idpr

[wmm27]

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• Repository: https://github.com/wmm27/idpr

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[bioc-issue-bot]

Hi @wmm27

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: idpr
Type: Package
Title: Profiling and Analyzing Intrinsically Disordered Proteins in R
Version: 0.99.0
Authors@R: c(person("William", "McFadden", 
      email = "wmm27@pitt.edu", 
      role = c("cre", "aut")),
   person("Judith", "Yanowitz", 
      email = "yanowitzjl@mwri.magee.edu",
      role = c("aut", "fnd")),
   person("Michael", "Buszczak", 
      email = "michael.buszczak@utsouthwestern.edu",
      role = c("ctb", "fnd")))
Description: ‘idpr’ aims to integrate tools for the computational analysis of 
    intrinsically disordered proteins (IDPs) within R. This package is used to 
    identify known characteristics of IDPs for a sequence of interest with 
    easily reported and dynamic results. Additionally, this package includes 
    tools for IDP-based sequence analysis to be used in conjunction with other R 
    packages. 
BugReports: https://github.com/wmm27/idpr/issues
License: LGPL-3
Encoding: UTF-8
LazyData: true
biocViews: StructuralPrediction, Proteomics, CellBiology
RoxygenNote: 7.1.1
Depends: 
    R (>= 4.0.0)
Imports: 
    ggplot2 (>= 3.3.0),
    seqinr (>= 3.6.1),
    magrittr (>= 1.5),
    dplyr (>= 0.8.5),
    plyr (>= 1.8.6),
    jsonlite (>= 1.6.1),
    rlang (>= 0.4.6)
Suggests: 
    knitr,
    rmarkdown,
    Biostrings,
    msa,
    ape,
    testthat
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: "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/idpr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mtmorgan]

DESCRIPTION

• Since this is a Bioconductor package, it seems like Biostrings is a better, more interoperable, choice than seqinr for biological string processing?

NEWS.md

• is this file up-to-date? If not, and this is not part of your programming discipline, it is better to have no NEWS.

vignettes

• good to see several vignettes

• Indicate, e.g., idpr-vignette.Rmd:123, that the package should be installed with BiocManager::install("idpr") or from Github with BiocManager::install("wmm27/idpr").

• It should not be necessary to use ::: for users to access objects (TP53Sequences) in the package. Make sure symbols mean for users are exported from the package NAMESPACE.

R

• Generally, I think it is better practice to cleanly separate computation and plotting (e.g., via separate functions) rather than conditionally evaluating plotting code. Whether you adopt this suggest is at your discretion.

• Perhaps the data are generally 'small', but the pattern in chargeHydropathyPlot() where an empty data.frame is created and then individual elements updated is usually very expensive -- the entire data.frame is updated each time an element is updated. It is better to, e.g., create a list of results, one element for each row, and then something like do.call(rbind, rows).

• In idprofile.R it should not be necessary to prefix idpr functions with idpr::. Also consider adopting and indentation style that allows for more consitent formatting, e.g., indenting by four spaces rather than under an opening parenthesis. The consistent formatting is easier to read.

  rhPlot <- chargeHydropathyPlot(
      sequence = sequence,
      pH = pH,
      pKaSet = pKaSet,
      proteinName = proteinName
  )

man

• good

Please update your package in response to the comments above, as well as the issues generated by the build system, and post a brief comment here when it is ready for subsequent review.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: bc7ce9a4342f66e5093602e82a7b1c07b90eb8dc

[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/idpr 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: 8dc4814e5c59da5c6c4bd2a38bc94dc211fca960

[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/idpr 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: cbcdd6378f9a02fc8f78e7dfb7e73da3580e59dd

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

[wmm27]

Hello, Thank you for taking the time to look over the package and provide insight. This is the first package submission I have been a part of, so I apologize if I am unfamiliar with this process.

I have addressed the following issues, per your recommendation:

• Removal of the NEWS.md file.
• Added installation instructions to all vignettes.
• Switched to lists instead of an updating data frame for chargeHydropathyPlot()
• Removed unnecessary idpr:: for functions within idprofile and fixed its indentation alignments.
• Resolved the errors and warnings from the Bioconductor build system.

I may need additional details on the following issues, if possible:

• We chose to use seqinr because we wanted to support sequences as character strings, vectors of characters, and as .fasta files. seqinr was the most efficient way to allow input as several formats, though this can be changed if necessary.

• The idpr:::TP53Sequences is needed because the sequences are stored as internal data. Removing the triple colon causes the following error – TP53Sequences Error: object 'TP53Sequences' not found. This error occurs because TP53Sequences do not appear in the Namespace as they are not exported. We chose to make the sequences internal because they are not required for the functionality of the package - they are only used as example sequences in vignettes. Therefore, the documentation of these sequences was not truly needed so we kept it as internal.

• In terms of separating computation and plotting, this is good advice. In the future I will implement this, however, changing this would take a large overhaul of code for this package which we do not wish to do.

Once again, thank you very much for your time and your comments, it is greatly appreciated.

[mtmorgan]

Thanks for your updates.

Since TP53Sequences is used in the vignette, it is part of the public API of the package and should be exported / documented.

Biostrings supports each representation of sequence data, and is generally more efficient than seqinr. But the important point is to be interoperable with other Bioconductor packages. I strongly encourage you to switch to using Biostrings.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 73eecf429076136ec2264be9acf16c7d4b843c79

[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, skipped". 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/idpr 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: cfd91249c4a08faadae1628781cb4d23012026e9

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

[wmm27]

Thanks for your comments. The TP53 sequences have been added to the NAMESPACE and documented. Additionally, the seqinr::read.fasta() function has been replaced with Bioconductor::readAAStringSet. I believe I have addressed all of the suggestions. Thank you again for your help

[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.

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

https://bioconductor.org/packages/idpr

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.