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Repository: https://github.com/BioinfoMonzino/PIUMA

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Dec 04 '23 11:12 BioinfoMonzino

Hi @BioinfoMonzino

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: PIUMA
Type: Package
Title: Phenotypes Identification Using Mapper from topological data 
     Analysis(PIUMA)
Version: 0.99.0
Authors@R: c(
    person("Mattia", "Chiesa", , "[email protected]", 
	role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7427-9954")),
    person("Arianna", "Dagliati", , "[email protected]",
	role = "aut", comment = c(ORCID = "0000-0002-5041-0409")),
	person("Alessia", "Gerbasi", , "[email protected]",
	role = "aut", comment = c(ORCID = "0000-0003-4501-1777")),
	person("Giuseppe", "Albi", , "[email protected]",
	role = "aut"),
	person("Laura", "Ballarini", , "[email protected]",
	role = "aut"),
	    person("Luca", "Piacentini", , "[email protected]",
	role = "aut", comment = c(ORCID = "0000-0003-1022-4481"))
  )
Description: The PIUMA package offers a tidy pipeline of Topological
        Data Analysis frameworks to identify and characterize 
		communities in high and heterogeneous dimensional data.
License: GPL-2 (>= 2)
Encoding: UTF-8
LazyData: true
biocViews: Clustering, GraphAndNetwork, DimensionReduction, Network,
     Classification
VignetteBuilder: knitr
Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales,
    Hmisc, patchwork, grDevices, stats
Suggests: BiocStyle, knitr, testthat
Depends: R (>= 4.2), ggplot2
RoxygenNote: 7.2.3

Dec 04 '23 11:12 bioc-issue-bot

Your license in your description is GPL-2 but you provided the LICENSE file for GPL-3. It would be better to update to GPL-3 in your DESCRIPTION file for consistency.

Dec 11 '23 12:12 lshep

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.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

Dec 11 '23 14:12 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 22.04.2 LTS): PIUMA_0.99.0.tar.gz macOS 12.7.1 Monterey: PIUMA_0.99.0.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 [email protected]:packages/PIUMA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 11 '23 14:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8e3b04b231f9993ab7a7d85ac6c1b00303b6479a

Dec 12 '23 15:12 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: PIUMA_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 [email protected]:packages/PIUMA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 12 '23 15:12 bioc-issue-bot

Dear Lori @lshep, I fixed the two minor issues, but I got this warning:

* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                  old_size new_size compress
  vascEC_norm.rda    1.6Mb    984Kb       xz

I used to build packages with --resave-data argument; thus, I have never get this warning. What should I do to solve this issue? Thanks in advance, Mattia.

Dec 13 '23 09:12 BioinfoMonzino

You can either grab the files from the built tar on your system when you have run --resave-data that have the files compressed and then move them into your source package, or you can resave the data files using the suggested compression type (xz). This is an old mailing list post but accurate https://stat.ethz.ch/pipermail/r-devel/2012-March/063649.html .

Dec 13 '23 12:12 lshep

Received a valid push on git.bioconductor.org; starting a build for commit id: 7d089fddd0bd467893b1ef13c7e6c07ed60d4789

Dec 13 '23 15:12 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 22.04.2 LTS): PIUMA_0.99.2.tar.gz macOS 12.7.1 Monterey: PIUMA_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 [email protected]:packages/PIUMA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 13 '23 15:12 bioc-issue-bot

@lshep I got this error

    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel

It's quite strange since I am the mantainer of other two packages. However, I filled out the form again. But everytime I try to check the subscribers list with my account I got this message: Error Bioc-devel roster authentication failed

Dec 15 '23 08:12 BioinfoMonzino

That is odd. I do not see you registered in the list. Would you like me to register you manually?

Dec 15 '23 17:12 lshep

It would be great! Many thanks, Mattia

Il giorno 15 dic 2023, alle ore 18:09, lshep @.***> ha scritto:

That is odd. I do not see you registered in the list. Would you like me to register you manually?

