MPAC

[pliu55]

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[bioc-issue-bot]

Hi @pliu55

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: MPAC
Title: Multi-omic Pathway Analysis of Cancer
Version: 0.99.0
Authors@R: c(
    person(given="Peng",    family="Liu", email="pliu55.wisc@gmail.com", 
 role = c("aut", "cre"), comment=c(ORCID="0000-0001-5655-2259")),
    person(given="Paul",    family="Ahlquist", role = c("aut")),
    person(given="Anthony", family="Gitter",   role = c("aut")),
    person(given="Irene",   family="Ong",      role = c("aut")))
Description: Multi-omic Pathway Analysis of Cancer (MPAC), integrates 
    multi-omic data for understanding cancer mechanisms. It  
    predicts novel patient groups with distinct pathway profiles 
    as well as identifying key pathway proteins with potential clinical 
    associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA
    states (i.e., repressed, normal, or activated), which serve as the input 
    for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes
    DNA and RNA states to create a background distribution to filter IPLs as a 
    way to remove events observed by chance. It provides multiple methods for
    downstream analysis and visualization.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends: R (>= 4.3)
Imports: 
    data.table (>= 1.14.2),
    magrittr (>= 2.0.2),
    BiocParallel (>= 1.28.3),
    fitdistrplus (>= 1.1),
    igraph (>= 1.2.11),
    BiocSingular (>= 1.10.0),
    S4Vectors (>= 0.32.3),
    SingleCellExperiment (>= 1.16.0),
    SummarizedExperiment (>= 1.24.0),
    bluster (>= 1.4.0),
    fgsea (>= 1.20.0),
    scran (>= 1.22.1),
    ComplexHeatmap (>= 2.16.0),
    grid,
    stats,
    utils
Suggests: 
    rmarkdown,
    knitr,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: Software, Technology, Sequencing, RNASeq, Survival, Clustering, 
    ImmunoOncology
SystemsRequirements: The `runPrd()` function requires an external software 
    named PARADIGM. For details, please see the 'Required external software' 
    section in vignette's 'Run PARADIGM: runPrd()'.

[vjcitn]

Thanks for this submission. I'd suggest that code like

# a matrix of RNA-seq data with rows as genes and columns as tumor samples
rna_tumor_mat = system.file('extdata/TcgaInp/log10fpkmP1_tumor.rds',
                            package='MPAC') %>% readRDS()

should be enhanced so that a Bioconductor data structure like SummarizedExperiment
is used to manage the features and samples in an interoperable and self-describing way.

The way you handle the acquisition of PARADIGM is not standard. It is nice to offer the
user a helper that obtains a binary from github, but in general we do not advocate dependence
on resources lodged only in github because they can disappear at will. We prefer not to see
github URLs in code in packages in Bioc.

[pliu55]

Thanks for all the suggestions, @vjcitn. I will utilize SummarizedExperiment as you recommended.

For PARADIGM, I will remove the github URLs from the code. This will likely lead to reduced coverage for the testing function, but I will put a note in the vignette to describe this. Does this plan sound ok? I would like to have your input first before moving ahead. Thanks.

[lshep]

That sounds like a good approach

[pliu55]

Hi @vjcitn and @lshep,

Thanks again for your suggestions. I have improved the MPAC package accordingly. All the changes are listed in the NEWs.md. Specifically,

• Use of SummarizedExperiment objects
  • I replaced the matrix objects by SummarizedExperiment objects in the following functions:
    • ppCnInp()
    • ppRnaInp()
    • ppPermInp()
    • runPrd()
    • runPermPrd()
    • pltNeiStt()
  • In addition, the newly added ppRealInp() function also uses SummarizedExperiment object.
  • Please note that, for the input of ppCnInp(), ppRnaInp(), and ppRealInp(), I still keep matrix objects. The reason is because I hope this will save user efforts on converting matrix objects to SummarizedExperiment objects, given that most SummarizedExperiment objects are constructed from matrix.
• Remove PARADIGM GitHub URL
  • The URL has been removed from the R code. A message has been put in place in case user did not supply PARADIGM binary when running the function runPrd() and runPermPrd().
  • The testing function no longer downloads PARADIGM binary automatically.
  • A note has been put in the vignettes to explain the dependence of PARADIGM binary.

