TomVuod commented 5 months ago

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xiaosaiyao commented 2 months ago

@jianhong the build report is successful. Do you mind looking over our response to your review? We are hoping to make it to the 3.19 release. Thank you!

TomVuod commented 2 months ago

Hello @lshep , can the package epiregulon.extra be proceeded? The status is still awaiting moderation and we would like it to be included in the upcoming release.

lshep commented 2 months ago

My apologies that this was overlooked. Yes I am processing it now. @jianhong once the build report posts, please also do a review of the secondary related package.

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xiaosaiyao commented 2 months ago

@jianhong the packages need to be accepted by April 24 for 3.19 release. Can we still make it?

jianhong commented 2 months ago

Package 'epiregulon' Review

The package passed check and build. It is almost there. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

[ ] Important: R version should be no less than 4.4. Update R version dependency from 4.2 to 4.4.0.
[ ] Important: Remove blank lines from DESCRIPTION.
[ ] NOTE: Makevars and Makefile not within a package when CPP version is lower than 0.11.0 or not restricted.
The NAMESPACE file
[ ] Important: Function names use camelCase or snake_case and do not include ..
- in line 8 export(aggregateAcrossCells.fast)

R code

[ ] Important: no <<-
- In file R/motif.R:
  - at line 89 found ' regulon[which(regulon$tf == tf), field_name] <<- motifs[match(regulon$idxATAC[which(regulon$tf == tf)],'
    Documentation
[ ] To avoid the '* NOTE: Consider adding runnable examples to man pages that document exported objects.' in BiocCheck, could you please add runnable examples to
- aggregateAcrossCells.fast.Rd

C and Fortran code

[ ] Important: Using stop() instead of std::runtime_error
- file src/aggregate_across_cells.cpp
  - line 13: throw std::runtime_error("expected a non-zero number of grouping factors");
  - line 20: throw std::runtime_error("each factor should have the same length as the number of columns");
- file src/fast_chisq.cpp
  - line 28: throw std::runtime_error("'peak_ordered' and 'tf_by_peak' should have the same length");
  - line 31: throw std::runtime_error("'peak_ordered' and 'target_by_peak' should have the same length");
  - line 34: throw std::runtime_error("'peak_ordered' and 'target_ordered' should have the same length");
  - line 50: throw std::runtime_error("'peak_ordered' should be in ascending order");
  - line 66: throw std::runtime_error("'target_ordered' should be in ascending order");
  - line 73: throw std::runtime_error("expession and peak matrices should have the same number of columns");
[ ] Note: try to avoid keyword auto unless it will increase the readability or the data type are not determined.
- file src/aggregate_across_cells.cpp
  - line 7: const auto& mat = converted->ptr;
  - line 27: auto combined = scran::AggregateAcrossCells::combine_factors(NC, gptrs, fptr);
  - line 33: const auto& current = combined.factors[f];
- file src/AggregateAcrossCells.h
  - line 36: for (auto curf : factors) {
  - line 59: auto current = indices[i];
  - line 61: for (auto curf : factors) {
  - line 88: auto output = combine_factors(n, std::move(factors), combined.data());
  - line 140: auto ext = tatami::consecutiveextractor<row, sparse_>(p, s, l, opt);
  - line 144: auto NC = p->ncol();
  - line 159: auto NC = p->ncol();
  - line 160: auto ext = tatami::consecutiveextractor<row, sparse_>(p, 0, NC, s, l, opt);
  - line 165: auto current = factor[x];
  - line 168: auto col = ext->fetch(x, vbuffer.data(), ibuffer.data());
  - line 170: auto& cursum = sums[current];
  - line 177: auto& curdetected = detected[current];
  - line 184: auto col = ext->fetch(x, vbuffer.data());
  - line 187: auto cursum = sums[current] + s;
  - line 194: auto curdetected = detected[current] + s;
- file src/fast_chisq.cpp
  - line 40: auto& current_start = peak_start[peak_ordered[i]];
  - line 41: auto& current_end = peak_end[peak_ordered[i]];
  - line 56: auto& current_start = target_start[target_ordered[i]];
  - line 57: auto& current_end = target_end[target_ordered[i]];
  - line 103: auto regstart = peak_start[index];
  - line 104: auto regend = peak_end[index];
  - line 121: auto regstart = target_start[index];
  - line 122: auto regend = target_end[index];
- file src/fast_wilcox.cpp
  - line 24: auto& less_than = work.less_than;
  - line 40: auto& equal0 = work.equal0;
  - line 42: auto& equal1 = work.equal1;
  - line 46: const auto& current = input[pos];
  - line 53: auto& equal = (okay[c] ? equal1 : equal0);
  - line 64: auto& equal = (self_okay ? equal1 : equal0);
  - line 119: for (auto c : clusters) {
  - line 189: auto col_u = output_auc.column(i);
  - line 190: auto output_auc_ptr = static_cast<double*>(col_u.begin());
  - line 191: auto col_tie = output_ties.column(i);
  - line 192: auto output_tie_ptr = static_cast<double*>(col_tie.begin());
  - line 197: for (const auto& ss : sortspace) {
  - line 206: for (auto x : okay_indices) {
  - line 220: for (const auto& ss : sortspace) {
  - line 238: auto col_t0 = output_t0.column(i);
  - line 241: auto col_t1 = output_t1.column(i);
  - line 247: for (auto o : okay_indices) {

