fgga - Githubissues

fspetale commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/fspetale/fgga

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bioc-issue-bot commented 3 years ago

Hi @fspetale

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: fgga
Type: Package
Title: Hierarchical ensemble method based on factor graph
Version: 0.99.0
Date: 2021-04-13
Authors@R: c(person("Spetale", "Flavio", email = "spetale@cifasis-conicet.gov.ar", role = c("aut", "cre")),
         person("Elizabeth", "Tapia", role = c("aut", "ctb")))
biocViews: Software, StatisticalMethod, Classification, Network, NetworkInference, SupportVectorMachine, GraphAndNetwork, GO
Description: Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent GO annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.
Depends: R (>= 4.0.4), RBGL
Imports: graph, stats, e1071, methods, gRbase, jsonlite
Suggests: knitr, rmarkdown, GOstats, PerfMeas, BiocGenerics
License: GPL (>=3)
URL: https://github.com/fspetale/fgga
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 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 build report for more details. This link will be 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/fgga to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 93a420b7b72f0aa5f9d790f97156f4300a8f2983

bioc-issue-bot commented 3 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 build report for more details. This link will be 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/fgga to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 3 years ago

Please see initial review below:

build report

[ ] High amount of donttests in man pages?

NAMESPACE

[ ] Do not use exportPattern("^[[:alpha:]]+"). Please selectively export the functions that should be user facing and keep others internal.

NEWS

[ ] Do not have empty sections. Essentially this is a blank NEWS file. Please populate. Many choose to do an initial entry of Submitted to Bioconductor

vignette

[ ] Why is the code section in 4.2 and 4.3 in an eval=FALSE? it seems quick enough to run the code?
[ ] Section 4.4, I am not able to run as idsTrain is not exposed to user code anywhere

> modelFGGA <- fgga2bipartite(mygraphGO)
> varianceGOs <- varianceGO(tableGOs = CfData[["tableCfGO"]][idsTrain, ], 
+                         dxCharacterized = CfData[["dxCf"]][idsTrain, ], 
+                         kFold = 5, graphGO = mygraphGO, rootNode = rootGO, 
+                         kernelSVM = "radial")
Error in as.matrix(tableGOs[order(rownames(tableGOs)), ]) : 
  object 'idsTrain' not found

Please expose the code to correctly make this variable. It seems there is an include=FALSE code chunk that has this information.

[ ] In section 4.5 I can't run the code either

> matrixFGGATest <- t(apply(matrixGOTest, MARGIN = 1, FUN = msgFGGA, 
+                         matrixFGGA = modelFGGA, graphGO = mygraphGO,
+                         tmax = 50, epsilon = 0.001))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': missing value where TRUE/FALSE needed

[ ] Since I can't make the above variable, I cannot test that section 5 works or not.

man pages

[ ] We would recommend not having static information in the fgga-package.Rd that often gets forgotten to update

\tabular{ll}{
Package: \tab fgga\cr
Type: \tab Package\cr
Version: \tab 0.99.0\cr
Date: \tab 2021-04-06\cr
License: \tab GPL 3.0\cr
LazyLoad: \tab yes\cr

[ ] The example in the donttest doesn't work? That's generally why we don't encourage the use of dontest/dontrun
```
> fggaResults <- fgga(graphGO = CfData[["graphCfGO"]],
```
tableGOs = CfData[["tableCfGO"]],
dxCharacterized = dxCfTrainCharacterized,
dxTestCharacterized = dxCfTestCharacterized,
kFold = 5, tmax = 50, epsilon = 0.001) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'nodes' for signature '"matrix"'



**R code**

- [ ] In preCoreFG.R Files that are accessed from the web should be cached so that if the website goes down or becomes unavailable users could use already investigated data or a downloaded version of the files.

- [ ] Please use message instead of print so user could potentially silence messages.

Please make changes and when ready do a version bump to trigger a new build report.  Please also comment here on how the above concerns have been addressed.  

Cheers

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0df887a0faaddbfccdf7b26f9e7f6c395c70aed9

bioc-issue-bot commented 3 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 build report for more details. This link will be 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/fgga to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

fspetale commented 3 years ago

Thanks @lshep for the review! I'll reply below to the raised points.

build report

[x] High amount of donttests in man pages? Removed the use of donttests by redesigning the test samples

NAMESPACE
- [x] Do not use exportPattern("^[[:alpha:]]+"). Please selectively export the functions that should be user facing and keep others internal. ExportPattern was removed and the functions that should be user facing and keep others internal were selected
NEWS
[x] Do not have empty sections. Essentially this is a blank NEWS file. Please populate. Many choose to do an initial entry of Submitted to Bioconductor The NEWS file was modified based on the suggestion made by the reviewer

vignette
[x] Why is the code section in 4.2 and 4.3 in an eval=FALSE? it seems quick enough to run the code? Sections 4.2 and 4.3 have been modified and are being evaluated.
[x] Section 4.4, I am not able to run as idsTrain is not exposed to user code anywhere Section 4.1 has been modified and is being evaluated.
[x] In section 4.5 I can't run the code either Section 4.5 has been modified and is being evaluated. The result of matrixFGGATest is now available because all functions are evaluated in vignette
[x] Since I can't make the above variable, I cannot test that section 5 works or not. Section 5 has been modified and is being evaluated.

man pages

[x] We would recommend not having static information in the fgga-package.Rd that often gets forgotten to update Static information has been removed
[x] The example in the donttest doesn't work? That's generally why we don't encourage the use of dontest/dontrun The example was checked and is working. Additionally, the use of donttest was eliminated to check its operation in the package building.

R code

[x] In preCoreFG.R Files that are accessed from the web should be cached so that if the website goes down or becomes unavailable users could use already investigated data or a downloaded version of the files. The preCore function was modified to cache GO ontologies that are extracted from the web. This function uses the BiocFileCache package
[x] Please use message instead of print so user could potentially silence messages. The use of print was changed to message

Regards, Flavio

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

vjcitn commented 3 years ago

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/fspetale.keys is not empty), then no further steps are required. Otherwise, do the following:

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("fgga"). The package 'landing page' will be created at

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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.

Bioconductor / Contributions

fgga #2103