HTSanalyzeR2: A R/Bioconductor package for gene set enrichment and network analysis of various high-throughput data

[linazhu3]

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• Repository: https://github.com/CityUHK-CompBio/HTSanalyzeR2

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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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[bioc-issue-bot]

Hi @linazhu3

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: HTSanalyzeR2
Type: Package
Title: Gene set over-representation, enrichment and network analyses for high-
    throughput data and corresponding time-series data
Version: 0.99.0 
Author: Lina ZHU, Xiupei MEI, Feng GAO, Xin WANG
Maintainer: Lina ZHU<zhulina0609@gmail.com>, Xiupei MEI <meixiupei@gmail.com>, Feng GAO <gaofeng21cn@gmail.com>
Description: This package provides classes and methods for gene set over-
    representation, enrichment and network analyses on various high-throughput 
    data as well as corresponding time-series data.
License: Artistic-2.0
LazyData: TRUE
RoxygenNote: 6.0.1
Imports: 
    GO.db,
    cellHTS2,
    doParallel,
    Rcpp,
    foreach,
    stringr,
    igraph,
    BioNet,
    DT,
    shiny,
    shinydashboard,
    colourpicker,
    KEGGREST,
    data.table,
    htmlwidgets,
    methods,
    RankProd,
    AnnotationDbi,
    graphics,
    grDevices,
    stats,
    utils 
Collate: 
    'utils.R'
    'class_union.R'
    'Batch_class.R'
    'HTSanalyzeR2.R'
    'HTSanalyzeR4MAGeCK.R'
    'RcppExports.R'
    'd3plot.R'
    'data.R'
    'gscaTS.R'
    'gsca_class.R'
    'gsca_analyze.R'
    'gsca_enrichmap.R'
    'gsca_load_genesets.R'
    'gsca_preprocess.R'
    'gsca_report.R'
    'gsca_summarize.R'
    'gsca_view.R'
    'nwaTS.R'
    'nwa_class.R'
    'nwa_analyze.R'
    'nwa_preprocess.R'
    'nwa_report.R'
    'nwa_summarize.R'
    'nwa_view.R'
    'stat_test.R'
    'zzz.R'
LinkingTo: Rcpp
Suggests:
    BiocStyle,
    rmarkdown,
    testthat,
    knitr,
    Homo.sapiens,
    org.Hs.eg.db,
    org.Dm.eg.db,
    Biobase
VignetteBuilder: knitr
Depends: R(>= 3.4)
biocViews: GeneSetEnrichment, NetworkEnrichment, TimeCourse, 
 GeneExpression, GO, KEGG

[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.

[mtmorgan]

There can be several Authors: but only one Maintainer; the maintainer name and email address need to be formatted correctly. The vignettes directory should not contain the 'built' vignette products, i.e., Rmd but no html 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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/HTSanalyzeR2_buildreport_20171122104102.html

[bioc-issue-bot]

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

b03cfae fit for check!

[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 following build report for more details:

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[bioc-issue-bot]

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[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/HTSanalyzeR2_buildreport_20171123095957.html

[bioc-issue-bot]

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[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 following build report for more details:

http://bioconductor.org/spb_reports/HTSanalyzeR2_buildreport_20171126082251.html

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

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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:

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[bioc-issue-bot]

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

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[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:

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[bioc-issue-bot]

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[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:

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[llrs]

I am not the official reviewer but I noticed the packages and gave it a look at the vignette:

• It seems that is needed to access slots directly in the vignettes. Could you provide accessors to the relevant information of the objects ? This way will be easier for end users.
• You use the name GSCA for an object and it is not clear to me how is related to "hypergeometric test in order to find the gene sets sharing significant overlapping with hits". Also it reminds me of another package for Gene Set Coexpression Analysis. Could you clarify this object purpose?
• There is also the need to call new, instead of providing a function to create the object of GSCA class. This would help the users to know which kind of data is needed to build a GSCA object.

Hope this helps

[bioc-issue-bot]

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

d5b20a0 gsea plot color bar bug fix; Add illustration for ...