LTLA commented 2 months ago

Rcpp will automatically convert throw's into the corresponding stops.
I think the usage of auto improves readability/simplifies maintenance in all cases mentioned above.

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bioc-issue-bot commented 2 months ago

Dear Package contributor,

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

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

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xiaosaiyao commented 2 months ago

@jianhong We have addressed your comments to the best of our ability. Please point by point reply below

Package 'epiregulon' Review

The package passed check and build. It is almost there. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

[x] Important: R version should be no less than 4.4. Update R version dependency from 4.2 to 4.4.0.

[x] Important: Remove blank lines from DESCRIPTION.

[ ] NOTE: Makevars and Makefile not within a package when CPP version is lower than 0.11.0 or not restricted.

The NAMESPACE file

[x] Important: Function names use camelCase or snake_case and do not include ..

in line 8 export(aggregateAcrossCells.fast)

R code

[x] Important: no <<-

In file R/motif.R:

at line 89 found ' regulon[which(regulon$tf == tf), field_name] <<- motifs[match(regulon$idxATAC[which(regulon$tf == tf)],'

Documentation

[x] To avoid the '* NOTE: Consider adding runnable examples to man pages that document exported objects.' in BiocCheck, could you please add runnable examples to

aggregateAcrossCells.fast.Rd

C and Fortran code

[ ] Important: Using stop() instead of std::runtime_error See Aaron's reply above

file src/aggregate_across_cells.cpp

line 13: throw std::runtime_error("expected a non-zero number of grouping factors");

line 20: throw std::runtime_error("each factor should have the same length as the number of columns");

file src/fast_chisq.cpp

line 28: throw std::runtime_error("'peak_ordered' and 'tf_by_peak' should have the same length");

line 31: throw std::runtime_error("'peak_ordered' and 'target_by_peak' should have the same length");

line 34: throw std::runtime_error("'peak_ordered' and 'target_ordered' should have the same length");

line 50: throw std::runtime_error("'peak_ordered' should be in ascending order");

line 66: throw std::runtime_error("'target_ordered' should be in ascending order");

line 73: throw std::runtime_error("expession and peak matrices should have the same number of columns");

[ ] Note: try to avoid keyword auto unless it will increase the readability or the data type are not determined. See Aaron's reply above

file src/aggregate_across_cells.cpp

line 7: const auto& mat = converted->ptr;

line 27: auto combined = scran::AggregateAcrossCells::combine_factors(NC, gptrs, fptr);

line 33: const auto& current = combined.factors[f];

file src/AggregateAcrossCells.h

line 36: for (auto curf : factors) {

line 59: auto current = indices[i];

line 61: for (auto curf : factors) {

line 88: auto output = combine_factors(n, std::move(factors), combined.data());

line 140: auto ext = tatami::consecutiveextractor<row, sparse_>(p, s, l, opt);

line 144: auto NC = p->ncol();

line 159: auto NC = p->ncol();

line 160: auto ext = tatami::consecutiveextractor<row, sparse_>(p, 0, NC, s, l, opt);

line 165: auto current = factor[x];

line 168: auto col = ext->fetch(x, vbuffer.data(), ibuffer.data());

line 170: auto& cursum = sums[current];

line 177: auto& curdetected = detected[current];

line 184: auto col = ext->fetch(x, vbuffer.data());

