epidecodeR

[kandarpRJ]

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

• Repository: https://github.com/kandarpRJ/epidecodeR

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

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[bioc-issue-bot]

Hi @kandarpRJ

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: epidecodeR
Type: Package
Title: Analysis of dysregulation of genes by DNA and RNA epigenetic modifications and visualization
Version: 0.99.1
Authors@R: c(person("Kandarp", "Joshi", email = "kandarpbioinfo@gmail.com",
        role = c("aut", "cre")),
   person("Dan", "Ohtan Wang", email = "ohtan@riken.jp",
        role = "aut"))
Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, rstatix, ggpubr, methods, stats, utils, dplyr
biocViews: Software
Description: epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1

[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 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/epidecodeR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[kandarpRJ]

Hi Kayla-Morrell,

Currently I am pushing changes in repository from my lab system, for which I have added as public key to git. But in few days I am going to lose access to this system after which I will be working using my personal system. I tried pushing changes to bioconductor git using my system and it showed errors. I added public key of my personal system to git but I think its not working. Can you please suggest how to proceed? I have made changes to solve above errors and want to push changes to git and bioconductor.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5b44d411a5d098c5c3a7b772afec4d183f3e39c8

[kandarpRJ]

Ok so I added new ssh public key to bioconductor git credential app and made a new push for review. Sorry for the confusion on my side.

[bioc-issue-bot]

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.

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

[Kayla-Morrell]

@kandarpRJ - 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.

General package development

• [ ] REQUIRED: File LICENSE is not mentioned in the DESCRIPTION file. Since you are using a standard library this file is not necessary and should be removed.

DESCRIPTION

• [ ] REQUIRED: Set 'LazyData' to 'false' instead of 'true'. It is our experience that when this field is set to 'true' it can slow down the loading of the package, especially if they include data.

• [ ] SUGGESTION: Based on the biocViews tags you have included, consider adding the automatically suggest biocViews 'ChipOnChip'.

• [ ] SUGGESTION: We strongly encourage the use of the 'BugReports:' field that includes the relevant link to GitHub for reporting Issues.

NAMESPACE

• [ ] REQUIRED: There are packages listed under 'Imports:' in your DESCRIPTION file that are not listed in your NAMESPACE file. Please be sure you have all imports or importFroms listed here.

NEWS

• [ ] SUGGESTION: Consider adding a NEWS file so your package news will be included in the Bioconductor release announcements.

Data

• [ ] REQUIRED: Since you include data in the 'inst/extdata' directory there needs to be related scripts present in the 'inst/script' directory that very clearly documents how the data was generated. The scripts can vary but they should include source urls and any important information regard filtering or processing. It can be executible code, sudo code, or a text description. A user should be able to doownload and roughly reproduce the file or object that is present as data.

Vignette

• [ ] REQUIRED: The 'Installation' section could use some improvements. First of all it isn't necessary to install the packages that are listed as imports in your package. They will be loaded when the package is. You do not need to install 'devtools' so this code should be removed. When it comes to installing the package you should not be installing from GitHub, instead you should be demonstrating to the user how to install and load from Bioconductor. The code should look something like the following and include eval = FALSE.

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("epidecodeR")

• [ ] SUGGESTION: We strongly encourage the use of table of contents.

• [ ] REQUIRED: Use accessors; do not access S4 class slots via '@'. This is used in many of your code chunks in the vignette.

• [ ] REQUIRED: There are sections of code that are included in echo = FALSE sections. These sections need to be visible to the user so they know how the variable is created. This is the best practice for reproducible code in your vignette.

• [ ] REQUIRED: The 'More Examples' section should be removed unless you intend to include more examples (this includes line 225).

• [ ] REQUIRED: The final section of the vignette should be 'Session Information' and should include sessionInfo().

Man pages

• [ ] REQUIRED: For functions that are documented but aren't being exported add the @keywords internal tag to the documentation. This will remove the function from the documentation index. This will also clear up the BiocCheck about using dontrun{}/donttest{} in man page examples (for plottingfunc).

Unit tests

• [ ] SUGGESTION: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/.

R code

• [ ] REQUIRED: Clarify how 1 obejct is intialized. Maybe it is part of a data set loaded with data(), or perhaps part of an object referenced in with() or withing(). function (object) epidecodeR (IRanges)

• [ ] REQUIRED: Avoid 1:...; use seq_len() or seq_along() instead. Found in files: epidecodeR.R, lines 103, 301, and 361

• [ ] REQUIRED: Avoid the use of direct slot access with @ or slot(). Accessor methods should be created and utilized instead.

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 138 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of using tabs. There are 8 lines that contain tabs.

