(inactive) Lheuistic package submission

[alexsanchezpla]

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

• Repository: https://github.com/ASPresearch/Lheuristic

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[bioc-issue-bot]

Hi @alexsanchezpla

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: Lheuristic
Title: Detection of scatterplots with L-shaped pattern
Version: 0.99.0
Authors@R: c(
    person("Sanchez Pla", "Alex", email ="asanchez@ub.edu", role = c("aut", "cre"),
  comment = c(ORCID = "0000-0002-8673-7737")),
    person("Miro Cau", "Berta", email = "berta.miro@vhir.org", role = "aut", ,
  comment = c(ORCID = "0000-0001-6049-8697")))
Description: The Lheuristic package identifies scatterpots that
    follow and L-shaped, negative distribution. It can be used
    to identify genes regulated by methylation by integration of
    an expression and a methylation array. The package uses two
    different methods to detect expression and methyaltion L-
    shapped scatterplots. The parameters can be changed to
    detect other scatterplot patterns. 
Depends: R (>= 4.3.0)
biocViews: DNAMethylation, StatisticalMethod, MethylationArray
Imports:
    Hmisc,
    stats,
    energy,
    grDevices,
    graphics,
    utils
Suggests: 
    knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.3

[vjcitn]

 ERROR
Running the tests in 'tests/test_binScore.R' failed.
Last 13 lines of output:
  > # Test that binScore returns the expected output for a given input
  > test_that("binScore returns the expected output for a given input", {
  +   # Generate example data
  +   aGrid <- matrix(c(20, 3, 0, 10, 2, 2, 20, 10, 20), nrow = 3, ncol = 3, byrow = TRUE)
  +   aReq <- matrix(c(15, 5, 0, 0, 5, 5, 10, 10, 15), nrow = 3, ncol = 3, byrow = TRUE)
  +   
  +   # Test binScore with the example data
  +   expected_output <- TRUE
  +   output <- binScore(aGrid, aReq)
  +   expect_equal(output, expected_output, 
  +                info = "binScore should return TRUE for the example input data")
  + })
  Error in test_that("binScore returns the expected output for a given input",  : 
    could not find function "test_that"

[alexsanchezpla]

The code causing the error has been corrected and the error is not appearing anymore. Changes have been committed and pushed again to github

[alexsanchezpla]

Hello

I changed the code to solve the error reported and committed it again to GitHub. I realice however that I didn’t respond this mail letting you know I had done this.

Could you please tell me if there is anything else I must do (or just wait for review)

Thanks

Alex Sanchez

Enviado desde Correohttps://go.microsoft.com/fwlink/?LinkId=550986 para Windows

De: Vince @.> Enviado: domingo, 21 de mayo de 2023 0:03 Para: @.> CC: Alejandro Sanchez @.>; @.> Asunto: Re: [Bioconductor/Contributions] Lheuistic package submission (Issue #3039)

ERROR

Running the tests in 'tests/test_binScore.R' failed.

Last 13 lines of output:

Test that binScore returns the expected output for a given input

test_that("binScore returns the expected output for a given input", {

• Generate example data

• aGrid <- matrix(c(20, 3, 0, 10, 2, 2, 20, 10, 20), nrow = 3, ncol = 3, byrow = TRUE)

• aReq <- matrix(c(15, 5, 0, 0, 5, 5, 10, 10, 15), nrow = 3, ncol = 3, byrow = TRUE)

• Test binScore with the example data

• expected_output <- TRUE

• output <- binScore(aGrid, aReq)

• expect_equal(output, expected_output,

• info = "binScore should return TRUE for the example input data")

• })

  Error in test_that("binScore returns the expected output for a given input", :

  could not find function "test_that"

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3039#issuecomment-1556024998, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADKLYCPC7CVUQEURHE6CJM3XHE5RFANCNFSM6AAAAAAX7KOTM4. You are receiving this because you were mentioned.Message ID: @.***>

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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 the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: Lheuristic_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): Lheuristic_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 git@git.bioconductor.org:packages/Lheuristic to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi @alexsanchezpla Thank you for the submission. Before I go further, I would like to know how you will integrate Bioconductor into the package. It does not seem to re-use existing infrastructure. Best regards, Marcel

---

Lheuristic #3039

• The package does not seem to use Bioconductor infrastructure. Please note how you will integrate with the existing infrastructure either with SummarizedExperiment or other integrative represetations.

DESCRIPTION

• Add URL and BugReports fields.

NAMESPACE

• Perhaps the plot* function names can be more descriptive as to what type of plot is used.

vignettes

• Remove commented code in vignette chunks.
• Remove built HTML vignettes from the folder.
• For readability, the text width should not exceed 80 columns.
• Consider using a Bioconductor package to download expression and methylation data, e.g., GenomicDataCommons, TCGAbiolinks, curatedTCGAData, etc.
• Also consider using MultiAssayExperiment (disclaimer I am the maintainer) to correlate accross assays and avoid subsetting each individual assay.
• Use nrow and ncol instead of dim[n]
• Avoid saving plots to pdf. Only display the plots and allow users to choose their graphics format with the respective function of their choosing e.g., ggsave, png, pdf etc.

R

• unlist(list(...)) seem to have no effect on the input in distCorrs. If you want to remove names, perhaps use unname.
• When checking both nrow and ncol use dim instead in matDistCorr.