line 187: auto cursum = sums[current] + s;

line 194: auto curdetected = detected[current] + s;

file src/fast_chisq.cpp

line 40: auto& current_start = peak_start[peak_ordered[i]];

line 41: auto& current_end = peak_end[peak_ordered[i]];

line 56: auto& current_start = target_start[target_ordered[i]];

line 57: auto& current_end = target_end[target_ordered[i]];

line 103: auto regstart = peak_start[index];

line 104: auto regend = peak_end[index];

line 121: auto regstart = target_start[index];

line 122: auto regend = target_end[index];

file src/fast_wilcox.cpp

line 24: auto& less_than = work.less_than;

line 40: auto& equal0 = work.equal0;

line 42: auto& equal1 = work.equal1;

line 46: const auto& current = input[pos];

line 53: auto& equal = (okay[c] ? equal1 : equal0);

line 64: auto& equal = (self_okay ? equal1 : equal0);

line 119: for (auto c : clusters) {

line 189: auto col_u = output_auc.column(i);

line 190: auto output_auc_ptr = static_cast<double*>(col_u.begin());

line 191: auto col_tie = output_ties.column(i);

line 192: auto output_tie_ptr = static_cast<double*>(col_tie.begin());

line 197: for (const auto& ss : sortspace) {

line 206: for (auto x : okay_indices) {

line 220: for (const auto& ss : sortspace) {

line 238: auto col_t0 = output_t0.column(i);

line 241: auto col_t1 = output_t1.column(i);

line 247: for (auto o : okay_indices) {

bioc-issue-bot commented 2 months ago

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xiaosaiyao commented 2 months ago

@jianhong I just made some changes to our second package epiregulon.extra. It is a companion package that provides visualization and statistical tests. Ideally it should come out in the same release as epiregulon. Apologies for the late request. Do you think you could still review it in time for the 3.19 release?

bioc-issue-bot commented 2 months ago

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.

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jianhong commented 2 months ago

Thanks for the updates. I think about the discussion about the error handling part is complicate and may be out of my acknowledge to explain more how it will be affected in shared library. And sure this should not be an issue in your package.

bioc-issue-bot commented 2 months ago

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xiaosaiyao commented 2 months ago

@jianhong @lshep Thank you for accepting the main epiregulon package. Could you kindly advise the status of the second package epiregulon.extra? Is it accepted as well or it would require further changes?

jianhong commented 2 months ago

@xiaosaiyao @lshep Sorry, I will update the review for epiregulon.extra soon.

bioc-issue-bot commented 2 months ago

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

jianhong commented 2 months ago

Package 'epiregulon.extra' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The NAMESPACE file

[ ] Note: Selective imports using importFrom instead of import all with import.
- in line 23 import(SingleCellExperiment)
- in line 24 import(ggbeeswarm)
- in line 25 import(ggplot2)
- in line 26 import(igraph)

General package development

[ ] Important: Failure in test coverage for epiregulon.extra ── Failure ('test-visualization.R:20:3'): plotActivityViolin works correctly ─── Snapshot of testcase to 'visualization/violin-plot.svg' has changed Backtrace: ▆
1. └─vdiffr::expect_doppelganger(...) at test-visualization.R:20:3
2. ├─base::withCallingHandlers(...)
3. └─testthat::expect_snapshot_file(...)

R code

[ ] Important: aes_string() was deprecated in ggplot2 3.0.0. get.adjacency(), get.vertex.attribute(), and delete.vertices() was deprecated in igraph 2.0.0.
[ ] NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.
- In file R/graphs.R:
  - at line 412 found ' for (cluster in clusters) {'
- In file R/regulonSimilarities.R:
  - at line 55 found ' for (i in seq_along(all_tfs)) {'
  - at line 120 found ' for (iteration in seq_len(n)) {'
- In file R/visualization.R:
  - at line 452 found ' for (tf in names(regulon.split)) {'
  - at line 577 found ' for (cluster in unique(clusters)) {'
[ ] Important: Remove unused code.
- In file R/statisticalTests.R:
  - at line 123 found ' #print(da_genes)'
  - at line 129 found ' #print(top.list)'
[ ] NOTE: Avoid 'suppressWarnings'/'*Messages' if possible
- In file R/visualization.R:
  - at line 71 found ' suppressMessages(return(plotActivityDim_(sce,'
  - at line 239 found ' markers <- suppressMessages(getSigGenes(markers,'
  - at line 257 found ' df.plot <- suppressMessages(reshape2::melt(df.mean,'
    Documentation
[ ] Note: typos: WORD FOUND IN elment plotActivityDim.Rd:45 indciate enrichPlot.Rd:14 refering plotActivityDim.Rd:44,45 reprogam regulon.Rd:6,17

