scHiCcompare #3649

hamy12398 · 2024-11-06T23:45:28Z

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Repository: https://github.com/dozmorovlab/scHiCcompare

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bioc-issue-bot · 2024-11-06T23:45:31Z

Hi @hamy12398

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: scHiCcompare
Title: Differential Analysis of Single-cell Hi-C Data
Version: 0.99.0
Authors@R: c(
    person(given = "My", family = "Nguyen",
 email = "[email protected]",
 role = c("aut"),
 comment = c(ORCID = "0009-0003-1118-7085")),
    person(given = "Mikhail",
 family = "Dozmorov",
 role = c("aut", "cre"),
 email = "[email protected]",
 comment = c(ORCID = "0000-0002-0086-8358")))
Description: This package provides functions for differential chromatin interaction analysis 
    between two single-cell Hi-C data groups. It includes tools for imputation, normalization, 
    and differential analysis of chromatin interactions. The package implements pooling techniques 
    for imputation and offers methods to normalize and test for differential interactions across 
    single-cell Hi-C datasets.
Imports: 
    DT,
    data.table,
    dplyr,
    ggplot2,
    gtools,
    HiCcompare,
    lattice,
    mclust,
    mice,
    miceadds,
    rstatix,
    tidyr,
    gridExtra
Suggests: knitr,
    rmarkdown,
    testthat,
    BiocStyle
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
Depends: R (>= 4.2.0)
VignetteBuilder: knitr
biocViews: Software, SingleCell, HiC, Sequencing, Normalization
BugReports: https://github.com/dozmorovlab/ScHiCcompare/issues
URL: https://github.com/dozmorovlab/ScHiCcompare

bioc-issue-bot · 2024-11-25T15:48:31Z

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
WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting
up remotes to push to git.bioconductor.org. All changes should be
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version bump to git.bioconductor.org to trigger a new build report.

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bioc-issue-bot · 2024-11-25T15:57:29Z

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): scHiCcompare_0.99.0.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/scHiCcompare to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep · 2024-12-03T13:49:15Z

Please fix the ERROR and do a valid version bump to get a new build report before a reviewer will be assigned

bioc-issue-bot · 2024-12-11T19:13:35Z

Received a valid push on git.bioconductor.org; starting a build for commit id: ecbec6d826f3b4d4896cb4f87bae3155887e4a6c

bioc-issue-bot · 2024-12-11T19:30:04Z

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: "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.

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

bioc-issue-bot · 2024-12-22T08:26:14Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9abe068e23f8be33cd5f6107e53eacc1f4a168d5

bioc-issue-bot · 2024-12-22T08:42:44Z

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: "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.

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

hamy12398 · 2024-12-22T09:21:14Z

Hi @lshep,
My first report error is because I had extra file. To solve, I remove that file from my first push. As a result, I got the TIMEOUT problem when installing vignette. I have re-run and checked on my local laptop, but I did not have the TIMEOUT problem as the report. I wonder if there is a way I can check how my package looks like on Bioconductor environment. I am not too sure the cause of this problem.
Thank you so much.

lshep · 2024-12-23T13:56:36Z

I also just tried locally and killed it after 40 min!!! The package should be able to be build/checked in ideally under 15 min. Maybe a smaller dataset?

lshep · 2024-12-23T14:02:48Z

When I just did a Stangle to have just the R code to run manually, when I run manually it seems slow/stuck on the "fitting" step of scHiCcompare function call

> # scHiCcompare(file.path.1, file.path.2,
> #   select.chromosome, .... [TRUNCATED] 
Imputing Condition 1 group cells in: 
pooled band 1, 
pooled band 2, 
pooled band 3, 
pooled band 4, 
pooled band 5, 
pooled band 6, 
pooled band 7, 
pooled band 10, 
pooled band 11, 
pooled band 12, 
pooled band 8, 
pooled band 9, 

Imputing Condition 2 group cells in: 
pooled band 1, 
pooled band 2, 
pooled band 3, 
pooled band 4, 
pooled band 5, 
pooled band 6, 
pooled band 7, 
pooled band 8, 
pooled band 9, 
pooled band 10, 
pooled band 11, 
pooled band 12, 

Transfering into pseudo-bulk sparse matrix.

Transfering into pseudo-bulk sparse matrix.

Jointly normalizing pseudo bulk matrices 
Span for loess: 0.0399471795291325
GCV for loess: 0.00017267469496343
AIC for loess: -0.0149900024956055
`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

Processing detect differential chromotin interaction 
Span for loess: 0.0622079693724011
GCV for loess: 2.55798352175634e-05
AIC for loess: -1.94600566665868
Filtering out interactions with A < 1
fitting ...
  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |   0%

bioc-issue-bot · 2024-12-23T16:28:54Z

Received a valid push on git.bioconductor.org; starting a build for commit id: c8e6289d082d2e4ff05ba334cc0ef3969cb52b43

bioc-issue-bot · 2024-12-23T16:45:21Z

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: "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.