— Reply to this email directly, view it on GitHubhttps://urlsand.esvalabs.com/?u=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F3245%23issuecomment-1858209829&e=8c00e339&h=85a72527&f=y&p=n, or unsubscribehttps://urlsand.esvalabs.com/?u=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAGCR73G74NLISVGQJCIWVJTYJR74PAVCNFSM6AAAAABAFY3B5KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJYGIYDSOBSHE&e=8c00e339&h=1373af2f&f=y&p=n. You are receiving this because you were mentioned.Message ID: @.***>

Dec 15 '23 20:12 BioinfoMonzino

@lshep, please let me know when everything is ok so that I push a new build/check.

Dec 18 '23 09:12 BioinfoMonzino

I have manually added you to the bioc-devel mailing list. If you still get an ERROR we can ignore as I can confirm registration. Please try and push a new build/check at your earliest convenience

Dec 18 '23 12:12 lshep

Received a valid push on git.bioconductor.org; starting a build for commit id: 371f639dad0154478eaa524be62aa97a8f840da8

Dec 18 '23 13:12 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: PIUMA_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): PIUMA_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 [email protected]:packages/PIUMA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 18 '23 13:12 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.

Dec 21 '23 18:12 bioc-issue-bot

Hi @BioinfoMonzino

Thanks for submitting PIUMA :tada:! Below is my review of your package. Please reply here if anything is unclear or needs any further explanation.

What next?

Please address the comments as best as you can. When you are ready for me to check the package again please reply to let me know with a summary of changes you have made or any other responses. You can use the "Quote reply" option in the ... menu on this comment to reply directly to my points below.

Luke

Review

Key: :rotating_light: Required :warning: Recommended :green_circle: Optional :question: Question

General package development

[ ] :warning: I got some notes when checking the packages. The important ones should be mentioned below but please check the build report after making changes to see if there are any others.

DESCRIPTION file

[ ] :warning: Please check the formating of the title
[ ] :rotating_light: There is a check warning related to the License field. You either need to change the LICENSE: to GPL-3 + file LICENSE (preferred) or delete the LICENSE file.
[ ] :rotating_light: Bioconductor recommends setting LazyData: false
[ ] :warning: It is recommended to add a BugReports field. This is usually a link to the GitHub issues page for the package or the Bioconductor support forum.
[ ] :warning: It is recommended to add a URL field. This is usually a link to the GitHub repository for the package.

NAMESPACE file

[ ] :rotating_light: Please import functions from patchwork rather than importing the whole package.

The CITATION file

[ ] :rotating_light: The citation currently isn't read correctly. You can test this with readCitationFile("inst/CITATION").

Package data

[ ] :warning: The documentation of the datasets could be expanded. It should be clear what the source of each dataset is. I think there is some code in the vignette that could be included here.
[ ] :warning: I think the @format tag should be sufficient for data documentation and you don't need to include @return (double check this doesn't lead to warnings though)

Documentation

[ ] :green_circle: It wasn't clear to me from the documentation what data types the package is designed for. You may want to make this clearer.
[ ] :green_circle: I noticed a few typos in difference parts of the documentation. The {spelling} package can help with finding these.

README

[ ] :rotating_light: Please include Bioconductor installation instructions

Vignette

[ ] :rotating_light: Please name the first section Introduction for consistency with other Bioconductor packages
- [ ] This should include motivation for including the package in Bioconductor and comparions to similar packages (if applicable)
[ ] :warning: It is generally preferred to have a HTML rather than PDF website. These are better incorporated into the Bioconductor website and are more accessible to users.