[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:

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[linazhu3]

Dear IIrs,

Thanks for your suggestions! For the s4 class slot and 'new' function, we will polish them ASAP in a more suitable way. For the 'GSCA' class, we named it as gene set collection analysis which can perform both hypergeometric test and gene set enrichment analysis.

[bioc-issue-bot]

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

3946b75 Create constructors instead of directly using 'new...

[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:

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[bioc-issue-bot]

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

3dfc77d Add accessors

[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:

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[linazhu3]

Hi @LiNk-NY

I've revised some unsuitable parts as suggested by @llrs. Could you please take a look at my package? I would be very appreciated if you can check it and give some useful suggestions.

Best, Lina

[lgeistlinger]

Hi @linazhu3 ,

According to

https://www.bioconductor.org/developers/package-guidelines/#name

Bioconductor packages should avoid names that imply a temporal (e.g., ExistingPackage2) relationship.

In your case, it seems rather appropriate to modify/extend your existing package

http://bioconductor.org/packages/HTSanalyzeR

instead of submitting a new one.

[linazhu3]

Dear @lgeistlinger,

Thanks for your recommendation. Actually, this package has been totally rewritten in a more efficient way and add many new functions. So perhaps I can rename it and submit a new one?

Best, Lina

[LiNk-NY]

Hi Lina, @linazhu3 We prefer that you not duplicate the functionality in HTSanalyzeR. It is always better to improve the previous package with the new and rewritten functions.

I am inclined to close the issue and encourage collaboration since one of the authors of HTSanalyzerR is also part of the team on this package.

Any additional comments @mtmorgan ?

Regards, Marcel

[xinwang2hms]

@mtmorgan @lgeistlinger

Hi gentlemen,

This is ridiculous!!!! You are wasting our time!!

I'm Xin Wang, assistant professor at City Universtiy of Hong Kong, PI of this project. HTSanalyzeR2 is fundamentally different from HTSanalyzeR in the design, functionalities and user interface. These changes cannot be made simply by revising or rewriting functions in HTSanalyzeR!!!

We are astonished that we have submitted this application for a few weeks, but got only a simple feedback of "prefer that you not duplicate the functionality xxx". This is absolutely unacceptable. If you cannot provide any help, we will no longer consider Bioconductor as the repository any more.

Please kindly provide your professional feedback asap. Otherwise, we will submit to other platforms.

Regards,

-Xin

[lgeistlinger]

Dear @xinwang2hms,

Your response is inappropriate. Considering the NAMESPACE file of HTSanalyzeR and HTSanalyzeR2 reveals numerous duplicated functions. Rewriting code and adding new features is part of normal package maintenance.

Improving and extending your existing package is thereby advantageous, as it allows your existing user community of HTSanalyzeR to quickly adopt these new features (whereas a new package typically takes time until being noticed). The NEWS file is intended to make your users aware of such changes. Also publishing on substantial extensions to existing software is a good practice to spread the word.

[xinwang2hms]

@lgeistlinger

Are you judging the similarity only based on NAMESPACE? How funny! Let me repeat the design, interface and functionalities are very different from HTSanalyzeR. The reason why we deliberately keep the same function names and arguments is to exactly allow our users to more easily adapt to the new package.

I'll submit the package to somewhere else, and also, we will also withdraw the HTSanalyzeR package as well from bioconductor.

It took us a few weeks to get such a ridiculous feedback. Terrible!

[xinwang2hms]

@mtmorgan @lgeistlinger

Just curious! Have you guys ever looked into our package, or just spent a few minutes and wrote something ridiculously about the version number?

[llrs]

I am not a user of HTSanalyzeR but how is HTSanalyzeR different from HTSanalyzeR2? Which different/new functionalities does HTSanalyzeR2 have?

If I, as a user, should adapt to the new HTSanalyzeR2, why don't change the underlying code in HTSanalyzeR using the code in HTSanalyzeR2? Many thanks for your help.

[mtmorgan]

I'll take over the review from @LiNk-NY . 8 Hours ago you asked for prompt feedback and 5 hours ago that you would remove your package from the review queue and ask that HTSanalyzeR be removed from Bioconductor. I'm happy to do take either the 8 hour or 5 hour action, let me know.

