bugphyzz

[sdgamboa]

Update the following URL to point to the GitHub repository of
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• Repository: https://github.com/waldronlab/bugphyzz

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[bioc-issue-bot]

Hi @sdgamboa

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: bugphyzz
Title: A harmonized data resource and software for enrichment analysis of microbial physiologies
Version: 0.99.0
Authors@R: 
    c(
        person(
  given = "Samuel",
  family = "Gamboa",
  role = c("aut", "cre"),
  email = "Samuel.Gamboa.Tuz@gmail.com",
  comment = c(ORCID = "0000-0002-6863-7943")
        ),
        person(
  given = "Levi",
  family = "Waldron",
  role = c("aut"),
  email = "levi.waldron@sph.cuny.edu",
  comment = c(ORCID = "0000-0003-2725-0694")
        ),
        person(
  given = "Kelly",
  family = "Eckenrode",
  role = c("aut")
        ),
        person(
  given = "Jonathan",
  family = "Ye",
  role = c("aut")
        ),
        person(
  given = "Jennifer",
  family = "Wokaty",
  role = c("aut")
        )
    )
Description: bugphyzz is an electronic database of standardized microbial
  annotations. It facilitates the creation of microbial signatures based on
  shared attributes, which are utilized for bug set enrichment analysis. The
  data also includes annotations imputed with ancestra state
  reconstruction methods.
biocViews:
    MicrobiomeData,
    ReproducibleResearch
License: Artistic-2.0
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr
Depends: 
    R (>= 4.4)
Imports: 
    dplyr,
    utils,
    purrr,
    stringr,
    tidyr,
    tidyselect,
    BiocFileCache,
    httr2,
    tools
Suggests: 
    DT,
    forcats,
    ggplot2,
    htmltools,
    taxizedb,
    knitr,
    rmarkdown,
    sessioninfo,
    taxize,
    testthat,
    EnrichmentBrowser,
    MicrobiomeBenchmarkData,
    mia,
    stats,
    rlang,
    limma,
    mgsub,
    methods,
    readr,
    crayon,
    tibble,
    magrittr,
    tidytext,
    BiocStyle
URL: https://github.com/waldronlab/bugphyzz
BugReports: https://github.com/waldronlab/bugphyzz/issues

[lshep]

We don't allow data to be store in github. Please store data on zenodo or some other trusted server. If a trusted serve is not available please consider using ExperimentHub.

[sdgamboa]

@lshep, we have published our data on zenodo and use it as the default option in our main function.

A couple of functions still use data from external sites. One of them is not exported. The other is exported, but we wrote in the documentation that it should be used by curator/developers. These functions are not used in any other function meant for end users.

Finally, a dataset that was originally imported from a github repo is now included in the
inst/extadata directory with a description in inst/scripts.

Please let me know if I need to make more changes.

Thank you!

[lshep]

Please also include a section in the vignette that is similar to an abstract describing why you are submitting the package to bioconductor and a comparison to an existing Bioconductor packages.

[lshep]

We have added the package to git.bioconductor.org but I am having trouble kicking off an initial build of the package. I'm currently investigating.

[lshep]

For Now this should be true:

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.

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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 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 22.04.3 LTS): bugphyzz_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/bugphyzz to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Figured out the issue. If you have difficulty triggering builds with pushes to git.bioconductor.org let me know and I can try to reprocess the package but I think it should be okay.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 475801d3e42da79725446199ae4e90061ff70ffe

[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: "skipped, 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:
ERROR before build products produced.

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

[sdgamboa]

@lshep, I added an abstract to the vignette and expanded the introduction to describe the package in more detail. I explain how the package should fit within Bioconductor workflows and related packages. Please let me know if that fulfills the request.

I got an error in the build, but I think this is a problem with one of the dependencies of another package (mia):

===============================

 R CMD BUILD

===============================

* checking for file bugphyzz/DESCRIPTION ... OK
* preparing bugphyzz:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building bugphyzz.Rmd using rmarkdown

Quitting from lines 291-294 [unnamed-chunk-9] (bugphyzz.Rmd)
Error: processing vignette 'bugphyzz.Rmd' failed with diagnostics:
package or namespace load failed for 'mia' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'scuttle'
--- failed re-building bugphyzz.Rmd

SUMMARY: processing the following file failed:
  bugphyzz.Rmd

Error: Vignette re-building failed.
Execution halted

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 604ff536de53970333f79ff29006bc4af4dddf80

[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): bugphyzz_0.99.2.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/bugphyzz 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.