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rhinotypeR package #3454

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marthaluka opened this issue Jun 10, 2024 · 2 comments
Open
10 tasks done

rhinotypeR package #3454

marthaluka opened this issue Jun 10, 2024 · 2 comments
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1. awaiting moderation submitted and waiting clearance to access resources 3e. pending pre-review changes review has indicated blocking concern that needs attention

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

Repository: https://github.com/omicscodeathon/rhinotypeR
Confirm the following by editing each check box to '[x]'

  • I understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
    general public.

  • I have read the Bioconductor Package Submission
    instructions. My package is consistent with the Bioconductor
    Package Guidelines.

  • I understand Bioconductor Package Naming Policy and acknowledge
    Bioconductor may retain use of package name.

  • 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.

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

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    includes monitoring the support site for issues that users may
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@bioc-issue-bot
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Hi @marthaluka

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: rhinotypeR
Type: Package
Title: Rhinovirus genotyping
Version: 0.99.0
Authors@R: c(
    person("Martha", "Luka", role = c("aut")),
    person("Ruth", "Nanjala", role = c("aut", "cre"), email = "[email protected]"),
    person("Winfred", "Gatua", role = c("aut")),
    person("Wafaa M.", "Rashed", role = c("aut")),
    person("Olaitan", "Awe", role = c("aut"))
    )
Description: "rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, 
  streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, 
  this package makes genotype assignment accessible to researchers and public health professionals. 
  This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of 
  rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. 
  Additionally, "rhinotypeR" supports comprehensive visualization and analysis of 
  single nucleotide polymorphisms (SNPs) and amino acid substitutions, 
  facilitating in-depth genetic and evolutionary studies.
License: MIT License
Encoding: UTF-8
LazyData: false
biocViews: Sequencing, Genetics, Phylogenetics
Depends: 
    R (>= 4.4.0),
    Biostrings
Suggests:
  knitr,
  rmarkdown
VignetteBuilder: knitr
URL: https://github.com/omicscodeathon/rhinotypeR
BugReports: https://github.com/omicscodeathon/rhinotypeR/issues  

@bioc-issue-bot bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Jun 10, 2024
@lshep
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lshep commented Jun 24, 2024

The package currently cannot be built

R CMD build rhinotypeR 
* checking for file 'rhinotypeR/DESCRIPTION' ... OK
* preparing 'rhinotypeR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 46-47 [unnamed-chunk-4] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open file 'path/to/your/fasta/file'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted

Please ensure you have run R CMD build, R CMD check and BiocCheck on your package and fix any ERROR, Warning, Notes to continue.

@lshep lshep added the 3e. pending pre-review changes review has indicated blocking concern that needs attention label Jun 24, 2024
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