EnrichDO

[liangcheng-hrbmu]

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[bioc-issue-bot]

Hi @liangcheng-hrbmu

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: EnrichDO
Type: Package
Title: Disease ontology annotation and enrichment analysis
Version: 0.99.0
Author: c(person(given="Haixiu",family="Yang",email="yanghaixiu@ems.hrbmu.edu.cn",role=c("aut")),
person(given="Hongyu",family="Fu",email="15736262010@163.com",role=c("cre"))
)
Maintainer: Liang Cheng <liangcheng@hrbmu.edu.cn>
Description: This package combines topological properties of 
    disease ontology structure to implement disease ontology 
    enrichment analysis.Enrichment analyses including a variety 
    of statistical models and visualization schemes for discovering 
    the disease-gene relationship under biological big data.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: BiocGenerics, RColorBrewer, Rgraphviz, clusterProfiler,
    dplyr, ggplot2, graph, magrittr, methods, pheatmap,
    purrr, readr, stringr, tidyr
biocViews: Annotation, Visualization, 
        GeneSetEnrichment, Software
Depends: 
    R (>= 3.5.0)
RoxygenNote: 7.3.1
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr

[lshep]

Can you please expand the abstract/introduction in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope. Is it possible to show interoperability with any existing Bioconductor infrastructure classes?

The data in Meta should be moved to an official recognized directory, either data or inst/extdata and if in inst/extdata there should be an inst/script that describes the data, how it was created, source information, etc.

[liangcheng-hrbmu]

Can you please expand the abstract/introduction in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope. Is it possible to show interoperability with any existing Bioconductor infrastructure classes?

The data in Meta should be moved to an official recognized directory, either data or inst/extdata and if in inst/extdata there should be an inst/script that describes the data, how it was created, source information, etc.

We have modified the uploaded package according to your suggestion.

[lshep]

Can you please make sure any default print/save/writes are defaulted to write to a tempdir() rather than a working directory.

When I'm rerunning the vignette I'm getting different results for the plotting functions. Is there some random effect that is not shown or controlled? Or if all sections of the vignettes are run (as some seem to be designated eval=FALSE) , that means the object used in plotting is different?

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

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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 the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.1.tar.gz macOS 12.7.1 Monterey: EnrichDO_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[liangcheng-hrbmu]

Can you please make sure any default print/save/writes are defaulted to write to a tempdir() rather than a working directory.

When I'm rerunning the vignette I'm getting different results for the plotting functions. Is there some random effect that is not shown or controlled? Or if all sections of the vignettes are run (as some seem to be designated eval=FALSE) , that means the object used in plotting is different?

@lshep We have submitted some new changes.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 70471bab0ce1e7b9cac9611e87c832384cbca11f

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: EnrichDO_0.99.2.tar.gz Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: aef8420194e39f971e88a5541d44fe77141a49a5

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: EnrichDO_0.99.3.tar.gz Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: eb1a14b3d894a6f73243e6bff3efd1f4f0d93e36

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.4.tar.gz macOS 12.7.1 Monterey: EnrichDO_0.99.4.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e17482d9a5c4c628befb38ea2589998199e3ac69

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.5.tar.gz macOS 12.7.1 Monterey: EnrichDO_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e3d615b87d5d17ea7e00d3cd49d3699b3d98ce7c

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: EnrichDO_0.99.6.tar.gz Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.6.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[DarioS]

Major changes required to bring it to Bioconductor standard.

• Vignette needs to have an Installation section. See Installation.

• The vignette uses eval = FALSE. No code chunks are allowed to use eval = FALSE. Please see Vignettes.

• Vignette shouldn't repeat content of function Rd files.

  

• Function calls explicitly use same values as default. If not different, don't specify the values to avoid redundancy.

doEnrich(interestGenes = demo.data, 
          test         = "hypergeomTest", 
          method       = "BH", 
          m            = 1, 
          maxGsize     = 5000,
          minGsize     = 5,
          traditional  = FALSE,
          delta        = 0.01, 
          result_do    = NULL,
          penalize     = T)    

• Use spaces around binary operators. For example, weight_result<-doEnrich(interestGenes = demo.data) does not. Please refer to Use of Space in the chapter named R Code.
• The output is a plain data.frame. Please use Biocoductor's DataFrame class from S4Vectors instead.

