Contributions MetaProViz

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Repository: https://github.com/saezlab/MetaProViz

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Sep 26 '25 15:09 ChristinaSchmidt1

Dear @ChristinaSchmidt1,

The package version number, '3.99.0', does not start with 0. Expecting format: '0.99.z' for new packages. Starting with non-zero x of 'x.y.z' format is generally only allowed if the package has been pre-released.

We recommend fixing the version number. See Bioconductor version numbers Please also consider running BiocCheck::BiocCheck('new-package'=TRUE) on your package to look for other Bioconductor package requirements.

Sep 26 '25 15:09 bioc-issue-bot

Hi @ChristinaSchmidt1

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: MetaProViz
Type: Package
Title: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
Version: 3.99.0
Authors@R: c(
    person("Christina", "Schmidt",  email = "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-3867-0881")),
    person("Denes", "Turei", role = "aut",
 comment = c(ORCID = "0000-0002-7249-9379")),
    person("Dimitrios", "Prymidis", role = "aut",
 comment = c(ORCID = "0009-0000-0168-3841")),
    person("Macabe", "Daley", role = "aut",
 comment = c(ORCID = "0000-0002-8026-7068")),
    person("Jannik", "Franken", role = "aut"),
    person("Julio", "Saez-Rodriguez", role = "aut",
 comment = c(ORCID = "0000-0002-8552-8976")),
    person("Christian", "Frezza", role = "aut",
 comment = c(ORCID = "0000-0002-3293-7397"))
  )
Description: MetaProViz can analyse standard metabolomics and
    exometabolomics data (CoRe). It performs pre-processing including
    feature filtering, missing value imputation, normalisation and outlier
    detection. It performs functional analysis including differential
    metabolite analysis (DMA), clustering based on regulatory rules (MCA)
    and contains different visualisation methods to extract biological
    interpretable graphs and saves them in a publication ready format.
URL: https://saezlab.github.io/MetaProViz
BugReports: https://github.com/saezlab/MetaProViz/issues
biocViews: Metabolomics, QualityControl, SystemsBiology, Visualization
License: GPL-3 + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
LazyData: true
Depends:
    R (>= 4.4)
Imports:
    broom,
    ComplexUpset (>= 1.3.3),
    cosmosR,
    DBI,
    dplyr,
    EnhancedVolcano,
    factoextra,
    ggbeeswarm,
    ggfortify,
    ggplot2 (>= 3.3.5),
    ggpubr,
    ggrepel,
    grid,
    gridExtra,
    gtools,
    hash,
    igraph,
    inflection,
    limma,
    logger,
    magrittr,
    methods,
    OmnipathR (>= 3.17.4),
    SummarizedExperiment,
    patchwork,
    pheatmap,
    Polychrome,
    purrr,
    qcc,
    qvalue,
    rappdirs,
    readr,
    rlang,
    rstatix,
    stringr,
    tibble,
    tidyr,
    tidyselect,
    writexl
Suggests:
    BiocStyle,
    ggupset,
    ggVennDiagram,
    kableExtra,
    knitr,
    pkgdown,
    svglite,
    testthat (>= 3.1.4)
RoxygenNote: 7.3.3
Config/testthat/edition: 3

Sep 26 '25 15:09 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.

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Oct 03 '25 16:10 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, TIMEOUT". 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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 03 '25 16:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 9ecbd3367de570e10a69aa4a8c414184eea6bff8

Oct 08 '25 12:10 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 24.04.3 LTS): MetaProViz_3.99.1.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 [email protected]:packages/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 08 '25 12:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 35b8935bbee6bf77a265b89d1d7446bb7b1fc068

Oct 08 '25 13:10 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 24.04.3 LTS): MetaProViz_3.99.2.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 08 '25 13:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: fe6b26af2510924c91e4a60e69f4c087d423c854

Oct 08 '25 15:10 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 24.04.3 LTS): MetaProViz_3.99.3.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 08 '25 15:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 4e6a9a47b90a995fa9feac1b78449dcbb1805d52

Oct 08 '25 17:10 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: "WARNINGS". 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 24.04.3 LTS): MetaProViz_3.99.4.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 08 '25 17:10 bioc-issue-bot

@lshep could you please review the package?

I checked the warning and it's due to the package number. I understood that this will be fixed upon release as the package number should be bumped to 4.0.0 to indicating the first build on the Bioconductor system.

