FelixErnst commented 4 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/FelixErnst/EpiTxDb

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bioc-issue-bot commented 4 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.

bioc-issue-bot commented 4 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.

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FelixErnst commented 4 years ago

@LiNk-NY everthing is ready for review. Please disregard the WARNINGS, since the label is somewhat stuck probably due to the number of packages in this issue. All packages have cleared the build without ERROR or WARNINGS.

LiNk-NY commented 4 years ago

Hi Felix, @FelixErnst Apologies for the delay. It took me some time to go over the number of files in the packages. On the other hand, the review is pretty short due to the organization of the packages.

Please see below. Thank you for your submission. Best, Marcel

EpiTxDb #1387

DESCRIPTION

Looks good.

NAMESPACE

Looks good.
Perhaps you may want to go over some imports and see which ones you can do without (e.g., assertive)

vignettes

Looks good and straightforward.

Minor:

You can use multi-chunk options to include the library calls only in one chunk. For example, you can set results="hide",include=TRUE,message=FALSE,warning=FALSE to show the chunk but not the results or messages etc.

R

Good work. Keep in mind that some pain points would be that unexported helpers from GenomicFeatures can change at any time and you will have to support any changes to them.
Overall, the functions look modular and there are plenty of helper function to support the modulartiy of the package.
You could write SQL calls that are not string dependent but this is a minor point and may not be worth the dependencies overhead (see dbplyr).

FelixErnst commented 4 years ago

Hi Marcel, @LiNk-NY

thanks for the review and the comments.

I removed the non eval chunk from the vignette. I didn't know that chunk option setup since I never had a close look at how startup messages relate to normal messages. Thanks for the hint.

Regarding the use of dbplyr: I didn't want to add a layer on the AnnotationDbi interface and follow more closely what was done for the TxDb class.

I will push the changes next week.

Felix

FelixErnst commented 4 years ago

Hi Marcel, @LiNk-NY

thank you for the review and the suggestions.

I removed the single call to assertive and combined the first two chunks in the vignette. Thanks again for the hint with the chunk settings.

Regarding the use of dbplyr: I looked into it, but opted to take the challange to implement the two version of SQL generators. It was a helpful exercise to take suggestions from the TxDb class and rework and optimize space requirements, table relations and SQL statement generator to achieve the functionality for this use case. Certainly lifted some cobwebs from my SQL skills.

I will push the changes shortly.

Felix

bioc-issue-bot commented 4 years ago

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

215f363 included changes from Bioconductor review

bioc-issue-bot commented 4 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.

FelixErnst commented 4 years ago

Hi Marcel, @LiNk-NY

any news on the changes?

Cheers Felix

LiNk-NY commented 4 years ago

Hi Felix, @FelixErnst I've reviewed your changes and comments. Thank you for your quick response. I will accept the package. Don't forget to include an Installation section in the vignette. Best, Marcel

bioc-issue-bot commented 4 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 4 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/FelixErnst.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

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for working with this repository. See especially

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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

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

https://bioconductor.org/packages/EpiTxDb

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.

mtmorgan commented 4 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/FelixErnst.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("EpiTxDb.Hs.hg38"). The package 'landing page' will be created at

https://bioconductor.org/packages/EpiTxDb.Hs.hg38

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.

FelixErnst commented 4 years ago

@mtmorgan Thanks for adding the packages to Bioconductor's git repo. Could you also add EpiTxDb.Sc.sacCer3 and EpiTxDb.Mm.mm10? Thank you

lshep commented 4 years ago

@mtmorgan not sure where EpiTxDb.Hs.hg38 got added but these three packages are annotation packages so @Kayla-Morrell will probably have to do some magic.

mtmorgan commented 4 years ago

Re-opening for additional processing

mtmorgan commented 4 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/FelixErnst.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("EpiTxDb.Sc.sacCer3"). The package 'landing page' will be created at

https://bioconductor.org/packages/EpiTxDb.Sc.sacCer3

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.

mtmorgan commented 4 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/FelixErnst.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("EpiTxDb.Mm.mm10"). The package 'landing page' will be created at

https://bioconductor.org/packages/EpiTxDb.Mm.mm10

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

EpiTxDb #1387

EpiTxDb #1387

DESCRIPTION

NAMESPACE

vignettes

R