dreamlet submission #2955

GabrielHoffman · 2023-03-16T00:54:27Z

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bioc-issue-bot · 2023-03-16T00:54:29Z

Hi @GabrielHoffman

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: dreamlet
Type: Package
Title: Cohort-scale differential expression analysis of single cell data using linear (mixed) models
Version: 0.99.0
Date: 2023-03-15
Authors@R: person("Gabriel", "Hoffman", role=c("aut", "cre"), email="gabriel.hoffman@mssm.edu")
Description: Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.
VignetteBuilder: knitr
License: Artistic-2.0
Encoding: UTF-8
URL: https://DiseaseNeurogenomics.github.io/dreamlet
BugReports: https://github.com/DiseaseNeurogenomics/dreamlet/issues
Suggests:
    BiocStyle,
    knitr,
    pander,
    rmarkdown,
    muscat,
    ExperimentHub,
    RUnit,
    scater,
    scuttle
biocViews: RNASeq,
    GeneExpression,
    DifferentialExpression,
    BatchEffect,
    QualityControl,
    Regression,
    GeneSetEnrichment,
    GeneRegulation,
    Epigenetics,
    FunctionalGenomics,
    Transcriptomics,
    Normalization,
    SingleCell,
    Preprocessing,
    Software
Depends:
    R (>= 4.2.0),
    ggplot2,
    variancePartition (>= 1.28.3)
Imports:
    edgeR,
    SummarizedExperiment,
    SingleCellExperiment,
    DelayedMatrixStats,
    sparseMatrixStats,
    MatrixGenerics,
    Matrix,
    methods,
    purrr,
    GSEABase,
    data.table,
    zenith (>= 0.99.13),
    mashr (>= 0.2.52),
    ashr,
    dplyr,
    BiocParallel,
    S4Vectors,
    IRanges,
    limma,
    tidyr,
    BiocGenerics,
    HDF5Array,
    DelayedArray,
    gtools,
    reshape2,
    ggrepel,
    scattermore,
    Rcpp,
    lme4,
    MASS,
    Rdpack,
    utils,
    stats
RoxygenNote: 7.2.3
RdMacros: Rdpack
SystemRequirements: C++11
LinkingTo: 
    Rcpp,
    beachmat

vjcitn · 2023-03-20T11:07:23Z

crumblr is referenced in vignettes but not declared in DESCRIPTION

vjcitn · 2023-03-20T11:11:21Z

and i can't find it. private repo?

vjcitn · 2023-03-20T11:11:44Z

it has to be in CRAN or bioconductor for dreamlet to go in. please advise.

GabrielHoffman · 2023-03-20T19:13:44Z

I have removed reference to this package in the latest push to GitHub (v0.99.1).

Reference to this package in the vignette had already been commented out, so a user would never have seen it. But now I removed it completely.

crumblr is a secondary package that I'm developing, but dreamlet does not depend on it.

vjcitn · 2023-03-20T20:00:12Z

Package .tar.gz is 11MB on my linux system. Sound right?

 dreamlet/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
  dreamlet/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
  dreamlet/docs/deps/bootstrap-5.1.3/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff

do you want the docs folder or should it be in .Rbuildignore?

vjcitn · 2023-03-20T20:09:13Z

https://arxiv.org/pdf/2012.02936.pdf discusses inference post-clustering. Does the package address this concern?

GabrielHoffman · 2023-03-20T20:28:42Z

The new version adds docs to . Rbuildignore, so tar.gz is now 4.4M on my Mac.
The Gao, et al. work is very interesting, but separate from the primary problem addressed here. Gao, et al. consider finding genes that are differentially expressed between two clusters. dreamlet does include this capability just for convenience, and I am well aware that the p-values are poorly calibrated.

But the primary goal of dreamlet it to identify genes differentially expressed within a single cluster, but across subjects based on a variable of interest (i.e. case/control status). I submitted my manuscript to biorxiv on Friday, but they didn't post it yet. I will link to it as soon at it's up.

