(inactive) acorn

[tycheleturner]

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

• Repository: https://github.com/TNTurnerLab/acorn

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]

Hi @tycheleturner

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: acorn
Type: R Package
Title: This package is a toolkit for working with de novo variants.
Version: 0.99.0
Authors@R: 
    c(person(given = "Tychele",
    family = "Turner",
    role = c("aut", "cre"),
    email = "tychele@wustl.edu",
    comment = c(ORCID = "0000-0001-8246-6477")))
Description: Acorn works with de novo variants (DNVs) already called using a 
    DNV caller (e.g., https://github.com/TNTurnerLab/HAT). The toolkit is useful
    for extracting different types of DNVs and summarizing characteristics of the 
    DNVs.
License: MIT
Depends: R (>= 3.5.0)
Suggests: knitr
VignetteBuilder: knitr
biocViews: Software
biocViews: GenomicVariation

[vjcitn]

fails BiocCheck, multiple biocViews fields in DESCRIPTION; noted on issue at source repo

[vjcitn]

Type: R Package is in DESCRIPTION. This makes R CMD check fail. Please remove that line. Please make biocViews content occupy only one line.

[vjcitn]

* checking examples ... ERROR
Running examples in 'acorn-Ex.R' failed
The error most likely occurred in:

> ### Name: annotateCpG
> ### Title: Annotate the SNVs in the DNV dataset that reside at CpG sites.
> ### Aliases: annotateCpG
> 
> ### ** Examples
> 
> annotateCpG(CpGannotFile)
Error in annotateCpG(CpGannotFile) : object 'CpGannotFile' not found
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
  'hello.Rmd' using 'UTF-8'... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
  '/home/stvjc/SUBMISSIONS/JAN9/acorn.Rcheck/00check.log'

please run R CMD check on your package before submitting.

[tycheleturner]

Thank you. I fixed the DESCRIPTION file.

I am working on the second one. It seems that loading an rda file, as part of an R function, is not acceptable in a bioconductor package. Is that correct?

[vjcitn]

the typical way to deal with a .rda formatted file x.rda is to place it in the data folder and use data("x") in code to make it available in the session or code

[vjcitn]

it is best to save one named object in the .rda file, with the same name as the file prefix, even though it is possible to save multiple objects in one file.

[tycheleturner]

Okay, I think everything is working well now and the package passes the R CMD CHECK on my end. The repo is up to date on GitHub.

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘acorn’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘acorn_0.99.0.tar.gz’

* using log directory ‘/Users/tychele/Documents/Github/acorn/acorn.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘acorn/DESCRIPTION’ ... OK
* this is package ‘acorn’ version ‘0.99.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘acorn’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘hello.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[vjcitn]

Making progress. With the latest changes I hit

Running examples in 'acorn-Ex.R' failed
The error most likely occurred in:

> ### Name: calculateDeletionlengths
> ### Title: Calculates the length of the deletions in the DNV object
> ### Aliases: calculateDeletionlengths
> 
> ### ** Examples
> 
> calculateDeletionlengths(DNVobject)
Error in calculateDeletionlengths(DNVobject) : 
  could not find function "calculateDeletionlengths"
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
  'hello.Rmd' using 'UTF-8'... OK

That looks like a spelling error. I don't think you should call your vignette hello.Rmd ... use a meaningful name.

[tycheleturner]

Thank you! All very helpful comments. I have made several changes and it seems to be working now:

$ R CMD BUILD acorn 
* checking for file ‘acorn/DESCRIPTION’ ... OK
* preparing ‘acorn’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘acorn_0.99.0.tar.gz’

$ R CMD CHECK acorn_0.99.0.tar.gz 
* using log directory ‘/Users/tycheleturner/Desktop/acorn.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘acorn/DESCRIPTION’ ... OK
* this is package ‘acorn’ version ‘0.99.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘acorn’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘acorn_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[vjcitn]

Run BiocCheck too when you get a chance, to find:

  * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/

I am clearing acorn for review.

[tycheleturner]

Great, thank you! I have registered there now.

[lshep]

I'm not able to process this package as there is an ERROR concerning files over 5 Mb in size.

* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      '.git/objects/pack/pack-ade84c5177a4d6353379f9ac440716e8427aa0f4.pack
      releases/acorn_0.99.0.tar.gz'

You should not be storing built tar of the package inside the package itself. Please make sure you run BiocCheck on the package as it would have produce a WARNING about this.

http://contributions.bioconductor.org/git-version-control.html#remove-large-data-files-and-clean-git-tree

[tycheleturner]

Okay, thank you for the update. I have updated the GitHub. After running BiocCheck, the error count is now 0 on my run.

$error character(0)

Please let me know if there are other updates to make to the package. Thanks again.

[tycheleturner]

Hello,

Checking in to see if there's anything else required of me at this time to continue with the Bioconductor process.

Thank you,

Tychele

[bioc-issue-bot]

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]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/acorn 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: 8ba3dfeb5b6671ce45a3e35763f8ec81b3fc3362

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/acorn to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[tycheleturner]

Thank you. Will I get a message on here with further follow up items?

[lshep]

Yes general once a reviewer is assign and the package is passing without ERROR a formal review will be posted within 2-3 weeks.

[tycheleturner]

Okay, thank you for the update

[LiNk-NY]

Hi @tycheleturner

Sorry for the delay. Please see the review below. Thank you.

Best, Marcel

---

acorn #2853

• The package does not integrate with formal Bioconductor classes. The main representation in use is the data.frame. I am concerned with fragile operations that use numeric indices on said data.frames. The interfaces to the functions are minimal and can be grouped to reduce code repetition.

DESCRIPTION

• Please include BugReports and URL fields pointing to GitHub issue and repo links.
• (Optional) Include additional details in the Description field.
• Imports field seems to be missing.

NAMESPACE

• Include importFrom packages in the DESCRIPTION Imports field.
• Remove exportPattern("^[[:alpha:]]+")
• Perhaps the extract/calculate prefixes are a bit redundant? Could these be improved?

vignettes

• Vignette sections should be in title case.
• Remove lsf.str from the vignette. There is no need to print out all the exports. The vignette itself presents these functions in a coherent way.
• Organize the vignette by higher level sections (domains).
• Ideally, include a description in each section. Describe where the data are coming from, what does the functionality provide?, what are the benefits of using the functions?, etc.
• Include sessionInfo() at the end of the vignette.

R

• Use message instead of cat in annotateCpG.
• Using paste inside cat / message etc. is redundant.
• Validate inputs in annotateCpG and other functions.
• Make sure to return computable results rather than simply cat the result (e.g., in calculateDeletionInsertionratio).
• Use camelCase uniformly (e.g., calculateDeletionInsertionRatio vs calculateDeletionInsertionratio)
• Avoid using numeric indices on the data and use names instead.
• It seems calculate* functions return plots rather than statistics? The name does not match what the function is doing.
• Avoid repetitive code and combine functions that have similar operations (e.g., calculateDeletionLengths, calculateInsertionLengths, etc.)
• The character vector in extractAutosomes only works for data that has chr1 annotations.
• Consider using standard Bioconductor representations e.g., GRanges in GenomicRanges
• readDNV seems to be a thin wrapper to read.delim, consider removing it.

tests

• We highly encourage the use of unit tests to ensure the robustness of the code.

[tycheleturner]

Thank you Marcel,

I have been looking through these items and will let you know if I have questions. Thanks again.

Tychele

[lshep]

@tycheleturner may we expect any updates soon. We like to see updates in 3-4 weeks. If it will take more time we can close for now until you are ready for updates.

[tycheleturner]

I have been going through the comments. One question I have is whether you think this package may be more appropriate for submission to CRAN since it "does not integrate with formal Bioconductor classes"? Please let me know. Thank you.

[vjcitn]

I am sorry to read this question after all the effort that has been put into pre-review and review. I have now had a look at the vignette which does not at this time address the guidelines http://contributions.bioconductor.org/docs.html#vignette-introduction ... and there is no descriptive prose to orient the user on the purpose of the illustrated computations. I think the topic addressed by the package is well-suited for the Bioconductor ecosystem, but more effort will be required to comply with a number of important guidelines noted at contributions.bioconductor.org. If you prefer to distribute via CRAN, just let us know.

[tycheleturner]

Okay, it's okay to close this for now while I continue to work on the package.

[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.