(inactive) AIRs

[bioinfo16]

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

• Repository: https://github.com/bioinfo16/AIRs

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

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• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

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[bioc-issue-bot]

Hi @bioinfo16

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: AIRs
Type: Package
Title: Analyzer of Integrated Regions
Version: 0.99.0
Date: 2018-01-16
Author@R: c( person("Min-Jeong", "Baek", email =
        "mjbaek16@korea.ac.kr", role = c("aut", "cre")),
        person("In-Geol", "Choi", email = "igchoi@korea.ac.kr", role =
        c("aut")) )
Author: Min-Jeong Baek [aut, cre],
  In-Geol Choi [aut]
Maintainer: Computational & Synthetic Biology Lab <igchoi@korea.ac.kr>
Description: This package was developed for analysis of regions where viral vectors are integrated. 
   Find the location of integrated regions and analyze whether it is associated with important genomic factors. 
   Finally, user can conduct random analysis based on the results of the previous analysis.
Depends: R (>= 3.2.5)
Imports: data.table (>= 1.10.4), ggbio (>= 1.18.5), ggplot2 (>= 2.2.1),
        GenomeInfoDb (>= 1.6.3), GenomicRanges (>= 1.22.4), grDevices
        (>= 3.2.5), graphics (>= 3.2.5), IRanges (>= 2.4.8), seqinr (>=
        3.3), stats (>= 3.2.5), stringr (>= 1.2.0), S4Vectors (>=
        0.8.11), utils (>= 3.2.5)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-01-30 04:31:07 UTC; mjbaek

[mtmorgan]

Please review the Bioconductor package guidelines, in particular the need for a vignette with fully evaluated code chunks. Please post a comment when your package has been updated to conform to these guidelines.

[bioinfo16]

We added up vignettes folder to AIRs repository. Please check up this one.

[mtmorgan]

The code chunks in the vignette must have eval = TRUE. Often the examples for the vignette need to be carefully chosen to process in a reasonable time, as outlined in the package guidelines. The vignette directory should NOT contain the html or other derived build products.

[bioinfo16]

We rechecked our package vignette. Please check it again. Plus, we also updated a description file too.

[mtmorgan]

The package needs to be built by our build system. We cannot build the vignettes when file paths are hard-coded to locations on your computer. We also cannot build the vignette when additional software, e.g,. blastn, is required. It would not be sufficient to simply remove these essential steps from your vignette. You might be able to include the data files in your package, or in a separate 'experiment data' package, but the reliance on external tools remains problematic. Also if the data files are large, then it would not be appropriate to simply place them in a package.

I am very concerned that your package is not suitable for Bioconductor.

[bioinfo16]

Thank you for your comment. When we want to upload this package after modifying functions, should we open new issue again?

[mtmorgan]

If the updated package is in the same repository with the same package name, it is better to just post a comment here. If it is in a new repository, with a new package name, then it is better to open a new issue.