Submission: BaseSet

[llrs]

Submitting Author: Lluís (@llrs)
Repository: llrs/BaseSet
Version submitted: 0.0.10
Editor: @annakrystalli
Reviewer 1: @arendsee
Reviewer 2: @j23414
Archive: TBD
Version accepted: TBD

---

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

Package: BaseSet
Title: Provides classes for working with sets
Version: 0.0.10
Authors@R: 
    person(given = "Lluís ",
           family = "Revilla Sancho",
           role = c("aut", "cre"),
           email = "lluis.revilla@gmail.com")
Description: A set collection, while not "tidy" in itself, can
    be thought of as three tidy data frames describing sets, elements and
    relations respectively. 'BaseSet' provides an approach to manipulate,
    load and use these virtual data frames.
License: MIT + file LICENSE
URL: https://github.com/llrs/BaseSet
BugReports: https://github.com/llrs/BaseSet/issues
Depends: 
    R (>= 3.6.0)
Imports: 
    dplyr (>= 0.7.8),
    magrittr,
    methods,
    rlang,
    utils,
    xml2
Suggests: 
    BiocStyle,
    covr,
    forcats,
    ggplot2,
    GO.db,
    GSEABase,
    knitr,
    org.Hs.eg.db,
    reactome.db,
    rmarkdown,
    spelling,
    testthat (>= 2.1.0),
    Biobase
VignetteBuilder: 
    knitr
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.0.2
Collate: 
    'AllClasses.R'
    'AllGenerics.R'
    'GMT.R'
    'GeneSetCollection.R'
    'activate.R'
    'add.R'
    'add_column.R'
    'add_relation.R'
    'adjacency.R'
    'arrange.R'
    'basesets-package.R'
    'cartesian.R'
    'complement.R'
    'data_frame.R'
    'deactivate.R'
    'droplevels.R'
    'elements.R'
    'filter.R'
    'group.R'
    'group_by.R'
    'head.R'
    'incidence.R'
    'independent.R'
    'operations.R'
    'intersection.R'
    'length.R'
    'list.R'
    'move_to.R'
    'mutate.R'
    'names.R'
    'naming.R'
    'nested.R'
    'obo.R'
    'power_set.R'
    'print.R'
    'pull.R'
    'relations.R'
    'remove.R'
    'remove_column.R'
    'rename.R'
    'select.R'
    'set.R'
    'size.R'
    'subtract.R'
    'tidy-set.R'
    'union.R'
    'utils-pipe.R'
    'xml.R'
    'zzz.R'

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
  • workflow automataion
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • database software bindings
  • geospatial data
  • text analysis

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

The package implements methods to work on sets, doing intersection, union, complementary and other set operations in a "tidy" way. It also allows to import from several formats used in the life science world. Like the GMT and the GAF or the OBO format file for ontologies.

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

The idea is to use the package for working with sets and signatures of genes in scRNAseq or in pathways and ontologies but it might work with other fields.

• 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 is the sets package which implements a more generalized approach, that can store functions or lists as an element of a set (while mine it only allows to store a character or factor), but it is harder to operate in a tidy/long way. Also the operations of intersection and union need to happen between two different objects, while TidySet objects (the class implemented in BaseSet) can store a single set or thousands of them.
In BaseSet is easier to operate and implement new fuzzy logic operations. It is developed openly on github compared to sets which I couldn't track how it is being developed.

The GSEABase partially implements this, but it doesn't allow to store fuzzy sets and it is also quite slow as it creates several classes for annotating each set. Neither does the BiocSets the package, which don't use the fuzzy set logic.

There is also the hierarchicalSets package that is focused on clustering of sets that are inside other sets and visualizations. However, BaseSet is focused on storing and manipulate sets including hierarchical sets.

• 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.

Most of the replies are copied from #339, handeled by @melvidoni.

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.

[annakrystalli]

Hi @llrs! 👋

I'll be the editor handling your review. I'm starting the inital editors' checks shortly. Will check back in when they are done. 😊

[annakrystalli]

Hello again @llrs!