Gabriel

GabrielHoffman · 2023-03-21T13:23:32Z

Preprint is now posted on biorxiv: https://doi.org/10.1101/2023.03.17.533005 and included in inst/CITATION

bioc-issue-bot · 2023-03-23T12:53:26Z

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bioc-issue-bot · 2023-03-23T13:19:04Z

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, 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. This link will be active
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Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2023-03-27T15:59:09Z

Received a valid push on git.bioconductor.org; starting a build for commit id: dd740b27e8aebb9d984e3f6ae537f40582c460f7

bioc-issue-bot · 2023-03-27T16:08:36Z

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: "ERROR, 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. This link will be active
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Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2023-03-27T18:38:59Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7

bioc-issue-bot · 2023-03-27T19:00:13Z

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: "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. 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
git@git.bioconductor.org:packages/dreamlet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2023-08-09T13:39:53Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9571bf5e08048a93dccecc24ee085410abf5ac4c

bioc-issue-bot · 2023-08-09T13:58:35Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build
System:
macOS 12.6.5 Monterey: dreamlet_0.99.24.tar.gz
Linux (Ubuntu 22.04.2 LTS): dreamlet_0.99.24.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/dreamlet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2023-08-09T14:06:58Z

Received a valid push on git.bioconductor.org; starting a build for commit id: e7bf5d9c7880c12ab8ed3f4c0c6613c48dd52536

bioc-issue-bot · 2023-08-09T14:25:52Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build
System:
macOS 12.6.5 Monterey: dreamlet_0.99.25.tar.gz
Linux (Ubuntu 22.04.2 LTS): dreamlet_0.99.25.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.

GabrielHoffman · 2023-08-09T14:29:07Z

I fixed all the issues I could. Can you check?

Note, I could not add sessionInfo() to vignettes/mashr.Rmd since this vignette is pre-processed in my machine since it takes too link to run on the BioC machines

Gabriel

bioc-issue-bot · 2023-08-22T00:38:20Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 71c3f7fec32e926270ada9aea40013cfe3c9a910

bioc-issue-bot · 2023-08-22T01:00:08Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): dreamlet_0.99.26.tar.gz
macOS 12.6.5 Monterey: dreamlet_0.99.26.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/dreamlet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

GabrielHoffman · 2023-08-22T20:18:32Z

My package passes most checks except for:

* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man pages.

but it doesn't tell me which function this is in. And I don't get this warning locally.

How can I resolve this?

lshep · 2023-08-23T11:27:01Z

If you run BiocCheck locally there will be a directory dreamlet.BiocCheck that will have a file that has a more detailed 00BiocCheck.log that give the exact file name/line numbers

bioc-issue-bot · 2023-08-23T13:01:50Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 9c0572b57a124faf3afb17f858a4e4bf4b8a8fa6

bioc-issue-bot · 2023-08-23T13:20:38Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build
System:
macOS 12.6.5 Monterey: dreamlet_0.99.27.tar.gz
Linux (Ubuntu 22.04.2 LTS): dreamlet_0.99.27.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/dreamlet to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2023-09-07T17:52:45Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 8acb0eb005aa6df971cbfd5320c766938336df59

bioc-issue-bot · 2023-09-07T18:11:45Z

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build
System:
macOS 12.6.5 Monterey: dreamlet_0.99.28.tar.gz
Linux (Ubuntu 22.04.2 LTS): dreamlet_0.99.28.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.

GabrielHoffman · 2023-09-07T18:15:29Z

Can you push this package to the next stage of Bioconductor approval?

Best,
Gabriel

jianhong · 2023-09-12T12:40:13Z

Package 'dreamlet' Review

Thank you for your patience during the review process. The package is intricate, and I truly appreciate the substantial effort you've invested in it. 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.

General package development

Important: Package files exceed the 5MB size limit.
The docs fold need to be removed, otherwise the package size fill exceed the 5MB size limit.

