YuanningEric commented 2 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/gevaertlab/EpiMix.data

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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bioc-issue-bot commented 2 years ago

Hi @YuanningEric

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: EpiMix.data
Title: Data for the EpiMix package
Version: 0.99.0
Authors@R: c(
   person("Yuanning", "Zheng", email = c("yuanning.zheng@gmail.com"), role = c("aut", "cre")),
   person("Olivier", "Gevaert", email = c("ogevaert@stanford.edu"), role = c("aut"))
   )
Maintainer: Yuanning Zheng <yuanning.zheng@gmail.com>
Description:
  Supporting data for the EpiMix R package.
  It include:
   - HM450_lncRNA_probes.rda
   - HM450_miRNA_probes.rda
   - EPIC_lncRNA_probes.rda
   - EPIC_miRNA_probes.rda
   - EpigenomeMap.rda
   - LUAD.sample.annotation
   - TCGA_BatchData
   - MET.data
   - mRNA.data
   - microRNA.data
   - lncRNA.data
   - Sample_EpiMixResults_lncRNA
   - Sample_EpiMixResults_miRNA
   - Sample_EpiMixResults_Regular
  That is. 
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 3.5.0)
biocViews: AssayDomainData, TechnologyData, OrganismData
NeedsCompilation: no
RoxygenNote: 7.1.2
VignetteBuilder: knitr

vjcitn commented 2 years ago

Please do not use the name vignette.Rmd for your vignette. Also, when attempting to check your package I get

* creating vignettes ... ERROR
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: EpiMix.data
Quitting from lines 297-317 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "EpiMix"
--- failed re-building ‘vignette.Rmd’

Please be sure to install your package and check it with R CMD check on a clean system so that another person attempting this will succeed.

YuanningEric commented 2 years ago

Hi Vince,

Thanks for the review !

I have renamed the vignette.md. I tried to build the package in a clean environment but could not reproduce the issue. It was very surprised to see the error, because "EpiMix" is one of the main exported functions of this package. So, if the package has been installed, then the function should exist.

Could you please fetch the updated repository and build it again?

Thanks!

YuanningEric commented 2 years ago

@vjcitn Please also note that the "EpiMix.data" package is the supporting data package of "EpiMix". They are stored in two different git repositories. I assume that the error occurred when you tried to build the main "EpiMix" package.

vjcitn commented 2 years ago

I need to understand this better.

    else {
        cat("Searching lncRNA data for:", CancerSite, "\n")
        url = "https://github.com/gevaertlab/ncRNA_pancancer_new/raw/main/"
        destfile = paste0(TargetDirectory, "/", CancerSite, "_lncRNA.txt")
        downloader::download(paste0(url, CancerSite, "_lncRNA.txt"), 
            destfile)
        MAdirectories = destfile
    }
    return(MAdirectories = MAdirectories)
}
<bytecode: 0x11600ef30>

Is your package downloading data from github? Instead you have to use ExperimentHub.

vjcitn commented 2 years ago

@lshep ^^

lshep commented 2 years ago

@vjcitn / @YuanningEric Bioconductor does not allow data to be stored on github. It minimally must be on a public server at an Institution or something like Zenodo and implement a caching like system (like BiocFileCache) for managing downloads. Bioconductor provides opportunity for hosting data through Bioconductor provided location. We encourage data to be distributed through the ExperimentHub. Please see https://bioconductor.org/packages/devel/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html

YuanningEric commented 2 years ago

@vjcitn Hi, Vince! I have started the procedures to upload these data to ExperimentHub. After this has been accomplished, I will modify the corresponding code and notify you about the change. At the mean time, please let us know if there are any other problems we need to fix for our package. Thanks a lot!

vjcitn commented 2 years ago

Thanks for this. I guess a basic question is why you had to write code to use firehose instead of reusing code in TCGAbiolinks. Are the data of interest not provided in curatedTCGAData?

vjcitn commented 2 years ago

RTCGAToolbox also has similar functionality. Had you looked at these?

YuanningEric commented 2 years ago

@vjcitn Thanks for your question, Vince!

I took a close look at both packages you mentioned. The TCGAbiolinks first downloads data from the GDC portal, which includes one patient data per file, then it combined all the patient files together for additional preprocessing. This takes significant higher amount of time and disk space than using the firehose, from which the downloaded data has already been a single zipped file including preprocessed data for all the patients.

The RTCGAToolbox uses a very similar function than what we wrote. The reason we used our own code is that we built our current package by extending our previous Bioconductor package, called MethylMix. We did reuse a few bottom functionalities from MethylMix, because we know that those functions worked well. This also reduces the number of package dependency by avoiding to downloading another package.

