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DNEA
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
-Note: The package is currently stored on the Lab github but I do the maintenance and developement as a member of said lab. My github profile is chrispatsalis.
- Repository: https://github.com/Karnovsky-Lab/DNEA/
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Hi @chrispatsalis
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: DNEA
Title: Differential Network Enrichment Analysis for Biological Data
Version: 0.99.0
Authors@R: c(
person(given = "Christopher", family = "Patsalis",
email = "[email protected]", role = c("cre", "aut"),
comment = c(ORCID = "0009-0003-4585-0017")),
person(given = "Gayatri", family = "Iyer",
email = "[email protected]", role = c("aut")))
Description: The DNEA R package is the latest implementation of the
Differential Network Enrichment Analysis algorithm and
is the predecessor to the Filigree Java-application
described in Iyer et al. (2020). The package is designed
to take as input an m x n expression matrix for some -omics
modality (ie. metabolomics, lipidomics, proteomics, etc.)
and jointly estimate the biological network associations
of each condition using the DNEA algorithm described in
Ma et al. (2019). This approach provides a framework for
data-driven enrichment analysis across two experimental
conditions that utilizes the underlying correlation
structure of the data to determine feature-feature
interactions.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
output:
BiocStyle::html_document
vignette: >
%\VignetteIndexEntry{Vignette Title}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
Imports:
BiocParallel,
dplyr,
gdata,
glasso,
igraph,
janitor,
Matrix,
methods,
netgsa,
stats,
stringr,
utils
Collate:
'JSEM-internals.R'
'aggregate-features.R'
'all-classes.R'
'all-generics.R'
'all-methods.R'
'clustering-internals.R'
'initiator.R'
'start-here.R'
'utilities-internals.R'
'utilities-exported.R'
'primary.R'
Depends:
R (>= 4.3.0)
LazyData: false
Suggests:
BiocStyle,
ggplot2,
Hmisc,
kableExtra,
knitr,
pheatmap,
rmarkdown,
testthat (>= 3.0.0),
withr
URL: https://github.com/Karnovsky-Lab/DNEA
biocViews: Metabolomics, Proteomics, Lipidomics,
DifferentialExpression, NetworkEnrichment,
Network, Clustering, DataImport
Config/testthat/edition: 3
VignetteBuilder: knitr
The package advertises input as m x n expression matrix for some -omics modality (ie. metabolomics, lipidomics, proteomics, etc.) . The package should also be able to take standard Bioconductor class structures of for this data. Minimally a SummarizedExperiment.
I will have the updates pushed to the repository before the end of the week - sorry for the delay!
Chris
I've pushed the updates to the repository. Thanks again for your patience, it has been a busy summer. I included a new exported function, SumExp2DNEAobj, that initiates the workflow from a summarizedExperiment object. Additionally, I made several additional changes to ensure a smooth workflow for users beginning from a summarizedExperiment.
It appears you have data over the size limit.
Error in .precheck_filesize(wd) : files larger than 5Mb:
/inst/extdata/ST001386_AN002314_Results_and_metabolite_metadata.rds
We recommend compressing or subsetting the data down to a smaller size. If that is not possible, consider accessing the file through the ExperimentHub. This involves storing the data on a trusted serve like zenodo, microsoft data lake, S3, etc. See https://contributions.bioconductor.org/general.html and https://contributions.bioconductor.org/data.html
Being an rds file already, I was not able to compress any further. I have deleted the /inst/extdata folder that was housing this data and will look into providing access by other means. Just to clarify, the total size of the package should be under 5mb, not just each individual file be under 5mb, correct?
Thanks! Chris
See 3.2.8 https://contributions.bioconductor.org/general.html Individual file sizes must be under 5Mb. You could move the data into experimenthub or reduce the amount of data in your object.
Thanks for the clarification, we have identified an alternative way to provide access to the data. The aforementioned file has been removed from the package so we should be good to continue.
Thanks, Chris
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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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, skipped". 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/DNEA 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: 8f3cde437da340add7ffc16531f3638fa5490015
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): DNEA_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/DNEA 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.
Reviewers for our associated paper asked that we make this package compatible with the RforMassSpectrometry project. I intend to make some modifications to the initialization i.e., be able to initialize the workflow from more than just a data frame or summarizedExperiment object.
Can I push changes I make this week to the repository, or is that going to create an issue since the package is currently under review?
We can hold off on the review until the changes are pushed. Please remember to push changes with a valid version bump to git.bioconductor.org too as that is the code we will review.
