rgoslin submission

[nilshoffmann]

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

• Repository: https://github.com/lifs-tools/rgoslin

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[bioc-issue-bot]

Hi @nilshoffmann

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: rgoslin
Type: Package
Title: Lipid Shorthand Name Parsing and Normalization
Version: 0.99.1
Date: 2021-12-10
Authors@R: c(
    person("Nils", "Hoffmann", email = "nils.hoffmann@cebitec.uni-bielefeld.de", role=c("aut","cre"), comment = c(ORCID = "0000-0002-6540-6875")),
    person("Dominik", "Kopczynski", email = "dominik.kopczynski@univie.ac.at", role=c("aut"), comment = c(ORCID = "0000-0001-5885-4568")))
Description: The R implementation for the Grammar of Succint Lipid Nomenclature
    parses different short hand notation dialects for lipid names. It 
    normalizes them to a standard name. It further provides calculated 
    monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS
    Category and Class information. Also, the structural level and further structural
    details about the head group, fatty acyls and functional groups are returned, where applicable.
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.3)
LinkingTo: Rcpp, testthat
Suggests: 
    pkgKitten,
    testthat (>= 2.1.0),
    knitr,
    rmarkdown,
    kableExtra,
    dplyr,
    BiocManager
RoxygenNote: 7.1.2
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: Software, Lipidomics, Metabolomics, Preprocessing, Normalization, MassSpectrometry
BugReports: https://github.com/lifs-tools/rgoslin/issues
URL: https://github.com/lifs-tools/rgoslin

[bioc-issue-bot]

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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 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. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[nilshoffmann]

@PeteHaitch I have updated my repository at https://github.com/lifs-tools/rgoslin, removing the Rstudio project file that seems to have caused the build error, according to the logs. I do not seem to have rights to push to Bioconductor's git at this point. How should we proceed?

[lshep]

@nilshoffmann you should have permission to push to git.bioconductor.org. You will need to activate your GitCredentials account as mentioned about and add ssh-keys for access. https://git.bioconductor.org/BiocCredentials . Then follow the instructions for pushing to git.bioconductor.org https://bioconductor.org/developers/how-to/git/new-package-workflow/

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 921329133ff613d89623f4a0cd8a8c688fb3a7c8

[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.

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

Please see the build report for more details. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[PeteHaitch]

Thanks @nilshoffmann. I aim to do the initial review this week (mid-next week at the latest).

[PeteHaitch]

Hi @nilshoffmann,

I see that rgoslin provides R bindings to the 'Goslin grammars' and that there are analogous packages for other programming languages. I started to review rgoslin, but before I go too far I'd like to clarify why you chose to submit to Bioconductor rather than, say, CRAN? In asking this, I don't mean to discourage the submission of rgoslin to Bioconductor.

I appreciate that lipids could certainly fall under Bioconductor's broad aim of supporting the "analysis of data from current and emerging biological assays", but rgoslin currently does not depend on any Bioconductor packages nor do the examples demonstrate how rgoslin would fit into a workflow that makes use of existing Bioconductor software around lipidomics, metabolomics, etc.

Since a key aim of the Bioconductor project is package interoperatability, some demonstration of this is generally considered essential. Are there packages within the LipidOmics, Metabolomics, or MassSpectrometry biocViews terms that you could use in your vignette to demonstrate how rgoslin fits into a typical analysis to properly showcase its features and benefits to a user?

Cheers, Pete

[nilshoffmann]

Hi @PeteHaitch,

thanks for the review and feedback on rgoslin. Proper lipid naming and reporting is still an unsolved problem. Goslin and rgoslin for R, aim at simplifying the process of parsing different shorthand nomenclatures that are currently in active use and aims to standardize lipid naming by providing a normlized shorthand lipid name, following the latest recommendations of the lipidomics standards initiative. As such, it is also the first library to support this use case in R and, as you already checked, many other programming languages.

I am in contact or have been with the authors of lipidr @ahmohamed, xcms @sneumann, @michaelwitting and others. I will be happy to discuss different examples / use cases to include in the rgoslin vignette with them, or even direct inclusion of rgoslin in one of these libraries. Since rgoslin is a utility library I designed it to have minimal dependencies.

Cheers, Nils

[PeteHaitch]

Hi @nilshoffmann,

Thanks for the above response. Overall, the package is in good shape. For acceptance into Bioconductor, I have a few Required points, as well as some Recommended points, that I would ask you to first please address. I've also asked someone from the core Bioconductor team to chime in on a couple of points (tagging @vjcitn).

