RUCova #3620

astaburuaga-garcia · 2024-10-21T17:57:04Z

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bioc-issue-bot · 2024-10-21T17:57:07Z

Hi @astaburuaga-garcia

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: RUCova
Title: Removes unwanted covariance from mass cytometry data 
Version: 0.99.0
Authors@R: person("Rosario", "Astaburuaga-García", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1179-4080"))
Description: Mass cytometry data is high dimensional and contains unwanted covariance induced by variations in cell size, staining and other technical artefacts. This package uses a set of linear models to model and remove unwanted covariance from this data.   
License: use_gpl3_license()
Encoding: UTF-8
biocViews: Software, SingleCell
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: 
    knitr,
    rmarkdown,
    BiocManager
Imports:
    dplyr,
    tidyr,
    fastDummies,
    ggcorrplot,
    ggh4x,
    ggplot2,
    ggpubr,
    ggridges,
    stringr,
    tibble,
    Matrix,
    ComplexHeatmap,
    grid,
    remotes,
    circlize,
VignetteBuilder: knitr
Depends: 
    R (>= 2.10)
LazyData: true

lshep · 2024-11-14T20:41:11Z

Please update you DESCRIPTION for a valid license field.

You mention mass cytometry but I don't see an integration with our common
Bioconductor class for this data Spectra. Please provide interoperability with
this class.

Please remove commented out sections of vignette

astaburuaga-garcia · 2024-11-25T15:50:58Z

Please update you DESCRIPTION for a valid license field.

Updated.

You mention mass cytometry but I don't see an integration with our common Bioconductor class for this data Spectra. Please provide interoperability with this class.

Our package works for mass cytometry data, not mass spectrometry (Spectra).

Please remove commented out sections of vignette

Done

lshep · 2024-11-27T18:57:10Z

It still seems like this could interact with common Bioconductor classes like a SummarizedExperiment and flowSet? You can see HDCytoData for reference

lshep · 2024-12-16T19:38:36Z

May we expect any updates soon?

astaburuaga-garcia · 2024-12-17T10:31:24Z

Hi, yes. Sorry for the delay. I'm adapting the whole pipeline to interact with a SingleCellExperiment class. I'll write here as soon as it is implemented and in the devel branch.

astaburuaga-garcia · 2024-12-30T10:17:55Z

Hi! I updated the functions and vignette so the workflow interacts with a SingleCellExperiment. The new implementation is on the devel branch.

bioc-issue-bot · 2025-01-02T16:21:04Z

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bioc-issue-bot · 2025-01-02T16:26:57Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.0.tar.gz

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bioc-issue-bot · 2025-01-03T12:54:22Z

Received a valid push on git.bioconductor.org; starting a build for commit id: eb30353c7978f86ba0ac7cc9b18839a1199130c2

bioc-issue-bot · 2025-01-03T12:59:38Z

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Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.8.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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2025-01-03T13:49:05Z

Received a valid push on git.bioconductor.org; starting a build for commit id: d328d4a4c9b00a4035f2b1a8ce126a372e517c39

bioc-issue-bot · 2025-01-03T13:54:34Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.9.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
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bioc-issue-bot · 2025-01-03T14:19:19Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 16c5b776f1b3ed2b0edc5ff85661abd4afe66197

bioc-issue-bot · 2025-01-03T14:24:52Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_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
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bioc-issue-bot · 2025-01-03T15:05:35Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 700860a2fccc5abfc20cc45f683a3e9f6560e060

bioc-issue-bot · 2025-01-03T15:11:08Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.2.tar.gz

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bioc-issue-bot · 2025-01-03T15:22:16Z

Received a valid push on git.bioconductor.org; starting a build for commit id: c92f03f272f305a969ab5ad632a253a6488a6e23

bioc-issue-bot · 2025-01-03T18:31:04Z

Received a valid push on git.bioconductor.org; starting a build for commit id: e283238b1532fef06844b42614a3190205494fef

bioc-issue-bot · 2025-01-03T18:37:05Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.4.tar.gz

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bioc-issue-bot · 2025-01-03T18:46:53Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 2a97a3aa3f63c2ecaa53ccad140804cd98c20d0f

bioc-issue-bot · 2025-01-03T18:49:47Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
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bioc-issue-bot · 2025-01-06T10:12:39Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 849114e1f904ad570c1d1d8f5f2feccd8e7522ed

bioc-issue-bot · 2025-01-06T10:18:16Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.6.tar.gz

