ISAnalytics

[GiuliaPais]

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• Repository: https://github.com/calabrialab/ISAnalytics

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[bioc-issue-bot]

Hi @GiuliaPais

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: ISAnalytics
Title: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
Version: 0.99.5
Date: 2020-07-03
Authors@R: c(
  person(given = "Andrea",
         family = "Calabria",
         role = c("aut", "cre"),
         email = "calabria.andrea@hsr.it"),
  person(given = "Giulio",
         family = "Spinozzi",
         role = c("aut"),
         email = "spinozzi.giulio@hsr.it"),
  person(given = "Giulia",
         family = "Pais",
         role = c("aut"),
         email = "giuliapais1@gmail.com"))
Description: In gene therapy, stem cells are modified using viral vectors to deliver the therapeutic transgene and replace functional properties since the genetic modification is stable and inherited in all cell progeny. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites (IS), essential for monitoring the evolution of genetically modified cells in vivo. A comprehensive toolkit for the analysis of IS is required to foster clonal trackign studies and supporting the assessment of safety and long term efficacy in vivo. This package is aimed at (1) supporting automation of IS workflow, (2) performing base and advance analysis for IS tracking (clonal abundance, clonal expansions and statistics for insertional mutagenesis, etc.), (3) providing basic biology insights of transduced stem cells in vivo.
License: CC BY 4.0
URL: https://github.com//calabrialab/isanalytics
BugReports: https://github.com//calabrialab/isanalytics
biocViews: BiomedicalInformatics
Depends: 
    R (>= 4.0)
Imports: 
    methods,
    vctrs,
    utils,
    reactable,
    htmltools,
    dplyr,
    readr,
    tidyr,
    purrr,
    rlang,
    forcats,
    tibble,
    BiocParallel,
    magrittr,
    stringr,
    fs,
    zip,
    lubridate
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Suggests: 
    testthat,
    covr,
    knitr,
    BiocStyle,
    knitcitations,
    sessioninfo,
    rmarkdown,
    roxygen2
VignetteBuilder: knitr

[bioc-issue-bot]

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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 Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, 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. 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/ISAnalytics 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: 001396a1ef0b3a2d2e71e9951b7442589733dcd9

[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: "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. 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/ISAnalytics 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: 1f891d355c17bbd72eef6274d9c3a640ae40a90c

[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: "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. 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/ISAnalytics 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: 2eb43a7c9fe8133f2d0c159362c95d64dfd03d25

[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.

Congratulations! The package built without errors or warnings on all platforms.

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

[Kayla-Morrell]

Hello @GiuliaPais -

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 but we strongly encourage them. Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

• [ ] SUGGESTION: Consider adding these automatically suggested biocViews:

  • Sequencing, SingleCell, CellBiology, DataImport

• [ ] REQUIRED: The 'BugReports:' field should link the issues on the GitHub.

NAMESPACE

• [ ] REQUIRED: Exported functions should use camel case or underscoring and not include '.' which indicates S3 dispatch.

NEWS

• [ ] REQUIRED: The version in the NEWS.md file should be corrected.

Vignettes

The two points below apply to both vignettes.

• [ ] REQUIRED: Before loading in the package with library(ISAnalytics) you should demonstrate to the user how to download the package using Biconductor. The code should look like the following and include eval = FALSE,

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ISAnalytics")

• [ ] SUGGESTION: Under the reproducibility section, a lot of the code isn't needed. For instance, the user will most likely access the vignette of the package by using vignette(XXX) in R, not using render() and knit(). The date and time aren't really needed either, we normally just ask for a session info section which is enough for reproducibility.

how_to_import_functions

• [ ] REQUIRED: The example at line 181, these code chunks should not be set to eval = FALSE. This defeats the purpose of a having a reproducable vignette.

Man pages

• [ ] REQUIRED: Any function that isn't exported should include @keywords internal so that the function is removed from the documentation index. Usually man pages are only used for functions that are exported to the user.

• [ ] REQUIRED: Unknown package 'import_parallel_vispa2Matrices' in Rd xrefs

• [ ] REQUIRED: Consider adding runnable examples to the following man pages which document exported objects:

  • pipe.Rd
  • tidyeval.Rd
  • vec_restore.ISADataFrame.Rd

• [ ] REQUIRED: Usage of dontrun{} / donttest{} found in man page examples. All exported functions should have runnable examples. Found in the following file:

  • import_parallel_Vispa2Marices.Rd

R code

• [ ] REQUIRED: 'sysdata.rdata' should be removed.

• [ ] REQUIRED: What is the purpose of 'utils-pipe' and 'utils-tidy-eval'? You can just import these functions from the packages.

• [ ] REQUIRED: We prefer classes to be S4 as opposed to S3, is there a reason you chose to go with S3 for 'ISADataFrame'? Especially since 'DataFrame' is an S4 class (the naming is confusing).

• [ ] REQUIRED: While running R CMD build/check and BiocCheck on this package, there were 100 tabs that were opened on my browser. These popups should be an option in the function so that the user can chose whether they want these reports or not.

• [ ] REQUIRED: Avoid sapply(), use vapply(). Found in file:

  • internal-functions.R line 430 and 560

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 146 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 121 lines that are not.

Best, Kayla

[GiuliaPais]

Hello @Kayla-Morrell, thanks for reviewing our package. Can I ask a few questions before we commit for changes?

REQUIRED: We prefer classes to be S4 as opposed to S3, is there a reason you chose to go with S3 for 'ISADataFrame'? Especially since 'DataFrame' is an S4 class (the naming is confusing).

ISADataFrame needs to be an S3 object because it extends and uses tibble (aka tbl_df), which is an S3 object and all generics working for tibbles must work for our structure too. We can't really change this I'm afraid.

