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coMethDMR #2064

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fveitz opened this issue Apr 21, 2021 · 64 comments
Closed
9 tasks done

coMethDMR #2064

fveitz opened this issue Apr 21, 2021 · 64 comments
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@fveitz
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@fveitz fveitz commented Apr 21, 2021

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

Dear reviewer, I am submitting my package for the very first time.
I am a master student in the lab of @lxw391 and @gabrielodom
Thank you in advance for your feedback and your patience.

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

  • I understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
    general public.

  • I have read the Bioconductor Package Submission
    instructions. My package is consistent with the Bioconductor
    Package Guidelines.

  • 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.

  • My package addresses statistical or bioinformatic issues related
    to the analysis and comprehension of high throughput genomic data.

  • I am committed to the long-term maintenance of my package. This
    includes monitoring the support site for issues that users may
    have, subscribing to the bioc-devel mailing list to stay aware
    of developments in the Bioconductor community, responding promptly
    to requests for updates from the Core team in response to changes in
    R or underlying software.

  • I am familiar with the Bioconductor code of conduct and
    agree to abide by it.

I am familiar with the essential aspects of Bioconductor software
management, including:

  • The 'devel' branch for new packages and features.
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    months, for bug fixes.
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For help with submitting your package, please subscribe and post questions
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@bioc-issue-bot bioc-issue-bot commented Apr 21, 2021

Hi @fveitz

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: coMethDMR
Title: Accurate identification of co-methylated and differentially methylated
  regions in epigenome-wide association studies
Version: 0.99.1
Authors@R: c(
  person("Fernanda", "Veitzman", email = "fveit001@fiu.edu", role = c("cre")),
  person("Lissette", "Gomez", email = "lxg255@miami.edu", role = c("aut")),
  person("Lily", "Wang", email = "lily.wang@med.miami.edu", role = c("aut")),
  person("Gabriel", "Odom", email = "gabriel.odom@fiu.edu", role = c("aut"))
  )
Description: coMethDMR identifies genomic regions associated with continuous
  phenotypes by optimally leverages covariations among CpGs within predefined
  genomic regions. Instead of testing all CpGs within a genomic region,
  coMethDMR carries out an additional step that selects co-methylated
  sub-regions first without using any outcome information. Next, coMethDMR tests
  association between methylation within the sub-region and continuous phenotype
  using a random coefficient mixed effects model, which models both variations
  between CpG sites within the region and differential methylation simultaneously. 
Depends:
  R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports:
  BiocParallel,
  bumphunter,
  dplyr,
  GenomicRanges,
  IRanges,
  lmerTest,
  methods,
  rlang,
  sesameData,
  stats,
  tidyr,
  utils
Suggests: 
  BiocStyle,
  corrplot,
  GenoGAM,
  knitr,
  rmarkdown,
  testthat,
  IlluminaHumanMethylation450kanno.ilmn12.hg19,
  IlluminaHumanMethylationEPICanno.ilm10b2.hg19
biocViews:
    DNAMethylation,
    Epigenetics,
    MethylationArray, 
    DifferentialMethylation, 
    GenomeWideAssociation
VignetteBuilder: knitr

@gabrielodom
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@gabrielodom gabrielodom commented Apr 21, 2021

Dear Bioconductor Review Team,
Thank you for moderating this package. At the time of submission, we have 7 notes (2 from CRAN check and 5 from BioC).
We have relayed them here: TransBioInfoLab/coMethDMR#1
Respectfully yours,
Gabriel

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@bioc-issue-bot bioc-issue-bot commented Apr 22, 2021

A reviewer has been assigned to your package. Learn what to expect
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@bioc-issue-bot bioc-issue-bot commented Apr 22, 2021

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, 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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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@bioc-issue-bot bioc-issue-bot commented May 3, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 52490ece613295f9734d6fabb892e5b2be0237e2

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@bioc-issue-bot bioc-issue-bot commented May 3, 2021

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

@Kayla-Morrell
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@Kayla-Morrell Kayla-Morrell commented May 3, 2021

@fveitz - Thank you for working on your package to get it ready for review. Please keep in mind that the deadline to accept new packages into the Bioconductor 3.13 release is May 12th. Any packages accepted after this date will be included in the next release.