Received a valid push on git.bioconductor.org; starting a build for commit id: 9055dd9c248bb8680e1257cde212e9a9c62c551a
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/DNEA 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: de4f7a2244afbb7a0959bcacf313a241617c8f7e
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 24.04.1 LTS): DNEA_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/DNEA to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hello,
Thanks for your patience - I pushed a new build successfully for this package, but I have a question for you. One reviewer wanted this package to be compatible with the tidymass suite of tools, and I originally included 1 initiator function that would enable this but tidymass is not hosted on Bioconductor so the build failed. I removed this but am brainstorming a way to still provide this functionality. Do you have any suggestions on how to provide this code to users? I was thinking about just uploading a script with the function to our github.
I believe that you can put tidymass in the Enhances field. This is a "softer" Suggests in the sense that R CMD check does not require packages listed in Enhances to be installed, so our build system won't try to install tidymass. Then your "initiator function" (whatever that is), or any function that relies on tidymass, should contain something like this at the very beginning of its body:
if (!requireNamespace("tidymass", quietly=TRUE))
stop("Could not load package tidymass. Is it installed?\n ",
"Note that <name-of-your-function> requires the tidymass package.\n ",
"Please install it with 'BiocManager::install(\"tidymass\")'.")
Also make sure to mention this requirement in the man pages of these functions and to wrap their examples in:
if (require(tidymass, quietly=TRUE)) {
...
...
}
Hope this helps.
Let me know when the package is ready for another review.
Thanks, H.
Received a valid push on git.bioconductor.org; starting a build for commit id: c466ecedbd0c717eb5fd81b66f37c8f7bea98477
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 24.04.1 LTS): DNEA_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/DNEA 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: c66c5d4b369ced3fa7a659f624863e3802701eb8
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 24.04.1 LTS): DNEA_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/DNEA to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
By initiator I was referring to a helper function to create a DNEAobj from a mass_dataset object from the tidymass suite - bad habit, sorry for the confusion.
I re-added the function with the changes you suggested and pushed them to the repository. It looks like the package successfully built so I'm good on my end. It is ready for a review when have a chance. Thanks for all of your help!
Chris
Thanks for the changes. My plate is full this week so won't be able to review before next week, sorry. Thanks for your patience.
H.
Hi @chrispatsalis,
Sorry again for the delay. I ran into some significant issues with the package. See below.
Let me know or ask on the bioc-devel mailing list if you have questions or concerns about this, or if you need help.
Best, H.
-
The whole download section is unnecessarily complicated and misleading. Just replace it with:
if (!require("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("DNEA")Note that:
- The above is the standard way to install a Bioconductor package. See for example the landing page for Biobase: https://bioconductor.org/packages/Biobase
- It's almost never a good idea to install a Bioconductor package directly from GitHub.
BiocManager::install()knows how to resolve and install dependencies, so explicitely passing the list of all DNEA's dependencies is not needed.if (!require("somePackage", quietly=TRUE)) install.packages("somePackage")is a much more widely adopted and understood idiom thanif(!nzchar(system.file(package="somePackage"))) install.packages("somePackage"). In particular, usingnzchar(system.file(package="somePackage"))to detect whether a package is installed or not is unnecessarily cryptic and convoluted.
-
It's usually not considered good practice to add the "obj" or "object" suffix to a class name like in
DNEAobjorcollapsed_DNEAobj. Please drop the "obj" suffix. -
The
show()method forDNEAobjobjects (see why the "obj" suffix is not good here?) needs to print an EOL character (\n) at the very end of its output to avoid the following adverse effect:> DNEA DNEAobj Project Name - TEDDYmetabolomics Samples - There are 322 samples. Features - There are 134 Features. Conditions - control: DM:control case: DM:case Optimized Lambda - Parameter tuning not performed Metabolic modules: Consensus Clustering not performed netGSA results: Enrichment analysis not performed> <-- the R prompt is at the wrong place -
The man page for the
collapsed_DNEAobjclass has no example. -
The big code chunk in the Quick Start section is not evaluated which is problematic because it won't get validated by
R CMD check. In other words there's no way to guarantee that the code will remain valid in the future as the package evolves or some of its dependencies introduce potentially disruptive changes. -
The man pages for the various datasets in the package seem to be out-of-sync with the actual datasets. For example the man page for the
TEDDYdataset says: "A data frame with 100 rows and 144 columns". But the actual dataset looks very different:> data(TEDDY) > class(TEDDY) [1] "matrix" "array" > dim(TEDDY) [1] 134 322Similar problems for the T1Dmeta dataset (incorrect nb of columns reported in the man page). Please revisit the man pages for all datasets and make sure that they reflect the current datasets.