drugfindR

[AliSajid]

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• Repository: https://github.com/CogDisResLab/drugfindR

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[bioc-issue-bot]

Hi @AliSajid

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: drugfindR
Title: Investigate iLINCS for candidate repurposable drugs
Version: 0.99.547
Authors@R: c(
    person(given = c("Ali", "Sajid"),
 family = "Imami",
 role = c("aut", "cre"),
 email = "Ali.Sajid.Imami@gmail.com",
 comment = c(ORCID = "0000-0003-3684-3539")),
    person(given = c("Justin", "Fortune"),
 family = "Creeden",
 role = c("aut"),
 email = "Justin.Creeden@rockets.utoledo.edu",
 comment = c(ORCID = "0000-0003-3123-8401")),
    person(given = c("Evelyn", "Alden"),
 family = "Bates",
 role = c("aut"),
 email = "Evelyn.Bates@rockets.utoledo.edu",
 comment = c(ORCID = "0000-0002-4157-2481")),
    person(given = c("Smita"),
  family = "Sahay",
  role = c("aut"),
  email = "Smita.Sahay@rockets.utoledo.edu",
  comment = c(ORCID = "0009-0003-4377-8963")))
Description: This package provides a convenient way to access the
    LINCS Signatures available in the iLINCS database. These signatures include
    Consensus Gene Knockdown Signatures, Gene Overexpression signatures and
    Chemical Perturbagen Signatures. It also provides a way to enter your own
    transcriptomic signatures and identify concordant and discordant signatures
    in the LINCS database.
License: GPL-3 + file LICENSE
Encoding: UTF-8
URL: https://github.com/CogDisResLab/drugfindR
BugReports: https://github.com/CogDisResLab/drugfindR/issues
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: FunctionalPrediction, DifferentialExpression, GeneSetEnrichment
Imports:
    httr,
    magrittr,
    tibble,
    rlang,
    dplyr,
    purrr,
    readr,
    stringr,
    stats,
    lifecycle
Depends:
    R (>= 4.3.0)
Suggests:
    AnnotationDbi,
    biocthis,
    codemetar,
    devtools,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
X-schema.org-applicationCategory: Genomics
X-schema.org-keywords: LINCS, iLINCS, drug repurposing, drug discovery,
    transcriptomics, gene expression, gene knockdown, gene overexpression,
    chemical perturbagen, drugfindR
X-schema.org-isPartOf: https://bioconductor.org

[lshep]

We like to see a clean package branch for inclusion and distribution, and extra features and integration controlled on different branches. There seems to be a lot of extra top level directories/files that should probably not be included by default to a user: codemeta.json, data-raw, raw, renv, renv.lock, utilities. If these are necessary please explain.

[AliSajid]

Hi,

I can create a cleaner branch if necessary but almost all of the files that are in the repository are effectively necessary if someone is to clone the package and develop it.

Here's a brief description:

• codemeta.json: A standard JSON-LD metadata file
• data-raw and raw: These contain both scripts and the compressed data that is used to generate the internal data file (sysdata.rda)
• renv and its related files for ensuring consistent development environment

The only one that is not standardized is utilities. I use that to store files I use elsewhere but that are not a core part of the code itself.

Most, if not all of these files are in the .Rbuildignore file and do not impact the build process itself.

If necessary, I can create a bioconductor-submission branch that removes a lot of these files, although I'd prefer not to.

[lshep]

We prefer as clean of a branch as possible and there are standards for where additional scripts and such should be stored; normally something like inst/scripts but I will move this forward to start getting builds and you can work the locations out with a reviewer.

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the
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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:
Linux (Ubuntu 22.04.2 LTS): drugfindR_0.99.559.tar.gz
macOS 12.6.5 Monterey: drugfindR_0.99.559.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/drugfindR 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: 54b6fd5144e77d5b0e36b1b8b096a6fa2e84592a

[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:
Linux (Ubuntu 22.04.2 LTS): drugfindR_0.99.560.tar.gz
macOS 12.6.5 Monterey: drugfindR_0.99.560.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/drugfindR 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: e37083839e28a83a3d5b8150c4cc0c6ae10b21e4

[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.

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 Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): drugfindR_0.99.561.tar.gz
macOS 12.6.5 Monterey: drugfindR_0.99.561.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/drugfindR 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: eb54b0aa0f204aa7c644c9d092461c6de24f092d

[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.

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 Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): drugfindR_0.99.564.tar.gz
macOS 12.6.5 Monterey: drugfindR_0.99.564.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/drugfindR 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: fd3ed32629e8a0be7d244097818d5d28edcb507c

[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: "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 Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): drugfindR_0.99.565.tar.gz
macOS 12.6.5 Monterey: drugfindR_0.99.565.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/drugfindR 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: 48b4e4160a3de45ec701a7a353b74db70a7e697a

[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.

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 Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): drugfindR_0.99.566.tar.gz
macOS 12.6.5 Monterey: drugfindR_0.99.566.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/drugfindR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hpages]

What happened to the vignette? It's empty!

[lshep]

@AliSajid Do you plan on revising the package? We will not review a package that does not have a vignette as it is part of Bioconductor standards. Please review Bioconductor contributions guidelines

[AliSajid]

I'm sorry. I seem to have wires crossed. I'm revising and adding the vignette this week.

[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.

[AliSajid]

Hi,

I apologize for the delay. The vignette is updated and in the devel upstream,

[bioc-issue-bot]

Dear @AliSajid ,

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]

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

[lshep]

Please remember to bump your version number to trigger a new build for the reviewer.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f3be58c04b5ee0808301e8cba06804695b5cafa7

[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): drugfindR_0.99.581.tar.gz
macOS 12.7.1 Monterey: drugfindR_0.99.581.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/drugfindR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[DarioS]

• Unclear relationship to existing Bioconductor packages. Imports field has zero Bioconductor packages. Please refer to Common Bioconductor Methods and Classes. Switching from tibble and data.frame to DataFrame is a good start.
• Function names and parameters use snake_case style, not camelCase.See R Code chapter of developer's guide.
• Empty R files. utilities.R has no code in it and is 0 bytes in size.
• Vignette needs to have Bioconductor style. See Vignette and other accepted packages.
• Vignettte needs spell checking. For example "inpur" should be "input" and "signagture" should be "signature".
• Vignette code should be self-contained. It is not.

diffexp <- read_tsv("https://zenodo.org/records/10265182/files/dCovid_diffexp.tsv")

Packages that rely on access to web resources need to be written carefully. Web resources can change location, can be temporarily unavailable, or can be very slow to access and retrieve.

• Each function requires a self-contained example. Currently, every example is a trivial one. See Examples.

#' @examples
#' TRUE

• \description is identical for every function. Provide a meaningful paragraph for each one instead.

[AliSajid]

I appreciate the comments and I'm working on addressing them. Thank you!