Best,
Kayla

@gabrielodom
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@gabrielodom gabrielodom commented May 3, 2021

Hi @Kayla-Morrell!
Thank you so much for checking on us. We are currently deliberating about the best way to reduce the package size (currently, that is our only ERROR because Fernanda just added coMethDMR to her watched tags on the support site).

The data files in inst/extdata/ (11.3Mb) are there to save the users from having to re-compute them in each analysis. We are right now reading the documentation on creating an ExperimentHub package to store these data sets, but we see that this also requires us to get help from someone on the Bioconductor team.

Should we ask you for help with this?

@gabrielodom
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@gabrielodom gabrielodom commented May 5, 2021

We have moved the example data sets to a supplemental GitHub directory. The package now has an install size <5Mb. We will be pushing these changes upstream tomorrow morning.
Thank you for your patience.

@gabrielodom
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@gabrielodom gabrielodom commented May 5, 2021

Hi @Kayla-Morrell,
We need help. We have removed the large data files from the package and the .git/ history folder. According to these instructions (https://bioconductor.org/developers/how-to/git/remove-large-data/), we are to email you and ask for help forcing the update.

@Kayla-Morrell
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@Kayla-Morrell Kayla-Morrell commented May 6, 2021

Hello @gabrielodom - Thank you for reaching out. I believe @nturaga should be able to help with this.

Best,
Kayla

@nturaga
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@nturaga nturaga commented May 6, 2021

@gabrielodom
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@gabrielodom gabrielodom commented May 6, 2021

Hi @nturaga,
We emailed bioc-devel@r-project.org yesterday at 7PM Eastern (I also commented here to cover my bases). The email address in your comment has been replaced with "*". Is that the email we were supposed to use, or should we use a different one?

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@bioc-issue-bot bioc-issue-bot commented May 6, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: ae98b938139084353628b9a69c436c56853c8d78

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@bioc-issue-bot bioc-issue-bot commented May 6, 2021

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

@bioc-issue-bot bioc-issue-bot added OK and removed ERROR labels May 6, 2021
@gabrielodom
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@gabrielodom gabrielodom commented May 6, 2021

We have extracted and documented the NOTEs here: TransBioInfoLab/coMethDMR#1.
We will work on a few of these shortly.

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@bioc-issue-bot bioc-issue-bot commented May 12, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: aa0c6ac3be74752f8348c56c998314d86489345f

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@bioc-issue-bot bioc-issue-bot commented May 13, 2021

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

@gabrielodom
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@gabrielodom gabrielodom commented May 13, 2021

Hi @Kayla-Morrell,
@fveitz and I worked on removing some of these notes (particularly the LazyData and redundant paste() calls).
Please let us know if there is anything else you would like us to improve.
Best,
Gabriel

@Kayla-Morrell
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@Kayla-Morrell Kayla-Morrell commented May 28, 2021

@fveitz - 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.

DESCRIPTION

  • REQUIRED: Update R version dependency from 4.0.0 to 4.1.

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

Vignettes

vin1_Introduction_to_coMethDMR_geneBasedPipeline

  • SUGGESTION: For section headings you include the number in your title so in the table of contents it looks like '1 1. Quick start'. I would suggest removing the leading 1. or 2. since they will get numbered automatically (you have the right idea in the next vignette).

  • REQUIRED: In the 'Installation' section the package should be installed from Bioconductor, not your GitHub. The code on line 39 should be changed toBiocManager::install("coMethDMR").

