sagrikachugh commented 4 months ago

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

Repository: https://github.com/sagrikachugh/simPIC

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

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.

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

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

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 4 months ago

Hi @sagrikachugh

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: simPIC
Version: 0.99.0
Date: 2023-02-02
Type: Package
Title: simPIC: A uniform quantification based method for simulating Paired-Insertion count matrices for single-cell ATAC sequencing data
Authors@R: person("Sagrika", "Chugh", role=c("aut","cre"), email = "sagrika.chugh@gmail.com", comment = c(ORCID = "0000-0002-8050-5214"))
Depends: SingleCellExperiment
Imports: 
    BiocGenerics,
    checkmate (>= 2.0.0),
    fitdistrplus,
    matrixStats,
    Matrix,
    stats,
    SummarizedExperiment,
    actuar,
    rlang,
    S4Vectors,
    ggplot2,
    methods,
    scales,
    scuttle
Description: simPIC is a package for simulating single-cell ATAC-seq count data.
    It provides a user-friendly, well documented interface for data simulation.
    Functions are proided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.
biocViews: SingleCell, ATACSeq, Software, Sequencing, ImmunoOncology, DataImport
License: GPL-3
Encoding: UTF-8
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
RoxygenNote: 7.3.1
Config/testthat/edition: 3

lshep commented 3 months ago

Note: In your vignette you use counts <- readRDS("../inst/extdata/test.rds"); you should not hard code a path to the file and instead use what you did inside your examples counts <- readRDS(system.file("extdata","test.rds", package = "simPIC")) .

bioc-issue-bot commented 3 months ago

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

bioc-issue-bot commented 3 months ago

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: Linux (Ubuntu 22.04.3 LTS): simPIC_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/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

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

HelenaLC commented 3 months ago

Thanks for submitting your package to Bioc, it's in fantastic shape already! A few minor points (mostly suggestions/optional improvements); please report back with what's been addressed and how, or any questions you might have.

misc

[ ] in the DESCRIPTION, please add R version dependency 4.4.0 (see BiocCheck NOTE in the build report)
[ ] since the core functionality of the package is simulation, you might want to consider moving ggplot2 (or any other plotting-related dependency) to Suggests: (see here for details); this could make the package more robust/light-weight to install

code

[ ] looks like all code is indented by one tab/4 spaces; is this intentional? It's a little annoying as it shifts all code to the write/out of screen when viewing with an 80-character line limit
[ ] consider having a look at Bioc's coding style guidelines and implementing these; e.g., no space about argument =s, tab/4-space indentation rather vertical code alignment
[ ] might be an edge-case, but just to point out that matrix-subsetting should be done using x[i, j, drop=FALSE] (e.g., line 68 in simPICestimate.R); else, subsetting a single row/column will return a vector causing downstream code that expects a matrix to fail; this is generally a good habit to build
[ ] repeated if (verbose) message(...) statements could be combined into a single one in a few places
[ ] if (x == "a") ... else if (x == "b") kind of statements can be nicely written using switch(), e.g., in simPICsimulate.R:

switch(pm.distr, 
    gamma={ 
        ...
    },
    weibull={
        ...
    })

[ ] also, if an argument should match a specific value from a set of choices, you should list valid choices in the function definition and validate the argument inside the function using match.arg; e.g.

simPICsimulatePeakMean <- \(..., 
    pm.distr=c("gamma", "weibull", ...)) {
    pm.distr <- match.arg(pm.distr)
    ...
}

docs

[ ] we encourages having a package man page with an overview of the package and links to the main functions; users should be able to have a relevant page display with ?simPIC
[ ] please provide provenance and data structure information for any example data used in the package; for now, that's inst/extdata/test.rds only; (see here for details)
[ ] in the vignette, there're some inconsistencies in the use of code-style vs. plain text (e.g., "simPICcount object"); also, you might consider hyperlinking external packages (maybe the first time they're mentioned) using BiocStyle (e.g., `r BiocStyle::Biocpkg("SingleCellExperiment")`)
[ ] simPICcount.R lists some pretty specific default parameters; please document where these are coming from (e.g., source information, supplementary code in inst/script if there's some data processing involved, or whatever is appropriate)

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 686954114190a577860c47b992ab5383ee91bc66

bioc-issue-bot commented 3 months ago

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): simPIC_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 git@git.bioconductor.org:packages/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e876fcbb6129604f58ab5cafcebc66d150f865f5

bioc-issue-bot commented 3 months ago

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): simPIC_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/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 304c22f4cee7ccd0586e9b98ea5c185c3d569f21

bioc-issue-bot commented 3 months ago

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): simPIC_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/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

sagrikachugh commented 3 months ago

@HelenaLC @lshep Thank you for reviewing my package. I have addressed all the comments/suggestions but I am stuck with a new error from BiocCheck::BiocCheckGitClone(".") that says system file simPIC.Rproj found. I have tried multiple times and have this in my .gitignore and it should not be tracked. Here are the contents of my .gitignore file -

simPIC.Rproj .Rproj.user .Rhistory .RData .Ruserdata /doc/ /Meta/

Could you please advice me how to avoid this error?

sagrikachugh commented 3 months ago

Hi Bioconductor team,

I am having issues with BiocCheck::BiocCheckGitClone() that says system file simPIC.Rproj found. I have this file in my .gitignore so it should not be tracked. Despite multiple attempts the error still persists.

Could you please advice me how to fix this?