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

bioc-issue-bot · 2024-12-26T18:45:19Z

Received a valid push on git.bioconductor.org; starting a build for commit id: bd735d46945b15ef9d2aa18d2d6528da3a1913fc

bioc-issue-bot · 2024-12-26T18:51:14Z

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): scHiCcompare_0.99.4.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/scHiCcompare to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2024-12-26T22:18:29Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 6091b7d763f154ea3292239664f08499e19cb99c

bioc-issue-bot · 2024-12-26T22:25:46Z

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): scHiCcompare_0.99.5.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/scHiCcompare to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2025-01-02T12:40:26Z

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

PeteHaitch · 2025-01-02T22:47:12Z

Hi @hamy12398,

I've been assigned as reviewer for scHiCcompare.
I'll aim to provide my review within the next 3 weeks.

Before I get started, please remove scHiCcompare_0.99.3.tar.gz from the git repository; the git repo should only contain the source files and not the built package.
Please also consider and address the output of R CMD check and BiocCheck::BiocCheck() as you will be likely asked to do so in any subsequent review.

Cheers,
Pete

PeteHaitch · 2025-01-27T02:00:05Z

Hi @hamy12398,

Thank you for submitting scHiCcompare to Bioconductor.

I've completed my checklist review of scHiCcompare and overall the package is in good shape and close to being ready for acceptance.
My main suggestions are improvements to the vignette.

A general question I had was around the input format ("five-column tab-separated text files in a sparse matrix format").
I don't work with HiC data, but I wondered if this is a de facto standard format or if there are other input formats that should be considered?

In my checklist review below I have separated the issues into Required and Recommended points that I would ask you to address before the package can be accepted.
Would you please provide line-by-line comments to my initial review so that I know what changes I'm looking for in my re-review.

Cheers,
Pete

Required

Why is the return class of scHiCcompare() a checkNumbers object rather than, say, a simple list? In fact, the 'Value' section of the ?scHiCcompare man page states that the returned object is a list and doesn't mention checkNumbers. I didn't find any documentation of the checkNumbers class, which is required if you are introducing a new (user-facing) class.
The BP_param argument of scHiC_bulk_compare() and scHiCcompare() should be named BPPARAM for consistency with other BiocParallel-backed functions in Bioconductor.
Use an informative name for the vignette rather than 'preciseTAD'. This title is what the user sees when searching for the vignette with browseVignettes().
Your citation file is empty and incorrectly named. Please fix. It should work when readCitationFile('inst/CITATION') is run; see https://contributions.bioconductor.org/citation.html.
The 'Usage' section of the documentation is different for the 3 data files; why?
I think the example data directories inst/MGs_example and inst/ODCs_example should be inst/extdata/MGs_example and inst/extata/ODCs_example, respectively; see https://contributions.bioconductor.org/data.html?q=data#raw-data-and-the-instextdata-directory.
R CMD check complains of a few things via NOTES (see below) that should be addressed:
- usethis::use_mit_license() will address License stub is invalid DCF.
- R CMD check tells you how to fix some of the 'no visible global function definition for XXX' issues. However, others are related to the use of dplyr, tidyr or data.table and can be addressed via utils::globalVariables() or an alternative described in https://r-pkgs.org/package-within.html#echo-a-working-package.