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 154 lines that are not.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 43c9eddd81a097b951198fe9c536c9786d218306

[bioc-issue-bot]

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/epidecodeR 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: e64e3d3f03e59be66aeb62c41b8bc29957e98234

[bioc-issue-bot]

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.

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

[kandarpRJ]

Hi @Kayla-Morrell,

Thank you for reviewing our package. I have made the changes required and suggested by you.

@kandarpRJ - 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.

General package development

• [x] REQUIRED: File LICENSE is not mentioned in the DESCRIPTION file. Since you are using a standard library this file is not necessary and should be removed.

Removed LICENSE file from git commit

DESCRIPTION

• [x] REQUIRED: Set 'LazyData' to 'false' instead of 'true'. It is our experience that when this field is set to 'true' it can slow down the loading of the package, especially if they include data.

Changed LazyData to false

• [x] SUGGESTION: Based on the biocViews tags you have included, consider adding the automatically suggest biocViews 'ChipOnChip'.

Added 'ChipOnChip' tag to biocViews

• [x] SUGGESTION: We strongly encourage the use of the 'BugReports:' field that includes the relevant link to GitHub for reporting Issues.

Added BugReports: and link to post issues

NAMESPACE

• [x] REQUIRED: There are packages listed under 'Imports:' in your DESCRIPTION file that are not listed in your NAMESPACE file. Please be sure you have all imports or importFroms listed here.

  Added missing imports

NEWS

• [x] SUGGESTION: Consider adding a NEWS file so your package news will be included in the Bioconductor release announcements.

Added NEWS file to the package

Data

• [x] REQUIRED: Since you include data in the 'inst/extdata' directory there needs to be related scripts present in the 'inst/script' directory that very clearly documents how the data was generated. The scripts can vary but they should include source urls and any important information regard filtering or processing. It can be executible code, sudo code, or a text description. A user should be able to doownload and roughly reproduce the file or object that is present as data.

Included script dir in inst dir. This contains desc.txt file which describes sources of data included as example as well as pseudo code used to generated examples from raw data.

Vignette

• [x] REQUIRED: The 'Installation' section could use some improvements. First of all it isn't necessary to install the packages that are listed as imports in your package. They will be loaded when the package is. You do not need to install 'devtools' so this code should be removed. When it comes to installing the package you should not be installing from GitHub, instead you should be demonstrating to the user how to install and load from Bioconductor. The code should look something like the following and include eval = FALSE.

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("epidecodeR")

Included new instructions of installation of package from bioconductor and removed install_github()

• [x] SUGGESTION: We strongly encourage the use of table of contents.

Added table of content to vignette

• [x] REQUIRED: Use accessors; do not access S4 class slots via '@'. This is used in many of your code chunks in the vignette.

Added methods to access slots in S4 class instead of @

• [x] REQUIRED: There are sections of code that are included in echo = FALSE sections. These sections need to be visible to the user so they know how the variable is created. This is the best practice for reproducible code in your vignette.

Removed echo=FALSE from examples in vignette

• [x] REQUIRED: The 'More Examples' section should be removed unless you intend to include more examples (this includes line 225).

Removed line 225 from vignette

• [x] REQUIRED: The final section of the vignette should be 'Session Information' and should include sessionInfo().

Added sessionInfo() at the end of vignette

Man pages

• [x] REQUIRED: For functions that are documented but aren't being exported add the @keywords internal tag to the documentation. This will remove the function from the documentation index. This will also clear up the BiocCheck about using dontrun{}/donttest{} in man page examples (for plottingfunc).

Added @keywords internal to the documentation of plottingfunc function. However when I run biocCheck() locally I still get the note about dontrun(). Is this a problem?

Unit tests

• [ ] SUGGESTION: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/.

R code

• [x] REQUIRED: Clarify how 1 obejct is intialized. Maybe it is part of a data set loaded with data(), or perhaps part of an object referenced in with() or withing(). function (object) epidecodeR (IRanges)

Added initialization for epidecodeR(IRanges)

• [x] REQUIRED: Avoid 1:...; use seq_len() or seq_along() instead. Found in files: epidecodeR.R, lines 103, 301, and 361

  Added seq_len instead of 1:... at suggested places

• [x] REQUIRED: Avoid the use of direct slot access with @ or slot(). Accessor methods should be created and utilized instead.

  Added methods to access slots in S4 class instead of @

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 138 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of using tabs. There are 8 lines that contain tabs.

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 154 lines that are not.

Tried to minimize offending formatting

Best, Kayla

Hope the changes are satisfactory. Please tell me if any more changes are required.

Regards, Kandarp

[Kayla-Morrell]

@kandarpRJ - Thank you for making the necessary changes. There are still a few points that need to be addressed before I can accept the package.

General package development

• [ ] REQUIRED: The LICENSE file is still present in the git repo. Please be sure this gets removed.

