Closed richardheery closed 8 months ago
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: methodical_0.99.20.tar.gz Linux (Ubuntu 22.04.2 LTS): methodical_0.99.20.tar.gz
Links above 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/methodical
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Please ignore the bioc-devel mailing list ERROR; I can confirm the email is registered and we are looking into why BiocCheck is reporting an ERROR in mistake.
The package has been substantially improved.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.
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/richardheery.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("methodical")
. The package 'landing page' will be created at
https://bioconductor.org/packages/methodical
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.
Your package has been failing on our devel builders for over 6 weeks. Please fix to avoid removal from Bioconductor
Hello,
Sure I will take a look at the issues in the coming days.
Best wishes,
Richard
On Tue 9 Apr 2024, 14:56 lshep, @.***> wrote:
Your package has been failing on our devel builders for over 6 weeks. Please fix to avoid removal from Bioconductor
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3169#issuecomment-2045239130, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMP6CXDQTOTEDLA5ZMWEGMTY4PXO7AVCNFSM6AAAAAA5JUOCO6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBVGIZTSMJTGA . You are receiving this because you were mentioned.Message ID: @.***>
Since my package is on the devel version of Bioconductor, do I need to still push any changes to the devel branch of Bioconductor at git@git.bioconductor.org:packages or is it enough just to my Git repository?
Is there also a way to trigger a BBS build report without waiting for the nightly build?
You need to push to git.bioconductor.org. Bioconductor no longer makes any connection or reference to the github repo. You will need to push changes to git.bioconductor.org with a valid version bump in order for them to appear and propagate to users
Currently builds are only once a day. But I encourage you to run R CMD build and R CMD check on your own, perhaps with the bioconductor docker image to test changes.
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.