mist

[dxd429]

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[bioc-issue-bot]

Hi @dxd429

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: mist
Title: Differential Methylation Analysis for scDNAm Data
Version: 0.99.0
Depends: R (>= 4.3.0)
Authors@R: 
    person("Daoyu", "Duan", , "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-3147-2006"))
Description: mist (Methylation Inference for Single-cell along Trajectory) is a hierarchical 
 Bayesian framework for modeling DNA methylation trajectories and performing differential methylation 
 (DM) analysis in single-cell DNA methylation (scDNAm) data. It estimates developmental-stage-specific 
 variations, identifies genomic features with drastic changes along pseudotime, and, for two 
 phenotypic groups, detects features with distinct temporal methylation patterns. mist uses Gibbs 
 sampling to estimate parameters for temporal changes and stage-specific variations.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: Epigenetics, DifferentialMethylation, DNAMethylation, SingleCell, Software
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports:
    BiocParallel,
    MCMCpack,
    Matrix,
    S4Vectors,
    methods,
    rtracklayer,
    car,
    mvtnorm,
    SummarizedExperiment,
    SingleCellExperiment,
    BiocGenerics,
    stats
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr

[lshep]

Please also provide an inst/scripts directory that describes how the data in inst/extdata was generated. It can be code, pseudo-code, or text but should minimally list any source or licensing information.

I see you can take in a SummarizedExperiment object but only as a file path?

> Dat_path <- system.file("extdata", "sampleData_sce.rds", package = "mist")
> Dat_path
[1] "/home/lorikern/R-Libraries/R4.5-Bioc3.21/mist/extdata/sampleData_sce.rds"
> beta_sigma_list <- estiParamSingle(
    Dat_sce = Dat_path,
    Dat_name = "Methy_level_group1",
    ptime_name = "pseudotime"
)

Why not the object itself if it is loaded in R? In other words passing the SCE object itself to estiParamSingle and other functions?

[dxd429]

Please also provide an inst/scripts directory that describes how the data in inst/extdata was generated. It can be code, pseudo-code, or text but should minimally list any source or licensing information.

I see you can take in a SummarizedExperiment object but only as a file path?

> Dat_path <- system.file("extdata", "sampleData_sce.rds", package = "mist")
> Dat_path
[1] "/home/lorikern/R-Libraries/R4.5-Bioc3.21/mist/extdata/sampleData_sce.rds"
> beta_sigma_list <- estiParamSingle(
    Dat_sce = Dat_path,
    Dat_name = "Methy_level_group1",
    ptime_name = "pseudotime"
)

Why not the object itself if it is loaded in R? In other words passing the SCE object itself to estiParamSingle and other functions?

Hi Ishep, sure I will add a file in 'inst/scripts', change it to taking SCE object directly, and push it for updates later. Thank you!

[dxd429]

Please also provide an inst/scripts directory that describes how the data in inst/extdata was generated. It can be code, pseudo-code, or text but should minimally list any source or licensing information.

I see you can take in a SummarizedExperiment object but only as a file path?

> Dat_path <- system.file("extdata", "sampleData_sce.rds", package = "mist")
> Dat_path
[1] "/home/lorikern/R-Libraries/R4.5-Bioc3.21/mist/extdata/sampleData_sce.rds"
> beta_sigma_list <- estiParamSingle(
    Dat_sce = Dat_path,
    Dat_name = "Methy_level_group1",
    ptime_name = "pseudotime"
)

Why not the object itself if it is loaded in R? In other words passing the SCE object itself to estiParamSingle and other functions?

Hi Ishep, I have addressed your comments, but it seems like I cannot push to the [email protected]:packages/mist.git yet.

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the
pre-review process. A build report will be posted shortly. Please
fix any ERROR and WARNING in the build report before a reviewer is
assigned or provide a justification on why you feel the ERROR or
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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 the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
ERROR before build products produced.

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/mist 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 the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.1.tar.gz

Links above active for 21 days.

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

[dxd429]

Hi @lshep, I fixed the error but do not have access to the Bioconductor repository:

[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
-ne
(base) Daoyus-MacBook-Pro-3:mist daoyuduan$ git remote -v
origin https://github.com/dxd429/mist (fetch)
origin https://github.com/dxd429/mist (push)
upstream [email protected]:packages/mist.git (fetch)
upstream [email protected]:packages/mist.git (push)

[lshep]

have you activated the BiocCredentials account and added an ssh-key for access?

[dxd429]

have you activated the BiocCredentials account and added an ssh-key for access?