Thanks for your patience with the editors checks. I've been traveling but I've also been having some issues with the checks which I'm having to seek some help with. Will be with you shortly, if not with the full checks, at least with those that I am able to perform successfully.

[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

Installation issues

When I try to do a full install and build vignettes, some suggested bioconductor dependencies are not installing and causing errors when attempting to build the vignettes.

devtools::install_github("llrs/BaseSet", dependencies = T, build_vignettes = T)

#> Installing 7 packages: BiocStyle, GO.db, GSEABase, org.Hs.eg.db, reactome.db, Biobase, BH
#> Error: (converted from warning) packages 'BiocStyle', 'GO.db', 'GSEABase', 'org.Hs.eg.db', 'reactome.db', 'Biobase' are not available (for R version 3.6.0)

***
   
   Error: Vignette re-building failed.
   Execution halted
Error in (function (command = NULL, args = character(), error_on_status = TRUE,  : 
  System command error
  

Reviewevers as well as potential future collaborators that will need to run devtools::check() and devtools::document(), need a section in the README or a separate CONTRIBUTING.md documenting the installation instructions required to install all dependencies (including suggested).

eg:

BiocManager::install("BiocStyle")
BiocManager::install("org.Hs.eg.db", type = "source")
BiocManager::install("GO.db", type = "source")
BiocManager::install("reactome.db", type = "source")

# test that package install and docs build successfully
devtools::install_github("llrs/BaseSet", dependencies = T, build_vignettes = T, force = T)

You can check out more of the adventures I had troubleshooting in this issue comment for more details. If you have some extra insight (as I imagine you are more familiar with bioconductor) to add to the discussion it would be more than welcome!

check() and test()

All good

goodpractice::gp() output

A few flags for minor formatting.

It is good practice to

  ✖ avoid long code lines, it is bad for
    readability. Also, many people prefer editor windows
    that are about 80 characters wide. Try make your
    lines shorter than 80 characters

    R/AllClasses.R:105:1
    R/AllGenerics.R:149:1
    R/AllGenerics.R:163:1
    R/length.R:171:1
    R/obo.R:122:1
    ... and 16 more lines

This is actually a bit more important. Is there a reason you are importing methods and utils packages as a whole?

  ✖ not import packages as a whole, as this
    can cause name clashes between the imported
    packages. Instead, import only the specific
    functions you need.
──────────────────────────────────────────────────────────────── 

Test coverage

Test coverage is overall good but is there a reason there are some files that are not tested at all or below 75%?

See the files indicated below:

BaseSet Coverage: 89.13%
R/xml.R: 0.00%
R/elements.R: 62.50%
R/set.R: 62.50%
R/size.R: 71.43%
R/pull.R: 73.33%

@llrs, could you please add the rOpenSci under review badge to your README?

[![](https://badges.ropensci.org/359_status.svg)](https://github.com/ropensci/software-review/issues/359)

Other than these minor issues, I am happy to start seeking reviewers.

---

Reviewers:
Due date:

[llrs]

Many thanks for your review @annakrystalli

• Installation problems: Oh, sorry on travis and my computer I didn't had these installation problems. I would follow the BiocViews solution, but usually the easier solution might be to use BiocManager::install("llrs/BaseSet"). Lately there has been some problems with the Bioconductor binaries for Windows related to BiocStyle (Some of your problems might come from this, but I'm not sure as I have not submitted a data package).
• Regarding long lines: Some of I had considered them easier to read with slightly over 80 character per line, some of them will be me forgetting to reformat them. I'll check each one of those lines.
• {methods} & {utils}: I thought that it would be easier to work with the S4 class if I imported both packages and I use many functions of them. It is easier for me while writing the package too. They are both installed by default so I did not expect much problems, but I will import only the functions needed.
• Test coverage: I forgot to delete the xml.R file. I think there isn't a compromise on which format are written with sets on .xml files. The other few packages that are below 75% might be that I didn't check for some exceptions.
• rOpenSci badge: Will add it.