Given that you are managing a number of language-specific interfaces to goslin, if the Bioconductor-specific requirements seem too burdensome then you should consider submission to CRAN. As a utility library for biological data, I can see arguments for submission of rgoslin to either Bioconductor or CRAN. Bioconductor packages, such as lipidr and xcms, would still be able to depend on rgoslin if it was available on CRAN. Again, this is not intended to discourage submission to Bioconductor but I just wanted to make sure you aware of all the options :)

Required

• The vignette must demonstrate interoperability with other Bioconductor software. It sounds like some thought has been given to demonstrating use cases or examples, so if you add a section to the vignette that will suffice. (I would advise against directly including rgoslin in one of these other packages because I suspect it will complicate maintenance).
• The vignette must have an Introduction section (essentially the existing Prerequisites)
• The vignette must have an Installation instruction with the official Bioconductor installation instructions (see https://contributions.bioconductor.org/docs.html?q=installation#installation). Once the package is accepted into Bioconductor, these will look like

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rgoslin")

Please also add these to the README.md (replacing the current devtools::install_github()-based instructions).

• Please add a table of contents to the vignette

Recommended

• Is it worth simplifying the R-level API to essentially parseLipidNames()?
  • As far as I can tell, there is a one-to-one mapping between the length of lipidNames and the number of rows in the returned data.frame, so the 'non-pluralised' versions of the two main functions (parseLipidName() and parseLipidNameWithGrammar()) feel redundant.
  • Could parseLipidNames(lipidNames) change to something like parseLipidNames(lipidNames, grammer = NULL) where grammar = NULL is equivalent to the current parseLipidNames(lipidNames) with automagic guessing of the grammar and parseLipidNames(lipidNames, grammer = value) is equivalent to the current parseLipidNamesWithGrammar(lipidNames, grammer = value)?
  • If you want to retain parseLipidNames() and parseLipidNamesWithGrammar() as two separate functions, then if parseLipidNamesWithGrammar() is not supplied with a grammar (e.g., parseLipidNamesWithGrammar("PC 32:1")) then it should probably return an error to the effect of "Please supply a 'grammar'" rather than returning NULL.
• Consider adding a inst/CITATION file (see https://contributions.bioconductor.org/citation.html)
• What is renovate.json needed for?
• The BiocStyle package is encouraged for vignette formatting. (https://contributions.bioconductor.org/docs.html?q=vignette#installation)
• Vignette needs a table of contents
• Consider removing pkgdown. Once the package is accepted into Bioconductor, it will have a software landing page and links to the documentation and vignettes available from https://bioconductor.org/packages/rgoslin/. I'll ask @vjcitn to chime in with any 'official' advice on whether separate pkgdown-based sites are okay.
• Consider adding tests that cover the error cases.
  • E.g., a silly (perhaps unrealistic) example like parseLipidNames(c("A", "B")) and parseLipidNames(c(1, 2)) may not be triggering the intended error message?
  • You can run covr::report() for a standalone code coverage report (this is how I saw that these lines are not covered by the current unit tests).
• There's a broken link in the README and vignette to the C# implementation (https://github.com/lifs-tools/csgoslin)
• Again tagging @vjcitn, would a C-expert mind checking the src/Makevars?

[PeteHaitch]

Consider removing pkgdown. Once the package is accepted into Bioconductor, it will have a software landing page and links to the documentation and vignettes available from https://bioconductor.org/packages/rgoslin/. I'll ask @vjcitn to chime in with any 'official' advice on whether separate pkgdown-based sites are okay.

I've checked with the BioC core team and there's no need to remove pkgdown.

You probably no longer need pkgKitten in Suggests in the DESCRIPTION. As far as I'm aware, this is only needed/used to setup the initial structure of an R package and it's then no longer required.

[PeteHaitch]

Hi @nilshoffmann ,

Do you wish to proceed with the submission? We like to see some activity on the issue within 3 weeks. It's no problem if it's taking longer, but for now I will close the issue and you can re-open it if you wish to proceed and when you are ready.

Cheers, Pete

[nilshoffmann]

Hi @PeteHaitch ,

thanks for the heads up. I will try to address the remaining issues until the end of this week.

Cheers, Nils

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.

[nilshoffmann]

@PeteHaitch I am ready to recommence with the submission. How do I reopen the issue?

[bioc-issue-bot]

Dear @nilshoffmann ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fee0a456877a07d062ce0c3edc615bf44c720080

[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.

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

Please see the build report for more details. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[nilshoffmann]

Current status of requested changes:

Required

• [x] The vignette must demonstrate interoperability with other Bioconductor software. It sounds like some thought has been given to demonstrating use cases or examples, so if you add a section to the vignette that will suffice. (I would advise against directly including rgoslin in one of these other packages because I suspect it will complicate maintenance).
• [x] The vignette must have an Introduction section (essentially the existing Prerequisites)
• [x] The vignette must have an Installation instruction with the official Bioconductor installation instructions (see https://contributions.bioconductor.org/docs.html?q=installation#installation). Once the package is accepted into Bioconductor, these will look like

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rgoslin")

• [x] Please also add these to the README.md (replacing the current devtools::install_github()-based instructions).

