scHiCcompare

[hamy12398]

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[bioc-issue-bot]

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]

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.

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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.

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]

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]

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

[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: "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]

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

[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: "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]

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]

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]

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]

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

[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: "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]

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

[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): 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]

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

[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): 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]

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

[PeteHaitch]

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