Contributions gINTomics

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Repository: https://github.com/angelovelle96/gINTomics

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Mar 20 '24 00:03 angelovelle96

Hi @angelovelle96

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: gINTomics
Title: Multi-Omics data integration
Version: 0.99.0
Authors@R: c(person("Angelo", "Velle", role = c("cre", "aut"),
          email = "[email protected]",
          comment = c(ORCID = "0000-0002-4010-6390")),
   person("Francesco", "Patane'", role = "aut",
           email = "[email protected]", 
           comment = c(ORCID = "0009-0001-8619-447X")),
   person("Chiara", "Romualdi", role = "aut", 
          email = "[email protected]",
          comment = c(ORCID = "0000-0003-4792-9047")))
Description: gINTomics is an R package for Multi-Omics data integration and 
  visualization.
  gINTomics is designed to detect the associationbetween the 
  expression of a target and of its regulators, taking into account 
  also their genomics modifications such as Copy Number Variations 
  (CNV) and methylation. 
  What is more, gINTomics allows integration results visualizations 
  via a Shiny-based interactive app.
License: AGPL-3
biocViews: GeneExpression, RNASeq, Microarray, 
    Visualization, CopyNumberVariation, GeneTarget
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
    BiocParallel,
    biomaRt,
    OmnipathR,
    edgeR,
    ggplot2,
    ggridges,
    gtools,
    MultiAssayExperiment,
    miRBaseConverter,
    plyr,
    stringi,
    stringr,
    SummarizedExperiment,
    methods,
    stats,
    reshape2,
    randomForest,
    Homo.sapiens,
    Mus.musculus,
    limma,
    org.Hs.eg.db,
    org.Mm.eg.db,
    BiocGenerics,
    GenomicFeatures,
    ReactomePA,
    clusterProfiler,
    dplyr,
    AnnotationDbi,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    shiny,
    GenomicRanges,
    ggtree,
    shinydashboard,
    plotly,
    DT,
    MASS,
    InteractiveComplexHeatmap,
    ComplexHeatmap,
    visNetwork,
    shiny.gosling,
    ggvenn,
    RColorBrewer,
    utils,
    grDevices,
    callr,
    circlize
Depends: 
    R (>= 4.3.0)
LazyData: false
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
BugReports: https://github.com/angelovelle96/gINTomics/issues
URL: https://github.com/angelovelle96/gINTomics

Mar 20 '24 00:03 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.

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Mar 21 '24 16:03 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): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 21 '24 16:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 2d63cce2ecbb482127ba8156024e14c89c1fc88e

Mar 22 '24 21:03 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 22.04.3 LTS): gINTomics_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 [email protected]:packages/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 22 '24 21:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: e0f2b556abf0699093e70accd68e8e26ee778024

Mar 22 '24 23:03 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 22.04.3 LTS): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 22 '24 23:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 6596e7ad9a64fe35dfbfbd2722490c7f08f678e2

Mar 23 '24 00:03 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 22.04.3 LTS): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 23 '24 01:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: c476e766713487788d1e9f3f16d3b32de0267c1b

Mar 23 '24 01:03 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 22.04.3 LTS): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 23 '24 01:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: f0548672e0a577c772ef60557521d1a721f963df

Mar 23 '24 01:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: abe529ad32cec15fc24e84bc2f8c50dc5c999400

Mar 23 '24 01:03 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): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 23 '24 01:03 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 22.04.3 LTS): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 23 '24 01:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: b4b9afe3462383a999c316c229986d124c8cf081

Mar 23 '24 02:03 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 22.04.3 LTS): gINTomics_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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 23 '24 02:03 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 11aa9b4143a58d54b0aa447144eb5dade0c963a3

Mar 23 '24 02:03 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): gINTomics_0.99.8.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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Mar 23 '24 02:03 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.

Mar 25 '24 14:03 bioc-issue-bot

@angelovelle96 - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

[ ] REQUIRED: Update R version dependency from 4.3.0 to 4.4.0.

NAMESPACE

[ ] SUGGESTION: Consider adding 'importFrom("stats", "coef", "cov")' to your NAMESPACE file.

CITATION

[ ] SUGGESTION: (Optional) CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'.

Data

[ ] REQUIRED: Data in the data/ directory needs to have a man page for documentation. I see the documentation within inst/scripts but it should be moved into a data.Rd file.

