GAprediction

[JonBohlin]

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• Repository: https://github.com/JonBohlin/GAprediction

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[bioc-issue-bot]

Hi @JonBohlin

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: GAprediction
Date: 2016-07-04
Type: Package
Title: Prediction of gestational age with Illumina HumanMethylation450
        data
Version: 0.99.0
Author: Jon Bohlin
Authors@R: c(person("Jon", "Bohlin", role=c("cre"), email="jon.bohlin@fhi.no"))
Maintainer: Jon Bohlin <jon.bohlin@fhi.no>
Description: [predictGA] predicts gestational age using Illumina HumanMethylation450 CpG data.
License: GPL (>=2)
LazyData: TRUE
Depends: R (>= 3.2.1)
Imports: glmnet, stats, utils, Matrix
biocViews: DNAMethylation, Epigenetics, Regression,
        BiomedicalInformatics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-07-06 06:32:50 UTC; jonb

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new 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.

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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160708053416.html

[JonBohlin]

I think I know what the problem is. I originally called the package predictGA, but had to change the name because I hadn't uploaded the R files properly the first time. The case was closed and I had to use a new name. Is it possible to open the old predictGA repository?

[mtmorgan]

Sorry for my slow response. You could close this issue, rename your github repository, revert the DESCRIPTION file and other changes with the new package name,, and open another issue. I'll assign myself to it. Alternatively, you could update your current code (e.g., in the vignette, where you say require(predictGA) to match the new package name.

[JonBohlin]

OK -thanks! The package is called "GAprediction" and all files have been updated. I have now tested the package multiple times with both windows and linux and it seems to (R CMD) run, build and check(BiocCheck) fine now, so please try again!

[mtmorgan]

To trigger a build, make a commit to the master branch where the version number in the DESCRIPTION file is changed from 0.99.0 to 0.99.1

[JonBohlin]

OK, it's done,

[dtenenba]

Have you set up a webhook?

It seems that our system did not detect your commit and push.

Please add a web hook and then bump the version again, to 0.99.2, and commit and push that change.

[bioc-issue-bot]

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

ea5b677 Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160714124604.html

[bioc-issue-bot]

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

50d1196 Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160714132819.html

[bioc-issue-bot]

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

6b1815b Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160714134121.html

[bioc-issue-bot]

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

b93042b Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160714160718.html

[bioc-issue-bot]

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

3fcc2a5 Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160715033215.html

[mtmorgan]

Looks like the remaining issue is because the package lists your address @fhi.no whereas you are subscribed to biocDevel as @gmail.com

[JonBohlin]

OK -thanks, I was starting to wonder...

[bioc-issue-bot]

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

831d0a0 Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160715042642.html

[bioc-issue-bot]

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

c3d2812 Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160715044013.html

[bioc-issue-bot]

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

fce662d Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160715044956.html

[mtmorgan]

Thanks for your package.

• Since the central function of the package processes HumanMethylation450k arrays, it seems like predictGA should accept the output of common upstream software for processing this data, e.g., minfi(??). Likely this can be accomplished by writing a one-line test / coercion inside predictGA that extracts the relevant matrix if the argument is of the appropriate type. Likely this also requires at least adding the relevant package where the class and accessor are defined to the Suggests: field of the DESCRIPTION file, or better Import:'ing the relevant package and functions.
• A LICENSCE file is not needed for GPL-2; please remove it
• use message() rather than cat() to communicate with the user; messages can be suppressed via suppressMessages()

• include context in error messages, rather than printing the error message to the screen and stopping uninformatively, e.g., at predictGA.R:32 write

  stop("Missing essential CpGs needed for prediction\n"
        predictorSites[temp], "\n")

• vectorize rather than iterate, for instance at predictGA.R:53

  for(i in predictorSites)
    predMatr[,i]<-mldat[,i]

  is I think just predMatr[, predictorSites] <- mldat[, predictorSites]

• explicitly invoking the garbage collector, e.g., at predictGA.R:68 is seldom necessary; these objects will be available for garbage collection as soon as the function ends, i.e., after the next line.
• It seems like the UL.mod.cv data is a central component of the model, and its derivation should be described explicitly (e.g., as a script in inst/script/.
• consider adding spaces around <- in the man pages; this makes the code more readable.

[JonBohlin]

Thank you very much for you comments! I am now on vacation but will look into this and get bet back to you!

[JonBohlin]

Thank you very much for taking the time to review my code and for your excelent comments. I have included a point-to-point response to them below. Your comments start with a bulletpoint, my responses are in italic

• Since the central function of the package processes HumanMethylation450k arrays, it seems like predictGA should accept the output of common upstream software for processing this data, e.g., minfi(??). Likely this can be accomplished by writing a one-line test / coercion inside predictGA that extracts the relevant matrix if the argument is of the appropriate type. Likely this also requires at least adding the relevant package where the class and accessor are defined to the Suggests: field of the DESCRIPTION file, or better Import:'ing the relevant package and functions.

Yes, this is a good idea. However, there are many different packages used for treating HumanMethylation450k data having myself used Minfi, WateRmellon and Methylumi. Unfortunately, there is no standard method (yet?) for extracting the beta-matrix which is required by the GA predictor. All the packages mentioned above are quite comprehensive and I’d like to keep this program as small and independent as possible.

• A LICENSCE file is not needed for GPL-2; please remove it

Removed

• use message() rather than cat() to communicate with the user; messages can be suppressed via suppressMessages()

OK, thanks!

• include context in error messages, rather than printing the error message to the screen and stopping uninformatively, e.g., at predictGA.R:32 write stop("Missing essential CpGs needed for prediction\n" predictorSites[temp], "\n")

OK

• vectorize rather than iterate, for instance at predictGA.R:53 for(i in predictorSites) predMatr[,i]<-mldat[,i] is I think just predMatr[, predictorSites] <- mldat[, predictorSites]

Thanks!

• explicitly invoking the garbage collector, e.g., at predictGA.R:68 is seldom necessary; these objects will be available for garbage collection as soon as the function ends, i.e., after the next line.

Thanks!

• It seems like the UL.mod.cv data is a central component of the model, and its derivation should be described explicitly (e.g., as a script in inst/script/.

An accompanying paper is under review and there everything is explained in detail. One of the reviewers wanted us to write a package to do GA prediction and so I did. Hopefully, the paper will be accepted soon.

• consider adding spaces around <- in the man pages; this makes the code more readable.

OK

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

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

3d5c7fb Update DESCRIPTION

[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 following build report for more details:

http://bioconductor.org/spb_reports/GAprediction_buildreport_20160725095153.html

[mtmorgan]

I'm sorry for my slow response. The changes look great and I'm marking this as 'accepted'. It'll be added to the nightly builds and the Bioc svn repository, with further instructions via email in the next several days.

[JonBohlin]

Great thanks!

Jon

On Thu, Aug 18, 2016 at 10:00 PM, Martin Morgan notifications@github.com wrote:

I'm sorry for my slow response. The changes look great and I'm marking this as 'accepted'. It'll be added to the nightly builds and the Bioc svn repository, with further instructions via email in the next several days.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/50#issuecomment-240838832, or mute the thread https://github.com/notifications/unsubscribe-auth/ATWudZVE8GxPuwY9HlqG4fW6SMjYuQFuks5qhLnmgaJpZM4JGTlE .