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EWCE #1904
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Hi @Al-Murphy Thanks for submitting your package. We are taking a quick The DESCRIPTION file for this package is:
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A reviewer has been assigned to your package. Learn what to expect IMPORTANT: Please read this documentation for setting Bioconductor utilized your github ssh-keys for git.bioconductor.org |
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: "ABNORMAL". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
The error seems to be down to a ggplot object part of the data object ctd (ctd[[1]]$plotting$ggdendro_vertical) I can't seem to reproduce this error locally and looking online the only related issue seems to be here: https://stackoverflow.com/questions/60187844/error-in-getas-characterfun-mode-function-envir-envir-object-guid. @lshep have you encountered an issue like this before? Sorry it's hard to correct since it isn't failing locally. The error: |
Please note you are also getting ERROR's for not being signed up for the mailing list and having some files that should not be git tracked. |
Thanks @lshep, that all makes sense and I have sorted all the errors and have bumped the version and pushed to my git repository. However, when I try and push upstream to bioconductor, I get the following error: To git.bioconductor.org:packages/ewceData.git |
Please show the full command with output. I assume you followed the instructions to set up the remotes but please be sure there is a upstream remote that points to |
I believe the upstream is set to bioconductor git, see the output of
Based on your advice, I reran
and then tried to push, I use main rather than master so I used Total 0 (delta 0), reused 0 (delta 0) |
Again -- our default branch is not main... please do |
Sorry I missed what you meant about master/main, I thought you could still use either (as per this documentation). I tried using master rather than main and I'm still getting an error:
Should I rename my main branch as master or would that make any difference? Also note I ran |
You should be able to leave yours as main while pushing to our master. Could you try |
That failed and I also tried forcing it which didn't seem to work either:
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@nturaga advice |
Received a valid push on git.bioconductor.org; starting a build for commit id: c69c7012261f6267fd4e3e374cb14e97ef06b3be |
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: "skipped, ERROR". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
Received a valid push on git.bioconductor.org; starting a build for commit id: 76deb36b06196b67a4829afd39f9ec88ff83a0a1 |
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: "skipped, ERROR". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
Received a valid push on git.bioconductor.org; starting a build for commit id: e3b1cf772bbcd9ad241a393fffbdbef6a833d230 |
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: "skipped, ERROR". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
Hey @lshep, the remaining issue is
which relates to |
@hpages do you know of any stipulations regarding windows for this use case? In the meantime I will review based on the other two platforms. Cheers |
Received a valid push on git.bioconductor.org; starting a build for commit id: bc3515a757b3bbaeb1e99a917d51d98f62681cac |
Received a valid push on git.bioconductor.org; starting a build for commit id: 4dcf3d25a1625b4b944955253156689483a3fee2 |
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". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
Received a valid push on git.bioconductor.org; starting a build for commit id: c3c4d3dc713c9e1c8e5d67e166f4f32b07438ee5 |
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". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
Hi @lshep, is it acceptable to use a |
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. |
Yep unit tests still cover 80+% of the code so they would be covered. I think with |
Yes that is acceptable then |
Received a valid push on git.bioconductor.org; starting a build for commit id: 4fd2bd628efa9efe9ecd83ffb5a8ff1e93b2de18 |
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". Please see the build report for more details. This link will be active Remember: if you submitted your package after July 7th, 2020, |
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. |
Yes this is acceptable. I try and review your packages over the next few days. |
Thank you! I won't be making any changes in the meantime then |
I can hold off if you would like to still make changes? |
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! |
Thank you for taking the time to apply the changes. The packages are in an acceptable state for inclusion into Bioconductor. |
Your package has been accepted. It will be added to the Thank you for contributing to Bioconductor! |
Thank you @lshep for all your help and work on this, I realise it wasn't the easiest of packages! Thanks, |
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/ 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 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. |
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/ 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 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. |
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