SVbyEye

[daewoooo]

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

• Repository: https://github.com/daewoooo/SVbyEye

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 @daewoooo

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: SVbyEye
Title: Visualization of genomic structural variants
Version: 0.99.0
Authors@R: 
    person(given = "David",
 family = "Porubsky",
 role = c("aut", "cre"),
 email = "david.porubsky@gmail.com",
 comment = c(ORCID = "0000-0001-8414-8966"))                 
Description: SVbyEye is an implements functions to detect and visualize genomic structural variation between two and multiple sequences.
  To achieve this, SVbyEye introduces 4 new ggplot2 geoms (geom_miropeats(), geom_arrowhead(), geom_roundrect(), and geom_wide_arc()) together
  with a number of other functions simplify oparations on FASTA alignments reported PAF format. A number of wrapper functions allows user to
  produce near publication ready figures.
Depends:
  R (>= 4.3.0)
Imports:
  ggplot2 (>= 3.4.0),
  ggnewscale,
  ggforce,
  gggenes,
  scales,
  grid,
  stats,
  dplyr,
  stringr,
  magrittr,
  data.table,
  S4Vectors,
  methods,
  tibble,
  utils,
  BSgenome,
  GenomicRanges,
  GenomicAlignments (>= 1.34.0),
  Biostrings,
  IRanges,
  GenomeInfoDb,
  Rsamtools,
  wesanderson,
  randomcoloR
Suggests:
  BSgenome.Hsapiens.UCSC.hg38,
  BiocStyle,
  testthat,
  knitr,
  gtools,
  rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
LazyLoad: yes
VignetteBuilder: knitr
biocViews: Software, GenomicVariation, StructuralVariation, VariantDetection, GenomeAnnotation, ComparativeGenomics, Sequencing, WholeGenome
URL: https://github.com/daewoooo/SVbyEye
BugReports: https://github.com/daewoooo/SVbyEye/issues
RoxygenNote: 7.3.2

[lshep]

you should also provide an inst/scripts directory that describes how the data in inst/extdata was generated. It can be code, pseudo-code, or text but should minimally list any source or licensing information.

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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 the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): SVbyEye_0.99.0.tar.gz

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