Hope this helps, and please let me know if you have any other questions!

bioc-issue-bot commented 2 years ago

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bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/EpiMix.data to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 54f9a747833374c11e80d5e7fd69ed58878c2e33

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

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YuanningEric commented 2 years ago

The data package has been built. Here is our main package:

https://github.com/gevaertlab/EpiMix

lshep commented 2 years ago

Please see the proper way to submit the related package at https://github.com/Bioconductor/Contributions#circular-dependencies you need to use an AdditionalPackage: indication

YuanningEric commented 2 years ago

AdditionalPackage: https://github.com/gevaertlab/EpiMix

bioc-issue-bot commented 2 years ago

Hi @YuanningEric, Thanks for submitting your additional package: https://github.com/gevaertlab/EpiMix. We are taking a quick look at it and you will hear back from us soon.

YuanningEric commented 2 years ago

@lshep @Kayla-Morrell
Hi Kayla! I saw there is a deadline for the new package to be built on Bioconductor in order for catching up the release of V3.15. Could you please move our additional package to the repo? Both our data package and the main (additional) package have been scrutinized during the pre-check phase (see comments above), and we want them to be released with Bioc 3.15 instead of waiting for the next release period.
We appreciate your time and effort!

lshep commented 2 years ago

Please be aware EpiMix currently has a mixture of biocViews. Please only use one hierarchy. I will manually force this in and designate EpiMix a software package.

lshep commented 2 years ago

@YuanningEric There also seems to be a discrepancy in our credentials app -- I assume the correct spelling of your email is eric2021@stanford.edu -- currently in the BiocCredentails app it is erci2021@stanford.edu. Would you like me to update the credentials app for you? I can't finish the processing without the name mismatch (and the biocViews) corrected.

YuanningEric commented 2 years ago

@YuanningEric There also seems to be a discrepancy in our credentials app -- I assume the correct spelling of your email is eric2021@stanford.edu -- currently in the BiocCredentails app it is erci2021@stanford.edu. Would you like me to update the credentials app for you? I can't finish the processing without the name mismatch (and the biocViews) corrected.

@lshep Thanks for checking this! Yes, please use eric2021@stanford.edu

bioc-issue-bot commented 2 years ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EpiMix to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

YuanningEric commented 2 years ago

@lshep Hi ! From the BiocCheck report, I saw an error: At least 80% of man pages documenting exported objects must have runnable examples" What if some of my functions take a really long time to run or need to save exported objects to the file system? For example, one of my functions is to download the gene expression data from the TCGA project. In this case, which folder should I save the download file?

lshep commented 2 years ago

Functions generally need to be run somewhere vignette or examples or tests. One of the reasons I think @vjcitn also mentioned the TCGAbiolinks is it already utilizes Bioconductor standards like experimenthub and biicfilecache. Anything downloaded from the internet should have a caching mechanism to download; that way the expensive download is done once and the a user can use the cached file in subsequent runs and only redownload if the file changes. I would see about implementing biocfilecache.

Also we would consider skipping running that example but implement a long test that would run and test functionality. http://contributions.bioconductor.org/long-tests.html

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bioc-issue-bot commented 2 years ago

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This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/EpiMix to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 18cfb0dbacb6f8768772ce0145babedd317e79e7

bioc-issue-bot commented 2 years ago

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Your package has been built on Linux, Mac, and Windows.

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YuanningEric commented 2 years ago

@lshep Thanks a lot for your advice! In a future release, we will consider to using TCGAbiolinks or RTCGAToolBox as mentioned by @vjcitn . Now, our package has passed the R CMD check. The only error and warning arising from the BiocCheck is that we need to test more chunks in vignette and/or examples.

For those functions I tested in the vignette, do I need to test it again in the function examples?

In addition, I plan to move those functions taking long time to run to the long test as you mentioned, but this may take me a few days. Whether this will affect the release of our package with Bioc 3.15?

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bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/EpiMix to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9278d7b9b6cad4e98b2e5887aa193d974e77e640

bioc-issue-bot commented 2 years ago

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bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5e1eab0e8be04988864ed3b839f1fbc2b836823a

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/EpiMix to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e2f054324088524953de43c32bc956599ec62911

bioc-issue-bot commented 2 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/EpiMix to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

YuanningEric commented 2 years ago

Hi @lshep @Kayla-Morrell, I have included the vast majority of functions as runnable examples in the Vignette. Since there is a time limit for R CMD check, the functions that have been run in the Vignette were not included as runnable examples in the man pages. Can you accept our package?

Thanks!

Kayla-Morrell commented 2 years ago

@YuanningEric - We do not accept packages simply based off the build report, there is a formal review process that must take place. I will begin reviewing both packages and post back here with required/suggested changes that should be made to the package before being accepted. I will attempt to get the review posted within the next week.

Best, Kayla

YuanningEric commented 2 years ago

@Kayla-Morrell Thanks, Kayla! Please let me know if you have any questions

Kayla-Morrell commented 2 years ago

@YuanningEric - Thank you for submitting to Bioconductor. Please see the initial review of the packages 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.

