HPiP

[mrbakhsh]

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• Repository: https://github.com/mrbakhsh/HPiP

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[bioc-issue-bot]

Hi @mrbakhsh

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: HPiP
Type: Package
Title: Host-Pathogen Interaction Prediction
Version: 0.99.7
Authors@R: c(
    person("Matineh", "Rahmatbakhsh", ,"matinerb.94@gmail.com",c("aut","trl","cre")),
    person("Mohan", "Babu", ,"mohan.babu@uregina.ca", c("led")))
Description: HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning 
    algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) 
    using structural and physicochemical descriptors computed from amino 
    acid-composition of host and pathogen proteins.The proposed package can effectively address 
    data shortages and data unavailability for HP-PPI network reconstructions. 
    Moreover, establishing computational frameworks in that regard will reveal 
    mechanistic insights into infectious diseases and suggest potential HP-PPI targets, 
    thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.
Depends: 
    R (>= 4.1)
Imports: 
    dplyr (>= 1.0.6),
    httr (>= 1.4.2),
    readr,
    tidyr,
    tibble,
    utils,
    stringr,
    magrittr,
    caret,
    corrplot,
    ggplot2,
    pROC,
    PRROC,
    igraph,
    graphics,
    stats,
    purrr
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
Suggests:
    knitr,
    rmarkdown,
    colorspace,
    protr,
    e1071,
    randomForest,
    gprofiler2,
    gridExtra,
    ggthemes,
    kableExtra,
    BiocStyle
biocViews: 
    Proteomics,
    SystemsBiology,
    NetworkInference,
    StructuralPrediction,
    GenePrediction,
    Network
RoxygenNote: 7.1.1

[bioc-issue-bot]

Dear @mrbakhsh ,

We have reopened the issue to continue the review process.
Please remember to push a version bump to git.bioconductor.org
to trigger a new build.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f2cf7449145781f3e73f889c0939a81129256dce

[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".
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/HPiP 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: 28a1931b7456e0c72f05b5914ce890aab728b268

[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. 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/HPiP 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: bb0f43aab45f4b735cd6827f664c7e6dfafd631d

[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. 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/HPiP to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Thank you for your submission. Please see initial review:

Build Report/General

• The License in the DESCRIPTION and the LICENSE file provided in the
  package do not match. Please choose one LICENSE type. It must be an open
  source LICENSE. We recommend one of the LICENSE distributed with R
  https://www.r-project.org/Licenses/

• Please address the coding practice NOTES in the build report.

• Please try to keep to an 80 character limit as the code will otherwise be
  difficult to read when displayed online. One suggested alternative is to
  include linebreaks after function arguments.

DESCRIPTION

• We recommend having a BugReport and Url field in the package description.

README

• Please also include Bioconductor installation instructions.

NEWS

• We highly recommend adding a NEWS file so package updates will be included
  in the bi-annual release announcements. See example release announcement
  http://bioconductor.org/news/bioc_3_13_release/. Without a NEWS file the
  package will not be included. See
  https://contributions.bioconductor.org/news.html for formatting.

Unit Tests

• We highly recommend unit test to test basic functionality of package

inst

• Please see https://cran.r-project.org/doc/manuals/r-release/R-exts.html
  for naming conventions. Generally data to be called by system.file are in a
  directory inst/extdata and internal system data is store in the R directory
  as a sysdata.rda file. This also explains it nicely
  https://r-pkgs.org/data.html

• All data provided in the inst directory, regardless of subdirectory,
  should have a inst/script file associated with how the data was
  generated. This should include source information, licensing if necessary, and
  any preprocessing to generate the data. It can be code, sudo-code, or text.

vignette

• There is no reuse of existing Bioconductor class structure. It seems like
  structures like BiocSet, SummarizedExpeirment, or at the very least
  BioStrings should be utilized.
  Biostrings seems highly approrpiate to be able to be used throughout the
  vignette as input option to all functions. And as FASTA import method.
  If you utilized SummarizedExperiment or an extention of SummarizedExperiment,
  you could potentially store the results of each of these processes in one
  object. Bioconductor standard object for rectangular feature x sample data is
  a SummarizedExperiment.

• Do not use deprecated functions. Please update as recommended by the dplyr
  warnings

> x_df <- calculateCTDD(x)
Warning messages:
1: `summarise_each_()` was deprecated in dplyr 0.7.0.
Please use `across()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: Expected 2 pieces. Additional pieces discarded in 273 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...]. 
3: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
> 

A deprecated function is intended to be removed and the functionality in your
package will then be broken

• Syntex errors in Summary of descriptors in the HPiP package

the Gold_ReferenceSet.csv data set.

**1. Load the gold-standard data:**

data is a dead link and this seems like it is wanted as a list header but does
not format properly.