• [x] Please add a table of contents to the vignette

Recommended

Is it worth simplifying the R-level API to essentially parseLipidNames()? As far as I can tell, there is a one-to-one mapping between the length of lipidNames and the number of rows in the returned data.frame, so the 'non-pluralised' versions of the two main functions (parseLipidName() and parseLipidNameWithGrammar()) feel redundant.

• [x] Could parseLipidNames(lipidNames) change to something like parseLipidNames(lipidNames, grammer = NULL) where grammar = NULL is equivalent to the current parseLipidNames(lipidNames) with automagic guessing of the grammar and parseLipidNames(lipidNames, grammer = value) is equivalent to the current parseLipidNamesWithGrammar(lipidNames, grammer = value)? If you want to retain parseLipidNames() and parseLipidNamesWithGrammar() as two separate functions, then if parseLipidNamesWithGrammar() is not supplied with a grammar (e.g., parseLipidNamesWithGrammar("PC 32:1")) then it should probably return an error to the effect of "Please supply a 'grammar'" rather than returning NULL.
• [x] Consider adding a inst/CITATION file (see https://contributions.bioconductor.org/citation.html)
• [x] What is renovate.json needed for? (removed)
• [x] The BiocStyle package is encouraged for vignette formatting. (https://contributions.bioconductor.org/docs.html?q=vignette#installation)
• [x] Vignette needs a table of contents
• [x] Consider removing pkgdown. Once the package is accepted into Bioconductor, it will have a software landing page and links to the documentation and vignettes available from https://bioconductor.org/packages/rgoslin/. I'll ask @vjcitn to chime in with any 'official' advice on whether separate pkgdown-based sites are okay. (removed)

Consider adding tests that cover the error cases.

• [x] E.g., a silly (perhaps unrealistic) example like parseLipidNames(c("A", "B")) and parseLipidNames(c(1, 2)) may not be triggering the intended error message?
• [x] You can run covr::report() for a standalone code coverage report (this is how I saw that these lines are not covered by the current unit tests).
  • [x] There's a broken link in the README and vignette to the C# implementation (https://github.com/lifs-tools/csgoslin)
  • [ ] Again tagging @vjcitn, would a C-expert mind checking the src/Makevars?

[PeteHaitch]

Thanks, @nilshoffmann. Please post a message once you're done addressing the review comments and I'll take another look

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2b776de70ffdee34613d4d0e1054af43c82d6a4c

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2a90a6937f0d893b4a6ee52c2afdbbdbcfa66ac5

[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.

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

Please see the build report for more details. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[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: "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. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 703e6222f8a1cc9709fda65818ff1e03dcb1f207

[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: "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. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 62b02b2642d603eab399ca18ec2b08b902f72f04

[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.

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

Please see the build report for more details. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 90cfedcf5cebbdf88948db6d7dabae7a547bc6f8

[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.

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

Please see the build report for more details. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[nilshoffmann]

Current status of requested changes:

Required

* [x]  The vignette must demonstrate interoperability with other Bioconductor software. It sounds like some thought has been given to demonstrating use cases or examples, so if you add a section to the vignette that will suffice. (I would advise against directly including rgoslin in one of these other packages because I suspect it will complicate maintenance).

* [x]  The vignette must have an Introduction section (essentially the existing Prerequisites)

* [x]  The vignette must have an Installation instruction with the official Bioconductor installation instructions (see https://contributions.bioconductor.org/docs.html?q=installation#installation). Once the package is accepted into Bioconductor, these will look like

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rgoslin")

* [x]  Please also add these to the README.md (replacing the current devtools::install_github()-based instructions).

* [x]  Please add a table of contents to the vignette

Recommended

Is it worth simplifying the R-level API to essentially parseLipidNames()? As far as I can tell, there is a one-to-one mapping between the length of lipidNames and the number of rows in the returned data.frame, so the 'non-pluralised' versions of the two main functions (parseLipidName() and parseLipidNameWithGrammar()) feel redundant.

* [x]  Could parseLipidNames(lipidNames) change to something like parseLipidNames(lipidNames, grammer = NULL) where grammar = NULL is equivalent to the current parseLipidNames(lipidNames) with automagic guessing of the grammar and parseLipidNames(lipidNames, grammer = value) is equivalent to the current parseLipidNamesWithGrammar(lipidNames, grammer = value)?
  If you want to retain parseLipidNames() and parseLipidNamesWithGrammar() as two separate functions, then if parseLipidNamesWithGrammar() is not supplied with a grammar (e.g., parseLipidNamesWithGrammar("PC 32:1")) then it should probably return an error to the effect of "Please supply a 'grammar'" rather than returning NULL.

