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Accio / KEGGgraph

The KEGGgraph package to parse KEGG pathways in R into graph objects
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convert KEGGgraph.Rnw to KEGGgraph.Rmd #16

Open sonali8434 opened 1 year ago

sonali8434 commented 1 year ago

@jwokaty kindly Review this PR before we ask @Accio for a final review.

@Accio We noticed that this pdf contains sections referring to pages, but it is not possible to refer to pages in new .Rmd file since we don't have a page no in an HTML document. So we have referred to sections instead of pages in the new KEGGgraph.Rmd file. If you have any suggestions about this, please don't hesitate to let us know.

We generally ask one of our team members to review the conversions before asking the maintainers to review them.

@Accio Generally, we give credits to the converter for converting Sweave documents. We ask maintainers if they want us to add ourselves as contributors in the description file and the. Rmd file. I wanted to ask if you would like me to add as a contributor for this conversion. It's totally fine to say no.

After your final review when you merge the PR, remember to bump the version in the DESCRIPTION file so that the Bioconductor build system will recognize the new changes and push the changes to Bioconductor's git repository.

sonali8434 commented 1 year ago

@jwokaty Thanks for the review, and I'm sorry for not pushing my changes to the description file. Thanks for reminding me.

I have made the changes you asked for. Please review.

Accio commented 1 year ago

Dear @sonali8434 and @jwokaty, I agree with the changes you proposed. Thank you for making them.

Do you mind adding yourself as contributors in the DESCRIPTION file? I am glad to merge the changes once the testing passes.

Have a good day and thanks again for the generous help, David.

sonali8434 commented 1 year ago

@Accio, I have completed the remaining changes. Please review the file and let me know if any more changes are required.

Thank you.