I'll modify the package to address your points by the beginning of next week I'll have them addressed. I'll let you know when I updated the package.

[annakrystalli]

Hello again @llrs,

Aha, it seems I have been trying to install the package the wrong way all this time, by using devtools::use_github() as I normally do for editors checks when I should be using BiocManager::install()

However, when I try to install using BiocManager::install("llrs/BaseSet", dependencies = TRUE, build_vignettes = TRUE) I still get the same errors for a couple of suggested bioconductor packages I removed to test it out.

I'm really intrigued by the fact that the packages builds successfully for you on TRAVIS. Looking at your travis.yml I see you are testing on r: bioc-devel only. I think this where the testing computational environment and my own (and of reviewers and future collaborators) would differ. I feel also testing on r: release at the very least would give a better idea of what challenges others would encounter. Would you mind trying that out for me?

[llrs]

Some of this errors might be due to a failed built on Bioconductor, they recently made some changes on the checks performed on packages. Could you please post the error you got?

On travis I am only testing on bioc-devel, but on my computer I am using R 3.6.1 with Bioconductor 3.10 and it builds successfully. I'm not sure this difference is the source of the problems you found. However, I'll add the build and test for r release.

[annakrystalli]

So the errors I am getting are the same as I was previously with using devtools::install_github(), namely, any missing bioconductor packages that need installing from source are missing. I've deleted package GO.db from my system and so now, the vignette that loads it is failing. Here's a condensed error output:

BiocManager::install("llrs/BaseSet", dependencies = TRUE, build_vignettes = TRUE)

E  creating vignettes (8.6s)
   --- re-building ‘advanced.Rmd’ using rmarkdown
   
   Attaching package: 'dplyr'
   
.
.
.

   Quitting from lines 49-56 (advanced.Rmd) 
   Error: processing vignette 'advanced.Rmd' failed with diagnostics:
   there is no package called 'GO.db'
   --- failed re-building ‘advanced.Rmd’
   
   --- re-building ‘basic.Rmd’ using rmarkdown
   --- finished re-building ‘basic.Rmd’
   
   --- re-building ‘fuzzy.Rmd’ using rmarkdown
   --- finished re-building ‘fuzzy.Rmd’
   
   SUMMARY: processing the following file failed:
     ‘advanced.Rmd’
   
   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'BaseSet' from GitHub:
  System command error, exit status: 1, stdout + stderr (last 10 lines):
E> --- finished re-building ‘basic.Rmd’
E> 
E> --- re-building ‘fuzzy.Rmd’ using rmarkdown
E> --- finished re-building ‘fuzzy.Rmd’
E> 
E> SUMMARY: processing the following file failed:
E>   ‘advanced.Rmd’
E> 
E> Error: Vignette re-building failed.
E> Execution halted

The reason this would not fail on your system is because you already have all the necessary package installed, but reviewers or new contributors won't necessarily. The reason I think the travis tests are passing is because of you are testing on bioc-devel. I can't think of why else installation on TRAVIS works while it doesn't for me. Testing on r: release feels like it would give you a more realistic situtation of what manual install steps would be required at any point by developers/ reviewers to be able to fully test and check the package.

Out of interest, you could try removing GO.db locally on your system and see what happens. For info, here's my session info too, ie I'm on a mac not windows.

> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.0 (2019-04-26)
 os       macOS Mojave 10.14.3        
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       America/Los_Angeles         
 date     2020-01-30                  