R code

Important: No paste in message(), message, stop
- In file R/misc.R:
  - at line 43 found ' stop("Variables in formula are not found in data:\n ", paste(v[!found], collapse = ", "))'
NOTE: Vectorize: for loops present, try to replace them by *apply funcitons.
- In file R/aggregateNonCountSignal.R:
  - at line 122 found ' for (i in seq(nrow(obj$weights))) {'
- In file R/aggregateToPseudoBulk.R:
  - at line 34 found ' for (i in seq_along(ys)) {'
  - at line 163 found ' for (i in by) {'
  - at line 197 found ' for (i in names(cd)) {'
  - at line 349 found ' for (i in seq_along(mat.out)) {'
- In file R/aggregateVar.R:
  - at line 100 found ' for (i in seq(nrow(obj$weights))) {'
- In file R/colsum2.R:
  - at line 60 found ' for (j in seq_len(grid_ncol)) {'
  - at line 98 found ' for (key in names(group)) {'
- In file R/dreamletCompareClusters.R:
  - at line 394 found ' for (i in seq(1, 100)) {'
- In file R/dropRedundantTerms.R:
  - at line 68 found ' for (x in excludeVar) {'
- In file R/removeConstantTerms.R:
  - at line 79 found ' for (x in excludeVar) {'
Important: Remove unused code. If you are not confident with the change, please try to add unit test for the changes.
- In file R/aggregateToPseudoBulk.R:
  - at line 35 found ' # message(i)'
- In file R/colsum2.R:
  - at line 16 found ' # grid <- DelayedArray:::normarg_grid(grid, x)'
  - at line 86 found ' # colsum(block, group2, reorder=FALSE, na.rm=na.rm)'
- In file R/dreamlet.R:
  - at line 829 found ' # if (!quiet) message("\n")'
- In file R/dropRedundantTerms.R:
  - at line 69 found ' # fterms_new = gsub(x, '1', fterms_new)'
  - at line 78 found ' # old: fterms_new = array(sapply(excludeVar, function(x) gsub(x, '1', fterms)))'
- In file R/plotHeatmap.R:
  - at line 117 found ' # bquote(log[2]~CPM)'
- In file R/processAssays.R:
  - at line 90 found ' # geneExpr <- tryCatch('
  - at line 91 found ' # voomWithDreamWeights(y[keep, ], formula, data, weights = w_cells, BPPARAM = BPPARAM, ..., save.plot = TRUE, quiet = quiet, span = span),'
  - at line 92 found ' # error = function(e) NULL'
  - at line 93 found ' # )'
- In file R/removeConstantTerms.R:
  - at line 80 found ' # old: fterms_new = gsub(x, '1', fterms_new)'
  - at line 89 found ' # old: fterms_new = array(sapply(excludeVar, function(x) gsub(x, '1', fterms)))'
- In file R/zenith_gsa.R:
NOTE: Avoid 'suppressWarnings'/'*Messages' if possible
- In file R/processAssays.R:
  - at line 71 found ' y <- suppressMessages(DGEList(y, remove.zeros = TRUE))'
  - at line 85 found ' keep <- suppressWarnings(filterByExpr(y, min.count = min.count, min.prop = min.prop))'
NOTE: Functional programming: code repetition.
- repetition in aggregateNonCountSignal and aggregateVar
  - in aggregateNonCountSignal
    - line 2: min.cells = 10, min.signal = 0.01, min.samples = 4, min.prop = 0.4,
    - line 3: verbose = TRUE, BPPARAM = SerialParam(progressbar = verbose))
    - line 4: {
    - line 5: pb <- aggregateToPseudoBulk(sce, assay = assay, cluster_id = cluster_id,
    - line 6: sample_id = sample_id, verbose = FALSE, fun = "mean",
    - line 7: BPPARAM = BPPARAM, checkValues = FALSE)
    - line 8: pb.sem <- aggregateToPseudoBulk(sce, assay = assay, cluster_id = cluster_id,
    - line 9: sample_id = sample_id, verbose = FALSE, fun = "sem",
    - line 10: BPPARAM = BPPARAM, checkValues = FALSE)
    - line 11: pb.number <- aggregateToPseudoBulk(sce, assay = assay,
    - line 12: cluster_id = cluster_id, sample_id = sample_id, verbose = FALSE,