  • REQUIRED: The code section at line 54 should not have eval = FALSE. Code chunks in your vignette (minus the installation ones) should be executable. I think this what is resulting in my local ERRORs when I try to build the vignettes. For example, under section 1.3 I get the following error:

system.time(  
   coMeth_ls <- CoMethAllRegions(    
       dnam = betasChr22_df,    
       betaToM = TRUE, #converts to mvalues    
        method = "pearson",
        CpGs_ls = CpGisland_ls,    
        arrayType = "450k",
        returnAllCpGs = FALSE,
        output = "CpGs",
        nCores_int = 1  )
)
## Error in stopAndCache(title): 
## File needs to be cached to be used in sesame.
## Please run
## > sesameDataCache("HM450")
## or cache all platforms by
## > sesameDataCacheAll()
## to retrieve and cache needed sesame data.
## Timing stopped at: 0.013 0.002 0.018# 12 seconds

coMeth_ls
## Error in eval(expr, envir, enclos): object 'coMeth_ls' not found

This makes the rest of the vignette almost non-reproducable since objects aren't found.

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

vin2_BiocParallel_for_coMethDMR_geneBasedPipeline

  • REQUIRED: Similar to the issue in the first vignette, when running the code at line 118, I get the error about sesameDataCacheAll() and that objects aren't found because this code is executable. Please fix this code.

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

Unit tests

  • REQUIRED: Running the tests in 'test/testthat.R' failed. I'm not sure exactly which test failed, but this is the output I got from R CMD check:
* checking tests ... ERROR 
   Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       4. └─coMethDMR::lmmTestAllRegions(...)
       5.   ├─BiocParallel::bplapply(...)
       6.   └─BiocParallel::bplapply(...)    
       7.     └─base::lapply(X, FUN_, ...)    
       8.       └─BiocParallel:::FUN(X[[i]], ...)    
       9.         └─BiocParallel:::FUN(...)   
       10.           ├─base::withCallingHandlers(...)   
       11.           └─base::tryCatch(...)   
       12.             └─base:::tryCatchList(expr, classes, parentenv, handlers)   
       13.               └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])   
       14.                 └─value[[3L]](cond)
  
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ]  
    Error: Test failures  
    Execution halted

R code

  • REQUIRED: Running examples in 'coMethDMR-Ex.R' failed. This is the output I got from R CMD check:
* checking examples ... ERROR
Running examples in ‘coMethDMR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CloseBySingleRegion
> ### Title: Extract clusters of CpGs located closely in a genomic region. 
> ### Aliases: CloseBySingleRegion 

### ** Examples
>
>
>    CpGs_char <- c(
     "cg02505293", "cg03618257", "cg04421269", "cg17885402", "cg19890033",
      "cg20566587", "cg27505880"
    )
>
>   cluster_ls <- CloseBySingleRegion(
      CpGs_char,
      genome = "hg19",
      arrayType = "450k",
      maxGap = 100,
      minCpGs = 3
    )
Error in stopAndCache(title) :
File needs to be cached to be used in sesame.
Please run
> sesameDataCache("HM450")
or cache all platforms by
> sesameDataCacheAll()
to retrieve and cache needed sesame data.
Calls: CloseBySingleRegion ... capture.output -> withVisible -> .sesameDataGet -> stopAndCache
Execution halted
  • SUGGESTION: Avoid redundant 'stop' and 'warn*' in signal conditions. Found in files: lmmTestAllRegions.R, line 140

  • SUGGESTION: For formating reasons, consider shorter lines. There are 201 lines that are > 80 characters long.

  • SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. There are 1001 lines that are not.

Best,
Kayla

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@bioc-issue-bot bioc-issue-bot commented Jun 10, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 76736cb40cf4dd756915cb6d7de9292d08aae290

@gabrielodom
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@gabrielodom gabrielodom commented Oct 21, 2021

Thank you Lori and Nitesh! Fernanda, please try this as soon as possible.

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@bioc-issue-bot bioc-issue-bot commented Oct 21, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 3e1e22cf98528d23c1a5c5ebad0087b21c00e538

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@bioc-issue-bot bioc-issue-bot commented Oct 21, 2021

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

@bioc-issue-bot bioc-issue-bot added ERROR and removed OK labels Oct 21, 2021
@fveitz
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@fveitz fveitz commented Oct 21, 2021

@gabrielodom
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@gabrielodom gabrielodom commented Oct 21, 2021

And we have another build error. Give us a minute. I think it's the sesameData package again.

