PPInfer - Githubissues

dongminjung commented 7 years ago

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Repository: https://github.com/dongminjung/PPInfer

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bioc-issue-bot commented 7 years ago

Hi @dongminjung

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: PPInfer
Type: Package
Title: Inferring functionally related proteins using protein
        interaction networks
Description: Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn urshered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins close to some interesting proteins. Then we can expect that they are often involved in the same or similar biological functions.
Version: 0.99.0
Date: 2017-01-08
Author: Dongmin Jung, Xijin Ge
Maintainer: Dongmin Jung <dmdmjung@gmail.com>
Depends: biomaRt, igraph, kernlab, stats, STRINGdb
License: Artistic-2.0
biocViews: Software, Statistical Method, Network, Graph And Network
BuildVignettes: FALSE
NeedsCompilation: no
Packaged: 2017-01-11 00:32:19 UTC; dongminjung

bioc-issue-bot commented 7 years ago

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 commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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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 following build report for more details:

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bioc-issue-bot commented 7 years ago

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.

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bioc-issue-bot commented 7 years ago

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

Version: 0.99.0

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bioc-issue-bot commented 7 years ago

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 commented 7 years ago

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

df600e1 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170111225810.html

bioc-issue-bot commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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

1b78927 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

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: "ABNORMAL". 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/PPInfer_buildreport_20170111231046.html

bioc-issue-bot commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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

415f422 Update

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170112000009.html

bioc-issue-bot commented 7 years ago

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 commented 7 years ago

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

69cd49a Update

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170112003857.html

bioc-issue-bot commented 7 years ago

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

4f76989 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

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 following build report for more details:

http://bioconductor.org/spb_reports/PPInfer_buildreport_20170203191118.html

bioc-issue-bot commented 7 years ago

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

c5e045d Update

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170203224527.html

hpages commented 7 years ago

Hi Dongmin,

Thanks for your submission. Please find below a list of issues with the PPInfer package. Please address them at your earliest convenience.

Cheers, H.

The build/ folder doesn't belong to PPInfer source tree. Please remove it. Also please remove the 'Packaged:...' line from the DESCRIPTION file. This line doesn't belong to the package source tree either.
Use <- instead of = for assignment. Make sure to put a space before and after the <-, like in
```
fblog <- upgrade_graph(fblog)
```
Please don't use \doublespacing in the vignette.

Indent your code properly. For example, in the \usage section of net.infer() man page:

 net.infer(list.proteins, kernel, top = NULL, cross = 0,
           C1 = 1, nu = 0.2, epsilon = 0.1, cache1 = 40, tol1 = 0.001, 
           shrinking1 = TRUE, C2 = 1, cache2 = 40, tol2 = 0.001,
           shrinking2 = TRUE)

instead of:

 net.infer(list.proteins, kernel, top = NULL, cross = 0,
 C1 = 1, nu = 0.2, epsilon = 0.1, cache1 = 40, tol1 = 0.001, 
 shrinking1 = TRUE, C2 = 1, cache2 = 40, tol2 = 0.001,
 shrinking2 = TRUE)

Or, in the \examples section:

 string.db.9606 <- STRINGdb$new(version='10',species=9606,
                                score_threshold = 999)

instead of:

 string.db.9606 = STRINGdb$new(version='10',species=9606,
 score_threshold = 999)

It doesn't make sense to return scores in a character vector like your net.infer() or ppi.infer.human() functions do.

It is also a very bad idea to prefix Ensembl protein ideas with a taxonomy id:

> infer$top
[1] "9606.ENSP00000348762" "9606.ENSP00000381768" "9606.ENSP00000351059"
[4] "9606.ENSP00000259154" "9606.ENSP00000337255" "9606.ENSP00000323856"
[7] "9606.ENSP00000374399" "9606.ENSP00000361548" "9606.ENSP00000336702"
[10] "9606.ENSP00000310623"

This hurts the usability of your package.