    - line 13: fun = "number", BPPARAM = BPPARAM, checkValues = FALSE)
    - line 14: data_constant <- droplevels(as.data.frame(colData(pb)))
    - line 15: resList <- lapply(assayNames(pb), function(CT) {
    - line 18: number <- assay(pb.number, CT)
    - line 19: obj <- new("EList", list(E = as.matrix(signal), weights = as.matrix(w)))
    - line 20: include <- (number[1, ] >= min.cells)
    - line 21: obj <- obj[, include, drop = FALSE]
    - line 22: keep <- apply(obj$E, 1, function(x) {
    - line 23: sum(x >= min.signal) >= min.prop * length(x)
    - line 24: })
    - line 25: obj <- obj[keep, , drop = FALSE]
    - line 26: if (any(!is.finite(obj$weights))) {
    - line 27: for (i in seq(nrow(obj$weights))) {
    - line 28: if (any(!is.finite(obj$weights[i, ]))) {
    - line 29: idx <- which(!is.finite(obj$weights[i, ]))
    - line 30: if (length(idx) > 0) {
    - line 31: obj$weights[i, idx] <- max(obj$weights[i,
    - line 32: -idx])
    - line 33: }
    - line 34: }
    - line 35: }
    - line 36: }
    - line 37: if (ncol(obj) < min.samples) {
    - line 38: return(NULL)
    - line 39: }
    - line 40: obj
    - line 41: })
    - line 42: names(resList) <- assayNames(pb)
    - line 43: resList <- resList[!vapply(resList, is.null, FUN.VALUE = logical(1))]
    - line 44: new("dreamletProcessedData", resList, data = data_constant,
    - line 45: metadata = metadata(pb)$aggr_means, by = metadata(pb)$agg_pars$by)
  - in aggregateVar
    - line 2: min.var = 0.01, min.samples = 4, min.prop = 0.4, verbose = TRUE,
    - line 3: BPPARAM = SerialParam(progressbar = verbose))
    - line 4:{
    - line 5: pb.sem <- aggregateToPseudoBulk(sce, assay = assay, cluster_id = cluster_id,
    - line 6: sample_id = sample_id, verbose = FALSE, fun = "sem",
    - line 7: BPPARAM = BPPARAM, checkValues = FALSE)
    - line 8: pb.number <- aggregateToPseudoBulk(sce, assay = assay, cluster_id = cluster_id,
    - line 9: sample_id = sample_id, verbose = FALSE, fun = "number",
    - line 10: BPPARAM = BPPARAM, checkValues = FALSE)
    - line 11: data_constant <- droplevels(as.data.frame(colData(pb.sem)))
    - line 12: resList <- lapply(assayNames(pb.sem), function(CT) {
    - line 15: w <- 1/assay(pb.sem, CT)^2
    - line 16: obj <- new("EList", list(E = as.matrix(var), weights = as.matrix(w)))
    - line 17: include <- (number[1, ] >= min.cells)
    - line 18: obj <- obj[, include, drop = FALSE]
    - line 19: keep <- apply(obj$E, 1, function(x) {
    - line 20: sum(x >= min.var) >= min.prop * length(x)
    - line 21: })
    - line 22: obj <- obj[keep, , drop = FALSE]
    - line 23: if (any(!is.finite(obj$weights))) {
    - line 24: for (i in seq(nrow(obj$weights))) {
    - line 25: if (any(!is.finite(obj$weights[i, ]))) {
    - line 26: idx <- which(!is.finite(obj$weights[i, ]))
    - line 27: if (length(idx) > 0) {
    - line 28: obj$weights[i, idx] <- max(obj$weights[i,
    - line 29: -idx])
    - line 30: }
    - line 31: }
    - line 32: }
    - line 33: }
    - line 34: if (ncol(obj) < min.samples) {
    - line 35: return(NULL)
    - line 36: }
    - line 37: obj
    - line 38: })
    - line 39: names(resList) <- assayNames(pb.sem)
    - line 40: resList <- resList[!vapply(resList, is.null, FUN.VALUE = logical(1))]
    - line 41: new("dreamletProcessedData", resList, data = data_constant,
    - line 42: metadata = metadata(pb.sem)$aggr_means, by = c(cluster_id,