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: aec704abd39f6fe6fdb9fab5ecf233c2fd051618

bioc-issue-bot commented 2 months ago

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: "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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): epiregulon.extra_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 git@git.bioconductor.org:packages/epiregulon.extra to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

xiaosaiyao commented 2 months ago

Thank you @jianhong for reviewing the package so promptly. We have addressed your comments below. The build report throws an error on macOS because R on merida1 is still 4.3. Linux builds without error

Package 'epiregulon.extra' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The NAMESPACE file

[x] Note: Selective imports using importFrom instead of import all with import.

in line 23 import(SingleCellExperiment)

in line 24 import(ggbeeswarm)

in line 25 import(ggplot2)

in line 26 import(igraph)

General package development

[x] Important: Failure in test coverage for epiregulon.extra ── Failure ('test-visualization.R:20:3'): plotActivityViolin works correctly ─── Snapshot of testcase to 'visualization/violin-plot.svg' has changed Backtrace: ▆

└─vdiffr::expect_doppelganger(...) at test-visualization.R:20:3

├─base::withCallingHandlers(...)

└─testthat::expect_snapshot_file(...)

R code

[x] Important: aes_string() was deprecated in ggplot2 3.0.0. get.adjacency(), get.vertex.attribute(), and delete.vertices() was deprecated in igraph 2.0.0.

[x] NOTE: Vectorize: for loops present, try to replace them by *apply funcitons. We decide to leave for loops over clusters because the number of clusters is expected to be small. Moreover in for loop in regulonSimilarities.R:120 the output object of appropriate size is created in advance and is populated during loop execution, so the using of lapply would not improve performance. We vectorized two other for loops.

In file R/graphs.R:

at line 412 found ' for (cluster in clusters) {'

In file R/regulonSimilarities.R:

at line 55 found ' for (i in seq_along(all_tfs)) {'

at line 120 found ' for (iteration in seq_len(n)) {'

In file R/visualization.R:

at line 452 found ' for (tf in names(regulon.split)) {'

at line 577 found ' for (cluster in unique(clusters)) {'

[x] Important: Remove unused code.

In file R/statisticalTests.R:

at line 123 found ' #print(da_genes)'

at line 129 found ' #print(top.list)'

[ ] NOTE: Avoid 'suppressWarnings'/'*Messages' if possible
We would like to suppress unnecessary warnings

In file R/visualization.R:

at line 71 found ' suppressMessages(return(plotActivityDim_(sce,'

at line 239 found ' markers <- suppressMessages(getSigGenes(markers,'

at line 257 found ' df.plot <- suppressMessages(reshape2::melt(df.mean,'

Documentation

[x] Note: typos: WORD FOUND IN elment plotActivityDim.Rd:45 indciate enrichPlot.Rd:14 refering plotActivityDim.Rd:44,45 reprogam regulon.Rd:6,17

jianhong commented 2 months ago

It is almost there. Please update the news file.

TomVuod commented 2 months ago

Hello @jianhong , I have just pushed updated NEWS to the Bioconductor devel.

jianhong commented 2 months ago

Please also update the NEWS for epiregulon.extra and bump the version number.

TomVuod commented 2 months ago

It's done.

jianhong commented 2 months ago

Please push the change to git.bioconductor.org

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: bbee48b9bd542cf4a238df3a6e3d30fb4fc201ef

bioc-issue-bot commented 2 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1aa00b24a4c3334fe2bcddfcdb56b40a4179c7f4

Bioconductor / Contributions

epiregulon #3271

Package 'epiregulon' Review

The DESCRIPTION file

The NAMESPACE file

R code

Documentation

C and Fortran code

Package 'epiregulon' Review

The DESCRIPTION file

The NAMESPACE file

R code

Documentation

C and Fortran code

Package 'epiregulon.extra' Review

The NAMESPACE file

General package development

R code

Documentation

Package 'epiregulon.extra' Review

The NAMESPACE file

General package development

R code

Documentation