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MPAC
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/pliu55/MPAC
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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="[email protected]",
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()'.
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.
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.
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(), andppRealInp(), 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.
- I replaced the matrix objects by SummarizedExperiment objects in the following functions:
- 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()andrunPermPrd(). - The testing function no longer downloads PARADIGM binary automatically.
- A note has been put in the vignettes to explain the dependence of PARADIGM binary.
- 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
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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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
[email protected]:packages/MPAC 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: f344270b0887b006e608cbd962060ca638ebcdcc
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
[email protected]:packages/MPAC 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: caa8351bb01db1b757527dab0af65e8b9f47dacc
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
[email protected]:packages/MPAC 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: ff6b0289080a3e9a81006f2c37e0d0a07a16ae52
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
[email protected]:packages/MPAC 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: b537f11f3ec6b095b2feab7c8b1e42f07d031f90
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/MPAC 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: b3175f148bd64c95cb69ff40cac5a7e5f7c1fd26
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
[email protected]:packages/MPAC 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: 1c203cd32898fedd7ca1e1ff1ac7f4224a27515f
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
[email protected]:packages/MPAC 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: 287b75f73717ae22961f8a78dc41f37f57086dec
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
[email protected]:packages/MPAC 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: 8c39dc35d6e31f9291bdaecc1ea07255cccffadb
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
[email protected]:packages/MPAC to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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 ([email protected]) 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.
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?
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 ([email protected]) 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 [email protected] mailing list!
To post to this list, send your message to:
General information about the mailing list is at:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at:
https://stat.ethz.ch/mailman/options/bioc-devel/wrk.smnr%2Bbioconductor%40gmail.com
You can also make such adjustments via email by sending a message to:
[I omitted the rest .... ]
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.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
@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 aninst/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
Received a valid push on git.bioconductor.org; starting a build for commit id: 1d9993c2d677c5bd4c1df611c01d44ee779a51e5