Here is my .gitignore file

simPIC.Rproj .Rproj.user .Rhistory .RData .Ruserdata /doc/ /Meta/

Thanks, Sagrika

On Sun, 10 Mar 2024 at 12:26 am, bioc-issue-bot @.***> wrote:

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 http://bioconductor.org/spb_reports/simPIC_buildreport_20240309082627.html for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): simPIC_0.99.3.tar.gz https://bioconductor.org/spb_reports/simPIC_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 @.***:packages/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here https://contributions.bioconductor.org/git-version-control.html#new-package-workflow .

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3323#issuecomment-1986857088, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFNN4ONZQTCAB5XTB7AM2EDYXMEZXAVCNFSM6AAAAABD67HR4CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWHA2TOMBYHA . You are receiving this because you were mentioned.Message ID: @.***>

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 575c79a8a7ba5a07f5f9304725b7e0ccbeaf13df

bioc-issue-bot commented 3 months ago

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: Linux (Ubuntu 22.04.3 LTS): simPIC_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/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

sagrikachugh commented 3 months ago

@HelenaLC Thank you for taking the time to review my package. I have addressed all your comments/suggestions. Also, I was able to solve my recent .gitignore issue that I raised earlier. Here is a detail of all the addressed suggestions-

misc

[ ] R version dependency has been updated to 4.4.0
[ ] ggplot2 dependency has been moved to Suggests:

code

[ ] Indentation has been fixed using styler::tidyverse_style (tab/4space indentation)
[ ] repeated if (verbose) message(...) statements have been combined
[ ] switch has been used instead of if/else statements in simPICsimulate.R and simPICestimate.R

docs

[ ] package man page with links to all main functions has been added
[ ] provenance and data structure for test data has been provided in inst/script. Supplementary code inst/script/testdata.R has been added to demonstrate how the test data was generate and inst/script/testdata.txt provides all the necessary information for creating test data
[ ] Vignette inconsistencies have been fixed and external packages are now hyperlinked

@lshep I have addressed your suggestion and updated counts <- readRDS(system.file("extdata","test.rds", package = "simPIC")) in the vignette. Also, I was able to resolve my earlier issue with .gitignore

Thanks, Sagrika

HelenaLC commented 3 months ago

Thanks for this; I think most comments have been sufficiently addressed. Couple comments outstanding...

[ ] simPICcount.R lists some pretty specific default parameters; please document where these are coming from [...] (see above) ... if they are estimated from a specific dataset (maybe what's in inst?), please say so in the simPICcount documentation
[ ] I think moving ggplot2 to Suggests: makes a lot of sense here; however, you should check that it's available in the relevant function(s) following these instructions
[ ] I'd suggest adding drop=FALSE at simPICestimate.R line 67 and any other time a matrix is being subsetted (see comment above)
[ ] Remember to track changes in the NEWS file; package is at v0.99.4 as opposed to v0.99.1 in the NEWS file (especially for release, where latest changes these will be put on the website)

Also, please try and address any NOTEs in the build report above, e.g.

In the DESCRIPTION, provide URL: and BugReports: fields pointing to https://github.com/sagrikachugh/simPIC and .../issues, respectively
avoid sapply and use vapply instead; avoid 1:n and use seq_len/along instead (simPICestimate.R line 238+; see here for details)
code style still doesn't align with Bioc guidelines; but this is really optional and I am leaving it to you if you really prefer using a linter...

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3b626a3237934afb0b58f7e1fb060e4499454413

bioc-issue-bot commented 3 months ago

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: Linux (Ubuntu 22.04.3 LTS): simPIC_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 git@git.bioconductor.org:packages/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

sagrikachugh commented 3 months ago

@HelenaLC Thanks for the additional comments. I have now addressed them as follows

[ ] simPICcount.R documentation has been updated providing information on the default parameters and how to generate them. The default parameters are based on PBMC10k dataset and can be reproduced using test data and script provided in inst/script
[ ] I have added drop= FALSE to line65 in simPICestimate.R where the matrix is being subsetted.
[ ] NEWS.md has been updated to reflect latest updates.
[ ] DESCRIPTION now includes URL: and BugReports: fields
[ ] 1:nCells has been updated to seq_len(nCells) in simPICsimulate.R. simPICestimate.R doesn't have 1:nCells
[ ] I have kept sapply as the output from simPICsimulateTrueCounts function is consistent across iterations and doesn't require explicit control.
[ ] The NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters long is related to two URLs in vignette, hence I cannot reduce the character limit

HelenaLC commented 3 months ago

Thanks for this. Just to say that "the output from [...] is consistent across iterations" is exactly what vapply is made for; see ?vapply: "vapply is similar to sapply, but has a pre-specified type of return value, so it can be safer (and sometimes faster) to use." Here, the output should always be an integer vector of length nPeaks, so you'd use vapply(seq_len(nCells), sim_true_counts, integer(nPeaks)). I'd recommend getting in the habit of using lapply when outputs are not consistent, and vapply when they are! I'll accept once that NOTE is cleared as I feel it is very simple to resolve (and in our experience doesn't happen usually after acceptance...)

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0980afdc48e9762a75743e1afa00c520c29b690d

bioc-issue-bot commented 3 months ago

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: Linux (Ubuntu 22.04.3 LTS): simPIC_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 git@git.bioconductor.org:packages/simPIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

sagrikachugh commented 3 months ago

@HelenaLC Thanks, I have updated simPICsimulateTrueCounts function of simPICsimulate.R to use vapply.

bioc-issue-bot commented 3 months ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

jwokaty commented 3 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/sagrikachugh.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("simPIC"). The package 'landing page' will be created at

https://bioconductor.org/packages/simPIC

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Bioconductor / Contributions

simPIC #3323

misc

code

docs

misc

code

docs