Step 4 is also not displaying properly

**4.Map the amino acid composition (AAC) descriptor to the gold-standard data:**

• Because there are multiple filter methods loaded, I originally got an
  error trying to run your code but if you specify the package it should come
  from it works:

> pred_interactions <- filter(pred_interactions, ensemble_score > 0.6)
Error in filter(pred_interactions, ensemble_score > 0.6) : 
  object 'ensemble_score' not found

## but if you specify the correct filter it works
> pred_interactions <- dplyr::filter(pred_interactions, ensemble_score > 0.6)

• For plotting results with plots=TRUE in pred_ensemel, I don't get to see
  all three plots interactively as they are overwritten in the same device
  window. I only end up with a ROC plot.

• I get more errors trying to run the code

> S_interc <- filter(pred_interactions, 
+                            str_detect(Pathogen_protein, "^E:"))
Error in str_detect(Pathogen_protein, "^E:") : 
  could not find function "str_detect"

• All the ERROR trying to mimic your vignette is why we never recommend
  eval=FALSE in the vignettes. If possible run the code as much as possible.

R code

• Large sections of repeated code should be avoided and moved into a single
  function. For example calculateCTDD and CalculateCTDT share most of the same
  code base. These easily could be merged into one function and have sections
  specific to which method is being called. Same with calculateF1 and
  calculateF2. The main functions are the exact same except which function to
  call in the lapply at the end. This should be one function with an argument
  for F1 or F2. These are only two examples but all functions that have high
  overlapped should be merged or the sections of code that are the same should
  be its own internal function that each of the main functions call.

• Remove inefficiencies. For example calculatedCTDD have two fastaSplitted. Please
  evaluate in all R files.

• Results of webqueries should be cached so users may reproduce
  results. See BiocFileCache. webqueries occur in both get_FASTA and
  get_positivePPI

• It seems very bad practice to share an access key? I assume this key was
  assigned to you or your group for access; is access to this website restricted
  use with an account? If so then users should register on their own and the
  function should take an argument of their own assigned access key.

Thank you for your submission. Please address the above issues. When ready please make sure there is a version bump to trigger a new build report and comment back here on the above issues and requesting a re-review.

Cheers,

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2bee610cad4684a8567b05861eb5a6888d64605e

[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".
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/HPiP 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: bf6a30d455f5635a4f0935e903600aeae9ea7eda

[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. 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/HPiP to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mrbakhsh]

Hi @lshep - I have pushed the following updates. Thank you!

Build report

• The License in the DESCRIPTION and the LICENSE file provided in the
  package do not match. Please choose one LICENSE type. It must be an open
  source LICENSE. We recommend one of the LICENSE distributed with R
  https://www.r-project.org/Licenses/.
  Answer: I have changed the LICENSE to MIT + file LICENSE.
• Please address the coding practice NOTES in the build report.
  Answer: I have addressed almost all the notes as suggested.
• Please try to keep to an 80-character limit as the code will otherwise be
  difficult to read when displayed online. One suggested alternative is to
  include linebreaks after function arguments.
  Answer: Thank you for the suggestion. Line breaks have been added to keep an 80-character limit.

Description

• We recommend having a BugReport and Url field in the package description.
  Answer: Thank you for the suggestion. They added to the package description.

README

• Please also include Bioconductor installation instructions.
  Answer: Bioconductor installation instructions is added to the README file.

NEWS

• We highly recommend adding a NEWS file so package updates will be included in the bi-annual release announcements. See example release announcement http://bioconductor.org/news/bioc_3_13_release/. Without a NEWS file the package will not be included. See https://contributions.bioconductor.org/news.html for formatting.
  Answer: NEWS file included in the package.

Unit Tests

• We highly recommend unit test to test basic functionality of package.
  Answer: Done.

inst

• Please see https://cran.r-project.org/doc/manuals/r-release/R-exts.html for naming conventions. Generally, data to be called by system.file are in a directory inst/extdata and internal system data is store in the R directory as a sysdata.rda file. This also explains it nicely https://r-pkgs.org/data.html.
  Answer: Thank you for the suggestion. Raw data now stored in inst/extdata, while package data are stored in data/ directory. In addition, scripts that generate package data in are now available in data-raw directory.
• All data provided in the inst directory, regardless of subdirectory, should have an inst/script file associated with how the data was generated. This should include source information, licensing if necessary, and any preprocessing to generate the data. It can be code, sudo-code, or text.
  Answer: Done.