Vignette

[ ] REQUIRED: Code blocks should not include eval = FALSE.

Man pages

[ ] SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?gINTomics.
[ ] SUGGESTION: Rd file 'dot_poly.Rd' \examples lines wider than 100 characters. These lines will be truncated in the PDF manual.

R code

[ ] REQUIRED: There are ':::' calls to the package's namespace in its code. A package almost never needs to use ':::' for its own objects. You can just use .def_enrich.
[ ] SUGGESTION: Checking R code for possible problems. Undefined global functions or variables: Freq chr_cov cnv cnv_meet coef cov met mirna_cnv omics pval significance
[ ] REQUIRED: Use accessors; don't access S4 class slots via '@' in examples/vignettes.
[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 48 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 386 lines that are not.

Best, Kayla

Apr 02 '24 19:04 Kayla-Morrell

Received a valid push on git.bioconductor.org; starting a build for commit id: 05ec4c2aca2b1423bece72c5b1771c37b669a584

Apr 04 '24 13:04 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): gINTomics_0.99.9.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/gINTomics to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Apr 04 '24 13:04 bioc-issue-bot

@Kayla-Morrell Thank you for your time and for the comments and suggestions regarding our package. All the required and some of the suggested updates have been implemented, now we are ready for a re-review:

DESCRIPTION

[x] REQUIRED: Update R version dependency from 4.3.0 to 4.4.0.

Version updated

NAMESPACE

[ ] SUGGESTION: Consider adding 'importFrom("stats", "coef", "cov")' to your NAMESPACE file.

coef and cov are columns of a dataframe used for building a ggplot. I noticed that R check gives NOTES when using the standard ggplot2 workflow (giving a dataframe as input and then calling the variables using column’s names). Anyway I would like to leave it this way, since this should be the correct structure to use with ggplot2.

CITATION

[x] SUGGESTION: (Optional) CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'.

We don’t have a publication or preprint yet

Data

[x] REQUIRED: Data in the data/ directory needs to have a man page for documentation. I see the documentation within inst/scripts but it should be moved into a data.Rd file.

I noticed that the names of the rda files in data/ didn’t match the names of their respective R objects and Rd files. Now the two rda files in data/ are mmultiassay_ov.rda and mirna_hsa.rda. You can find their documentations in man/mmultiassay_ov.Rd and man/mirna_hsa.Rd

Vignette

[x] REQUIRED: Code blocks should not include eval = FALSE.

I removed the eval = FALSE, now the only chunk that has it is the one for the package installation

Man pages

[x] SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?gINTomics.

I added the package man page

[x] SUGGESTION: Rd file 'dot_poly.Rd' \examples lines wider than 100 characters. These lines will be truncated in the PDF manual.

Now the example lines are shorter

R code

[x] REQUIRED: There are ':::' calls to the package's namespace in its code. A package almost never needs to use ':::' for its own objects. You can just use .def_enrich.

I removed the ::: for .def_enrich

[ ] SUGGESTION: Checking R code for possible problems. Undefined global functions or variables: Freq chr_cov cnv cnv_meet coef cov met mirna_cnv omics pval significance

This is the same ggplot2 issue of the NAMESPACE section

[x] REQUIRED: Use accessors; don't access S4 class slots via '@' in examples/vignettes.

I removed the '@', now the accessors are used

[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 48 lines that are > 80 characters long.

All the lines exceeding 80 characters are contained in text sections of manual/vignette

[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 386 lines that are not.

We used the styler package for the indentation, almost all the lines are correctly indented. Part of the lines that are not correctly indented are contained in text sections of manual/vignette

Best, Angelo

Apr 04 '24 14:04 angelovelle96

@angelovelle96 - Thank you for making the necessary changes. I have reviewed everything and it all looks good. I'm more than happy to accept the package.

Best, Kayla

Apr 24 '24 01:04 Kayla-Morrell

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.

Apr 24 '24 01:04 bioc-issue-bot

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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

https://bioconductor.org/packages/gINTomics

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.

Apr 25 '24 13:04 lshep

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gINTomics

DESCRIPTION

NAMESPACE

CITATION

Data

Vignette

Man pages

R code

DESCRIPTION

NAMESPACE

CITATION

Data

Vignette

Man pages

R code

Contributions
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