[mtmorgan]

@xinwang2hms let me know where you want to go with this; if I don't hear from you tomorrow I'll close the issue but wait for explicit instructions (Martin.Morgan at RoswellPark.org) before removing HTSanalyzeR.

[bioc-issue-bot]

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

4b54808 Vignette update b9de4b4 Merge branch 'master' of https://github.com/CityUH... c4458e0 color legend bug fix

[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/HTSanalyzeR2_buildreport_20171215015622.html

[mtmorgan]

Thanks for your contribution. I'll assume that the recent commits imply that you wish to continue with the review process.

• Because one of the authors has expressed a desire to not submit the package, please have each author confirm, via posting a comment in this issue or emailing me (Martin.Morgan at RoswellPark.org) directly, that inclusion in Bioconductor is acceptable.
• As noted in earlier contributed comments, we strongly discourage packages with names such as HTSanalyzeR_2_. We would prefer that this contribution were simply an update to HTSanalyzeR. If it is completely new version, then we would prefer to deprecate HTSanalyzeR in the 'devel' branch this release cycle, and then remove it next release cycle. This will give developers and users almost a year to adapt their code to the new version, following the standard package end-of-life process. It will remove the burden of maintaining two packages from the authors. Users wishing the original functionality can install and use older versions of R and Bioconductor.
• I assume that you will increment the version number to trigger a re-build.
• post a comment summarizing your responses here when done.

DESCRIPTION, NAMESPACE

• Good

vignettes

• Required. Please do NOT include the PDF version of the vignette; it will be built by R CMD build for distribution with the package.
• The vignette provides a nice overview of package functionality; good!
• Recommended. I am concerned about the number of eval = FALSE code chunks, in particular the opportunity for the code chunks to become invalid. What steps are you taking to ensure that the code in these chunks remains valid?

R

• Batch_class.R:13. Recommended. Generally 'initialize' methods have a difficult 'contract' to fulfill. For instance, it is generally required that new("GSCABatch") succeeds, else writing a derived class will not work. Because of the complexity of this contract, the best practice is to write constructors (like your GSCABatch()) that serve as an interface between the arguments provided by users and the instantiation of a class, and to NOT implement initialize() methods.
• Batch_class.R:46. Recommended. Each assignment .Object@... <- copies the entire object; consider callNextMethod() instead (this is obviously not a concern if no initiailize methods are defined).
• E.g., Batch_class.R:127: Recommended / required. Best practice is to implement slot 'accessors' for all slots, and to use them throughout, rather than to use direct slot access @. The accessors do not have to be methods on generics, and do not have to be exported to the user.
• class_union.R: Recommended. Class unions are very tricky, changing the semantics of existing classes. Consider carefully whether the class union statements here are essential to your package.
• gsca_analyze.R:229. Required. lengths(listOfGeneSetCollections) instead of sapply(); also elsewhere in the code.
• Required. vapply() rather than sapply(), throughout
• Required. stop(...), rather than stop(paste(...)); likewise for cat(), message(), warning().
• Required. message() rather than cat() when producing diagnostic (e.g., update progress) output; message() / warning() / stop() write to stderr, whereas cat(), print() write to stdout.
• Required. Use seq_len() or seq_along() rather than 1:..., to avoid problems in, e.g., 1:numGeneSetCollections when numGeneSetCollections == 0.

• gsca_analyze.R:280. Required. Use a simple helper function to avoid repetitive code, e.g.,

  helper <- function(x, cidx) {
      if (nrow(x) == 0)
          return(NULL)
      a <- x[[cidx]] < pValueCutoff
      x <- x[a, , drop = FALSE]
      if (any(a))
          x <- x[order(x[[cidx]]), , drop = FALSE]
      x
  }
  sign.hgt <- lapply(HGTresults, helper, "Pvalue")
  sign.hgt.adj <- lapply(HGTresults, helper, "PAdjusted.Pvalue")