[bioc-issue-bot]

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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.

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): MPAC_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/MPAC 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: f344270b0887b006e608cbd962060ca638ebcdcc

[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): MPAC_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/MPAC 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: caa8351bb01db1b757527dab0af65e8b9f47dacc

[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): MPAC_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/MPAC 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: ff6b0289080a3e9a81006f2c37e0d0a07a16ae52

[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): MPAC_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
git@git.bioconductor.org:packages/MPAC 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: b537f11f3ec6b095b2feab7c8b1e42f07d031f90

[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".
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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
git@git.bioconductor.org:packages/MPAC 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: b3175f148bd64c95cb69ff40cac5a7e5f7c1fd26

[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): MPAC_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
git@git.bioconductor.org:packages/MPAC 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: 1c203cd32898fedd7ca1e1ff1ac7f4224a27515f

[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): MPAC_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
git@git.bioconductor.org:packages/MPAC 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: 287b75f73717ae22961f8a78dc41f37f57086dec

[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): MPAC_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
git@git.bioconductor.org:packages/MPAC 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: 8c39dc35d6e31f9291bdaecc1ea07255cccffadb

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

[pliu55]

Hi @lshep and @vjcitn,

According to the build report above, my package has pass all the tests except the error below:

ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel

I have subscribed to the Bioc-devel mailing list using the email (wrk.smnr+bioconductor@gmail.com) listed in DESCRIPTION this morning, therefore, I am not sure why the error above is still reported. Please advice how to proceed next. Thank you.

[lshep]

There is often a confirmation email that gets sent. Can you please check your spam folders to see if it ended up being marked as spam?

[pliu55]

Hi @lshep,

Thanks for your response. I did receive a confirmation email. I clicked the confirmation link and received a 'Welcome' email as below. In addition, I can visit the subscriber list by my email (wrk.smnr+bioconductor@gmail.com) and password. Also, I received two Bioc-devel email threads yesterday and this morning, one on 'Important Bioconductor Release Deadlines' and one on "duplicated entries with 'ExperimentHub(localHub=TRUE)'". Therefore, I think my email has subscribed to the Bioc-devel list.

Welcome to the Bioc-devel@r-project.org mailing list!

To post to this list, send your message to:

bioc-devel@r-project.org

General information about the mailing list is at:

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If you ever want to unsubscribe or change your options (eg, switch to
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[I omitted the rest .... ]

[lshep]

interesting. I don't see it in the member management section nor am I able to manually enter the email and see it. We will reach out to the list administrators to try and get more information but for now when you are assigned a reviewer they can ignore this error.

[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.

[Kayla-Morrell]

@pliu55 - Thank you for submitting to Bioconductor. The package is in really good shape, I have just one requirement that needs to be addressed before I can accept it. Please see the requirement below. Please let me know when you are ready for a re-review.

Data

• REQUIRED: For all the data in inst/extdata/ there needs to be documentation for in an inst/scripts/ directory. The scripts in this directory can vary. It's most important to have a related script that documents clearly how the data was generated and source information. It should include any source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.

Best,
Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1d9993c2d677c5bd4c1df611c01d44ee779a51e5

[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): MPAC_0.99.10.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/MPAC to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[pliu55]

Hi @Kayla-Morrell,

Thank you for reviewing this package and your helpful suggestion. I added documentation in inst/scripts/ to describe the source and derivation of all the data in inst/extdata/. Each Rmd file in inst/scripts/ corresponds to a folder in inst/extdata/. The Rmd files contain text describing where the data was obtained as well as related URLs. It also contains R code showing how files were generated. Hope this documentation is clear.

I pushed a new version of this package as above. For some reason, the build report has an error saying my email address (wrk.smnr+bioconductor@gmail.com) is not subscribed to Bioc-devel. But this email address has been subscribed to Bioc-devel and it keeps receiving emails. Also this email address is in the subscriber list. So, this error is not true.