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GRETTA #3011

Closed ytakemon closed 11 months ago

ytakemon commented 1 year ago

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

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 1 year ago

Hi @ytakemon

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: GRETTA
Title: Genetic Interaction and Essentiality Mapper
Version: 0.99.0
Authors@R:
    c(person(given = "Yuka",
        family = "Takemon",
        role = c("aut", "cre", "cph"),
        email = "yuka.takemon@gmail.com",
        comment = c(ORCID = "0000-0002-3538-4409")),
      person(given = "Marco",
        family = "Marra",
        role = c("ths"),
        email = "mmarra@bcgsc.ca",
        comment = c(ORCID = "0000-0001-7146-7175")))
Description: Genetic inteRaction and EssenTiality mApper, or `GRETTA`, performs in-silico genetic screens and generate essentiality network maps. 
  To do this, `GRETTA` leverages publicly available data generated by the Cancer Dependency Map (DepMap) project. Users can define versions of DepMap 
  to analyze, and can also query DepMap data directly from the tool. A pre-print with detailed explanations on `GRETTA` can be found here: 
  https://doi.org/10.1101/2022.09.21.508787. 
biocViews: Genetics, SystemsBiology, Transcriptomics, Proteomics, BiomedicalInformatics, GenePrediction, FunctionalPrediction, GeneTarget, NetworkInference, Network
URL: https://github.com/ytakemon/GRETTA
BugReports: https://github.com/ytakemon/GRETTA/issues
BiocType: Software
Depends: 
    R (>= 4.2.0)
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.2
Suggests:
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports:
    dplyr,
    magrittr,
    forcats,
    rlang,
    stringr,
    utils,
    tidyr,
    doMC,
    broom,
    diptest,
    parallel,
    rcompanion,
    foreach,
    readr,
    tidyselect,
    stats,
    ggplot2,
    ggrepel,
    RootsExtremaInflections,
    tibble
VignetteBuilder: knitr
ytakemon commented 1 year ago

Hello, This submission is part of a manuscript revision for a journal, and our deadline is the end of May. Would it be possible to have my tool reviewed as soon?

vjcitn commented 1 year ago

in your vignette you have

## Path to data to pre-processed data
gretta_data_dir <- "/projects/marralab/ytakemon_prj/DepMap/GRETTA_data/22Q2/data/"
gretta_output_dir <- "/projects/marralab/ytakemon_prj/DepMap/GRETTA_troubleshooting/"

there is no way this can work, it involves code specific to your machine. Please verify that your package can be installed, pass R CMD check, pass BiocCheck, on a completely clean machine and let us know when this has occurred.

ytakemon commented 1 year ago

Hi @vjcitn ,

The purpose of my package is to be able to process publicly available data, and this data (~11 Gb) is required to be downloaded separately (~11 Gb, see below) for the tutorial on the vignette to process. I saw there is a limit to the size of a Bioconductor package, so I wasn't quite sure how to achieve this without linking to an external path. Do you have any suggestions?

# Make a new directory/folder called GRETTA_project and go into directory
mkdir GRETTA_project
cd GRETTA_project

# Download data from the web
wget https://www.bcgsc.ca/downloads/ytakemon/GRETTA/22Q2/GRETTA_DepMap_22Q2_data.tar.gz

# Extract data and data documentation
tar -zxvf GRETTA_DepMap_22Q2_data.tar.gz
vjcitn commented 1 year ago

We can have packages that work with large data bundles but neither the submissions or the checking themselves should require the large bundle. Can't you produce an extract that is of modest size that accomplishes the testing and demonstration of the package, leaving it up to the user to obtain the large bundle when required for the user's work?

vjcitn commented 1 year ago

If the bundle is made available BiocFileCache should be used to manage its storage and retrieval for the user.

ytakemon commented 1 year ago

Thank you for the suggestion. I will see how small I can make this test data bundle and will push an update soon.

ytakemon commented 1 year ago

Please take another look @vjcitn. I've generated a small bundle, as you suggested. This bundle is now used by both the vignette, examples, and tests.