* [x]  Consider adding a inst/CITATION file (see https://contributions.bioconductor.org/citation.html)

* [x]  What is renovate.json needed for? (_removed_)

* [x]  The BiocStyle package is encouraged for vignette formatting.
  (https://contributions.bioconductor.org/docs.html?q=vignette#installation)

* [x]  Vignette needs a table of contents

* [x]  Consider removing pkgdown. Once the package is accepted into Bioconductor, it will have a software landing page and links to the documentation and vignettes available from https://bioconductor.org/packages/rgoslin/. I'll ask @vjcitn to chime in with any 'official' advice on whether separate pkgdown-based sites are okay. (_removed_)

Consider adding tests that cover the error cases.

* [x]  E.g., a silly (perhaps unrealistic) example like parseLipidNames(c("A", "B")) and parseLipidNames(c(1, 2)) may not be triggering the intended error message?

* [x]  You can run covr::report() for a standalone code coverage report (this is how I saw that these lines are not covered by the current unit tests).

* [x]  There's a broken link in the README and vignette to the C# implementation (https://github.com/lifs-tools/csgoslin)

* [ ]  Again tagging @vjcitn, would a C-expert mind checking the src/Makevars?

@PeteHaitch I have added an example usage with lipidr in the vignette and have addressed all of your remarks. Only the external check of Makevars by @vjcitn is still open.

[PeteHaitch]

Thanks, @nilshoffmann! I'll take a look in the next few days (although might not be until next week)

[PeteHaitch]

Hi @nilshoffmann

Some additional comments based on the changes:

• [x] Shouldn't have testthat in LinkingTo
• [x] Consistent use of <- instead of = in vignette (this was automatically fixed by running styler::style_pkg(filetype = "Rmd"))
• [x] Need library(stringr) and library(ggplot2) in echoed and evaluated chunk in vignette, otherwise a user copy-pasting the code from the rendered vignette won't be able to run the example.
• [x] lipidr example is a great addition to vignette but code (and comments) are a bit hard to read (some of this was automatically fixed by running styler::style_pkg(filetype = "Rmd") and the rest with some manual tweaks to spacing and indentation).
• [ ] No need to mention RTools in installation instructions. In any case, RTools is only applicable to those on Windows building from source, which will be a tiny minority of users because BioC will serve Windows (and macOS) binaries.
• [ ] I got a lot of errors when running lipidNames <- parseLipidNames(rowData(d)$clean_name) from the vignette (vignette shows the same errors); it sort of seems like this error is expected but could perhaps be made clearer and explained in vignette.

I implemented fixes for those ticked ones, which I planned to submit as a PR to https://github.com/lifs-tools/rgoslin. However, this github-hosted repo wasn't in-sync with the Bioconductor-hosted git repo so I couldn't do that. Instead, I've attached the output of git diff bioc-re-review > bioc-re-review-diff.txt, i.e. comparing the master branch of the Bioconductor-hosted git to my bioc-re-review branch. You may need to manually apply the changes I ticked off, but hopefully the patch helps somewhat.

Once those last issues are address I think we'll be ready to accept the package.

Thanks, Pete bioc-re-review-diff.txt

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 0892bb4d6adeb3805b06b8643f83a552c5aea890

[nilshoffmann]

Hi @PeteHaitch thanks for the style fixes. Spaces versus tabs, I see :-).

• I have incorporated the fixes from your diff patch.
• I have added all libraries required to run the lipidr example to an eval = FALSE block.
• I have removed RTools from the vignette, it is now only mentioned in the README.md with an explicit remark that only installation from source code may require that, but not regular installation via bioconductor.
• I have added further NOTE blocks and inline explanations to the vignette about expected messages, warnings and errors.

As to why there is a difference between the GitHub repo and the one on Bioconductor: We have quite some large files included in the cppgoslin and goslin subtrees that would not pass the bioc-checks and would not need to be included for the R implementation to run. I am currently merging the contents manually between the two repos, but will switch to using proper patches due to your remark.

Thanks for this great and interactive review!

[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.

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

Please see the build report for more details. This link will be 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/rgoslin to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

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[PeteHaitch]

Hi @nilshoffmann,

Congratulations 🎉 I'm marking the package as accepted. Thank you for your contribution to Bioconductor.

I would still recommend running styler::style_pkg(filetype = "Rmd") on your package to make some cosmetic changes to the code in the vignette because it seems like these weren't incorporated when you manually applied the patch.

Cheers, Pete

[lshep]

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/nilshoffmann.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

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("rgoslin"). The package 'landing page' will be created at

https://bioconductor.org/packages/rgoslin

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.