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bugphyzz
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- Repository: https://github.com/waldronlab/bugphyzz
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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
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.
@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!
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.
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.
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.
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
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.
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 475801d3e42da79725446199ae4e90061ff70ffe
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.
@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
Received a valid push on git.bioconductor.org; starting a build for commit id: 604ff536de53970333f79ff29006bc4af4dddf80
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.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 496e8d6e661db1e90f4574c81fb1749afa964085
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.
bugphyzz is a package that stores annotations regarding microbiomes and enables enrichment analysis to be done. It will be a useful addition for Bioconductor microbiome researchers. However, there are some modifications required for it to conform to the Bioconductor Developer's Guide.
-
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. -
Uses unnecessary
forloops. For example,
output <- vector("list", length(files))
for (i in seq_along(output)) {
output[[i]] <- utils::read.csv(files[i], header = TRUE, skip = 1) |>
dplyr::mutate(Attribute = tolower(.data$Attribute))
}
return(output)
Please refer for Vectorize and change all such instances to vapply or lapply.
- Package seems incomplete.
## Function for importing fatty acid compositions
## TODO This dataset needs more curation.
## TODO Names of the Fatty Acids should be more "user-friendly"
## TODO Maybe a threshold should be decided to consider a FA as present or not.
and
## TODO correct plant pathogenicity name earlier in the workflow or
## better yet, directly in the curation
See Comments section.
Commenting TODO’s should be avoided in published package code
Please add the missing functionality descibed in TODO sections.
-
Lack of input parameter checking. For example,
@param tax_id_type A character string. Valid options: NCBI_ID, Taxon_name.However, the function specification hastax_id_type = "NCBI_ID"but it should instead betax_id_type = c("NCBI_ID", "Taxon_name")and inside the function should betax_id_type <- match.arg(tax_id_type). See R at Work for an introductory tutorial about parameter checking in R. -
Package has good interoperability with existing Bioconductor infrastructure but could be better. For example, it relies on
data.framebut it does not handleDataFramefoundational class from S4Vectors.
> bp[["aerophilicity"]] <- as(bp[["aerophilicity"]], "DataFrame")
> makeSignatures(dat = bp[["aerophilicity"]], tax_id_type = "Taxon_name", tax_level = "genus")
Error in UseMethod("filter") :
no applicable method for 'filter' applied to an object of class "c('DFrame', 'DataFrame', 'SimpleList', 'RectangularData', 'List', 'DataFrame_OR_NULL', 'Vector', 'list_OR_List', 'Annotated', 'vector_OR_Vector')"
- Vignette is not discoverable from the command line.
> browseVignettes("bugphyzz")
No vignettes found by browseVignettes("bugphyzz")
- Vignette uses limma's voom approach for linear modelling. Justify why you use count modelling for non-count data.
limma::voom(counts = assay(se), design = design, plot = FALSE)$E
> assay(se)[1:5, 1:5] # Not count data.
700103497 700106940 700097304 700099015 700097644
Streptococcus 17.18097 18.50818 16.03412 15.40698 17.148602
Neisseria 16.82849 16.12832 15.12273 15.20496 13.653478
Porphyromonas 12.80149 12.73703 16.37312 15.05930 4.935801
Capnocytophaga 16.79096 15.31840 16.58074 17.05846 17.598692
Actinomyces 17.66332 17.65465 11.65284 16.26541 13.892903
counts: A numericmatrixcontaining raw counts, or anExpressionSetcontaining raw counts, or aDGEListobject. Counts must be non-negative andNAs are not permitted.
@lshep, yes. Thanks for following up. I've already made the required changes. I'll bump the version today.
Received a valid push on git.bioconductor.org; starting a build for commit id: 96dae082e576c0690e52df7ba0be965f4c15afae
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 74ffe67004db23383bcbcb24392ee30adb70f296
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 9dc230555d8581b5a4a198f81ff7d92d9c0c2ca5
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.
@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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 12b69a764fde049a09e0f7a5f8588fb5e64baa7a
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.
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
importBugphyzzfunction. 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.