vjcitn commented 1 year ago

Still does not run out of the box

> ### Name: get_GeneNameID
> ### Title: Get unique DepMap-compatible gene IDs
> ### Aliases: get_GeneNameID get_DepMapID
> 
> ### ** Examples
> 
> gretta_data_dir <- '/projects/marralab/ytakemon_prj/DepMap/GRETTA_data/22Q2/data'
> 
> get_GeneNameID('A1CF', data_dir = gretta_data_dir)
Error in get_GeneNameID("A1CF", data_dir = gretta_data_dir) : 
  DepMap data directory does not exists. Please check again and provide the full path to the DepMap data directory.

git:

stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/MAY16/GRETTA$ git log |head
commit 4821cd82d0bc77b75a7989fc296333a4244f2fb1
Author: ytakemon <yuka.takemon@gmail.com>
Date:   Sat May 20 18:42:52 2023 -0700

    v0.99.1 to fix paths for bioconductor pre-check
ytakemon commented 1 year ago

Thanks for your patients. This is my first time creating an R package. I've now tried running examples and checks on another device, and this time GRETTA should run out of the box. Please check again.

bioc-issue-bot commented 1 year ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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

bioc-issue-bot commented 1 year ago

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, 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: macOS 12.6.5 Monterey: GRETTA_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): GRETTA_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 git@git.bioconductor.org:packages/GRETTA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 1 year ago

@ytakemon - Just checking it to see what the status of this package is. If no progress is made to fix the errors within the next couple of weeks I will have to close the issue due to inactivity.

Best, Kayla

ytakemon commented 1 year ago

Hi @Kayla-Morrell , the build report link leads to a "Page not found" site. Is there another way for me to see what is causing the issue?

lshep commented 1 year ago

http://staging.bioconductor.org:8000/job/19188/

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: edb702061cf6449498b4e1e2b02edb9049e7d790

bioc-issue-bot commented 1 year ago

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): GRETTA_0.99.3.tar.gz macOS 12.6.5 Monterey: GRETTA_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 git@git.bioconductor.org:packages/GRETTA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ytakemon commented 1 year ago

I see that the builds show warnings due to "WARNING: directory GRETTA/man/figures is empty". However, these are figures that are useful to illustrate how the package works in the README page. Could I get some advice on how to deal with this?

Kayla-Morrell commented 1 year ago

@ytakemon - I would suggest moving these figures into an 'inst/figures/' directory and access them from there. Usually the man page directories should only contain the man pages, nothing else.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6c4801a8b7d124bbc1a57633fe642774f2210909

bioc-issue-bot commented 1 year ago

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: macOS 12.6.5 Monterey: GRETTA_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): GRETTA_0.99.4.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/GRETTA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ytakemon commented 1 year ago

Hi @Kayla-Morrell, Thank you for your suggestion. I've moved the figures into "inst/figures". However, the build shows a warning indicating that the directory is empty, but 3 .png files should be contained. I can see them on my own repo and .png isn't part of the .gitignore file either, so I am not quite sure why this is occuring. Do you have any suggestions for how I can resolve this?

Kayla-Morrell commented 1 year ago

@ytakemon - I'm not sure how to fix this warning, but I can ask others on the team. I can do my review based on the current state of the package since there are no ERRORs. I'll have the review posted in the next couple of days.

Best, Kayla

Kayla-Morrell commented 1 year ago

@ytakemon - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

DESCRIPTION

NAMESPACE

Vignette

Man pages

Best, Kayla

Kayla-Morrell commented 1 year ago

@ytakemon - Just checking in to see the status of this submission. The deadline for accepting new packages into the Bioconductor 3.18 release is 10/18/23. Any packages accepted after this date will be included in the next release.

Best, Kayla

ytakemon commented 1 year ago

Hi @Kayla-Morrell, Sorry I am currently trying to write my up PhD thesis and won't be able to address them in the next two days. When is the next release planned? I will aim to address them by then.

Kayla-Morrell commented 1 year ago

@ytakemon - No worries, the next release will be roughly 6 months from now.

lshep commented 11 months ago

@ytakemon should we close this issue until you are ready to make updates?

ytakemon commented 11 months ago

Sure that would be fine. thanks