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bioc-issue-bot · 2025-01-06T12:09:24Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 5e8fa7f949bf596321de2f5fdf88e5f5422fd83f

bioc-issue-bot · 2025-01-06T12:15:03Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.65.tar.gz

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Remember: if you submitted your package after July 7th, 2020,
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bioc-issue-bot · 2025-01-06T12:47:45Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 81ba88dc5d15f1bd43844322f093b4400c95ce85

bioc-issue-bot · 2025-01-06T12:53:21Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.66.tar.gz

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bioc-issue-bot · 2025-01-06T12:55:54Z

Received a valid push on git.bioconductor.org; starting a build for commit id: dfa081b91d614202cb8629b565698301bb21bb5f

bioc-issue-bot · 2025-01-06T13:01:28Z

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The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): RUCova_0.99.67.tar.gz

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Remember: if you submitted your package after July 7th, 2020,
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bioc-issue-bot · 2025-01-07T12:08:45Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 057908fed9ca2c615e61f63ad3f1adb78369ab14

bioc-issue-bot · 2025-01-07T12:14:31Z

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bioc-issue-bot · 2025-01-07T13:33:13Z

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bioc-issue-bot · 2025-01-07T13:38:58Z

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bioc-issue-bot · 2025-01-14T15:01:03Z

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

ttriche · 2025-01-30T19:31:13Z

Package Review Checklist

Version 1.0.1

This checklist is intended to aid and guide the reviewer through the review
process.
The individual checkboxes match the package review criteria listed here.
The package review itself (including comments) should be posted in the corresponding issue on the submission tracker.

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The functionality should be sufficiently documented in man pages with runnable examples and package vignette(s).

package name: RUCova
link to issue: #3620

Package name

Package name complies the criteria listed on the Package name section of the development guide.

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[NO] Unit tests present and covering large part of core functionality.

R code

C and Fortran code

[N/A] Internal functions from R's C library used (e.g. R_alloc).
[N/A] C function registration used (See Registering native routines.
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[N/A] Inclusion of third-party code follows the guideline.

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Unacceptable files

No unacceptable files present (see .gitignore for a listing).

lshep · 2025-01-31T12:46:06Z

In addition to checklist @ttriche mentioned above my summary comments:

build report

Please clean up as many notes as possible

vignette

update your installation section to include bioconductor
In running the code there are a few warnings messages of deprecated
functions. If you are using these deprecated functions directly, it is
recommended to fix now to avoid ERRORs and immediate action later.

man

Please include a package level man page so a naive user that does
?RUCova gets some starting information

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Oct 21, 2024

lshep added the Post Release Deadline package submitted after posted deadline. reviewer will only review if time allows label Oct 25, 2024

lshep removed the Post Release Deadline package submitted after posted deadline. reviewer will only review if time allows label Nov 8, 2024

lshep added 3e. pending pre-review changes review has indicated blocking concern that needs attention 3d. needs interop Package must explicitly use Bioconductor structures and methods labels Nov 14, 2024

lshep added pre-check passed pre-review performed and ready to be added to git and removed 3e. pending pre-review changes review has indicated blocking concern that needs attention 3d. needs interop Package must explicitly use Bioconductor structures and methods labels Jan 2, 2025

bioc-issue-bot added the ERROR label Jan 2, 2025

bioc-issue-bot added WARNINGS and removed ERROR labels Jan 3, 2025

bioc-issue-bot added ERROR and removed WARNINGS labels Jan 3, 2025

bioc-issue-bot added WARNINGS and removed ERROR labels Jan 6, 2025

bioc-issue-bot added OK and removed WARNINGS labels Jan 7, 2025

lshep added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed pre-review on bioconductor git and access to on demand build but not assigned reviewer until build report clean labels Jan 14, 2025

bioc-issue-bot assigned lshep Jan 14, 2025

RUCova #3620

RUCova #3620

Comments

astaburuaga-garcia commented Oct 21, 2024

bioc-issue-bot commented Oct 21, 2024

lshep commented Nov 14, 2024

astaburuaga-garcia commented Nov 25, 2024 • edited Loading

lshep commented Nov 27, 2024

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ttriche commented Jan 30, 2025 • edited Loading

Package Review Checklist

Package name

General package development

The DESCRIPTION file

The NAMESPACE file

The NEWS file

The CITATION file

Package data

Documentation

Unit tests

R code

C and Fortran code

Third-party code

Shiny apps

Unacceptable files

lshep commented Jan 31, 2025

astaburuaga-garcia commented Nov 25, 2024 •

edited

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ttriche commented Jan 30, 2025 •

edited

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