RandomWalkRestartMH

[alberto-valdeolivas]

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• Repository: https://github.com/alberto-valdeolivas/RandomWalkRestartMH

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[bioc-issue-bot]

Hi @alberto-valdeolivas

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: RandomWalkRestartMH
Type: Package
Title: Random walk with restart on multiplex and heterogeneous Networks
Version: 0.99.0
Date: 2018-03-28
Author: Alberto Valdeolivas Urbelz <alvaldeolivas@gmail.com>
Maintainer: Alberto Valdeolivas Urbelz <alvaldeolivas@gmail.com>
Description: This package performs Random Walk with Restart on multiplex and
    heterogeneous networks. It is described in the following article:
    "Random Walk With Restart On Multiplex And Heterogeneous Biological 
    Networks". 
License: GPL (>= 2)
URL: https://www.biorxiv.org/content/early/2017/08/30/134734
Encoding: UTF-8
LazyData: true
Imports: igraph, Matrix, dnet, methods
Depends: R(>= 3.4.0)
RoxygenNote: 6.0.1
biocViews: GenePrediction, NetworkInference, SomaticMutation,
        BiomedicalInformatics, MathematicalBiology, SystemsBiology,
        GraphAndNetwork, Pathways, BioCarta, KEGG, Reactome, Network
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2018-04-08 10:25:37 UTC; alvaldeolivas

[mtmorgan]

This seems like a general statistical method without dependencies on or use of Bioconductor; why not submit to CRAN instead? If you'd like to target Bioconductor, then update the user-visible functions so that they accept or return, as appropriate, standard Bioconductor objects. Please let me know if you do make this change by adding a brief comment. I will then add your package to the review queue.

[alberto-valdeolivas]

Hello. Thanks for your answer. This package is based on an algorithm we developed for an article submitted to the Bioinformatics journal. They proposed us to deposite our software in Bioconductor, since the algorithm is dealing with a graph theory method applied to Bioinformatics. Therefore, to enable a wider audience to apply our methods, we developed this package in order to be more user friendly and generally applicable.

I would still like to target Bioconductor, since our method is applied to Bioinformatics.

[mtmorgan]

Great! Please then update your package to interoperate with standard Bioconductor objects, as indicated in the previous comment.

[alberto-valdeolivas]

Dear Martin,

We carefully checked the Bioconductor objects, but all the 4 packages (igraph, Matrix, dnet, methods) and objects we are using are either new or from CRAN. So, even if our package is dedicated to the bioinformatics community, to navigate biological multiplex networks, we do not see any way of using Bioconductor objects for input or output. If this is mandatory for Bioconductor, we unfortunately have to dismiss our submission.

Sincerely,

Alberto

[bioc-issue-bot]

A reviewer has been assigned to your package Learn what to expect during the review process.

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: "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:

