tidysbml

[veronicapaparozzi]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/veronicapaparozzi/tidysbml

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[bioc-issue-bot]

Hi @veronicapaparozzi

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: tidysbml
Type: Package
Title: Extract SBML's data into dataframes
Version: 0.99.0
Authors@R: person("Veronica", "Paparozzi", role = c("aut", "cre"), email = "veronicapaparozzi1@gmail.com")
Author: Veronica Paparozzi [aut, cre]
Maintainer: Veronica Paparozzi <veronicapaparozzi1@gmail.com>
Description: Starting from one SBML file, it is possible to extract its information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the 'notes' subelement and one set of columns for the content of the 'annotation' subelement. 
License: CC BY 4.0
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: 
  xml2,
  methods
Suggests: 
    rmarkdown,
    knitr,
    BiocStyle
biocViews: GraphAndNetwork, Network, Pathways, Software
VignetteBuilder: knitr

[vjcitn]

Thanks for this submission. Please provide some scientific context in the vignette. It would be great to show how information organized using SBML can be used with existing Bioconductor workflow or annotation processes. This would really help fit the package into the ecosystem. At present the package software focuses on xml transformation.

[veronicapaparozzi]

Thanks for the feedback. I have updated vignette file with required info. If I understand correctly from submission instructions, at this stage the version bump is not required, so I have not made changes in Description file. Please let me know if any adjustment is required. Thank you.

[lshep]

We recommend the vignette have a more distinct name (like your package name). Something generic like introduction can have naming conflicts depending on package load order. For instance just doing library of your package and doing a vignette("introduction") actually pulls up cowplot vignette without explicitly stating your package

> library(tidysbml)
> vignette("introduction")
starting httpd help server ... done
Warning message:
vignette 'introduction' found more than once,
using the one found in '/home/lorikern/R-Libraries/R4.4-Bioc3.19/cowplot/doc' 

You also don't show any examples still that use Bioconductor structures or packages? Unless I missed it?

[veronicapaparozzi]

Dear @lshep, I apologise for delayed reply. I’ve renamed the vignette file adding the package name. About interoperability examples, I've previously inserted at the beginning of the vignette a very short description of interoperability, just quoting the packages name, but your last answer suggest me that maybe it is not enough. Currently I am close to finish an article which describes the package and its applications. In particular, I’ve described some use cases of workflows in R to enable tidysbml output (R dataframes) as input to use other R packages. Specially, I show the R commands to run for:

• igraph package: in order to create an igraph graph starting from a portion of one of the output data frames;
• RCy3 package: starting from both igraph graph and dataframe (in form of edgelist)
• biomaRt package: to manipulate dataframes for accessing annotation databases

I suppose that these cases can be used for interoperability examples as well (please correct me if I’m wrong), but only one document can incorporate them. Thus I have some questions:

• Are these examples suitable for your request?
• If yes, could I report interoperability examples in the vignette just by adding citation to the article once it will be published? (The journal is open-access and the two submissions will be carried out in parallel); otherwise, could I describe inside vignette a similar example (for instance using biomaRt) ?
• If not, which are the type of examples needed?

Many thanks for your patience and availability.

[lshep]

Yes those examples (in particular RCy3 and biomaRt as Bioconductor packages) are suitable. We prefer to have some executed code in the vignette in a similar example to ensure runnable code/examples perform as advertised. If you could add examples showing how to incorporate with RCy3 and boimaRt that would be sufficient.

[lshep]

May we expected updates soon?

[veronicapaparozzi]

Yes, by tomorrow or at the latest the day after tomorrow I will update the package with the requested changes.

[veronicapaparozzi]

Dear @lshep, I've completed the changes discussed: I've update the vignette inserting two example of interoperability (with RCy3 and biomaRt). I've also put an additional file in external data.

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: ERROR before build products produced.

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/tidysbml to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.