- repetition in dropRedundantTerms and removeConstantTerms
  - in dropRedundantTerms
    - line 1: data, tol = 0.001)
    - line 2:{
    - line 3: stopifnot(is(formula, "formula"))
    - line 4: stopifnot(is(data, "data.frame"))
    - line 5: data <- data[, colnames(data) %in% unique(all.vars(formula)),
    - line 6: drop = FALSE]
    - line 7: data <- droplevels(data)
    - line 8: checkFormula(formula, data)
    - line 9: trmf <- terms(formula)
    - line 10: intercept <- attr(trmf, "intercept")
    - line 11: fterms <- attr(trmf, "term.labels")
    - line 28: if (length(excludeVar) > 0) {
    - line 29: fterms_new <- fterms
    - line 30: for (x in excludeVar) {
    - line 31: fterms_new <- gsub(paste0(x, "$"), "1", fterms_new)
    - line 32: fterms_new <- gsub(paste0(x, "\)"), "1)", fterms_new)
    - line 33: }
    - line 34: fterms_new <- unique(fterms_new)
    - line 35: fterms_new <- fterms_new[fterms_new != ""]
    - line 36: fterms_new <- fterms_new[fterms_new != "1"]
    - line 37: }
    - line 38: else {
    - line 39: fterms_new <- fterms
    - line 40: }
    - line 41: exclude <- grep(":1|1:|\| 1", fterms_new)
    - line 42: if (length(exclude) > 0) {
    - line 43: fterms_new <- fterms_new[-exclude]
    - line 44: }
    - line 45: response <- all.vars(update.formula(formula, . ~ NULL))
    - line 46: if (attr(trmf, "response") == 0)
    - line 47: response <- NULL
    - line 48: if (length(fterms_new) > 0) {
    - line 49: form_new <- reformulate(fterms_new, response = response)
    - line 50: }
    - line 51: else {
    - line 52: form_new <- ~1
    - line 53: }
    - line 54: if (intercept == 0) {
    - line 55: form_new <- update.formula(form_new, ~. - 1)
    - line 56: }
    - line 57: environment(form_new) <- environment(formula)
    - line 58: form_new
  - in removeConstantTerms
    - line 1: data)
    - line 2:{
    - line 3: stopifnot(is(formula, "formula"))
    - line 4: stopifnot(is(data, "data.frame"))
    - line 5: data <- data[, colnames(data) %in% unique(all.vars(formula)),
    - line 6: drop = FALSE]
    - line 7: data <- droplevels(data)
    - line 8: checkFormula(formula, data)
    - line 9: trmf <- terms(formula)
    - line 10: intercept <- attr(trmf, "intercept")
    - line 11: fterms <- attr(trmf, "term.labels")
    - line 30: if (length(excludeVar) > 0) {
    - line 31: fterms_new <- fterms
    - line 32: for (x in excludeVar) {
    - line 33: fterms_new <- gsub(paste0(x, "$"), "1", fterms_new)
    - line 34: fterms_new <- gsub(paste0(x, "\)"), "1)", fterms_new)
    - line 35: }
    - line 36: fterms_new <- unique(fterms_new)
    - line 37: fterms_new <- fterms_new[fterms_new != ""]
    - line 38: }
    - line 39: else {
    - line 40: fterms_new <- fterms
    - line 41: }
    - line 42: exclude <- grep(":1|1:|\| 1", fterms_new)
    - line 43: if (length(exclude) > 0) {
    - line 44: fterms_new <- fterms_new[-exclude]
    - line 45: }
    - line 46: response <- all.vars(update.formula(formula, . ~ NULL))
    - line 47: if (attr(trmf, "response") == 0)
    - line 48: response <- NULL
    - line 49: if (length(fterms_new) > 0) {
    - line 50: form_new <- reformulate(fterms_new, response = response)
    - line 51: }
    - line 52: else {
    - line 53: form_new <- ~1
    - line 54: }
    - line 55: if (intercept == 0) {
    - line 56: form_new <- update.formula(form_new, ~. - 1)
    - line 57: }
    - line 58: environment(form_new) <- environment(formula)
    - line 59: form_new

