Roma

[klarakaleb]

• Repository: https://github.com/klarakaleb/roma

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor [Package Submission][2] instructions. My package is consistent with the Bioconductor [Package Guidelines][1].

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the [support site][3] for issues that users may have, subscribing to the [bioc-devel][4] mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

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• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using [Git][5] (optionally [via GitHub][6]).

[bioc-issue-bot]

Hi @klarakaleb

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: roma
Title: R wrapper for the OMA REST API
Version: 0.99.0
Author: Klara Kaleb 
Maintainer: Klara Kaleb <klarakaleb@outlook.com>
Description: A package for the orthology prediction data download from OMA database.
Depends: R (>= 3.3.2), jsonlite (>= 1.5), httr (>= 1.2.1),plyr(>= 1.8.4), utils
Imports: jsonlite, httr, plyr
License: GPL-2
LazyData: true
RoxygenNote: 6.0.1.9000
Suggests: knitr,
    rmarkdown
VignetteBuilder: knitr
biocViews: Software, Comparative Genomics, Functional Genomics, Genetics, Annotation, GO

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". 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 following build report for more details:

http://bioconductor.org/spb_reports/roma_buildreport_20170922150417.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

8c34c9e third commit

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". 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 following build report for more details:

http://bioconductor.org/spb_reports/roma_buildreport_20170922152348.html

[lawremi]

There needs to be a layer that integrates this information somehow with Bioconductor. The vignette just documents the functions; it needs to provide a tutorial/workflow --- how would someone use this package in the broader context? This should not have low-level packages like jsonlite listed in Depends. Just keep them in Imports.

[lshep]

Thank you for your submission please see the following comments:

• [ ] Michael's comment above is valid and should be addressed. Until there is a more thorough vignette, it is hard to evaluate your package. There should be some integration with Bioconductor, like the output being converted into a standard Bioconductor object to be used with other existing pipelines.

• [ ] also fix all ERROR, WARNING, and NOTES from the build report.

• [ ] When I tried to clone your repo locally I also ran into the following ERROR's trying to build:

  
  R CMD build roma/

• checking for file 'roma/DESCRIPTION' ... OK

• preparing 'roma':

• checking DESCRIPTION meta-information ... OK

• installing the package to build vignettes

• creating vignettes ... ERROR Loading required package: jsonlite Loading required package: httr Loading required package: plyr Quitting from lines 22-27 (my-vignette.Rmd) Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: 'fromJSON' is not an exported object from 'namespace:httr' Execution halted

  After I fixed that locally:

  R CMD build roma/

• checking for file 'roma/DESCRIPTION' ... OK

• preparing 'roma':

• checking DESCRIPTION meta-information ... OK

• installing the package to build vignettes

• creating vignettes ... ERROR Loading required package: jsonlite Loading required package: httr Loading required package: plyr No encoding supplied: defaulting to UTF-8. Quitting from lines 22-27 (my-vignette.Rmd) Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: lexical error: invalid char in json text.