[on hold...]

[alexsanchezpla]

Dear Marcel,

Thank you very much for your e-mail and first review. Below are our comments to each of your points:

• The package does not seem to use Bioconductor infrastructure. Please note how you will integrate with the existing infrastructure either with SummarizedExperiment or other integrative represetations.
  • We were not aware that we were expected to re-use BioC infrastructure. However, it is something we have been considering for some time. Indeed both SummarizedExperiment and MultiAssayExperiment can be used. So, if you recommend us to do so, we will make the necessary changes to re-use them.
• Add URL and BugReports fields.
  • Ok. We'll find out how to do it.
• Perhaps the plot* function names can be more descriptive as to what type of plot is used.
  • We'll look fore more self-explanatory names

vignettes

• Remove commented code in vignette chunks.
• Remove built HTML vignettes from the folder.
• For readability, the text width should not exceed 80 columns.
  • OK, with everythin
• Consider using a Bioconductor package to download expression and methylation data, e.g., GenomicDataCommons, TCGAbiolinks, curatedTCGAData, etc.
  • Not sure we need it, right now because there has to be some data preprocessing before the package can be used. In any case we will explore these resources and we may consider using some of these in the vignette.
• Also consider using MultiAssayExperiment (disclaimer I am the maintainer) to correlate accross assays and avoid subsetting each individual assay.
  • OK, seems natural here
• Use nrow and ncol instead of dim[n]
  • Ok, we'll check and change
• Avoid saving plots to pdf. Only display the plots and allow users to choose their graphics format with the respective function of their choosing e.g., ggsave, png, pdf etc.
  • OK. We'll give it a look. The main reason why we send plots to pdf is because there are cases where we plot hundreds of genes, but we will review it so that there is always the option to send to pdf or not (e.g. by avoiding to display them allif the number is very high).

R

* unlist(list(...)) seem to have no effect on the input in distCorrs. If you want to remove names, perhaps use unname.

• OK, we'll check and change it.
  • When checking both nrow and ncol use dim instead in matDistCorr.
• OK, we'll check and change it.

---

Dr. Alex Sánchez-Pla

Professor. Genetics Microbiology and Statistics Department. Universitat de Barcelona.

Facultat de Biologia UB. Avda Diagonal 643. 08028 Barcelona. Spain e-mail: asanchez_at_ub.eduhttp://asanchez_at_ub.edu/

web (UB) https://webgrec.ub.edu/webpages/tmp/cat/asanchez.ub.edu.html

Statistics and Bioinformatics research group (EstBioinfo); https://sites.google.com/view/estbioinfo

Biostatistics and Bioinformatics Research Group (GRBio); http://grbio.upc.eduhttps://sites.google.com/view/estbioinfo telf: (+34) 934020949

---

---

De: Marcel Ramos @.> Enviado: viernes, 8 de septiembre de 2023 18:03 Para: Bioconductor/Contributions @.> Cc: Alejandro Sanchez Pla @.>; Mention @.> Asunto: Re: [Bioconductor/Contributions] Lheuistic package submission (Issue #3039)

Hi @alexsanchezplahttps://github.com/alexsanchezpla Thank you for the submission. Before I go further, I would like to know how you will integrate Bioconductor into the package. It does not seem to re-use existing infrastructure. Best regards, Marcel

---

Lheuristic #3039https://github.com/Bioconductor/Contributions/issues/3039

• The package does not seem to use Bioconductor infrastructure. Please note how you will integrate with the existing infrastructure either with SummarizedExperiment or other integrative represetations.

DESCRIPTION

• Add URL and BugReports fields.

NAMESPACE

• Perhaps the plot* function names can be more descriptive as to what type of plot is used.

vignettes

• Remove commented code in vignette chunks.
• Remove built HTML vignettes from the folder.
• For readability, the text width should not exceed 80 columns.
• Consider using a Bioconductor package to download expression and methylation data, e.g., GenomicDataCommons, TCGAbiolinks, curatedTCGAData, etc.
• Also consider using MultiAssayExperiment (disclaimer I am the maintainer) to correlate accross assays and avoid subsetting each individual assay.
• Use nrow and ncol instead of dim[n]
• Avoid saving plots to pdf. Only display the plots and allow users to choose their graphics format with the respective function of their choosing e.g., ggsave, png, pdf etc.

R

• unlist(list(...)) seem to have no effect on the input in distCorrs. If you want to remove names, perhaps use unname.
• When checking both nrow and ncol use dim instead in matDistCorr.

[on hold...]

— Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/3039#issuecomment-1711903648, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADKLYCMTNYZCSFOX7QPDPP3XZM6URANCNFSM6AAAAAAX7KOTM4. You are receiving this because you were mentioned.Message ID: @.***>

Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver.

Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener.

This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

[LiNk-NY]

Hi Alex, @alexsanchezpla Thank you for your response. Yes, we would like maintainers to re-use existing infrastructure where possible as other packages use e.g., SummarizedExperiment as the main data representation. Please see https://contributions.bioconductor.org/ for more details. Note. Bump the patch version of the package and push to git.bioconductor.org when the changes are ready.

[lshep]

@alexsanchezpla is there any updates on the recommended changes? may we expected an updated package for re-review soon?

[lshep]

We are closing this issue for now. When you are ready to continue please comment back here and we will reopen.

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.