> class(enrich)
  "data.frame"

• No biological interpretation. Please explain what the important biological aspects are, not just a list of definitions.

  

  Which disease terms were statistically significant? What does this suggest about the disease? Interpret the results.

• The vignette still writes to the currently working directory: writeDoTerms(doterms,file = "doterms.txt").

• Inconsistent variable naming style e.g. weight_matrix, fisherTest. Bioconductor requires camelCase for consistency.

• Too much copying and pasting of code. Please restructure your functions to remove redundancy.

• Don't use for loops e.g. for(i in max(enrich$level):m) but vectorise with lapply or vapply. See Vectorize.

• Unnecessary usage of global variables.

enrich <<- enrich %>% arrange(p)
enrich <<- mutate(enrich, p.adjust=p.adjust(p, method=method))

• Package submitted for review should not contain EnrichDO.Rproj file. See Undesirable Files.
• Package lacks unit tests. Please read Chapter 14: Unit Tests and add some meaningful correctness tests.
• There are many data files in extdata folder such as PAAD_GSE16515.csv. They are not used in examples or the vignette,
• Function parameters that have a limited set of valid values are not properly implemented. For example,

test: One of "fisherTest","hypergeomTest","binomTest","chisqTest" and "logoddTest". Default is hypergeomTest.

is implemented as test = "hypergeomTest" and inside the function there is no validity check. See match.arg and use it.

• Don't use cat for user messages. Use message instead. See End-user Messages.
• doEnrich function's described return type does not match the actual type that is returned.

Value: A enrich instance.

> class(demo_result3)
  "data.frame"

• Figure 3 of vignette has poor readability due to an unfortunate default colour scheme.

  

• Vignette needs a session information section at the end of it. See Session Information.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2df2436c4329b9d2ce1f94c84a8ab86add144238

[liangcheng-hrbmu]

Thank you for your suggestion！We have made corresponding modifications.

for(i in max(enrich$level):m), among them, regarding the use of the for loop, our algorithm needs to be calculated layer by layer and cannot calculate all levels simultaneously. Thus, except for the for loop, we have not come up with a better approach.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: EnrichDO_0.99.7.tar.gz Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.7.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[liangcheng-hrbmu]

hi @DarioS , I am getting this warning on Bioconductor server at macOS, not sure yet what's the reason: WARNING: R CMD check exceeded 10 min requirement

[DarioS]

That warning is fine to have. I will re-review your package soon.

[DarioS]

The package has been moderately improved. However, some major issues remain.

• The software doesn't implement Functional Programming. It has widespread use of global assignment.

• The unit test is not meaningful. It tests whether the p-value is between 0 and 1.

res <- sapply(c("fisherTest","hypergeomTest","binomTest","chisqTest","logoddTest" ), function(test){
  aa<-doEnrich(interestGenes = demo.data, test = test) ;return(aa@enrich$p)})
  expect_true(all(res >= 0) && all(res <= 1))

The p-values are calculated by base R functions and would never produce values outside of 0 and 1. For example,

p<-phyper(wa-1,wa+wb,wc+wd,wa+wc,lower.tail = FALSE)

• The code does not use whitespace around binary operators. For example,

p<-phyper(wa-1,wa+wb,wc+wd,wa+wc,lower.tail = FALSE)

• An S4 class was defined. But, it has no accessor functions and the examples ask the user to use @ e.g. demo_result@enrich. @ should only ever be used by a package developer, not by a package user. Please refer to Class Design.

• Result floods the R console because the S4 class lacks a required show method.

From Class Design section,

Implement a show() method to effectively convey information to your users without overwhelming them with detail.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 439befc54ce91f96eeca4bb13a341cfdb93a5002

[liangcheng-hrbmu]

@DarioS Thank you for your suggestion！We have made corresponding modifications.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.8.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[DarioS]

The package improves but outstanding issues remain.