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@bioc-issue-bot bioc-issue-bot commented Oct 21, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 64f54b826f1713142814afab2a93c38cdfe0b126

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@bioc-issue-bot bioc-issue-bot commented Oct 21, 2021

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

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@bioc-issue-bot bioc-issue-bot commented Oct 23, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 1edd8558764f32bd1425c5f9aced233af0bc8d68

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@bioc-issue-bot bioc-issue-bot commented Oct 23, 2021

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

@bioc-issue-bot bioc-issue-bot added OK and removed ERROR labels Oct 23, 2021
@lshep
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@lshep lshep commented Nov 5, 2021

Were you ready for a re-review?

@gabrielodom
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@gabrielodom gabrielodom commented Nov 5, 2021

@lshep -- if you have time. We aren't in a huge hurry (the paper was already accepted), and we know you have a million other things.

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@lshep lshep commented Nov 12, 2021

In vin1 section 2.3. I still cannot reproduce your results.After the run
where we get ##NULL and change to Cgi_ls[5], your results show and answer. Mine
are still ##NULL and subsequently the rest of the code in 2.4 is also non
reproducible.

> Cgi_ls <- readRDS(
+   system.file(
+     "extdata",
+     "CpGislandsChr22_ex.rds",
+     package = 'coMethDMR',
+     mustWork = TRUE
+     )
+ )
> 
> coMeth_ls <- CoMethAllRegions(
+   dnam = resid_mat,
+   betaToM = FALSE,
+   method = "pearson",
+   CpGs_ls = Cgi_ls[1],
+   arrayType = "450k",
+   returnAllCpGs = FALSE,
+   output = "CpGs"
+ )
> 
> coMeth_ls
NULL
> coMeth_ls <- CoMethAllRegions(
+   dnam = resid_mat,
+   betaToM = FALSE,
+   CpGs_ls = Cgi_ls[5],
+   arrayType = "450k",
+   returnAllCpGs = FALSE, 
+   output = "CpGs"
+ )
> 
> coMeth_ls
NULL
> coMethData_df <- CoMethAllRegions(
+   dnam = resid_mat,
+   betaToM = FALSE,
+   CpGs_ls = Cgi_ls[5],
+   arrayType = "450k",
+   returnAllCpGs = FALSE, 
+   output = "dataframe"
+ ) [[1]]
Error in CoMethAllRegions(dnam = resid_mat, betaToM = FALSE, CpGs_ls = Cgi_ls[5],  : 
  subscript out of bounds

@gabrielodom
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@gabrielodom gabrielodom commented Nov 12, 2021

@lshep, I know this is a huge ask, but do you have time for a Zoom call? We have tried everything we can think of to replicate this error, but to no avail.

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@lshep lshep commented Nov 12, 2021

That can be arranged. When were you thinking?

@gabrielodom
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@gabrielodom gabrielodom commented Nov 12, 2021

Our time is yours to command. I have @fveitz in my office at this instant

@lshep
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@lshep lshep commented Nov 12, 2021

I'm free now if you wanted to set up a zoom and email me or slack me the information to login

@gabrielodom
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@gabrielodom gabrielodom commented Nov 12, 2021

Setting it up now

@gabrielodom
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@gabrielodom gabrielodom commented Nov 12, 2021

I sent it to the roswell park email. Is that still ok?

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@bioc-issue-bot bioc-issue-bot commented Nov 12, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 5762fddc9c20815a94120212991d81448df0393b

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@bioc-issue-bot bioc-issue-bot commented Nov 12, 2021

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

@gabrielodom
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@gabrielodom gabrielodom commented Nov 12, 2021

@lshep, we have fixed the issue, and the build passes (see above).
Thank you, again, for your patience. I think we are ready for that re-review.

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@bioc-issue-bot bioc-issue-bot commented Nov 24, 2021

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

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@lshep lshep commented Nov 24, 2021

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/fveitz.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("coMethDMR"). The package 'landing page' will be created at

https://bioconductor.org/packages/coMethDMR

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.

@lshep lshep closed this as completed Nov 24, 2021
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