I just tried, but it says "[email protected] is not associated with a maintainer of a Bioconductor package.". The email address in my description file is not correct but I already fixed in the GitHub Repository.

[lshep]

since the description is all we have to go on when submitting we created the account with [email protected]. I will delete this and create an account with the email above. I will let you know when to try again

[dxd429]

since the description is all we have to go on when submitting we created the account with [email protected]. I will delete this and create an account with the email above. I will let you know when to try again

Thank you so much! Please take your time.

[lshep]

We have created the new account. let us know if there are any further issues

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 6eb6f49b0079698e13fce022d8348b68c4ba580a

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/mist 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: 89ebd53b70622f82697920eeedd7f242c91b5f78

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/mist 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: 805816a07d41922ccebd4ff216c9e776711a374d

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.11.tar.gz

Links above active for 21 days.

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

[dxd429]

misc

• Remember tracking changes in the NEWS file (it's still at 0.99.0);
  this is also helpful during review (see here for guidance).
• Please consider implementing thorough unit tests; we strongly encourage them.
• Please provide URL and BugReports fields in DESCRIPTION.
• Since visualization is not essential to the packages analytical capabilities,
  I'd recommend placing ggplot2 (and other plotGene-specific dependencies) under
  Suggests:; see here for guidance on what/what not to depend on.

docs

• \dontrun{} should be removed from plotGene.R.
• We encourage the use of BiocStyle for formatting with html_document as rendering
  target; see here.
• To simplify installation instructions, one can use
  BiocManager::install("user/repo") to install from GitHub.
• Please provide source and provenance information for any example data, e.g.,
  ?small_sampleData_sce should open a help page. I can see that there's info under
  inst/scripts, so simply exposing a corresponding .man page should do the trick.

code

• Anywhere where message/warning()s are given, it'd be recommendable to expose
  a verbose=TRUE/FALSE argument that let's the user control printing to the console.
• I can see that BiocParallel is being used under the hood, but don't see
  how the user would know about/leverage parallelization capabilities. Please either
  explicitly document this, or (as many packages do), expose an BPPARAM argument
  (passed to bplapply) that let's users be aware of and control parallelization.
• One of the beauties of standardized data structures like SingleCellExperiment,
  is to have homotypic functions, i.e., input = output. For example, estiParamSingle
  returns a list of fixed length for every feature. Why not put this in the rowData,
  and return the input data as a SCE object again? Example below:

> data <- readRDS(system.file("extdata", 
+     "small_sampleData_sce.rds", 
+     package = "mist"))
> beta_sigma_list <- estiParamSingle(
+     Dat_sce = data,
+     Dat_name = "Methy_level_group1",
+     ptime_name = "pseudotime")
Pseudotime cleaning and normalization to [0, 1] completed.
Removal of genomic features with too many 0/1 values completed.
> rowData(data)$mist_pars <- do.call(rbind, beta_sigma_list)
> head(rowData(data)$mist_pars)
                     Beta_0       Beta_1      Beta_2      Beta_3
ENSMUSG00000000001 1.216481 -0.405602702  0.44646806  0.29288724
ENSMUSG00000000003 1.608948  1.656889618  1.85377836 -1.84281325
ENSMUSG00000000028 1.289076 -0.005897583  0.06094288  0.03824746
ENSMUSG00000000037 1.019306 -3.765516788 10.12709049 -3.47833929
ENSMUSG00000000049 1.017952 -0.106286707  0.08811738  0.09461149

• dmSingle() could then work on data, rather than beta_sigma_list,
  and again be homotypic, i.e., rowData(data)$mist_dm <- dm_results.
  Overall, this would enable a nice-ish workflow where the same input
  is input, updated, output, and eventually passed down to plotting:

sce <- estiParamSingle(sce)
sce <- dmSingle(sce)
plotGene(sce)

Hi Helena,

I addressed all your comments already, but now I got 1 warning about CMD check exceeding 10 mins, I wonder if it is a must to get rid of it?

Thank you!

