coMethDMR #2064

fveitz · 2021-04-21T19:15:23Z

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Repository: https://github.com/TransBioInfoLab/coMethDMR

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.

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bioc-issue-bot · 2021-04-21T19:15:24Z

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 · 2021-04-21T19:18:43Z

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

bioc-issue-bot · 2021-04-22T11:12:57Z

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bioc-issue-bot · 2021-04-22T13:18:44Z

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.
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bioc-issue-bot · 2021-05-03T14:36:52Z

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

bioc-issue-bot · 2021-05-03T14:59:08Z

Dear Package contributor,

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

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

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Kayla-Morrell · 2021-05-03T18:54:24Z

@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 · 2021-05-03T19:00:57Z

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 · 2021-05-05T02:46:25Z

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 · 2021-05-05T22:59:12Z

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 · 2021-05-06T13:22:52Z

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

Best,
Kayla

nturaga · 2021-05-06T13:30:39Z

Hi, Please send an email as instructed to ***@***.******@***.***> . We like to keep a track of packages when we manually interfere and make big changes like this, for the purpose of back tracing if needed. Best, Nitesh From: Kayla-Morrell ***@***.***> Date: Thursday, May 6, 2021 at 9:23 AM To: Bioconductor/Contributions ***@***.***> Cc: Nitesh Turaga ***@***.***>, Mention ***@***.***> Subject: Re: [Bioconductor/Contributions] coMethDMR (#2064) Hello @gabrielodom<https://github.com/gabrielodom> - Thank you for reaching out. I believe @nturaga<https://github.com/nturaga> should be able to help with this. Best, Kayla — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#2064 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAU6QS3PU6SL27RZD2U6XLDTMKJ4BANCNFSM43K6PDMQ>.

gabrielodom · 2021-05-06T13:39:37Z

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?

bioc-issue-bot · 2021-05-06T16:07:44Z

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

bioc-issue-bot · 2021-05-06T16:26:33Z

Dear Package contributor,

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

Congratulations! The package built without errors or warnings
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Please see the build report for more details. This link will be active
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gabrielodom · 2021-05-06T16:49:45Z

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

bioc-issue-bot · 2021-05-12T19:09:38Z

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

bioc-issue-bot · 2021-05-13T12:25:30Z

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,
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gabrielodom · 2021-05-13T15:06:19Z

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 · 2021-05-28T14:06:53Z

@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

bioc-issue-bot · 2021-06-10T15:37:49Z

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

gabrielodom · 2021-10-21T14:49:57Z

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

bioc-issue-bot · 2021-10-21T16:05:18Z

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

bioc-issue-bot · 2021-10-21T16:07:47Z

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

fveitz · 2021-10-21T16:08:12Z

Hi Lori, Nitesh and Gabriel, Using my internet at home I could push successfully. "Fernandas-MacBook-Pro:coMethDMR fernandaveitzman$ git push upstream master Enumerating objects: 179, done. Counting objects: 100% (179/179), done. Delta compression using up to 16 threads Compressing objects: 100% (128/128), done. Writing objects: 100% (128/128), 32.08 KiB | 290.00 KiB/s, done. Total 128 (delta 104), reused 0 (delta 0) remote: Resolving deltas: 100% (104/104), completed with 48 local objects. To git.bioconductor.org:packages/coMethDMR.git 507e5d3..3e1e22c master -> master" Thank you!

…

On Thu, Oct 21, 2021 at 10:50 AM Gabriel J. Odom ***@***.***> wrote: Thank you Lori and Nitesh! Fernanda, please try this as soon as possible. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2064 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASCHHMX5UJA34OL4DO6FVDDUIASCDANCNFSM43K6PDMQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

gabrielodom · 2021-10-21T16:12:28Z

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

bioc-issue-bot · 2021-10-21T21:01:54Z

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

bioc-issue-bot · 2021-10-21T21:04:20Z

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.
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Please see the build report for more details. This link will be active
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when making changes to your repository push to
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bioc-issue-bot · 2021-10-23T12:54:35Z

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

bioc-issue-bot · 2021-10-23T13:11:28Z

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
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lshep · 2021-11-05T14:27:12Z

Were you ready for a re-review?

gabrielodom · 2021-11-05T15:01:52Z

@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.

lshep · 2021-11-12T14:52:37Z

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 · 2021-11-12T14:56:58Z

@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.

lshep · 2021-11-12T15:01:04Z

That can be arranged. When were you thinking?

gabrielodom · 2021-11-12T15:04:10Z

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

lshep · 2021-11-12T15:05:35Z

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

gabrielodom · 2021-11-12T15:10:15Z

Setting it up now

gabrielodom · 2021-11-12T15:12:22Z

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

bioc-issue-bot · 2021-11-12T17:05:49Z

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

bioc-issue-bot · 2021-11-12T17:20:27Z

Dear Package contributor,

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

Congratulations! The package built without errors or warnings
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Please see the build report for more details. This link will be active
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gabrielodom · 2021-11-12T18:12:35Z

@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.

bioc-issue-bot · 2021-11-24T12:52:15Z

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

Thank you for contributing to Bioconductor!

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lshep · 2021-11-24T12:53:07Z

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:

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.

bioc-issue-bot added the 1. awaiting moderation label Apr 21, 2021

bioc-issue-bot added 2. review in progress and removed 1. awaiting moderation labels Apr 22, 2021

bioc-issue-bot assigned Kayla-Morrell Apr 22, 2021

bioc-issue-bot added the TIMEOUT label Apr 22, 2021

bioc-issue-bot added ERROR and removed TIMEOUT labels May 3, 2021

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

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

bioc-issue-bot added OK and removed ERROR labels Oct 23, 2021

lshep added 3a. accepted and removed 2. review in progress labels Nov 24, 2021

lshep closed this as completed Nov 24, 2021

coMethDMR #2064

coMethDMR #2064

Comments

fveitz commented Apr 21, 2021

bioc-issue-bot commented Apr 21, 2021

gabrielodom commented Apr 21, 2021

bioc-issue-bot commented Apr 22, 2021

bioc-issue-bot commented Apr 22, 2021

bioc-issue-bot commented May 3, 2021

bioc-issue-bot commented May 3, 2021

Kayla-Morrell commented May 3, 2021

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DESCRIPTION

Vignettes

Unit tests

R code

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lshep commented Nov 12, 2021 • edited

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edited