4d1d56c Delete NAMESPACE d6b300e Delete DESCRIPTION 8ae208f Delete Bioc.bib 0116bd5 Delete RandomWalkRestartMH1-fig.pdf d396a2f Delete RandomWalkRestartMH1.Rnw 556745b Delete AllFunctions.R ec49daf Delete data.R f02801b Delete vignette.rds 279577b Delete Disease_Network.rda 11001f2 Delete GeneDiseaseRelations.rda d582290 Delete PPI_Network.rda 54c676d Delete Pathway_Network.rda 3a1fa31 Delete NEWS bded1bc Delete RandomWalkRestartMH1.R 03c44cd Delete RandomWalkRestartMH1.Rnw 5fc54f3 Delete RandomWalkRestartMH1.pdf ce22e69 Delete testthat.R 050034c Delete test_matricesComputation.R 412aee2 Delete test_objectstype.R 11672d6 Delete test_randomWalkResults.R 94fc448 Delete Disease_Network.Rd 0b57648 Delete GeneDiseaseRelations.Rd 0a5de3e Delete PPI_Network.Rd 28c4edb Delete Pathway_Network.Rd de31517 Delete Random.Walk.Restart.Multiplex.Rd 126a44a Delete Random.Walk.Restart.MultiplexHet.Rd 01bd601 Delete compute.adjacency.matrix.Rd da262b9 Delete compute.transition.matrix.Rd 171f29c Delete create.multiplex.Rd 4247bf4 Delete create.multiplexHet.Rd 85147c9 Delete create.multiplexHetNetwork.topResults.Rd e9e4360 Delete create.multiplexNetwork.topResults.Rd f366107 Delete is.RWRM.Results.Rd 246aa16 Delete is.RWRMH.Results.Rd 1401ef0 Delete is.multiplex.Rd b9f4ea1 Delete is.multiplex.het.Rd 02c5e2c Delete normalize.multiplex.adjacency.Rd e653e6e Add files via upload 6e2087e Create foo.txt fe5a967 Add files via upload 479310b Delete foo.txt 3878474 Create foo.txt 71099b0 Add files via upload 8e9e32e Delete foo.txt eeefc4b Create foo.txt 4a19358 Add files via upload 2658225 Add files via upload 560e039 Add files via upload f47e7f3 Delete foo.txt d60cd98 Create foo.txt 19f45a7 Add files via upload 1f86615 Delete foo.txt 97486fc Create foo.txt 350327c Add files via upload 72dd47f Delete foo.txt 40bbbe7 Create foo.txt 39322f8 Add files via upload 5eb0352 Delete foo.txt a23f61a Create foo.txt 7178e71 Add files via upload 5e484bc Delete foo.txt fbdc80c Create foo.txt e6ec062 Add files via upload 7d66bd3 Delete foo.txt b76aa72 Create foo.txt a4ef921 Add files via upload 5778214 Delete foo.txt d2d3a9b Merge pull request #1 from alberto-valdeolivas/v_0...

[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:

57926f1 Update DESCRIPTION 890f4a9 Merge pull request #3 from alberto-valdeolivas/v_0...

[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:

52a1d48 Update DESCRIPTION 304d06d Delete RandomWalkRestartMH1.R 9fc3816 Delete RandomWalkRestartMH1.Rnw c1604d9 Delete RandomWalkRestartMH1.pdf e4bcd48 Merge pull request #4 from alberto-valdeolivas/v_0...

[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.

[mtmorgan]

Thanks for submitting your package. Please revise according to the following and post a comment briefly summarizing changes when you are ready for a second review.

• please remove the the build/ directory from git; this is generated during the R CMD build process.

DESCRIPTION

• provide a Description: field that does not force the user to find the publication

vignette

• good

R

• AllFunctions.R:33 etc test class membership with is(x, "Multiplex")
• Avoid function names that can be confused for S3 methods -- isMultiplex or is_Multiplex; this is more than just a style issue.
• AllFunctions.R:156 consider vapply() rather than explicit for loop to avoid need to pre-allocate and fill. Similar issues for many for () loops that populate lists or vectors to be replaced by lapply() or vapply().

• AllFunctions.R:325 (and elswhere) vectorize as

  Layers_Name <- paste0("Layer_", seq_len(Number_of_Layers), ":")

• AllFunctions.R:330 adopt a style that allows for longer lines, e.g., new-line after {, consistent indentation by 4 spaces

  if (!is.character(Layers_Name)) {
      stop("The name of the layer should be a vector of characters")
  }
  ...
      Transition_Multiplex_SecondNet <- get.transition.multiplex.secondNet(
          N, L, M, SupraBipartiteMatrix, lambda
      )
      ## alternatively...
      Transition_Multiplex_SecondNet <- 
          get.transition.multiplex.secondNet(N, L, M, SupraBipartiteMatrix, lambda)

• Please spell-check documentation and error messages; one example AllFunctions.R:630 "The lenght" -> "The length"
• AllFunctions.R:751 Avoid 'copy-and-append' (x <- character(); for (...) x <- c(x, ...) which scales quadratically w/ vector size; pre-allcoate and fill or use lst <- lapply(); x <- do.call(c, lst). See also use of rbind() at AllFunctions.R:1545