Oct 09 '25 06:10 ChristinaSchmidt1

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

Oct 09 '25 13:10 bioc-issue-bot

Hi @cvanderaa, I'm another developer working on MetaProViz. Because Wednesday is the deadline for new packages to complete the review, we're wondering if there is any chance we can make it into the upcoming release? We know there are a number of points that should be improved (shorter functions, better organization and quality of code, cleaner style, etc), some of these also show up as BiocCheck notes. We're currently completing a comprehensive refactoring plan to address these (we can share if you're interested). At the same time, the current version is quite stable and thoroughly tested, and does a number of useful things. For this reason, we thought it would be good to have in BioC already this version, while the major quality improvements would be ready for the next release. Most of the BiocCheck notes we can address this week if that's a concern in this regard. Let us know what you think.

Oct 20 '25 09:10 deeenes

Hello @deeenes and @ChristinaSchmidt1,

Thank you for your contribution. I took last week off so I couldn't have a look yet at your submission. I'll do my best to look at it as soon as possible...

Oct 20 '25 13:10 cvanderaa

I'll manage to find time to review your package today, but the schedule will be tight. You can already address the warning that your package version is not starting with a 0. The DESCRIPTION mentions v3.99.4. 2 options:

MetaProtViz 1 and 2 have already been released elsewhere, then you could rename your package MetaProtViz3 and provide version 0.99.4.
Rename the version to 0.99.4 without changing the package name.

Oct 22 '25 07:10 cvanderaa

@cvanderaa https://github.com/Bioconductor/Contributions/issues/3966 I think this is okay if they justify previously released use

Oct 22 '25 11:10 lshep

Congratulations on this interesting package 🎉 I appreciated the big efforts you've put to thoroughly document the package. However, I have comments that need to be solved/discussed before it passes the submission process.

⚠️ Please let's first discuss the major comment below which determines whether your package will be able to be accepted for this release or not ⚠️

Major comment:

Your data is amenable for common Bioconductor classes, namely the SummarizedExperiment class. Please provide a convincing argument explaining why you don't rely on that class by default. We can discuss approaches to implement support for this class, but this won't be possible before next release. Note, your processing() function documents the possibility to return a SummarizedExperiment object, but this is not implemented.

Minor comments:

Remove the following artefact/non-standard files: omnipathr-log/, .bumpversion.cfg
Move _pkgdown.yml to the pkgdown directory
README: Fix the large code chunk in README.Rmd, it seems to create a figure which cannot be generate. Personnal opinion: add a script in inst/scripts that generates a static image, which you can then include in the README. There is also an artefact chunk with eval = FALSE, remove it.
DESCRIPTION: Add Software to BiocView
DESCRIPTION: set LazyData: false (see https://contributions.bioconductor.org/description.html#description-lazydata)
NEWS: add a NEWS file (and don't forget to update it later on, see https://contributions.bioconductor.org/news.html)
vignettes: why having a separate pkgdown directory with vignettes? It is expected that all vignettes are under vignettes.
(recommended, not mandatory) vignettes: Use BiocStyle::html_document: in the vignette headers
vignettes: I don't understand your vignette organisation. Why is quick-start.Rmd not with the other vignettes?
vignettes: there are duplicated code chunks, with and without eval=FALSE. eval=FALSE should not be used, please remove those. It seems you are doing this to obtain scrollable plots, but this is a bad idea regarding code maintenance.
vignettes: you can remove MetaProViz:: in front of functions since you run library(MetaProViz) at the beginning.

Upon acceptance, please ensure you do the following:

Fix the NOTES with refactored code as you mentioned in your previous comment
Update the README installation instruction with BiocManager (see https://contributions.bioconductor.org/readme.html)

Oct 22 '25 14:10 cvanderaa

Received a valid push on git.bioconductor.org; starting a build for commit id: 1cfb3b14d2ea2d061177eff8ded82be9cdb225a8

Oct 30 '25 17:10 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: "WARNINGS". 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 24.04.3 LTS): MetaProViz_3.99.14.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 30 '25 18:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8f122b35da767ae92e14cd52d472d6f29908fabb

Oct 31 '25 06:10 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: "TIMEOUT". 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 24.04.3 LTS): MetaProViz_3.99.17.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 31 '25 06:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 06811fcdb5a4cc52185613d4bdf5a2e380ed8f37

Oct 31 '25 14:10 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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 03 '25 17:11 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8442f67b8d5f9f803eda9667198c02f27aa290cf

Nov 05 '25 07:11 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 24.04.3 LTS): MetaProViz_3.99.20.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 05 '25 07:11 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 1b508251e43f4b83dbd363fec60f42e8da294f91

Nov 07 '25 07:11 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: "WARNINGS". 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 24.04.3 LTS): MetaProViz_3.99.21.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/MetaProViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 07 '25 07:11 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 3e11bbba1ad8ed64a791892bc97437eff7dbcb01

Nov 10 '25 09:11 bioc-issue-bot