• gsca_analyze.R:326. Required. Avoid 'copy and append' pattern were a result is grown, implicitly, via overlap = list(); ...; overlap[[i]] <- ;, instead, 'pre-allocate and fill', overlap = vector("list", length(numGeneSetCollections)); ...; overlap[[i]] <-. This avoids unnecessary copying when the list is extended.
• gsca_analyze.R:511 and throughout. Recommended. Consider using BiocParallel rather than foreach, to better integrate with the Bioconductor ecosystem.
• gsca_load_genesets.R:183. Required unlist(sapply(...)) does not make sense, use unlist(lapply(...), use.names=FALSE)
• gsca_summarize.R:3. Recommended. When a generic has several arguments, and only one or a few of those arguments will be used for dispatch, use signature = to restrict dispatch to the specific arguments for which dispatch is required.

• nwa_analyze.R:103. Recommended. Load but do not attach annotation packages, e.g,

  nmspc < - loadNamespace(anno.db.species)
  obj <- get(anno.db.species, nmspc)

  Use newer select() and mapIds() rather than the 'bimap' interface to annotation resources, e.g.,

  AnnotationDbi::mapIds(obj, vertex_attr(module, "name"), "SYMBOL", "ENTREZID")

• nwa_preprocess.R:298 Recommended. Use BiocFileCache to reduce the number of times resources are downloaded and to limit the need for users to manage files on disk. This also increases reliability of the nightly build system.

• nwa_view.R:135. Recommended. Avoid highly nested calls

  unique(Reduce(rbind, lapply(extractedValues, function(li){li$vertices[colsInCommon]})))

  in favor of more readable versions

  values <- lapply(extractedValues, function(li) li$vertices[colsInCommon])
  unique(Reduce(rbind, values))

• stat_test.R:117 et seq. Required. Simply assign the result of sapply() rather than pre-allocate and fill. No need to use an index if the object itself can be used.

  t.test.pvalues.one.sample <- sapply(replicates, function(replicate) {
      if (sum(!is.na(replciate)) < 2)
          return(1)
      t.test(replicate, mu, alternative)$p.value
  })

• zzz.R:2. Required. No need for this message.

man

• Recommended. A best practice is to organize the man pages into files identical to R code files, so that the file structure is 'parallel'. This is good practice because it emphasizes the logical coherence of source code in terms of functionality.
• Recommended. Please give additional consideration to the naivete of your users when describing data sets. For instance indicating that Biogrid_HS_Mat is an 'interactome matrix' is not helpful without knowing what an 'interactome matrix' is.

misc

• Required. Remove sys/symbols.rds.
• Required. Format inst/NEWS for parsing by news(), or remove.

[linazhu3]

Hi, @mtmorgan

Thanks for your time and suggestions!

[mtmorgan]

@linazhu3 can you let me know what your plans are with this package? Thanks

[mtmorgan]

@linazhu3 I'll close the issue next week unless I hear from you. If you resume development the issue can be reopened.

[bioc-issue-bot]

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

ba974b6 hyperGeo Pvalue visualization

[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:

a86e229 Vignette 475638c pvalue in table Merge branch 'master' of https://...

[LiNk-NY]

@linazhu3,

Do you intend to have your package reviewed for submission by Bioconductor? If so, I can reopen the issue. Otherwise, please remove the webhook in your package settings.

Regards, Marcel

[xinwang2hms]

LIna, pls remove the webhook, as we would never consider Bioconductor anymore in the future for any of our packages.

-Xin

On Wed, Jun 13, 2018 at 11:41 PM, Marcel Ramos notifications@github.com wrote:

@linazhu3 https://github.com/linazhu3,

Do you intend to have your package reviewed for submission by Bioconductor? If so, I can reopen the issue. Otherwise, please remove the webhook in your package settings.

Regards, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/561#issuecomment-396984530, or mute the thread https://github.com/notifications/unsubscribe-auth/AFIt_CBxIWGdGbIK6PGHLtGlzvDIkx3Eks5t8TKsgaJpZM4QnkRj .

[linazhu3]

Dear Dr. Wang,

Yep, I've already removed the webhook.