I'm not convinced it's pertinent/relevant to dedicate 3 pages of an 8-page vignette to illustrate the functionality of your package with an example based on the 'fblog' dataset (French political blogs). Furthermore, you also have these fblog-based examples in the man pages. Please treat use cases and provide examples that are relevant to the Bioinformatics community.

bioc-issue-bot commented 7 years ago

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

a48cd04 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170228194921.html

bioc-issue-bot commented 7 years ago

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

c231783 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170228211029.html

dongminjung commented 7 years ago

Hi. hpages

I appreciate your comments. I corrected all issues. Please see below.

Thanks, Dongmin

The build/ folder doesn't belong to PPInfer source tree. Please remove it. Also please remove the 'Packaged:...' line from the DESCRIPTION file. This line doesn't belong to the package source tree either.

Correction : I removed the file in the build folder and the line in the DESCRIPTION file.

Use <- instead of = for assignment. Make sure to put a space before and after the <-, like in

fblog <- upgrade_graph(fblog)

Correction : I changed from = to <-. For example, infer <- net.infer(list.proteins,K.9606,10).

Please don't use \doublespacing in the vignette.

Correction : I use \linespread{1.5} instead of \doublespacing.

Indent your code properly.

Correction : I did it.

It doesn't make sense to return scores in a character vector like your net.infer() or ppi.infer.human() functions do.

Correction : I changed from pred.svm$score <- as.vector(new.sort.pred2[1:top,2]) ppi.pred.9606$score <- as.vector(na.omit.new.protein_score[1:top,2]) ppi.pred.10090$score <- as.vector(na.omit.new.protein_score[1:top,2]) to pred.svm$score <- as.numeric(new.sort.pred2[1:top,2]) ppi.pred.9606$score <- as.numeric(na.omit.new.protein_score[1:top,2]) ppi.pred.10090$score <- as.numeric(na.omit.new.protein_score[1:top,2]) for each function, respectively.

It is also a very bad idea to prefix Ensembl protein ideas with a taxonomy id:

> infer$top [1] "9606.ENSP00000348762" "9606.ENSP00000381768" "9606.ENSP00000351059" [4] "9606.ENSP00000259154" "9606.ENSP00000337255" "9606.ENSP00000323856" [7] "9606.ENSP00000374399" "9606.ENSP00000361548" "9606.ENSP00000336702" [10] "9606.ENSP00000310623" This hurts the usability of your package.

Correction : I removed the prefix before taking the input. This problem comes from the name of columns and rows of a kernel matrix. So I used rownames(K.9606) <- sub('.*\\.','',rownames(K.9606)) colnames(K.9606) <- sub('.*\\.','',colnames(K.9606)). So such corrections are not necessary for getBM() in ppi.infer.human() and ppi.infer.mouse(). We have > infer$top [1] "ENSP00000348762" "ENSP00000381768" "ENSP00000351059" [4] "ENSP00000259154" "ENSP00000337255" "ENSP00000323856" [7] "ENSP00000374399" "ENSP00000361548" "ENSP00000336702" [10] "ENSP00000310623"

I'm not convinced it's pertinent/relevant to dedicate 3 pages of an 8-page vignette to illustrate the functionality of your package with an example based on the 'fblog' dataset (French political blogs). Furthermore, you also have these fblog-based examples in the man pages. Please treat use cases and provide examples that are relevant to the Bioinformatics community.

Correction : The data litG of the package yeastExpData is used in the vignette. So the package containing 'fblog' is not necessary anymore.

bioc-issue-bot commented 7 years ago

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

8f67643 Update DESCRIPTION

bioc-issue-bot commented 7 years ago

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/PPInfer_buildreport_20170312185300.html

hpages commented 7 years ago

Hi Dongmin,

Thanks for addressing the issues. I'm marking the package as accepted. We will add it to our Subversion repo and build system in the next days. You'll receive an email with more information about this.

Thanks for contributing to the Bioconductor project!

Regards, H.

dongminjung commented 7 years ago

Thank you for taking the time to review the package.

Dongmin

Bioconductor / Contributions

PPInfer #241