Documentation

Important: remove unused file vignettes/mashr.Rmd.orig.

C and Fortran code

Important: remove unused code in the colsum_beachmat.cpp. You have test functions to validate the code.

Unit test

Important: remove unused code in the inst/unitTests/test\_pseudobulk.R
Important: move the library function to outside of the test\_functions. You may want to put all the library load into file tests/runTests.R

bioc-issue-bot · 2023-09-12T13:41:55Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 870d92718b3e8c929fdcae959581bea7386f7015

bioc-issue-bot · 2023-09-12T14:05:14Z

Dear Package contributor,

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Your package has been built on the Bioconductor Build System.

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 Bioconductor Build
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Linux (Ubuntu 22.04.2 LTS): dreamlet_0.99.29.tar.gz
macOS 12.6.5 Monterey: dreamlet_0.99.29.tar.gz

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GabrielHoffman · 2023-09-12T14:08:09Z

@jianhong I have addressed all the important issues. Confirm?

Gabriel

GabrielHoffman · 2023-09-18T19:42:24Z

@jianhong Following up to finalize this submission

Best,
Gabriel

bioc-issue-bot · 2023-09-18T19:59:28Z

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

lshep · 2023-09-21T13:15:23Z

The default branch of your GitHub repository has been added to Bioconductor's
git repository as branch devel.

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/GabrielHoffman.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

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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

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(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("dreamlet"). The package 'landing page' will be created at

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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 submitted and waiting clearance to access resources label Mar 16, 2023

vjcitn added the 3e. pending pre-review changes review has indicated blocking concern that needs attention label Mar 20, 2023

vjcitn added pre-check passed pre-review performed and ready to be added to git and removed 3e. pending pre-review changes review has indicated blocking concern that needs attention labels Mar 20, 2023

bioc-issue-bot assigned jianhong Mar 23, 2023

bioc-issue-bot added WARNINGS TIMEOUT labels Mar 23, 2023

bioc-issue-bot added ERROR and removed WARNINGS TIMEOUT labels Mar 27, 2023

bioc-issue-bot added WARNINGS and removed ERROR labels Mar 27, 2023

bioc-issue-bot added the ERROR label Aug 8, 2023

bioc-issue-bot added WARNINGS and removed ERROR labels Aug 9, 2023

LiNk-NY mentioned this issue Aug 16, 2023

include macros location when using Rdpack Bioconductor/BiocCheck#196

Closed

bioc-issue-bot added the OK label Aug 23, 2023

bioc-issue-bot removed the WARNINGS label Sep 7, 2023

jianhong added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Sep 18, 2023

lshep closed this as completed Sep 21, 2023

dreamlet submission #2955

dreamlet submission #2955

Comments

GabrielHoffman commented Mar 16, 2023

bioc-issue-bot commented Mar 16, 2023

vjcitn commented Mar 20, 2023 • edited

vjcitn commented Mar 20, 2023

vjcitn commented Mar 20, 2023

GabrielHoffman commented Mar 20, 2023

vjcitn commented Mar 20, 2023

vjcitn commented Mar 20, 2023

GabrielHoffman commented Mar 20, 2023

GabrielHoffman commented Mar 21, 2023

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GabrielHoffman commented Aug 9, 2023

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GabrielHoffman commented Aug 22, 2023

lshep commented Aug 23, 2023

bioc-issue-bot commented Aug 23, 2023

bioc-issue-bot commented Aug 23, 2023

bioc-issue-bot commented Sep 7, 2023

bioc-issue-bot commented Sep 7, 2023

GabrielHoffman commented Sep 7, 2023

jianhong commented Sep 12, 2023

Package 'dreamlet' Review

General package development

R code

Documentation

C and Fortran code

Unit test

bioc-issue-bot commented Sep 12, 2023

bioc-issue-bot commented Sep 12, 2023

GabrielHoffman commented Sep 12, 2023

GabrielHoffman commented Sep 18, 2023

bioc-issue-bot commented Sep 18, 2023

lshep commented Sep 21, 2023

vjcitn commented Mar 20, 2023 •

edited