CasedUgr commented 5 years ago

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

Repository: https://github.com/CasedUgr/KnowSeq

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 5 years ago

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

ea69fc5 KnowSeq V0.99.27

bioc-issue-bot commented 5 years ago

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: "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.

bioc-issue-bot commented 5 years ago

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

f86b9b1 KnowSeq V0.99.28

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

CasedUgr commented 5 years ago

Dear @Kayla-Morrell :

Thanks for you revision, I am going to proceed to answer you questions.

vignette

[x] CLARIFICATION: You said that Table of Contents were added to the file, but when I build the vignette I don't see it. Since it is just a suggestion, it isn't needed but I thought I would point it out since you said you made the change. I am very confused with this point, because when I compile the documentation in PDF or HTML the Table Of Content (toc) is added successfully. As you can see in the code, toc is setted to TRUE in order to achieve that.

_output: pdf_document: toc: true toc_depth: 3 number_sections: true highlight: tango citation_package: natbib html_document: toc: true toc_depth: 3 number_sections: true highlight: tango citationpackage: natbib

Are you trying to compile the documentation in a different format that PDF or HTML? Thank you again for your help.

[x] REQUIRED: All R code chunks need to contain '{}' so that the code is evaluated as R code. There are many code chunks that do not contain these curly braces, please correct this (line 76, 86, 146, 194, etc.). These pieces of code are related to the alignment step. This step requires the user interaction and the download of a precompiled tools. Due to that considerations, it is not possible to evaluated these pieces of code in the vignette. The rest of the code, when the count files are available, can be evaluated without problems. However, the example code includes the alignment step to execute it. If the chunks of R code shouldn't be evaluated then you should add 'eval = FALSE' but they still need to contain '{ }' so they are recognized as R code and not just text.

Done.

Best,

Daniel

Kayla-Morrell commented 5 years ago

@CasedUgr - I seem to have been able to compile the vignette with the table of contents. To do so I had to make a slight change to the code in your vignette file. Please see the code below:

vignette: >
  %\VignetteIndexEntry{The KnowSeq users guide} 
  \usepackage[UTF-8]{inputenc} 
  %\VignetteEngine{knitr::rmarkdown}

The vignette needs to be built using rmarkdown. Another minor note is that when the package is built it creates the vignette in only one format. Therefore you must chose which format you would prefer your vignette to be in (either PDF or HTML) and remove the other from the 'output:' code.

Thank you, Kayla

bioc-issue-bot commented 5 years ago

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

735a796 KnowSeq V0.99.30

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

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

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

Kayla-Morrell commented 5 years ago

@CasedUgr -

Thank you for making the changes, everything looks good and I'm happy to accept the package!

Best, Kayla

bioc-issue-bot commented 5 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/CasedUgr.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("KnowSeq"). The package 'landing page' will be created at

https://bioconductor.org/packages/KnowSeq

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Bioconductor / Contributions

KnowSeq R package #1121

vignette