Man pages

[ ] :warning: It is recommended to add a package man page

Unit tests

[ ] :rotating_light: Tests should be placed inside a test_that() block. Something like:

test_that("function A works", {

  out <- functionA(...)

  expect_equal(out, ...)
})

Code

R

[ ] :rotating_light: Please use vapply instead of sapply
[ ] :warning: Please try to used named indicies instead of numeric indices
[ ] :rotating_light: Please use message() instead of cat() or print()
[ ] :rotating_light: Currently your package does not depend on any other Bioconductor packages or data structures. Can your functions be adjusted to use standard objects to increase compatibility with other Bioconductor pacakges.
[ ] :rotating_light: Please remove commented code that is no longer used
[ ] :warning: It is better to have separate functions for analysis and visualisation rather than doing both in one function (eg. checkScaleFreeModel(), dfToProjection())
[ ] :warning: It is generally better to avoid nested functions
[ ] :warning: Chained allocation (x <- y <- z) can be confusing and is generally not recommended
[ ] :green_circle: The styling is inconsistent in some places, you might want to consider using the {styler} package to help with this.

Jan 12 '24 15:01 lazappi

@lazappi Thanks a lot for the valuable feedbacks which surely help us to improve PIUMA. We will try to address all your concerns. I ill give you a feedback in the next upcoming weeks. Thanks again, Mattia

Jan 23 '24 11:01 BioinfoMonzino

Received a valid push on git.bioconductor.org; starting a build for commit id: 66f9bcc97b0c43d85f11247389982144ec7581a2

Mar 22 '24 10:03 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: "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.

The following are build products from R CMD build on the Single Package Builder: ERROR before build products produced.

Links above active for 21 days.

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

Mar 22 '24 10:03 bioc-issue-bot

Dear @lazappi We tried to fix all your concerns. The flagged checkbox means that the task has been accomplished, in accordance with your suggestions. The bold text gives you motivation about our choices .

I still see a check error about vignette generation that I cannot reproduce in my systems. I try to look a bit deeper.

Mar 22 '24 10:03 BioinfoMonzino

Hi @BioinfoMonzino

Thanks for submitting PIUMA 🎉! Below is my review of your package. Please reply here if anything is unclear or needs any further explanation.

What next?

Please address the comments as best as you can. When you are ready for me to check the package again please reply to let me know with a summary of changes you have made or any other responses. You can use the "Quote reply" option in the ... menu on this comment to reply directly to my points below.

Luke

Review

Key: 🚨 Required ⚠️ Recommended 🟢 Optional ❓ Question

General package development

[x] ⚠️ I got some notes when checking the packages. The important ones should be mentioned below but please check the build report after making changes to see if there are any others. Thanks for the feedback. We fixed almost all the relevant notes from Check and BiocCheck. In addition, no Errors and Warnings happened from our side during check and biocCheck.

DESCRIPTION file

[x] ⚠️ Please check the formating of the title

[x] 🚨 There is a check warning related to the License field. You either need to change the LICENSE: to GPL-3 + file LICENSE (preferred) or delete the LICENSE file.

[x] 🚨 Bioconductor recommends setting LazyData: false

[x] ⚠️ It is recommended to add a BugReports field. This is usually a link to the GitHub issues page for the package or the Bioconductor support forum.

[x] ⚠️ It is recommended to add a URL field. This is usually a link to the GitHub repository for the package.

NAMESPACE file

[x] 🚨 Please import functions from patchwork rather than importing the whole package.

The CITATION file

[x] 🚨 The citation currently isn't read correctly. You can test this with readCitationFile("inst/CITATION").

Package data

[x] ⚠️ The documentation of the datasets could be expanded. It should be clear what the source of each dataset is. I think there is some code in the vignette that could be included here. We extended the data documentation for those datasets used for vignette, highlighting the paper purposes, the data repository and adding a brief description. **

[x] ⚠️ I think the @format tag should be sufficient for data documentation and you don't need to include @return (double check this doesn't lead to warnings though) Removing @return tag from data documentation leads to a Warning, during the check. Therefore, we re-added this tag to each dataset.

