proBatch submission

[ChloeHJ]

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

• Repository: https://github.com/symbioticMe/proBatch/

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.

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• [x] The 'devel' branch for new packages and features.
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[ChloeHJ]

One more important thing for developing a new R/Bioconductor package is the interoperability with other existing / established packages in the same area.

Interoperability is strongly encouraged in Bioconductor and would help with the usage of your own package. Consider interoperability with packages included in RforProteomics, and mzR which uses CDF (Common Data Format) to represent MS data in R without completely loading data into memory? Check here for other MS related R / Bioconductor packages: http://bioconductor.org/packages/release/BiocViews.html#___MassSpectrometry

Regards to interoperability, the example data is in the same format as the ones in e.g. SWATH2stats, which is the output from openSWATH. However, we needed a data that explicitly shows the presence of batch effects, both continuous mass spectrometry-associated signal drifts and discrete batch effects. The data included in our package was one of the first large-scale proteomics dataset that explicitly showed the batch effects, which raised the notion to develop tools to correct for them. Therefore, we included a reduced openSWATH output of the data to show that the batch effect can be improved by utilizing our proBatch tool.

[bioc-issue-bot]

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

59f35a5 version bump to 0.99.12 9808e30 Merge branch 'master' of https://github.com/symbio...

[ChloeHJ]

Hi Qian,

I modified the scripts based on the your comments, and resolved most of them, except for test/ and the vignette problem. I will soon generate tests and get back to you :)

Best regards, Chloe

[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, 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]

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

19a4dd5 add affiliation to vignette

[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, 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.

[Liubuntu]

Hi @ChloeHJ ,

Thanks for those updates and sorry for delaying the review of your short vignette. I'll review them altogether next week.

Best, Qian

[Liubuntu]

HI @ChloeHJ ,

Please see the following comments:

vignette

• Remove proBatch_vignette_brief.R and only keep the .Rmd files and .png files. Seems like it is generating one warning from your build report.
• Rename your vignette as proBatch.Rmd and proBatch_brief.Rmd so it's more spontaneous and easier for users to browse your vignette using vignette("proBatch").
• proBatch_vignette_brief.Rmd.

R

• fit_non_linear.R:L14, mismatched braces in (\code[loess_regression}).

tests

test Unit tests are highly recommended. We find them indispensable for both package development and maintenance. Two of the main frameworks for testing are RUnit and testthat. Examples and explanations are provided here.

I am emphasizing the unit test again here. As a large package with many functionalities and hopefully to be widely used by users, good unit tests could help you accurately locate issue source for later maintenance. Otherwise, it's big pain when your package fails in some day, and you spend huge amount of time trying to figure out where the bug is. It would greatly enhance your package by adding unit tests (and glad to hear that you are working on this).

Meta/vignette.rds

• What is this file for? Why is it here?

Other Suggestions:

• Data Structure: The Biobase::ExpressionSet data structure represents datasets as assayData, phenoData, featureData, and protocolData. Note this has been updated into SummarizedExperiment which has similar representations using Assay, colData, rowData and metadata. In any case that you want to use Biobase::ExpressionSet, use SummarizedExperiment::SummarizedExperiment instead! Modern data structures for representing DNA/RNA/MS datasets extends SummarizedExperiment class, including those I have mentioned in the interoperability section.

  Try the following example of a SummarizedExperiment object called airway.

library(airway)
data(airway)
airway
is(airway)
assay(airway)[1:5, 1:5]
rowData(airway)
colData(airway)
metadata(airway)

Use methods(class = "SummarizedExperiment") for more details about available methods.

• Interoperability

  Interoperability is strongly encouraged in Bioconductor and would help with the usage of your own package. Consider interoperability with packages included in RforProteomics, and mzR which uses CDF (Common Data Format) to represent MS data in R without completely loading data into memory? Check here for other MS related R / Bioconductor packages: http://bioconductor.org/packages/release/BiocViews.html#___MassSpectrometry

It's fine that you are using in-memory loading of the MS datasets for now. But as you said, the dataset is "large-scale", and it's common that genomic datasets are going out-of-memory large, you should consider the above mentioned data structure for representation of the big data in a lazy way that you don't actually load the whole data into memory for doing analysis using your methods, but you have an interface of the data in R that it seems like you are working with the whole dataset. It's the trend of lazy data representation in R/Bioconductor. For a long-term / next-phase goal of your package, your functions should support these kind of data structures. In your case, the MS lazy interfaces.

[Liubuntu]

The short vignette settings looks fine. Two suggestions:

1. use smaller data (under data/*.rda) in examples / tests / vignette. The current one is 535*233. Cut it down but big enough to show the functionality.
2. Do not print twice the figures in the vignettes (seems you are summarizing all figures in the beginning and then separately in lower sections).

The only error comes from the tarball size. Please try to do the above and let's see if this could be fixed.

Best, Qian

[ChloeHJ]

Hi Qian,

Thank you for your comments, I will go through them and get back to you soon,

Best regards, Chloe

[bioc-issue-bot]

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

2313b56 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.