$ R_ENVIRON_USER=~/.Renviron.bioc R CMD check scHiCcompare_0.99.5.tar.gz 
<snip>
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.txt
Most likely ‘inst/CITATION’ should be used instead.
* checking R code for possible problems ... NOTE
.all_progressive_pooling: no visible global function definition for
  ‘tail’
.randomize_IFs: no visible global function definition for ‘rnorm’
GMM_layer: no visible global function definition for ‘shapiro.test’
RF_impute.outrm.schic: no visible global function definition for
  ‘boxplot.stats’
RF_impute.outrm.schic: no visible global function definition for
  ‘na.omit’
RF_impute.outrm.schic: no visible global function definition for
  ‘aggregate’
RF_impute.outrm.schic: no visible binding for global variable
  ‘Single_cell’
RF_impute.outrm.schic: no visible binding for global variable ‘IF’
RF_process: no visible global function definition for ‘boxplot.stats’
RF_process: no visible global function definition for ‘na.omit’
RF_process: no visible global function definition for ‘aggregate’
RF_process: no visible binding for global variable ‘Single_cell’
RF_process: no visible binding for global variable ‘IF’
best_A: no visible global function definition for ‘is’
best_A: no visible global function definition for ‘quantile’
differential_result_plot: no visible binding for global variable
  ‘adj.M’
differential_result_plot: no visible binding for global variable ‘D’
differential_result_plot: no visible binding for global variable
  ‘Difference.cluster’
find.collinear: no visible global function definition for ‘cor’
mice.rf_impute: no visible global function definition for ‘quantile’
mice.rf_impute: no visible global function definition for ‘IQR’
mice.rf_impute: no visible global function definition for ‘na.omit’
mice.rf_impute: no visible global function definition for ‘aggregate’
plot_HiCmatrix_heatmap: no visible global function definition for
  ‘colorRampPalette’
plot_imputed_distance_diagnostic: no visible binding for global
  variable ‘IF’
plot_imputed_distance_diagnostic: no visible binding for global
  variable ‘Group’
pools_impute : process_pool: no visible global function definition for
  ‘na.omit’
pools_impute : process_pool: no visible binding for global variable
  ‘Single_cell’
pools_impute : process_pool: no visible binding for global variable
  ‘IF’
print.checkNumbers: no visible global function definition for ‘na.omit’
read_files: no visible global function definition for ‘read.delim’
scHiC_bulk_compare: no visible global function definition for ‘bpparam’
scHiCcompare: no visible global function definition for ‘bpparam’
scHiCcompare: no visible binding for global variable ‘cell_id’
scHiCcompare: no visible binding for global variable ‘region1’
scHiCcompare: no visible binding for global variable ‘region2’
scHiCcompare: no visible binding for global variable ‘IF’
scHiCcompare : <anonymous>: no visible global function definition for
  ‘write.table’
scHiCcompare: no visible global function definition for ‘write.table’
scHiCcompare_impute: no visible global function definition for
  ‘boxplot’
scHiCcompare_impute: no visible binding for global variable
  ‘Single_cell’
scHiCcompare_impute: no visible binding for global variable ‘IF’
withoutNorm_hicTable: no visible global function definition for ‘:=’
withoutNorm_hicTable: no visible binding for global variable ‘A’
Undefined global functions or variables:
  := A D Difference.cluster Group IF IQR Single_cell adj.M aggregate
  boxplot boxplot.stats bpparam cell_id colorRampPalette cor is na.omit
  quantile read.delim region1 region2 rnorm shapiro.test tail
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "colorRampPalette")
  importFrom("graphics", "boxplot")
  importFrom("methods", "is")
  importFrom("stats", "D", "IQR", "aggregate", "cor", "na.omit",
             "quantile", "rnorm", "shapiro.test")
  importFrom("utils", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
</snip>

BiocCheck::BiocCheck() similarly reports some issues. Some are recommendations about coding style and removing redundancy, and I encourage you to consider these points and the advice offered, but for the following specific points I ask you to follow the advice or explain why you haven't:
- NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
- NOTE: Avoid 'suppressWarnings'/'*Messages' if possible

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scHiCcompare #3649

scHiCcompare #3649

hamy12398 commented Nov 6, 2024

bioc-issue-bot commented Nov 6, 2024

bioc-issue-bot commented Nov 25, 2024

bioc-issue-bot commented Nov 25, 2024

lshep commented Dec 3, 2024

bioc-issue-bot commented Dec 11, 2024

bioc-issue-bot commented Dec 11, 2024

bioc-issue-bot commented Dec 22, 2024

bioc-issue-bot commented Dec 22, 2024

hamy12398 commented Dec 22, 2024

lshep commented Dec 23, 2024

lshep commented Dec 23, 2024

bioc-issue-bot commented Dec 23, 2024

bioc-issue-bot commented Dec 23, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Jan 2, 2025

PeteHaitch commented Jan 2, 2025 •

edited

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PeteHaitch commented Jan 27, 2025

PeteHaitch commented Jan 30, 2025

scHiCcompare #3649

scHiCcompare #3649

Comments

hamy12398 commented Nov 6, 2024

bioc-issue-bot commented Nov 6, 2024

bioc-issue-bot commented Nov 25, 2024

bioc-issue-bot commented Nov 25, 2024

lshep commented Dec 3, 2024

bioc-issue-bot commented Dec 11, 2024

bioc-issue-bot commented Dec 11, 2024

bioc-issue-bot commented Dec 22, 2024

bioc-issue-bot commented Dec 22, 2024

hamy12398 commented Dec 22, 2024

lshep commented Dec 23, 2024

lshep commented Dec 23, 2024

bioc-issue-bot commented Dec 23, 2024

bioc-issue-bot commented Dec 23, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Dec 26, 2024

bioc-issue-bot commented Jan 2, 2025

PeteHaitch commented Jan 2, 2025 • edited Loading

PeteHaitch commented Jan 27, 2025

Required

Recommended

PeteHaitch commented Jan 30, 2025

PeteHaitch commented Jan 2, 2025 •

edited

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