outsider -- submission

[DomBennett]

Submitting Author: Dom Bennett (@DomBennett)
Repository: https://github.com/AntonelliLab/outsider
Version submitted: 0.0.0
Editor: @annakrystalli
Reviewer 1: @nuest
Reviewer 2: @hrbrmstr
Archive: TBD
Version accepted: 0.1.0

---

• Paste the full DESCRIPTION file inside a code block below:

Package: outsider
Type: Package
Title: Install and run programs, outside of R, inside of R
Version: 0.0.0
Authors@R: person("Dom", "Bennett", role = c("aut", "cre"),
    email = "dominic.john.bennett@gmail.com",
    comment = c(ORCID = "0000-0003-2722-1359"))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: Install and run external command-line programs in R through use of
    'Docker' <https://www.docker.com/> and 'GitHub' <http://github.com/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
SystemRequirements: docker (>=18.0.0)
URL: https://antonellilab.github.io/outsider
BugReports: https://github.com/antonellilab/outsider/issues
Language: en-GB
Depends:
    R (>= 3.3.0)
Imports:
    utils (>= 3.1),
    crayon,
    devtools (>= 1.1),
    jsonlite (>= 1.1),
    sys (>= 2.1),
    yaml (>= 2.0),
    callr (>= 3.0.0),
    withr (>= 2.0),
    stringr,
    tibble,
    cli,
    praise
Suggests:
    testthat (>= 2.0),
    knitr (>= 1.0)

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • database access
  • data munging
  • data deposition
  • reproducibility
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

The aim of the package is to enable R users to install and run, within R, software, packages and programs external to R. This allows users to more readily create workflows and pipelines that are portable, reproducible and make use of a wide range of available methods outside of R.

• Who is the target audience and what are scientific applications of this package?

The target audience are data scientists, bioinformaticians and general scientists interested in running external programs within R.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

There are many available packages that allow the interfacing between software external to R (e.g. packages for interacting with python or java). There does not, however, seem to be any packages that make use of docker (www.docker.com) to import external software as this package does. The closest packages to this one appear to be things like rocker. Rocker, however, uses docker to make R more portable, not external software accessible within R.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Technical checks

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:

JOSS Options

• The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

• The package is novel and will be of interest to the broad readership of the journal.
• The manuscript describing the package is no longer than 3000 words.
• You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
• (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (Please do not submit your package separately to Methods in Ecology and Evolution)

Code of conduct

• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[sckott]

thanks for your submission @DomBennett - in Repository: AntonelliLab/outsider can you give the url instead please

[DomBennett]

Done!

[sckott]

we're discussing now

[sckott]

thanks for your submission. @annakrystalli has been assigned as handling editor

[annakrystalli]

Hello @DomBennett!

Just starting with the editors checks now. Will get back to you with any initial feedback and next steps shortly.

[annakrystalli]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Many thanks again @DomBennett for your submission. A really interesting package!

I've completed the editor checks and am happy to start looking for reviewers. In the meantime, there are a couple of monior issues the initial checks have thrown up.

---

Test failure on oldrel

There's a test failure that pops up in examples when running on oldrel. Forking your repo and adding:

language: r
r:
  - oldrel
  - release

to travis.yml to also test on the old release of R indicates there's an API change between 3.4 and 3.5 R that affects package functionality, as oldrel fails.

In particular:

Checks

Throw an error in one of the module_details examples:

Running examples in ‘outsider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: module_details
> ### Title: Look up details on module(s)
> ### Aliases: module_details
> 
> ### ** Examples
> 
> library(outsider)
> # return table of ALL available modules on GitHub
> # NOT RUN - takes too long
> # (available_modules <- module_search())
> 
> # look-up whether specific module exists
> # NOT RUN
> # repo <- 'dombennett/om..goodbye.world'
> # (suppressWarnings(module_exists(repo = repo)))
> repo <- 'dombennett/om..hello.world'
> (module_exists(repo = repo))
dombennett/om..hello.world 
                      TRUE 
> # get details on specific module(s)
> (module_details(repo = repo))
Error in if (inherits(X[[j]], "data.frame") && ncol(xj) > 1L) X[[j]] <- as.matrix(X[[j]]) : 
  missing value where TRUE/FALSE needed
Calls: module_details -> lapply -> FUN -> as.matrix.data.frame
Execution halted

Tests

Again the same function fails the tests

* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [10s/74s]
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Container status 'This is a mock'
  ────────────────────────────────────────────────────────────────────────────────────────
  ── 1. Error: module_details() works (@test-search.R#94)  ───────────────────────────────
  missing value where TRUE/FALSE needed
  1: module_details(repo = c(repo, repo)) at testthat/test-search.R:94
  2: lapply(X = github_res, FUN = as.matrix)
  3: FUN(X[[i]], ...)
  4: as.matrix.data.frame(X[[i]], ...)
  

I've checked the CI section in our guide and admittedly we don't have any guidance on this currently, so we are discussing updating it as a result. In the meantime, can I ask that you:

• set up travis.yml to also test on devel, release and oldrel (I can make a PR if you like)?
• address the errors in oldrel? If you need any help debugging, just let us know.

Good practice

Firstly, goodpractice() throws a couple of warnings. it seems a few files don't end in a new line. I'm not sure how consequential that is to functionality. In any case, it probably means the files aren't being parsed correctly during goodpractice checks so it's best to address it we can check all the code.

• ensure complete final lines in files:

Preparing: lintr
incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/R/identities.R'incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/tests/test-all.R'incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/tests/test-all.R'incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/tests/testthat/test-outsider.R'incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/tests/testthat/test-outsider.R'incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/tests/testthat/test-test.R'incomplete final line found on '/Users/Anna/Documents/workflows/rOpenSci/editorials/outsider/tests/testthat/test-test.R'

Finally an issue that needs addressing

• remove call to require()

It is good practice to

  ✖ avoid the library() and require() functions, they change the
    global search path. If you need to use other packages, import them. If you
    need to load them explicitly, then consider loadNamespace() instead, or as
    a last resort, declare them as 'Depends' dependencies.

    R/test.R:18:22

Could you also please:

• add the rOpenSci under review badge to your README?

[![](https://badges.ropensci.org/282_status.svg)](https://github.com/ropensci/onboarding/issues/282)

If you could try and address these before review begins officially, that would be great. I'll ping back in when I've secured reviewers. In the meantime, feel free to reach out with any questions

---

Reviewers:
Due date:

[DomBennett]

Hi @annakrystalli

Thanks for the editor checks. I hope I've managed to correct the issues you raised!

Do you have any advice on running tests across different R versions (oldrel, release and devel) locally? Looks like I'd need to set up multiple virtual environments and install and run tests in each one; a bit of a palava.

Thanks!
Dom

[annakrystalli]

Hi @DomBennett,

Thanks for the swift action!

So we've opened an issue in the dev_guide regarding this (feel free to contribute to the discussion) and have outlined a couple of suggestions.

The main approach to test locally would be to use Rocker Docker images with different tags. Get different version with eg docker run -v $(pwd):/pkg rocker/verse:devel Rscript "devtools::check('/pkg')".

In your case It will be a bit trickier, because the package needs access to Docker itself. But it's doable. If you write a dockerfile that installs the docker client on top of a Rocker image, and mounts the docker socket when running the container, it should work.

Hope this helps and let us know if you have any more questions 😸

[DomBennett]

Thanks @annakrystalli! I'll look into using rocker and keep an eye on the issue in the dev_guide.