[HelenaLC]

• Since ggplot2 is under Suggest: now, good practice would be to check for its availability upfront in plotGene(); see here for how to do this.
• There's a build/check report NOTE to please "Update R version dependency from 4.3.0 to 4.5.0".
• Unfortunately yes, it should take less than 10' (see here for guidelines) ...beware the Bioc build system is periodically building and checking 2k+ packages on multiple operating systems, hence there are per-package memory and time limits in place that should be respected.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e682f9b27c27d3192200d0279aa094001b3e219f

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.12.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/mist 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: 74bf7571e753df45048ebc70b4e7f764d322b312

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.13.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/mist 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: c8d6fe1fd98e7ed0562addd587064037e3518ee6

[HelenaLC]

Alright, the following is a wild guess/I am not sure, but:

• the report states ~100s for a couple examples, but these take ~10s when I run them locally
• you are hard-coding bplapply(..., BPPARAM=SnowWorkers()), which "chooses the number of workers"
• that might cause overly long computation (because job distribution comes with a lot of overhead, which isn't worth it when the data is small/fast to compute)
• whether or not this is the root of the issue, I'd suggest exposing a BPPARAM argument EVERYWHERE were it is being used so that users are in control of how to parallelize; e.g., SerialParam() might already be faster in the examples here

[dxd429]

Alright, the following is a wild guess/I am not sure, but:

• the report states ~100s for a couple examples, but these take ~10s when I run them locally
• you are hard-coding bplapply(..., BPPARAM=SnowWorkers()), which "chooses the number of workers"
• that might cause overly long computation (because job distribution comes with a lot of overhead, which isn't worth it when the data is small/fast to compute)
• whether or not this is the root of the issue, I'd suggest exposing a BPPARAM argument EVERYWHERE were it is being used so that users are in control of how to parallelize; e.g., SerialParam() might already be faster in the examples here

Hi Helena, thank you for taking your time for this! I already revised the function estiParamTwo() so it only uses bplapply once. It should reduce the computation time by a lot, but i have not gotten any results from my latest push (Maybe the server is not currently running now?).

[HelenaLC]

Did you git push upstream? Build report says v0.99.13, but your GitHub repo has v0.99.14.

[dxd429]

Did you git push upstream? Build report says v0.99.13, but your GitHub repo has v0.99.14.

I did, it is this push: "Received a valid push on git.bioconductor.org; starting a build for commit id: c8d6fe1fd98e7ed0562addd587064037e3518ee6
"

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.14.tar.gz

Links above active for 21 days.

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

[dxd429]

Did you git push upstream? Build report says v0.99.13, but your GitHub repo has v0.99.14.

Oh, it just returned the results, and it seems to be working fine now.

[HelenaLC]

Alright, good, we are below the time limit now. I'd still ask you to

• expose a BPPARAM argument anywhere where there are bplapply calls; otherwise parallelization is either not obvious to control, or uncontrollable, which isn't so nice.
• add @importFrom stats setNames in estiParamTwo.R to address an outstanding NOTE in the report.
• use ggplot2::aes in plotGene.R to address another NOTE.
• avoid sapply and use vapply instread; two instances (see report)
  ...apologies for the pedanticism, but it'd be nice to start off with as clean of a report as possible, as these tend to only worsen over time. Should be ready to accept with the next update!

[dxd429]

Alright, good, we are below the time limit now. I'd still ask you to

• expose a BPPARAM argument anywhere where there are bplapply calls; otherwise parallelization is either not obvious to control, or uncontrollable, which isn't so nice.
• add @importFrom stats setNames in estiParamTwo.R to address an outstanding NOTE in the report.
• use ggplot2::aes in plotGene.R to address another NOTE.
• avoid sapply and use vapply instread; two instances (see report)
  ...apologies for the pedanticism, but it'd be nice to start off with as clean of a report as possible, as these tend to only worsen over time. Should be ready to accept with the next update!

No worry! I appreciate the time you spent identifying these problems, and will make these changes.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 41130ad8e13235d9a8236e852e37c7b0e46e4bd3

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.15.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
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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: 8c26f4d0efecbfa2e638b488b172f74776efb6cc

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): mist_0.99.16.tar.gz

Links above active for 21 days.

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

[dxd429]

Alright, good, we are below the time limit now. I'd still ask you to

• expose a BPPARAM argument anywhere where there are bplapply calls; otherwise parallelization is either not obvious to control, or uncontrollable, which isn't so nice.
• add @importFrom stats setNames in estiParamTwo.R to address an outstanding NOTE in the report.
• use ggplot2::aes in plotGene.R to address another NOTE.
• avoid sapply and use vapply instread; two instances (see report)
  ...apologies for the pedanticism, but it'd be nice to start off with as clean of a report as possible, as these tend to only worsen over time. Should be ready to accept with the next update!

I think it is good now looking at the report.

[HelenaLC]

Super, thanks for all your efforts!

[bioc-issue-bot]

Your package has been accepted. It will be added to the
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[lshep]

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