─ Packages ───────────────────────────────────────────────────────────────────────────
 package     * version     date       lib source                             
 assertthat    0.2.1       2019-03-21 [1] CRAN (R 3.6.0)                     
 backports     1.1.5       2019-10-02 [1] CRAN (R 3.6.0)                     
 BiocManager   1.30.10     2019-11-16 [1] CRAN (R 3.6.0)                     
 callr         3.4.1       2020-01-24 [1] CRAN (R 3.6.0)                     
 cli           2.0.1       2020-01-08 [1] CRAN (R 3.6.0)                     
 clipr         0.7.0       2019-07-23 [1] CRAN (R 3.6.0)                     
 crayon        1.3.4       2017-09-16 [1] CRAN (R 3.6.0)                     
 curl          4.3         2019-12-02 [1] CRAN (R 3.6.0)                     
 desc          1.2.0       2018-05-01 [1] CRAN (R 3.6.0)                     
 devtools    * 2.2.1       2019-09-24 [1] CRAN (R 3.6.0)                     
 digest        0.6.23      2019-11-23 [1] CRAN (R 3.6.0)                     
 ellipsis      0.3.0       2019-09-20 [1] CRAN (R 3.6.0)                     
 evaluate      0.14        2019-05-28 [1] CRAN (R 3.6.0)                     
 fansi         0.4.1       2020-01-08 [1] CRAN (R 3.6.0)                     
 fs            1.3.1       2019-05-06 [1] CRAN (R 3.6.0)                     
 glue          1.3.1       2019-03-12 [1] CRAN (R 3.6.0)                     
 htmltools     0.4.0       2019-10-04 [1] CRAN (R 3.6.0)                     
 knitr         1.27        2020-01-16 [1] CRAN (R 3.6.0)                     
 magrittr      1.5         2014-11-22 [1] CRAN (R 3.6.0)                     
 memoise       1.1.0       2017-04-21 [1] CRAN (R 3.6.0)                     
 packrat       0.5.0       2018-11-14 [1] CRAN (R 3.6.0)                     
 pkgbuild      1.0.6       2019-10-09 [1] CRAN (R 3.6.0)                     
 pkgload       1.0.2       2018-10-29 [1] CRAN (R 3.6.0)                     
 prettyunits   1.1.1       2020-01-24 [1] CRAN (R 3.6.0)                     
 processx      3.4.1       2019-07-18 [1] CRAN (R 3.6.0)                     
 ps            1.3.0       2018-12-21 [1] CRAN (R 3.6.0)                     
 R6            2.4.1       2019-11-12 [1] CRAN (R 3.6.0)                     
 Rcpp          1.0.3       2019-11-08 [1] CRAN (R 3.6.0)                     
 remotes       2.1.0       2019-06-24 [1] CRAN (R 3.6.0)                     
 reprex      * 0.3.0       2019-05-16 [1] CRAN (R 3.6.0)                     
 rlang         0.4.3       2020-01-24 [1] CRAN (R 3.6.0)                     
 rmarkdown     2.1         2020-01-20 [1] CRAN (R 3.6.0)                     
 rprojroot     1.3-2       2018-01-03 [1] CRAN (R 3.6.0)                     
 rstudioapi    0.10.0-9000 2019-05-30 [1] Github (rstudio/rstudioapi@31d1afa)
 sessioninfo   1.1.1       2018-11-05 [1] CRAN (R 3.6.0)                     
 testthat    * 2.3.1       2019-12-01 [1] CRAN (R 3.6.0)                     
 usethis     * 1.5.1.9000  2020-01-29 [1] Github (r-lib/usethis@4194fd6)     
 whisker       0.4         2019-08-28 [1] CRAN (R 3.6.0)                     
 withr         2.1.2       2018-03-15 [1] CRAN (R 3.6.0)                     
 xfun          0.12        2020-01-13 [1] CRAN (R 3.6.0)                     

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

[llrs]

I've updated the package as requested on your initial review.

However, I think that the configuration for .travis.yaml that better matches CRAN is using bioc-release. Because otherwise it doesn't install the Bioconductor packages. I hope that with the new instructions to install the Bioconductor packages reviewers and users will be able to install all of its dependencies.

[annakrystalli]

Hi @llrs,

Sorry, I probably didn't make myself clear enough. For sure you should be testing on bioc-release (perhaps on bioc-devel also). What I was suggesting is that you run a matrix of jobs that include testing on r-release and including any manual setup code during the build to both test that any awkward dependencies required for a reviewer/collaborator to work with the source code locally have:
a) been identified
b) their installation has been successfully specified.

Does that make sense? I've opened a PR to your repo with my attempt at implementing this. Let's see if it's successful!