Documentation

[x] 🟢 It wasn't clear to me from the documentation what data types the package is designed for. You may want to make this clearer.

[x] 🟢 I noticed a few typos in difference parts of the documentation. The {spelling} package can help with finding these.

README

[x] 🚨 Please include Bioconductor installation instructions

Vignette

[x] 🚨 Please name the first section Introduction for consistency with other Bioconductor packages

[x] This should include motivation for including the package in Bioconductor and comparions to similar packages (if applicable)

[x] ⚠️ It is generally preferred to have a HTML rather than PDF website. These are better incorporated into the Bioconductor website and are more accessible to users.

Man pages

[x] ⚠️ It is recommended to add a package man page

Unit tests

[x] 🚨 Tests should be placed inside a test_that() block. Something like:
test_that("function A works", {

  out <- functionA(...)

  expect_equal(out, ...)
})
Code

R

[x] 🚨 Please use vapply instead of sapply

[ ] ⚠️ Please try to used named indicies instead of numeric indices In most cases, our functions loop over the features of matrices and data.frames, than can exhibit different names, each time. In such cases, we believe that numeric indices are more practical than named indices.

[x] 🚨 Please use message() instead of cat() or print()

[x] 🚨 Currently your package does not depend on any other Bioconductor packages or data structures. Can your functions be adjusted to use standard objects to increase compatibility with other Bioconductor pacakges. We stressed this point even more in the vignette. TDA can be performed on any high-dimensional and sizable datasets, such as scRNA-seq experiment. To be compliant with the Bioconductor data compatibility we generated a 'TDAobj' (S4) object which can easily interact with the most popular Bioconductor data types, such as SummarizedExperiment, as shown in the vignette.

[x] 🚨 Please remove commented code that is no longer used

[ ] ⚠️ It is better to have separate functions for analysis and visualisation rather than doing both in one function (eg. checkScaleFreeModel(), dfToProjection()) We have designed these functions so as to provide the user with immediate visual feedbacks that allows appreciating the effect of parameters combination. However, we agree that in some cases, such as in a 'grid-search' test, the generation of several images can be heavy and not very useful. Accordingly, we decided to set to false by default the arguments that control the graphs generation, without create additional dedicated functions.

[ ] ⚠️ It is generally better to avoid nested functions We used nested functions in two situations: scaling data and calculating Jaccard's indexes; these functions are 1) very small (1 to 5 lines) and 2) used just one time inside the 'outer function'. Therefore, we do not believe that it is necessary to generate a dedicated script (with documentation, test, manual and so on).

[x] ⚠️ Chained allocation (x <- y <- z) can be confusing and is generally not recommended

[x] 🟢 The styling is inconsistent in some places, you might want to consider using the {styler} package to help with this.

Mar 22 '24 10:03 BioinfoMonzino

Received a valid push on git.bioconductor.org; starting a build for commit id: eeb78895a59ddf16b898caf11b2176b73ecaef07

Mar 25 '24 09:03 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): PIUMA_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 [email protected]:packages/PIUMA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 25 '24 09:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 0b48fe985e1c92ce255cb8bfc21e68aaca0869c9

Mar 25 '24 09:03 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: Linux (Ubuntu 22.04.3 LTS): PIUMA_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 [email protected]:packages/PIUMA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 25 '24 09:03 bioc-issue-bot

[x] ⚠️ I got some notes when checking the packages. The important ones should be mentioned below but please check the build report after making changes to see if there are any others. Thanks for the feedback. We fixed almost all the relevant notes from Check and BiocCheck. In addition, no Errors and Warnings happened from our side during check and biocCheck.

There is an error on the build report now, please check and correct this

[x] 🚨 The citation currently isn't read correctly. You can test this with readCitationFile("inst/CITATION").

If you don't currently have a citation available I would suggest removing this file. Bioconductor will generate a full reference full the package including DOI etc. but that will be overwritten by what is in the file.

