mnem

[MartinFXP]

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

• Repository: https://github.com/cbg-ethz/mnem

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 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.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[MartinFXP]

I have done both and got nothing.

The last Bioc-devel email I received was from September 26: https://stat.ethz.ch/pipermail/bioc-devel/2018-September/014098.html Nothing after that.

However, the error appeared for the first time on October 25. October 18 was still fine (https://github.com/Bioconductor/Contributions/issues/805#issuecomment-430947789). It just seems weird to me, that I didn't get any Bioc-devel mail in October, even though apparently there were some (https://stat.ethz.ch/pipermail/bioc-devel/2018-October/thread.html).

Is it a coincidence, that the final package acceptance deadline for Bioconductor 3.8 was October 24? https://stat.ethz.ch/pipermail/bioc-devel/2018-September/014073.html

I appreciate the help.

[mtmorgan]

I manually subscribed you to the mailing list.

[bioc-issue-bot]

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

9b8489d fixed bug in case of overlapping S-gene names; add...

[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: "skipped, TIMEOUT, 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.

[bioc-issue-bot]

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

024f0c8 added optimization of the expectation of the compl...

[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: "skipped, ERROR, 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.

[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: "skipped, 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.

[bioc-issue-bot]

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

1cce1b8 bugfix multi knock-down; added helper function and...

[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: "skipped, 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.

[hpages]

Hi @MartinFXP ,

Looks like the epiNEM package was missing on celaya2 last time our Single Package Builder checked mnem, which caused mnem to fail on this machine. However, according to the following page, epiNEM is now installed on celaya2. Please bump mnem version again in order to trigger a new build by our Single Package Builder. Thanks!

H.

[bioc-issue-bot]

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

8d30970 small bugfixes

[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.

[MartinFXP]

Hi @hpages ,

looks like the epiNEM ERROR is gone. However, it also seems like I am again unsubscribed from the bioc-devel list. Btw, after @mtmorgan manually added me the last time, I did not receive any bioc-devel emails. Should I try to subscribe again by myself?

Thanks, Martin

[mtmorgan]

I again resubscribed you, and you should have received an email. Please check carefully, including in your spam and junk (instititutional) email filters.

[bioc-issue-bot]

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

d77efd2 version bump

[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.

[MartinFXP]

Dear @mtmorgan ,

there actually has been a configuration error at the ETH Zurich mail service since September, which resulted in blocked r-project emails to some accounts (like mine). It has been fixed. However, since it was only fixed after my inquiry yesterday, I did not get the confirmation email after you subscribed me. Does that mean I will get unsubscribed again at one point?

Best, Martin

[mtmorgan]

You are still subscribed; thank you for investigating on your end.

[bioc-issue-bot]

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

77d1212 bugfix: data averaging with probabilistic perturba...

[MartinFXP]

Is there any reason this is not building? Seems to be a problem with only this package. Should I do a version bump?

[lshep]

Sorry. I have manually kicked off a build and it should post soon. Future version bumps should trigger a build.

[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.

[MartinFXP]

Hi,

since today is supposed to be the last day for new packages, is there anything still wrong with this package? No errors or warnings and as far as I can see, I fixed all issues addressed in the review(s).

Best, Martin

[hpages]

Hi Martin,

Sorry for the late answer. We've delayed the BioC 3.9 release by a few days. mnem will be part of it.

Cheers, H.

[bioc-issue-bot]

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]

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/MartinFXP.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("mnem"). The package 'landing page' will be created at

https://bioconductor.org/packages/mnem

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.