EWCE - Githubissues

Al-Murphy commented 3 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/neurogenomics/ewceData

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

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[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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Al-Murphy commented 3 years ago

Hi @lshep, I seem to still be getting errors which seem to be related to the caching (if you could check the latest build report). This is only on the data package and I haven't tried the main package - I'll run it again once this is resolved.

lshep commented 3 years ago

In the latest build report I do not see ERROR's related to caching. I see an ERROR related to registration on the support site. This is a new check but it is relevant and an easy fix by altering your profile on the support site to have your package name in the watched tags.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6ddd027e4199c1903cc56b1529ceca598696812c

bioc-issue-bot commented 3 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. 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/ewceData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 96ca915ed6a557cae844f03cf76e874bd59af2a1

bioc-issue-bot commented 3 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: "TIMEOUT, 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 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 826ced68d6daf123c7bce3e69c2bd96a51945130

bioc-issue-bot commented 3 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: "TIMEOUT, 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 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Al-Murphy commented 3 years ago

Hi @lshep , thanks for your help already today but it seems I still have time out issues with the package for windows and a warning for Linux. Is there any advice on what I should do next to get around this? I imagine I must be close with the time seeing as it passed on Mac? @hpages just commenting you in on this as I know we discussed timeouts previously.

Thanks, Alan.

lshep commented 3 years ago

It may be close but it is still a very long time for a package to build and check. Is there a way to use a smaller subset of data for the vignettes and examples?

Al-Murphy commented 3 years ago

I've subsetted the examples as much as possible and unfortunately the vignette can't really be sped up since it replicates the associated paper's results. I know the most time consuming parts are the tests and examples.

lshep commented 3 years ago

I'll continue with the review. I should have a re-review in the next few days

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b3957a1c5b75b4cdf83a36d1585fa1a9b0a670fe

bioc-issue-bot commented 3 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: "TIMEOUT, 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 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ef071a431cf358bb1142fef8ecb278961d6a9561

bioc-issue-bot commented 3 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: "TIMEOUT, 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 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ab37f0f582b7f32844afa484f8902473e1ccf9e4

bioc-issue-bot commented 3 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: "TIMEOUT". 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4dcf3d25a1625b4b944955253156689483a3fee2

bioc-issue-bot commented 3 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, skipped". 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c3c4d3dc713c9e1c8e5d67e166f4f32b07438ee5

bioc-issue-bot commented 3 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: "TIMEOUT". 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Al-Murphy commented 3 years ago

Hi @lshep, is it acceptable to use a donttest wrapper for two examples in my exported functions? I will still have greater than 80% with running examples but this will greatly improve my runtime.

lshep commented 3 years ago

Are there other tests or anything for the functions that would be in the donttest? I think that would be reasonable as long as the majority are run.

Al-Murphy commented 3 years ago

Yep unit tests still cover 80+% of the code so they would be covered. I think with dontest checks that it's valid R code anyway. Thanks!

lshep commented 3 years ago

Yes that is acceptable then

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4fd2bd628efa9efe9ecd83ffb5a8ff1e93b2de18

bioc-issue-bot commented 3 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: "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 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/EWCE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Al-Murphy commented 3 years ago

Hi @lshep , is the warning for a run time over 20 minutes on Windows acceptable? Note that the run time is below 10 for Linux and I assume the same on Mac.

lshep commented 3 years ago

Yes this is acceptable. I try and review your packages over the next few days.

Al-Murphy commented 3 years ago

Thank you! I won't be making any changes in the meantime then

lshep commented 3 years ago

I can hold off if you would like to still make changes?

Al-Murphy commented 3 years ago

No no I have no more changes I want to make, sorry I was just confirming for you so you know things won't change while you are in the middle of a review!

lshep commented 3 years ago

Thank you for taking the time to apply the changes. The packages are in an acceptable state for inclusion into Bioconductor.

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

Al-Murphy commented 3 years ago

Thank you @lshep for all your help and work on this, I realise it wasn't the easiest of packages!

Thanks, Alan.

vjcitn commented 3 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/Al-Murphy.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("ewceData"). The package 'landing page' will be created at

https://bioconductor.org/packages/ewceData

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.

vjcitn commented 3 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/Al-Murphy.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("EWCE"). The package 'landing page' will be created at

https://bioconductor.org/packages/EWCE

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

EWCE #1904