REQUIRED: 'sysdata.rdata' should be removed.

Is this mandatory? Sysdata contains very useful internal variables for us. Should we convert them into functions instead?

REQUIRED: Exported functions should use camel case or underscoring and not include '.' which indicates S3 dispatch.

Also related to the previous point, all functions containing a dot are in fact implementations of S3 generics, except for internal functions which begin with a dot as specified here https://bioconductor.org/developers/how-to/coding-style/

REQUIRED: What is the purpose of 'utils-pipe' and 'utils-tidy-eval'? You can just import these functions from the packages.

These were added automatically by devtools::use_pipe and devtools::use_tidy_eval. It allows our package to use the pipe operator %>% and tidy evaluation automatically. Since we're extensively using function from the tidyverse these steps were reccomended, should we change it anyway?

REQUIRED: Usage of dontrun{} / donttest{} found in man page examples. All exported functions should have runnable examples. Found in the following file:

• import_parallel_Vispa2Marices.Rd

  REQUIRED: The example at line 181, these code chunks should not be set to eval = FALSE. This defeats the purpose of a having a reproducable vignette.

These two problems are related to the fact that the function in question is interactive, meaning it requires input from the user in the console, therefore it's not possible to run examples for this function.

Please let us know what to do with the above, in the meantime we're going to work on the other problems. Thank you in advance

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: baaf2b063cb81638ef5a330793cc1ac7172886e5

[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.

Congratulations! The package built without errors or warnings on all platforms.

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

[GiuliaPais]

Hi @Kayla-Morrell, our package has been modified and is ready to be reviewed again. Here are our comments on changes:

DESCRIPTION

• [X] SUGGESTION: Consider adding these automatically suggested biocViews:

  • Sequencing, SingleCell, CellBiology, DataImport

    We added "Sequencing" and "SingleCell" to the DESCRIPTION file, we don't find appropriate the other biocViews for our package

• [X] REQUIRED: The 'BugReports:' field should link the issues on the GitHub.

NAMESPACE

• [X] REQUIRED: Exported functions should use camel case or underscoring and not include '.' which indicates S3 dispatch.

The only function that include dots are now only unexported functions

NEWS

• [X] REQUIRED: The version in the NEWS.md file should be corrected.

Vignettes

• [X] REQUIRED: Before loading in the package with library(ISAnalytics) you should demonstrate to the user how to download the package using Biconductor. The code should look like the following and include eval = FALSE

Now all vignettes include an "Installation" section and also a section referencing package options and settings.

• [X] SUGGESTION: Under the reproducibility section, a lot of the code isn't needed. For instance, the user will most likely access the vignette of the package by using vignette(XXX) in R, not using render() and knit(). The date and time aren't really needed either, we normally just ask for a session info section which is enough for reproducibility.

• [ ] REQUIRED: The example at line 181, these code chunks should not be set to eval = FALSE. This defeats the purpose of a having a reproducable vignette.

As stated in my previous post, these chunks refer to interactive functions, meaning they require input from the user in the console, therefore it is impossible to execute those chunks of code. Despite this we think it might be actually helpful for the user to have this code in the vignette even if it's not automatically executed. Please let us know your feedback on this.

Man pages

• [X] REQUIRED: Any function that isn't exported should include @keywords internal so that the function is removed from the documentation index. Usually man pages are only used for functions that are exported to the user.

• [X] REQUIRED: Unknown package 'import_parallel_vispa2Matrices' in Rd xrefs

This was removed

• [X] REQUIRED: Consider adding runnable examples to the following man pages which document exported objects:
  • pipe.Rd
  • tidyeval.Rd
  • vec_restore.ISADataFrame.Rd

All of these files were removed

• [ ] REQUIRED: Usage of dontrun{} / donttest{} found in man page examples. All exported functions should have runnable examples. Found in the following file:
• import_parallel_Vispa2Marices.Rd

As stated before this example refers to an interactive function and can not be run

R code

• [X] REQUIRED: 'sysdata.rdata' should be removed.

• [X] REQUIRED: What is the purpose of 'utils-pipe' and 'utils-tidy-eval'? You can just import these functions from the packages.

These files were removed

• [X] REQUIRED: We prefer classes to be S4 as opposed to S3, is there a reason you chose to go with S3 for 'ISADataFrame'? Especially since 'DataFrame' is an S4 class (the naming is confusing).

We decided to drop this structure entirely and use tibble directly

• [X] REQUIRED: While running R CMD build/check and BiocCheck on this package, there were 100 tabs that were opened on my browser. These popups should be an option in the function so that the user can chose whether they want these reports or not.

This should be fixed now, please let us know if more problems arise

• [X] REQUIRED: Avoid sapply(), use vapply(). Found in file:

• internal-functions.R line 430 and 560

• [X] SUGGESTION: For formatting reasons, consider shorter lines. There are 146 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 121 lines that are not.

We actually styled every file in the package now but BiocCheck is still giving us this note for man files (these files are generated automatically by roxygen2 and we can't modify them)

Please let us know if all of the changes were sufficent, hope to hear from you soon, Giulia

[Kayla-Morrell]

@GiuliaPais - Thank you for making the necessary changes. I have looked them over and everything looks good. With the interactive functions not being run in the vignettes and examples, this is fine. We want to be sure the the exported functions are being run/tested somewhere (usually in vignettes and examples) to be sure that it is known when these functions may be broken. There are ample tests that utilize these functions so that should suffice. I am more than happy to accept the package now.

Best, Kayla

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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/GiuliaPais.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

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("ISAnalytics"). The package 'landing page' will be created at

https://bioconductor.org/packages/ISAnalytics

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.