• AllFunctions.R:753 hoist vectorizable calculations out of for loops, e.g.,

  i <- seq_len(Number_Layers)
  Position_ini_row <- 1 + (i - 1) * Number_Nodes_1
  Position_end_row <- Number_Nodes_1 + (i - 1) * Number_Nodes_1
  for (i in seq_len(Number_Layers)) {
      ...
      idx <- seq(Position_ini_row[i], Position_end_row[i])
      Supra_Bipartite_Matrix[idx,] <- Bipartite_matrix
  }

• AllFunctions.R:892 use message() instead of print() for diagnositic / verbose output
• AllFunctions.R:938 it seems like this form

      for (j in seq_len(Number_Nodes_secondNet)){
      if (Col_Sum_Bipartite[j] != 0){
          Transition_Multiplex_SecondNet[,j] <-
              (lambda*SupraBipartiteMatrix[,j]) /Col_Sum_Bipartite[j]
      }

  can be vectorized

    m <- lambda * t(t(Supra_Bipartite_Matrix) / Col_Sum_Bipartite)
    idx <- Col_Sum_Bipartite != 0
    Transition_Multiplex_SecondNet[,idx] = m[,idx]

  and similar elsewhere in the code

• use (internal) functions to avoid code repetition, e.g., the above transformation appears repeatedly in the get.transition.* functions.
• consider structuring your code into (a few) separate files with common functionality in each; structure the man pages and unit tests in similar fashion so that the user has easy access to related documentation / the relationshp between code / test / man is less of a hunt-and-search exercise.

man

• documentation is generally great!

NEWS

• should be parse-able by utils::news() and contain meaningful NEWS, otherwise delete.

[bioc-issue-bot]

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

222e19d Add files via upload 50b9761 Add files via upload ce25c8a Delete RandomWalkRestartMH1-fig.pdf 2ecf601 Add files via upload 2f7b36a Add files via upload a9b0c4d Add files via upload 2194f65 Delete is.multiplex.Rd 37705c8 Delete is.multiplex.het.Rd 9c726ad Delete is.RWRMH.Results.Rd 8871336 Delete is.RWRM.Results.Rd 52d05fd Delete Disease_Network.Rd 4add78a Delete GeneDiseaseRelations.Rd 0c4691a Delete PPI_Network.Rd e190f9a Delete Pathway_Network.Rd f874857 Delete Random.Walk.Restart.Multiplex.Rd 5b7e17d Delete Random.Walk.Restart.MultiplexHet.Rd afeef8c Delete compute.adjacency.matrix.Rd 1554ebe Delete compute.transition.matrix.Rd cd1d1b0 Delete create.multiplex.Rd 806669c Delete normalize.multiplex.adjacency.Rd aba0a98 Delete create.multiplexHet.Rd b4dd7ba Delete create.multiplexHetNetwork.topResults.Rd 61ab11b Delete create.multiplexNetwork.topResults.Rd 4c5b944 Add files via upload 508e8e8 Delete NEWS ab2b029 Add files via upload bf1e392 Delete vignette.rds 9eb4539 Add files via upload c70dc51 Delete AllFunctions.R 501ac6d Merge pull request #5 from alberto-valdeolivas/v.0...

[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.

[alberto-valdeolivas]

Dear Martin,

We carefully checked your comments and we reviewed our code according to them. In fact, your comments were very useful to improve the computational efficiency of our algorithms. Thanks very much.

I briefly summarize the changes:

• We spell-check documentation, vignette and error messages. We removed unused files and directories.

• We provide a link to the related publication in the DESCRIPTION FILE.

R code

• We replaced for () loops by apply or do.call functions. In addition, we applied vectorization in some cases following your recommendations. Just a couple of for () loops remain in our code, since we think they can ease future modifications or user's understanding.

• We replaced some potentially confusing names of S3 methods, and we tested class membership in the way you proposed.

• We replaced print() by message() for verbose output.

• We structured our code into different files with related functionality and according the unitary test files.

Therefore, we consider to be ready for a second review.

Sincerely,

Alberto

[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/alberto-valdeolivas.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 biocLite(\"RandomWalkRestartMH\"). The package 'landing page' will be created at

https://bioconductor.org/packages/RandomWalkRestartMH

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.