NEWS

• [ ] REQUIRED: Thank you for including a NEWS file but it does not seem to be formatted correctly. Please see our NEWS documentation here - https://bioconductor.org/developers/package-guidelines/#news.

Vignette

• [ ] REQUIRED: The only files that should be present in this directory are the vignette file (.Rmd) and the necessary images (.png). Please remove the .html file.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fc8b861f5ce3921551181ac8646138baef4545ef

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: eb8653c731b1b1e15bbe2a8cda97e6b72d3188fe

[bioc-issue-bot]

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, 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. 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/epidecodeR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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, 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. 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/epidecodeR 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: 06d95fdd53adc48f7b4c0981739b01b0d0a06de5

[bioc-issue-bot]

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, 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. 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/epidecodeR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[kandarpRJ]

Hi @Kayla-Morrell, sorry for making the mistakes in uploading wrong files. I have made following changes.

@kandarpRJ - Thank you for making the necessary changes. There are still a few points that need to be addressed before I can accept the package.

General package development

• [ ] REQUIRED: The LICENSE file is still present in the git repo. Please be sure this gets removed.

Apologies, I thought I had removed the file but somehow missed it. I have removed the file this time.

NEWS

• [ ] REQUIRED: Thank you for including a NEWS file but it does not seem to be formatted correctly. Please see our NEWS documentation here - https://bioconductor.org/developers/package-guidelines/#news.

I have added NEWS.rd file in inst/ dir, I hope this one is in correct format.

Vignette

• [ ] REQUIRED: The only files that should be present in this directory are the vignette file (.Rmd) and the necessary images (.png). Please remove the .html file.

Removed the html file from vignette folder

Best, Kayla

I pushed to git after making the changes but now build and check is giving me error.

For windows build it is saying rtracklayer package not found, but I was using this package earlier too and it was building fine then. I dont know how to solve this error.

For linux and mac check error it says "Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags.". I dont know what this error means and checking the internet didnt provide any solutions. Can you please help me out in solving these errors?

Regards, Kandarp

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 67756b3faaa717d41f56d14250417766b9b74396

[bioc-issue-bot]

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, 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. 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/epidecodeR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[kandarpRJ]

Hi @Kayla-Morrell, I figured out that I need to add my package name to watched tag field in profile of support.bioconductor.org and did it (Please see attached screenshot) But after pushing package to git I am still getting error in the checks for linux and mac. Am I doing something wrong here?

[Kayla-Morrell]

@kandarpRJ - This is a new check that has been added to BiocCheck. I will check with the devel team to see if I can get you any suggestions to clear up this ERROR.

[lshep]

@kandarpRJ When you added the watched tag, did you remember to go to the bottom of the page and hit "submit" to save the updates to the profile?

[lshep]

Admittedly this is confusing and we will change the button to say "save" in the future but you must hit "submit" in order for the changes to your profile to actively save.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: db29552b8e733931a322acdb9a9d43cb849d601a

[bioc-issue-bot]

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, WARNINGS, 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. 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/epidecodeR 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: ec04ebe516f743c93a7a3d1cd537517d8f740de0

[bioc-issue-bot]

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, WARNINGS, 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. 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/epidecodeR 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: 8113e36c9caa78f367c97fcadf0dab12d5af6c4f

[bioc-issue-bot]

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, WARNINGS, 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. 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/epidecodeR 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: 4e1959d877e25a55dbdc41112a581c3d8512db7a

[bioc-issue-bot]

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, 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. 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/epidecodeR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[kandarpRJ]

Hi @Kayla-Morrell & @lshep Thank you for helping me out. Sorry it was my bad, I didn't save after adding the tag. I have added the tag and that error has disappeared now.

However, I am still getting error on windows build "ERROR: dependency 'rtracklayer' is not available for package 'epidecodeR'". I used this package previously and the build was successful then. I don't know what to do about this error.

[lshep]

We Updated R which flushed the available packages. Currently rtracklayer has an ERROR in windows and is breaking hundreds of package on the builders; the maintainers are aware and in the process of fixing the package but it will be unavailable until they push up a fix. You can ignore the windows error right now as long as the other two platforms are clean.

[kandarpRJ]

@lshep Thank you for the clarification and help.

@Kayla-Morrell since we can ignore windows error for now, can we proceed with the review based on build reports of mac and linux to access the changes I made in the latest push?

[kandarpRJ]

@Kayla-Morrell hi please let me know what more needs to be done to improve the package to get accepted. Awaiting your reply. Thanks

[Kayla-Morrell]

@kandarpRJ - I have reviewed the required changes and everything looks good. I'm more than happy to accept the package.

Best, Kayla

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/kandarpRJ.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

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

https://bioconductor.org/packages/epidecodeR

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.