• The authors implemented an S4 show method. However, there is still a vast amount of text in console. This is attempted to be hidden by using comments in R chunks and hiding the real output of the variable. show method needs to be used.

• The code still does not use whitespace around binary operators.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b32752ee5ad51643a88ff820a7bf293413bbc9ff

[liangcheng-hrbmu]

hi，@DarioS .The feature of our algorithm lies in calculating the ontology structure layer by layer. Thus, we aim to present the calculation status of each layer to the user. The running time of the algorithm is approximately 10 seconds, indicating that the calculation results can prevent the user from waiting for an extended period. If the above explanation does not conform to the rules, we will revise it again. We have modified the binary operators, thank you for your reminding！

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.9.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4792d1332036e86a73b4056f6447188df8572121

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.10.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 16a8e7d656bd89fbd316cc5f8f493a4df888647f

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.11.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[DarioS]

The result of doEnrich function now has a nice show method. However, the result of EnrichTab floods the R console with text. The request to use DataFrame was previously made and it would easily address this issue.

• The output is a plain data.frame. Please use Biocoductor's DataFrame class from S4Vectors instead.
• The support for DataFrame input is variable across the package.

  > DOterms <- DataFrame(doterms)
  > writeDoTerms(DOterms, file = file.path(tempdir(), "doterms.txt"))
  Error in UseMethod("mutate") : 
  no applicable method for 'mutate' applied to an object of class "c('DFrame', 'DataFrame', 'SimpleList',
  'RectangularData', 'List', 'DataFrame_OR_NULL', 'Vector', 'list_OR_List', 'Annotated', 'vector_OR_Vector')"

• Lack of robustness to edge cases. For example, gene_n = 1:

  > drawHeatmap(interestGenes = demo.data, enrich = Enrich,gene_n = 1, fontsize_row = 8, readable = TRUE)
  gene symbol conversion result: 
  Error in hclust(d, method = method) : must have n >= 2 objects to cluster

  Input parameters need validity checking by package code.

Always use space after a comma. This: a, b, c.

from Section 15.2.7.2 has also not been done.

• Warnings from ggplot2 need to be avoided.

  drawPointGraph(enrich=enrich,delta = 0.05) Warning message: Using size for a discrete variable is not advised.

• The code still does not use whitespace around binary operators. For example,

  enrichWeight<-get("enrichWeight",envir = .EnrichDOenv)
  enrichPvalue<-get("enrichPvalue",envir = .EnrichDOenv)
  enrichgeneArr<-get("enrichgeneArr",envir = .EnrichDOenv)
  
  genes<-enrichgeneArr[[DOID]]
  weights<-enrichWeight[[DOID]]

  Another round of modifications and review is warranted.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fe90d13033918cc32784ffb993f732e6e7134c72

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): EnrichDO_0.99.13.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[liangcheng-hrbmu]

Hi @DarioS , I am sorry for the repeated problems. Fortunately, we have found a suitable way to solve the above problems.

• We have corrected the format using formatR.
• Our package currently does not use plain data.frame and also supports DataFrame input.
• In addition, the parameter Settings of other functions are also limited, and inappropriate parameter input will be warned.

besides，for the internal data--doterms, although it is a data.frame, we set up the appropriate showDoTerms(doterms) to show the structure of doterms, and the function writeDoTerms supports DataFrame(doterms) as input.

Thank you for your review over the past two months. We look forward to hearing from you.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 880eb7c7c9b97a7143585d1bcc9ef550e282c500

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): EnrichDO_0.99.14.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EnrichDO to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[liangcheng-hrbmu]

Hello @DarioS , thank you for your review and encouragement. Additionally, we need a download address for EnrichDO provided by Bioconductor for our paper, but EnrichDO has not been deployed to the devel branch yet. How long does it usually take to successfully deploy it, or is there another download address we can use?

[DarioS]

It is performed manually by Lori Kern of the Bioconductor core team. It usually happens once per week.

[lshep]

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/liangcheng-hrbmu.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("EnrichDO"). The package 'landing page' will be created at

https://bioconductor.org/packages/EnrichDO

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.