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]

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

985975b version 0.99.15

[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, 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:

93d515c version bump to 0.99.16

[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.

[bioc-issue-bot]

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

aa23d59 version bump to 0.99.17

[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, 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.

[bioc-issue-bot]

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

fa011d9 version 0.99.18

[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.

[bioc-issue-bot]

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

4126272 0.99.19 check latest version

[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, 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]

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

255b4d7 version bump to 0.99.20

[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.

[bioc-issue-bot]

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

6dd1e31 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.

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.

[bioc-issue-bot]

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

6325f77 version bump 0.99.22

[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.

[ChloeHJ]

Hi Qian,

Thank you for the suggestions and comments. We tried to improve our package based your comments and please see the descriptions below for details:

• For the vignette, there was still the problem of exceeding time limits and weird generation of vignette_brief.R in the process of building the package. So for now, I have put the shorter vignette into another branch called RELEASE_2.0. If it’s okay for the initial release, is it okay that we handle the problems with the shorter vignette in the next round of release as we would still have one detailed vignette to describe our package?
• I have added tests to our package.
• Thank you for the suggestions on data structure and interoperability. We will aim to let our functions support these data structures for the next phase of release.

After making these changes, I tried to build/check our package on the machine but it keeps giving me warning about timestamps:

checking for future file timestamps ...Warning in file(con, "r") : cannot open URL 'http://worldclockapi.com/api/json/utc/now': HTTP status was '403 Site Disabled' WARNING unable to verify current time

I was not sure how to handle this problem so may I ask for your suggestion to tackle this warning?

Thank you and best regards, Chloe

[Liubuntu]

HI @ChloeHJ ,

The newly added test functions look awesome. It's fine now to remove the brief vignette also.

Here are some minor issues to fix:

tests

• new test functions look great!

DESCRIPTION

• Maintainer: The package maintainer Chloe H. Lee <chloe.h.lee94@gmail.com> Only keep the name and email here.

NEWS

• add a NEWS file in the top folder. Initial version could be empty. See example here for later maintenance.

examples, dontrun tag.

• Be cautious with the dontrun tag. Make sure they are runnable before adding the tag. Since the building time doesn't seem to be an issue now, try removing the dontrun tag and see if the time could be within limit.
• Assign the returned complex values to a new R object. E.g., adjust_batch_trend() has very big output. When users run the example, it prints everything in the R console but hard to trace back. Same as the correct_batch_effects() example.

vignette

• remove the .html and .R file from the folder.

Coding issues.

• no visible global function defition for ... in building report. Follow the suggestions in building report to import corresponding packages.
• avoid sapply(), use vapply().
• avoid 1:..., use seq_len() or seq_along().
• Check your NOTE messages in the building report for details of above issues. Fix as much as possible for the NOTEs.

Best, Qian

[Liubuntu]

checking for future file timestamps ...Warning in file(con, "r") : cannot open URL 'http://worldclockapi.com/api/json/utc/now': HTTP status was '403 Site Disabled' WARNING unable to verify current time

Please ignore this warning for now. It's an R-devel issue, we'll update the R-devel and it will go away.

[bioc-issue-bot]

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

c57be5c multiple of 4 spaces for indentataion 37b476e 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.

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:

a77d8cd 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.

[bioc-issue-bot]

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

4182ac6 version 0.99.25

[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.

[ChloeHJ]

Dear Qian,

Thank you so much for your quick review. I revised our packaged based on your comments:

• Added NEWS file
• Added examples with a smaller example data matrix and removed dontrun tag
• I tried to remove the most of NOTES

For the vignette, you commented to remove the .html and .R form the folder but I could not find these files in my local folder. I tried to remove gitignore from vignette folder to see if these folders can be found from elsewhere but I still could not find them. May I ask you for help with this?

Thank you very much for your kind revisions,

Best regards, Chloe

[Liubuntu]

Hi @ChloeHJ ,

All you changes are looking great. Just one more note for the NEWS file. I'll accept this package now. Thanks for your contribution to Bioconductor!

NEWS

• No need to change. Just updating with you the official guideline for NEWS file: htttp://bioconductor.org/developers/package-guidelines/#news

Cheers, Qian

[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!

[ChloeHJ]

Hi @ChloeHJ ,

All you changes are looking great. Just one more note for the NEWS file. I'll accept this package now. Thanks for your contribution to Bioconductor!

NEWS

• No need to change. Just updating with you the official guideline for NEWS file: htttp://bioconductor.org/developers/package-guidelines/#news

Cheers, Qian

Thank you so much for your revisions all the way Qian!!

[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/ChloeHJ.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("proBatch"). The package 'landing page' will be created at

https://bioconductor.org/packages/proBatch

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.

[symbioticMe]

Dear reviewers, we have made updates to the package & changed the maintainer (from now on it's me). How to we proceed now to make sure the updates will appear on BioConductor? It seems like BiocCredentials don't work for me