iNETgrate

[habilzare]

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

• Repository: https://github.com/habilzare/iNETgrate

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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[nilseling]

Hi @habilzare are there any updates on this? Otherwise we can temporarily close the issue due to inactivity.

[habilzare]

Hi @nilseling , I am almost done with addressing your comments. Please do not close the issue. I'll send an update soon.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a0e65c8557cb5d667d77ab43821261d780716ac3

[habilzare]

Hi @nilseling, I address all your comments below:

• [ ] In the vignette, please replace the R CMD INSTALL iNETgrate_x.y.z.tar.gz line with the devel installation BiocManager::install("habilzare/iNETgrate"). In general the package should be installed via BiocManager::install("iNETgrate").

Updated to only BiocManager::install("iNETgrate").

• [ ] I'm not quite sure if the warnings regarding the standard deviation should be suppressed. In the vignette there is another warning:

## Warning in stats::cor(balancedData, as.matrix(eigengenes[rownames(balancedData),
: the standard deviation is zero

Could this be avoided by filtering out features with sd == 0? If not, you could add instructions to the vignette if the user can ignore this but also the other warnings that occur during analysis.

I removed warnings as much as I could. The remaining warnings are beyond the scope of this package:

1- read_block is caused by loading loading SummarizedExperiment and HDF5Array packages. 2- dopar is caused by WGCNA. 3- stats::cor(balancedData,..) and get.enriched.pw are caused by Pigengene (hopefully, will be addressed in the next release of Pigengene).

• [ ] In general all chunks of the vignette except the installation instructions need to be executed. To reach this aim, you can remove the downloadData chunk and please evaluate the oneStep chunk.

Done.

Please let me know if you have any other suggestion.

[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: "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/iNETgrate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[nilseling]

Thanks @habilzare. Is there any way you could reduce the R CMD check time to less than 10 minutes?

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fe72943bf684e20658559f639a8ffda2b4ea0597

[habilzare]

Thanks @habilzare. Is there any way you could reduce the R CMD check time to less than 10 minutes?

Yes, if you allow me to refer to the one step iNETgrate() documents instead of running it in the vignette like what I did in version 0.99.68. Is this OK?

[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: "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/iNETgrate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[habilzare]

Hi @nilseling , Is the current package acceptable? Thanks!

[nilseling]

It still gets a timeout when checking. Is there any way to reduce the check time?

[habilzare]

@nilseling

It is very difficult to make the toy data smaller because it may not lead to a reasonable network. With the new updated on the TCGAbiolonks package, I cannot even make the toy data again. I have asked the authors for help in this post:

https://support.bioconductor.org/p/9152425/#9152427

[habilzare]

Hi @nilseling , I tried with a smaller toy data, which is 2/3 of the current data. A network cannot be made using this smaller toy data because there won't be enough genes to form clusters (modules). Is there any possibility the package be accepted as is?

[lshep]

The R CMD check call didn't even start checking examples and tests; It timeouts after 16 min which is still pretty significant. Is it possible to use a different toy example set that is smaller and has enough genes? Also please fix the data files suggestion for compression R CMD build --resave-data and update your R version dependency.

[habilzare]

Hi @lshep ,

The R CMD check call didn't even start checking examples and tests; It timeouts after 16 min which is still pretty significant.

The check on Bioc stops after checking for missing documentation entries. It takes only 5 minutes to reach this on my laptop and the whole check takes 12 minutes for me. I do not know why it takes so long on the Bioc server. Could the server be busy with multiple tasks?

Also please fix the data files suggestion for compression R CMD build --resave-data

The build command on the Bioc server uses the --no-resave-data option and I have control over it.

BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data iNETgrate --

and update your R version dependency.

@nilseling told me to remove dependency to R (see above).

[lshep]

Re: the data save. save the data either by using tools::resaveRdaFiles() or save(something, file = "something.rda", compress = "xz") . We have now implemented the SPB to check on both linux and mac builders -- when you make the above change with appropriate version bump we can see if it is platform specific and/or gets better.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9a5a9aa0f2f643408de62b070a864b9ea2e5dbf7

[habilzare]

I used save(compress = "xz", ....) and the total data folder size decreased by 20% in Version 0.99.74. However, the check time increased from 12 minutes to 15 minutes on my laptop probably because it takes longer to load xz-compressed files.

[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: "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/iNETgrate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 36b34c5ea45d73e12913833f2672fff87de68d20

[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: "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/iNETgrate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 6ccb773611a0cb967720e7d388f59e657657154e

[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: "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/iNETgrate to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[habilzare]

The R version and file compression issues were resolved in Version 0.99.80.

[nilseling]

Hi @habilzare

is there any attempt to decrease the check time by using a smaller toy dataset?

[habilzare]

Yes @nilseling , I tried, but with smaller data, a network cannot be made using the smaller toy data because there won't be enough genes to form clusters (modules) unfortunately.

[lshep]

The core team has discussed and will allow the exception on the timeout. Please understand that exceptions are not granted lightly and if you develop future packages they should meet the time requirements.

[lshep]

@nilseling please add any other comments but ignore the timeout

[nilseling]

With this we can then accept the package.

[bioc-issue-bot]

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.

[habilzare]

Thank you @nilseling and @nilseling for accepting our package! We appreciate the the core team's flexibility.

When we started this package, I was careful to have a toy dataset to limit the check time below 4 minutes. However, as we added more functions and examples, the check time increased. Also, I did not expect the check time on the Bioc server to be significantly higher than our laptop. In future packages, I'll be more careful about the check time.

[habilzare]

It is not on the Bioc 3.18 list yet. Does it take more for this to happen?

https://www.bioconductor.org/checkResults/3.18/bioc-LATEST/

[lshep]

I am away at a conference this week and will process al packages when I get back. Thank you for your patience

[lshep]

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/habilzare.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("iNETgrate"). The package 'landing page' will be created at

https://bioconductor.org/packages/iNETgrate

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.

[habilzare]

Thanks @lshep for adding iNETgrate to the build list. I already have an 'ssh' key associated with my github username.

Can I keep the package updated only on the Bioconductor repository and remove it from my github? I think updating and synchronizing two remotes is extra, unnecessary work.

[lshep]

Yes if you like. the location Bioconductor will use will always be the git.bioconductor.org location so if you only wish to maintain that location that is up to you.

[habilzare]

Thanks @lshep for the confirmation! I'll remove the iNETgrate repository from my GitHub after I review nightly builds.