EpiMix.data

DESCRIPTION

[ ] REQUIRED: Since this is a data package we recommend not including 'LazyData: TRUE'. It's our experience that it only slows down the loading of the package. Either set to 'FALSE' or remove.
[ ] REQUIRED: Update R version dependency from 4.1.0 to 4.2.0.
[ ] SUGGESTION: We strongly encourage including the 'BugReports:' field with a relevant link to GitHub for reporting issues.

NEWS

[ ] REQUIRED: It is great that a NEWS file is included with the package. However, it seems that the file is not formated properly. Please see the following link on how to format your file: https://contributions.bioconductor.org/news.html

Unit tests

[ ] SUGGESTION: We strongly encourage the use of unit tests.

R code

[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 17 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 7 lines that are not.

EpiMix

DESCRIPTION

[ ] REQUIRED: Either set 'LazyData' to false or remove it.
[ ] REQUIRED: Update R version dependency from 4.1.0 to 4.2.0.
[ ] SUGGESTION: Consider adding this automatically suggested biocView Preprocessing
[ ] SUGGESTION: It is encouraged to include the 'BugReports:' field with relevant links to GitHub for reporting issues.

NAMESPACE

[ ] REQUIRED: Exported functions should use camel case or underscoring and not include '.' which indicates S3 dispatch.

NEWS

[ ] REQUIRED: It is great to include a NEWS file but yours does not seem to be formatted properly. Please see the following link for correct format of NEWS files: https://contributions.bioconductor.org/news.html.

Vignette

[ ] REQUIRED: The name of the vignette should be more descriptive.
[ ] REQUIRED: There should be no eval = FALSE sections of code besides the installation code chunk.
[ ] SUGGESTION: We strongly encourage the use of BiocStyle for formatting of the vignette.
[ ] REQUIRED: The last section of the vignette should be 'Session Information' and should include sessionInfo().
[ ] REQUIRED: Only the source vignette file and any necessary static images should be in the vignette directory (the style file is fine as well). Please remove any unnecessary files, I could only find reference to the Workflow.png file. All others should be removed if not needed.
[ ] REQUIRED: Use accessors; don't access S4 slots via '@'.
[ ] REQUIRED: There is a lot of repeated code in your vignette that could be simplified. You don't need call library() in each code chunk, once is sufficient. The same goes for the data() calls.
[ ] REQUIRED: When running through the vignette code, the code chunk starting at line 312 and line 331 does not run resulting in the following error. This is why it is crucial to have all code chunks evaluated so you know when code is not working properly.
```
Error in wilcox.test.default(expr.high.values, expr.low.values, alternative = ifelse(correlation ==  :
not enough 'y' observations
>
```
[ ] REQUIRED: Line 481, Correlation is misspelled. If I run this line of code I get NULL. If I change to plots$CorrelationPlot then a plot is produced.
[ ] REQUIRED: All saved files/results should be in a temp directory. When running through the code I ended up with two directories that results were saved to, "Test" and "ReferenceEpigenomes".

Man pages

[ ] REQUIRED: At least 80% of man pages documenting exported objects must have runnable examples.
[ ] REQUIRED: If examples must not be run we prefer using donttest{} over dontrun{} since donttest{} requires valid R code.
[ ] REQUIRED: You mentioned examples being run in vignettes but the function TCGA_GetData is never actually run in the vignette, it's included in eval = FALSE code chunks. Therefore, the function is never being run to know if it is working properly. It must be run some where, whether that be in the vignette, with runnable man page examples, or unit tests.

Unit tests

[ ] SUGGESTION: Consider adding unit tests, we strongly encourage them.

R code

[ ] SUGGESTION: Undefined global function/variable, 'query'.
[ ] REQUIRED: Avoid sapply(); use vapply() instead.
[ ] REQUIRED: Avoid 1:...; use seq_len() or seq_along() instead.
[ ] REQUIRED: Avoid 'cat' and 'print' outside of 'show' methods.
[ ] REQUIRED: Avoid using '=' for assignment and use '<-' instead.
[ ] REQUIRED: Avoid the use of 'paste' in condition signals.
[ ] REQUIRED: Avoid 'suppressWarnings'/'*Messages' if possible, found 24 times.
[ ] REQUIRED: Function names should use camelCase, not use '.' within the name, and non-exported functions should have the prefix '.'.
[ ] REQUIRED: Make sure web resources follow the guidelines Querying Web Resources.
[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 1565 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of tabs. There are 5 lines that contain tabs.
[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 2931 lines that are not.

Best, Kayla

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Bioconductor / Contributions

EpiMix #2558

EpiMix.data

DESCRIPTION

NEWS

Unit tests

R code

EpiMix

DESCRIPTION

NAMESPACE

NEWS

Vignette

Man pages

Unit tests

R code