OmicsMLRepoR

[shbrief]

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[bioc-issue-bot]

Hi @shbrief

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: OmicsMLRepoR
Type: Package
Title: Search harmonized metadata created under the OmicsMLRepo project
Version: 0.99.0
Date: 2024-9-15
Authors@R: 
    c(person(given = "Sehyun",
   family = "Oh",
   role = c("aut", "cre"),
   email = "shbrief@gmail.com",
   comment = c(ORCID = "0000-0002-9490-3061")),
      person(given = "Kaelyn",
   family = "Long",
   email = "krlong586@gmail.com",
   role = "aut"))
Description: This package provides functions to browse and query the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology. 
Depends: 
    R (>= 4.2.0)
Imports: 
    dplyr, 
    stringr, 
    rols,
    tidyr,
    methods,
    stats,
    tibble,
    data.tree,
    jsonlite,
    plyr,
    BiocFileCache,
    readr,
    DiagrammeR,
    rlang,
    lubridate
Suggests: 
    arrow,
    knitr,
    BiocStyle,
    curatedMetagenomicData,
    testthat (>= 3.0.0),
    cBioPortalData
License: Artistic-2.0
biocViews: Software, Infrastructure, DataRepresentation
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/shbrief/OmicsMLRepoR
BugReports: https://github.com/shbrief/OmicsMLRepoR/issues

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the
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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.

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 24.04.1 LTS): OmicsMLRepoR_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/OmicsMLRepoR 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.

[HelenaLC]

misc

• Please update R version dependency from 4.2.0 to 4.4.0.
• LazyData: should be removed or set to false (see here).
• Date: field is invalid; see corresponding build report NOTE.
• Consider adding a NEWS file to keep track of changes, in non-technical language, in the code from one release version to the next.
• In the README, please add installation instructions using BiocManager::install().

docs

• Consider adding a package .man/help page (?OmicsMLRepoR) with a description of key functionality, links to key functions etc.
• Source and providence information on inst/extadata is currently hidden in inst/scripts; please provide a corresponding .man page so users can view these.
• Vignette- please replace devtools::install_github() installation instructions by ones using BiocManager::install().
• Vignette- you can hyperlink external packages using BiocStyle::Biocpkg() (or similar, for packages living on CRAN or GitHub).
• Vignette- please add sessionInfo() output, to be placed at the very end.
• Vignette- typo in line 94 (dadta > data).
• Vignette- eval=FALSE flags or similar are not permitted.
• Vignette- bug in line 234? There's a for-loop iterating through studies, but study <- studies[1] is fixed.

code

• Please address the NOTEs in the build report...
  • Avoid sapply(); use vapply() (6 instances).
  • Avoid 1:n; use seq_len/along (3 instances).
  • Avoid cat/print outside of show methods (2 instances); you could, e.g., use message() and expose an argument verbose=TRUE/FALSE that let's the user control this (some might want to suppress printing to the console).
• In ontoTreePlot(), you can use match.arg() to make valid argument choices visible in the documentation, and validate the users input. Also, here's a more concise alternative of the code:

ontoTreePlot <- function(..., display=c("Term", "Text")) {
  display <- match.arg(display)
  ...
  foo <- switch(display, Term=map$term, Text=map$text)
  edgelist <- edgelist_base %>%
      mutate(from = plyr::mapvalues(from, map$id, foo, warn_missing = FALSE)) %>%
      mutate(to = plyr::mapvalues(to, map$id, foo, warn_missing = FALSE))
}

[shbrief]

Hi @HelenaLC, I updated the following review points. Let me know if you need anything else. Thanks!

misc

• Please update R version dependency from 4.2.0 to 4.4.0.
• LazyData: should be removed or set to false (see here).
• Date: field is invalid; see corresponding build report NOTE.
• Consider adding a NEWS file to keep track of changes, in non-technical language, in the code from one release version to the next.
• In the README, please add installation instructions using BiocManager::install().

docs

• Consider adding a package .man/help page (?OmicsMLRepoR) with a description of key functionality, links to key functions etc.
• Source and providence information on inst/extadata is currently hidden in inst/scripts; please provide a corresponding .man page so users can view these.
• Vignette- please replace devtools::install_github() installation instructions by ones using BiocManager::install().
• Vignette- you can hyperlink external packages using BiocStyle::Biocpkg() (or similar, for packages living on CRAN or GitHub).
• Vignette- please add sessionInfo() output, to be placed at the very end.
• Vignette- typo in line 94 (dadta > data).
• Vignette- eval=FALSE flags or similar are not permitted.
• Vignette- bug in line 234? There's a for-loop iterating through studies, but study <- studies[1] is fixed.

code

• Please address the NOTEs in the build report...

  • Avoid sapply(); use vapply() (6 instances).
  • Avoid 1:n; use seq_len/along (3 instances).
  • Avoid cat/print outside of show methods (2 instances); you could, e.g., use message() and expose an argument verbose=TRUE/FALSE that let's the user control this (some might want to suppress printing to the console).

• In ontoTreePlot(), you can use match.arg() to make valid argument choices visible in the documentation, and validate the users input. Also, here's a more concise alternative of the code:

ontoTreePlot <- function(..., display=c("Term", "Text")) {
  display <- match.arg(display)
  ...
  foo <- switch(display, Term=map$term, Text=map$text)
  edgelist <- edgelist_base %>%
      mutate(from = plyr::mapvalues(from, map$id, foo, warn_missing = FALSE)) %>%
      mutate(to = plyr::mapvalues(to, map$id, foo, warn_missing = FALSE))
}

[HelenaLC]

Hm, I can see updates on your GH, however, you need to push changes (with a version bump in the DESCRIPTION) to the (upstream) Bioc branch, which will trigger a new build (and report) that should show up here. Please see here for guidance if that's unclear.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 87faed4ae5e4cbff01add86d602c09a25f481849

[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): OmicsMLRepoR_0.99.1.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/OmicsMLRepoR 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: 2fb5701a98a188954e5ed2ce41cce11cd790c43e

[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 24.04.1 LTS): OmicsMLRepoR_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/OmicsMLRepoR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

Super, thanks! Almost there now...

major-ish...

• example data documentation is still missing (specifically, hidden to the user); please provide corresponding .man pages (see previous comment)
• similarly, in the vignette, could you please add a comment clarifying where sampleMetadta is coming from? It appears in a code chunk without being previously assigned, and it took me a minute to understand that becomes available with library(curatedMetagenomicData)

very minor...

• from the build report: "consider adding @importFrom graphics text and @importFrom stats setNames" - I can find the 1st, but roxygen syntax requires a hash-dash (i.e., you have #, but should be #'); can't find the 2nd currently
• there are still 2 instances of sapply() (utils.R and treatment_columns.R, though the latter is only in inst/)
• similarly, a couple 1:n left in ancestors.R and mini_cmd.R; nothing major, but would be nice to get in the habit of using seq_len/along() consistently

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: aaeb13b56aae28734b437328f2e5a9e3417b7d0e

[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 24.04.1 LTS): OmicsMLRepoR_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
git@git.bioconductor.org:packages/OmicsMLRepoR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

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reviewer, please see Reviewers Expectations.

[lshep]

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