a bit strange, but maybe it helps.

Building docker image failed due to absence of `top` in the Debian base image

Describe the bug
rsuite docker img stopped working after upgraded to v0.37.253.

To Reproduce

rsuite docker img --tag test --tag-latest -p debian --version 0.0.1 --verbose

Expected behavior
A docker image is built like it used to be able to.

Logs

2019-06-19 13:35:13 INFO::Will use wlog/rsuite:debian_r3.6 as base image!
2019-06-19 13:35:13 INFO::Retrieving RSuite CLI exposed on S3 package index ...
2019-06-19 13:35:13 INFO::... found v0.37.253 (debian/rsuitecli_0.37.253-1_all.deb)
2019-06-19 13:35:13 INFO::Starting container rsbuild-b81f18694df4 based on wlog/rsuite:debian_r3.6_v0.37.253 ...
2019-06-19 13:35:13 DEBUG::running: /usr/local/bin/docker run --name rsbuild-b81f18694df4 -d wlog/rsuite:debian_r3.6_v0.37.253 sh -c top -b
2019-06-19 13:35:13 DEBUG::out> de4e691cf4fafc7c900e28c86aca3e4ad4002ea7d4eba60054f38944e28ed01a
2019-06-19 13:35:14 DEBUG::return code: 0
2019-06-19 13:35:14 INFO::Starting container rsbuild-b81f18694df4 based on wlog/rsuite:debian_r3.6_v0.37.253 ... done.
2019-06-19 13:35:14 INFO::RSuite build container rsbuild-b81f18694df4 started ...
2019-06-19 13:35:14 DEBUG::running: /usr/local/bin/docker ps -f name=rsbuild-
2019-06-19 13:35:14 DEBUG::out> CONTAINER ID        IMAGE                               COMMAND             CREATED             STATUS                  PORTS               NAMES
2019-06-19 13:35:14 DEBUG::out> de4e691cf4fa        wlog/rsuite:debian_r3.6_v0.37.253   "sh -c 'top -b'"    1 second ago        Up Less than a second                       rsbuild-b81f18694df4
2019-06-19 13:35:14 DEBUG::return code: 0
2019-06-19 13:35:14 DEBUG::running: /usr/local/bin/docker exec rsbuild-b81f18694df4 Rscript --version
2019-06-19 13:35:14 DEBUG::err> Error response from daemon: Container de4e691cf4fafc7c900e28c86aca3e4ad4002ea7d4eba60054f38944e28ed01a is not running
2019-06-19 13:35:14 DEBUG::return code: 1
2019-06-19 13:35:14 INFO:rsuite:Exporting project from /Users/freeyoung/code/test/test ...
2019-06-19 13:35:15 INFO:rsuite:Package R version set to Error response from daemon: Container de4e691cf4fafc7c900e28c86aca3e4ad4002ea7d4eba60054f38944e28ed01a is not running
2019-06-19 13:35:15 INFO:rsuite:Exporting project from /Users/freeyoung/code/test/test ... done
2019-06-19 13:35:16 INFO::Copying project pack into container rsbuild-b81f18694df4 ...
2019-06-19 13:35:16 DEBUG::running: /usr/local/bin/docker cp /private/var/folders/96/xg4qffjj0g19w945m_bqswjr0000gn/T/RtmpNN9KGD/prjpack_test_0.0.1x.zip rsbuild-b81f18694df4:/opt/
2019-06-19 13:35:17 DEBUG::return code: 0
2019-06-19 13:35:17 INFO::Copying project pack into container rsbuild-b81f18694df4 ... done.
2019-06-19 13:35:17 DEBUG::running: /usr/local/bin/docker exec rsbuild-b81f18694df4 Rscript -e if (dir.exists('/opt/test')) {   unlink('/opt/test', recursive = TRUE, force = TRUE); }
2019-06-19 13:35:17 DEBUG::err> Error response from daemon: Container de4e691cf4fafc7c900e28c86aca3e4ad4002ea7d4eba60054f38944e28ed01a is not running
2019-06-19 13:35:17 DEBUG::return code: 1
2019-06-19 13:35:17 INFO::[rsbuild-b81f18694df4] Running command 'unzip prjpack_test_0.0.1x.zip' ...
2019-06-19 13:35:17 DEBUG::running: /usr/local/bin/docker exec -i rsbuild-b81f18694df4 sh -c unzip prjpack_test_0.0.1x.zip
2019-06-19 13:35:17 DEBUG::err> Error response from daemon: Container de4e691cf4fafc7c900e28c86aca3e4ad4002ea7d4eba60054f38944e28ed01a is not running
2019-06-19 13:35:17 DEBUG::return code: 1
ERROR: Error response from daemon: Container de4e691cf4fafc7c900e28c86aca3e4ad4002ea7d4eba60054f38944e28ed01a is not running
2019-06-19 13:35:17 INFO::Removing container rsbuild-b81f18694df4 ...
2019-06-19 13:35:17 DEBUG::running: /usr/local/bin/docker rm -f rsbuild-b81f18694df4
2019-06-19 13:35:17 DEBUG::out> rsbuild-b81f18694df4
2019-06-19 13:35:17 DEBUG::return code: 0
2019-06-19 13:35:17 INFO::Removing container rsbuild-b81f18694df4 ... done.
ERROR: [rsbuild-b81f18694df4] Running command 'unzip prjpack_test_0.0.1x.zip' failed

Environment

OS: macOS 10.14.5
RSuite/RSuiteCLI version: 0.37.253
R version: 3.5.3 (locally)

Additional context
I think the issue was introduced in d61c296#diff-e4e6a904027035d673706be3cf18c62a .

And top is not installed.

$ docker run -it --name rsbuild-demo -d wlog/rsuite:debian_r3.6_v0.37.253 sh -c top -b
26aeb632475d63858a72bba563be51b3391cc736f31a4af7e618f8e634518a0b
$ docker logs rsbuild-demo
-b: 1: -b: top: not found

$ docker run -it --name rsbuild-demo2 -d wlog/rsuite:debian_r3.6_v0.37.253 bash
244533aa97bcd82bc531415a97a0a757380d6ddee50488acd7f04d440e600e02
$ docker exec -it rsbuild-demo2 bash
root@244533aa97bc:/opt# top
bash: top: command not found

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