[x] 🚨 Tests should be placed inside a test_that() block. Something like:

[ ] ⚠️ Please try to used named indicies instead of numeric indices In most cases, our functions loop over the features of matrices and data.frames, than can exhibit different names, each time. In such cases, we believe that numeric indices are more practical than named indices.

This is ok for loops, I was referring more to cases such as accessing a column from a data.frame using df[, "column_name"] rather than df[, 1]
It is clearer to use nrow(x)/ncol(x) rather than dim(x)[1]/dim(x)[2]

[x] 🚨 Currently your package does not depend on any other Bioconductor packages or data structures. Can your functions be adjusted to use standard objects to increase compatibility with other Bioconductor pacakges. We stressed this point even more in the vignette. TDA can be performed on any high-dimensional and sizable datasets, such as scRNA-seq experiment. To be compliant with the Bioconductor data compatibility we generated a 'TDAobj' (S4) object which can easily interact with the most popular Bioconductor data types, such as SummarizedExperiment, as shown in the vignette.

I did not see any mention of compatibility with SummarizedExperiment or other objects in the vignette, maybe I missed it?
It is not an absolute requirement but there would be much greater compatibility if you operated directly on something like a SummarizedExperiment directly rather than creating your own object. This would allow your package to be easily included in workflows involving other Bioconductor packages.
If you do choose to have your own custom object then you need to create getter, setter and constructor methods rather than using @ or slot()

[x] 🚨 Please remove commented code that is no longer used

Please check this again, I saw some in the tests but there may be more in other places

[ ] ⚠️ It is better to have separate functions for analysis and visualisation rather than doing both in one function (eg. checkScaleFreeModel(), dfToProjection()) We have designed these functions so as to provide the user with immediate visual feedbacks that allows appreciating the effect of parameters combination. However, we agree that in some cases, such as in a 'grid-search' test, the generation of several images can be heavy and not very useful. Accordingly, we decided to set to false by default the arguments that control the graphs generation, without create additional dedicated functions.

Having unexpected plots appear is one consideration but there are others. Having separate functions would make it easier to modify the plots (changing themes for example). It also makes the code easier to follow and maintain when functions only do one thing.

[ ] ⚠️ It is generally better to avoid nested functions We used nested functions in two situations: scaling data and calculating Jaccard's indexes; these functions are 1) very small (1 to 5 lines) and 2) used just one time inside the 'outer function'. Therefore, we do not believe that it is necessary to generate a dedicated script (with documentation, test, manual and so on).

Ok. I think the code would be easier to maintain if you moved these small functions to a utils.R file and you would not necessarily need separate tests for them but it is probably up to you.

Additional points:

Please give the test file a more meaningful name. The convention is to have one test file for each .R code file.

I think these lines in makeTDAobj() are identical, maybe check that is what you want?

# find numeric columns
indNumInt <- which(vapply(df, class, FUN.VALUE = character(1)) %in%
                     c("numeric", "integer"))

# find factor columns
indFact <- which(vapply(df, class, FUN.VALUE = character(1)) %!in%
                 c("numeric", "integer"))

You should use is() (or is.numeric() etc.) rather than class()
Please use seq_len()/seq_along() rather than 1:x

Mar 25 '24 14:03 lazappi

Received a valid push on git.bioconductor.org; starting a build for commit id: a8f8fcfc0af37dfc2e0f5e56650dfb9fc7f917d5

Apr 09 '24 12:04 bioc-issue-bot

Contributions Contributions copied to clipboard

PIUMA

Review

General package development

DESCRIPTION file

NAMESPACE file

The CITATION file

Package data

Documentation

README

Vignette

Man pages

Unit tests

Code

R

Review

General package development

DESCRIPTION file

NAMESPACE file

The CITATION file

Package data

Documentation

README

Vignette

Man pages

Unit tests

Code

R

Contributions
Contributions copied to clipboard