rBLAST

[mhahsler]

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

• Repository: https://github.com/mhahsler/rBLAST

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.

  ^ Notes to the reviewer: - The warnings about long lines are due to long lines in man pages created by the formatter in roxygen. I have no control over this. - One function is > 50 lines. Breaking it into several functions would not improve the code.

• [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 @mhahsler

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: rBLAST
Title: R Interface for the Basic Local Alignment Search Tool
Description: Seamlessly interfaces the Basic Local Alignment Search Tool 
  (BLAST) to search genetic sequence data bases. This work was partially 
  supported by grant no. R21HG005912 from the National Human 
  Genome Research Institute.
Version: 0.99.0
Date: 2024-03-22
Authors@R: c(person("Michael", "Hahsler",
      role = c("aut", "cre"),
      email = "[email protected]",
      comment = c(ORCID = "0000-0003-2716-1405")),
  person("Nagar", "Anurag",
      role = "aut"))
biocViews: Genetics, Sequencing, SequenceMatching, Alignment, DataImport
Depends: Biostrings (>= 2.26.2)
Suggests: knitr, rmarkdown, testthat
URL: https://github.com/mhahsler/rBLAST
BugReports: https://github.com/mhahsler/rBLAST/issues
Imports: methods, utils
SystemRequirements: ncbi-blast+
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)

[lshep]

Please include an INSTALL file for any needed system dependencies that need to be installed on a system so we can quickly find instructions. http://contributions.bioconductor.org/sysdep.html

We highly recommend caching any files used / needed for vignettes and examples if an example file cannot be included with the package in case internet is unavailable. See BiocFileCache

@hpages / @jwokaty Might need a system dependency install

[mhahsler]

@Ishep Thanks for the info. I have added the needed INSTALL file.

The BLAST databases are somewhat large, so I cannot include them in the package. The standard database most people use is 58 MB.

[mhahsler]

@ishep Thanks for your feedback. I have now addressed all your concerns in the devel branch of the repository.

• Added INSTALL file.
• Database files are now managed using BiocFileCache.

In addition, I have added the function has_blast() to check if the software dependency is installed.

[jwokaty]

Hi @mhahsler

In rBLAST's INSTALL, could you make the changes:

• [ ] add a link to the installation instructions for ncbi-blast+
• [ ] recommend the .dmg for mac, which should handle putting ncbi-blast+ on the path
• [ ] clarify if ncbi-blast+ is available for mac Intel or Apple Silicon

[mhahsler]

Hi @jwokaty

Thank you for the feedback. I have updated the installation instructions as recommended.

Best, -Michael

[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.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): rBLAST_0.99.3.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 [email protected]:packages/rBLAST to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[hpages]

Sorry for the delay. Package looks good and is on its way to Bioconductor 3.19.

Thanks for this contribution.

Best, H.

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[lshep]

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/mhahsler.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("rBLAST"). The package 'landing page' will be created at

https://bioconductor.org/packages/rBLAST

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.