vignette

• There is no reuse of existing Bioconductor class structure. It seems like structures like BiocSet, SummarizedExpeirment, or at the very least BioStrings should be utilized. Biostrings seems highly approrpiate to be able to be used throughout the vignette as input option to all functions. And as FASTA import method.If you utilized SummarizedExperiment or an extention of SummarizedExperiment,
  you could potentially store the results of each of these processes in one object. Bioconductor standard object for rectangular feature x sample data is a SummarizedExperiment.
  Answer: Thank you for the suggestion. Both objects are added to the vignette.
• Do not use deprecated functions. Please update as recommended by the dplyr warnings
  Answer: I updated the function.
• Syntex errors in Summary of descriptors in the HPiP package. Step 4 is also not displaying properly.
  Answer: fixed the errors.
• Because there are multiple filter methods loaded, I originally got an error trying to run your code but if you specify the package it should come from it works.
  Answer: Thank you for the suggestion. All the required packages for data manipulation or data handling are loaded in the beginning of the vignette.
• For plotting results with plots=TRUE in pred_ensembel, I don't get to see all three plots interactively as they are overwritten in the same device window. I only end up with a ROC plot.
  Answer: I already fixed the issue, and if argument plots set to TRUE, the pred_ensembel function will create three plots and save them as pdf file in a sub directory of the working directory.
• I get more errors trying to run the code.
  Answer: Thank you for the suggestion. All the required packages for data manipulation or data handling are loaded in the beginning of the vignette.
• All the ERROR trying to mimic your vignette is why we never recommend eval=FALSE in the vignettes. If possible run the code as much as possible.
  Answer: All eval arguments are now set to TRUE.

R code

• Large sections of repeated code should be avoided and moved into a single function. For example calculateCTDD and CalculateCTDT share most of the same code base. These easily could be merged into one function and have sections specific to which method is being called. Same with calculateF1 and calculateF2. The main functions are the exact same except which function to call in the lapply at the end. This should be one function with an argument for F1 or F2. These are only two examples but all functions that have high overlapped should be merged or the sections of code that are the same should be its own internal function that each of the main functions call.
  Answer: Thank you for the suggestions. F1 and F2 are merged into one function. Also, Autocorrelation descriptors (moran, geary and moreau_broto) are now merged into one function. For calculateCTDD and calculateCTDT, the section of the codes that were similar are now merged.
• Remove inefficiencies. For example calculatedCTDD have two fastaSplitted. Please evaluate in all R files.
  Answer: Done.
• Results of webqueries should be cached so users may reproduce results. See BiocFileCache. webqueries occur in both get_FASTA and get_positivePPI.
  Answer: Thank you for the suggestion. Changed the functions as suggested.
• It seems very bad practice to share an access key? I assume this key was assigned to you or your group for access; is access to this website restricted use with an account? If so then users should register on their own and the function should take an argument of their own assigned access key.
  Answer: Thank you for the suggestion. Changed the function as suggested.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 16a3bbd0f02e69b850223e260660c2f7c68a03a2

[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. 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/HPiP 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: c8ee81d29e25d3909ce5d15492a53f81c719bf9d

[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. 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/HPiP 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: 037f880e0f34cca02997a3e0e0b8d89788783c9a

[mrbakhsh]

Hi @lshep - Sorry to push new updates as I found some issues in the pred_ensembel ( ) function. Looking forward to hearing from you soon, thank you.

[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. 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/HPiP to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Thank you for the changes. A few more minor comments:

• In vignette, when plot.pdf is saved in pred_ensemel call

set.seed(102)
ppi <- pred_ensembel(ind_data,
                     gd,
                     classifier = c("svmRadial", "glm", "ranger"),
                     resampling.method = "cv",
                     ncross = 5,
                     verboseIter = TRUE,
                     plots = TRUE,
                     filename = "plots.pdf")

Please show using a tempdir(). filename=file.path(tempdir(), "plots.pdf")

• You are still technically sharing your access key with users by providing it as default argument to get_positivePPI. How necessary is it to show the example and usage in the vignette? This would be an appropriate place to use an eval=FALSE in vignette and donttest in man examples. If it is necessary to have the results of this function for subsequent examples in the vignette, I would suggest saving the necessary intermediate object in extdata and then in the vignette after an eval=FALSE (with dummy access.key value), load the object that performed the task with a code chunk in an echo=FALSE.

Cheers

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2b68d63b088c339d22c2a89237d49c68de36ae58

[mrbakhsh]

Hi @lshep, thanks a lot for all the help. I have pushed the following updates. Thank you!

• In the vignette, when plot.pdf is saved in pred_ensemel call filename=file.path(tempdir(), "plots.pdf")
  Answer: Thank you for the suggestion, changed the vignette as suggested.

• You are still technically sharing your access key with users by providing it as a default argument to get_positivePPI. How necessary is it to show the example and usage in the vignette? This would be an appropriate place to use an eval=FALSE in vignette and donttest in man examples. If it is necessary to have the results of this function for subsequent examples in the vignette, I would suggest saving the necessary intermediate object in extdata and then in the vignette after an eval=FALSE (with dummy access.key-value), load the object that performed the task with a code chunk in an echo=FALSE.
  Answer: Thank you for the suggestion. Changed both vignette and the man file as suggested.

[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. 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/HPiP to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mrbakhsh]

Hi @lshep, I have addressed the minor comments. Please let me know if you need anything further for the submission.

Thank you

[lshep]

Thank you.

[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.

[vjcitn]

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/mrbakhsh.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

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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("HPiP"). 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.