bugphyzz

[sdgamboa]

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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 = "[email protected]",
  comment = c(ORCID = "0000-0002-6863-7943")
        ),
        person(
  given = "Levi",
  family = "Waldron",
  role = c("aut"),
  email = "[email protected]",
  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
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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
[email protected]: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
[email protected]: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
[email protected]: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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 496e8d6e661db1e90f4574c81fb1749afa964085

[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_0.99.3.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/bugphyzz to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

@sdgamboa may we expected updates soon?

[sdgamboa]

@lshep, yes. Thanks for following up. I've already made the required changes. I'll bump the version today.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 96dae082e576c0690e52df7ba0be965f4c15afae

[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:
macOS 12.7.1 Monterey: bugphyzz_0.99.4.tar.gz
Linux (Ubuntu 22.04.3 LTS): bugphyzz_0.99.4.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/bugphyzz to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 74ffe67004db23383bcbcb24392ee30adb70f296

[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:
macOS 12.7.1 Monterey: bugphyzz_0.99.5.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/bugphyzz to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5

[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:
macOS 12.7.1 Monterey: bugphyzz_0.99.6.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/bugphyzz to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[sdgamboa]

@lshep, I think there could be some issues with the connection on nebbiolo2 (Ubuntu). I keep getting an error when building the vignette or running the tests of the package. The error seems to be related to the function that downloads the data. This doesn't happen on my local machine (I deleted the cache). It doesn't happen on GitHub either.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 12b69a764fde049a09e0f7a5f8588fb5e64baa7a

[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_0.99.7.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/bugphyzz to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[sdgamboa]

Dear @DarioS,

Thank you for your feedback. I think I've addressed all of the requested changes below:

• Inconsistent use of camelCase and snake_case coding. For example, makeSignatures, importBugphyzz, force_download, exclude_rarely. Please refer to Function Names and Variable Names of the Bioconductor Developer's Guide and amend accordingly.

I homogenized all function names, variables, and arguments to camelCase. Please see
issue#244.

• Uses unnecessary for loops.

I changed all for loops to lapply when a vector was being created. However,
I left some for loops that were used for printing messages or modifying existing
vectors. Please see issue#245.

• Lack of input parameter checking.

Added match.args. Please see issue#246

• Package seems incomplete...Please add the missing functionality described in TODO sections.

• The annotations could always be expanded or changed in the future through versioning on Zenodo. So I converted the TODO regarding the fatty acids annotations into an issue. Decision about inclusion or not of this data will be taken at another time. Please see issue#242.

• Removed code from the importBugphyzz function. Curation changes were made directly in the source file. Please see issues#247. A new version of the data was created on Zenodo.

• Package has good interoperability with existing Bioconductor infrastructure but could be better. For example, it relies on data.frame but it does not handle DataFrame foundational class from S4Vectors.

The makeSignatures function can now handle S4Vectors::DataFrame objects. Please see issue#243.

• Vignette is not discoverable from the command line.

I was not able to reproduce this issue. I'm able to open the vignettes in my browser (Linux machine) with either browseVignettes("bugphyzz") or vigentte("bugphyzz", "bugphyzz"). I can do this in the linux terminal and the Rstudio console. I was able to do this after installing the package locally with:

R CMD build <bugphyzz-directory>
R CMD INSTALL <generatered-tar.gz>

• Vignette uses limma's voom approach for linear modeling. Justify why you use count modeling for non-count data.

The input for limma::voom was count data. Please note that the "assay" slot in the SummarizedExperiment changes from counts to normalized counts (output of limma) in the code. This procedure was done following the recommendation of the GSEA method. Please see issue#248. I wrote all of this more explicitly in the main vignette.

Please let me know if other changes are required. Thanks.

[DarioS]

The issues raised have been addressed.

[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/sdgamboa.keys is not empty), then no further steps are required. Otherwise, do the following:

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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("bugphyzz"). The package 'landing page' will be created at

https://bioconductor.org/packages/bugphyzz

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.