cran-comments.md

In diegommcc/digitalDLSorteR_dev: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning

Test environments

• local Ubuntu 20.04, R 4.1.0
• local macOS BigSur 11.4, R 4.1.0
• win-builder (devel and release)
• macOS, Windows 10, and Ubuntu 20.04 (R release and devel) on Github Actions

R CMD check results

There were no ERRORs or WARNINGs. There was 1 NOTE:

• checking CRAN incoming feasibility ... NOTE Maintainer: ‘Diego Mañanes [e-mail]’

New submission

digitalDLSorteR 0.1.0 (2021-10-08)

Please do not start the description with "This package", package name,
title or similar.

Please add \value to .Rd files regarding exported methods and explain
the functions results in the documentation. Please write about the
structure of the output (class) and also what the output means. (If a
function does not return a value, please document that too, e.g.
\value{No return value, called for side effects} or similar)
Missing Rd-tags:
    barErrorPlot.Rd: \value
    barPlotCellTypes.Rd: \value
    blandAltmanLehPlot.Rd: \value
    corrExpPredPlot.Rd: \value
    installTFpython.Rd: \value
    plotTrainingHistory.Rd: \value
    preparingToSave.Rd: \value
    saveTrainedModelAsH5.Rd: \value

\dontrun{} should only be used if the example really cannot be executed
(e.g. because of missing additional software, missing API keys, ...) by
the user. That's why wrapping examples in \dontrun{} adds the comment
("# Not run:") as a warning for the user.
Does not seem necessary.

Please unwrap the examples if they are executable in < 5 sec, or replace
\dontrun{} with \donttest{}.

If you use a package which is only needed in examples, please list it in
'Suggests' and wrap these examples in if(requireNamespace("pkgname")){}
instead. However please omit the \dontrun{} warp around those examples.

Everything has been solved.

Problem with tests on SolarisOS:

Error in splatter::zinbEstimate(counts = ceiling(as.matrix(list.data[[1]])), BPPARAM = parallelEnv, design.samples = sdm, design.genes = gdm, O_mu = matrix(0, nrow = ncol(list.data[[1]]), ncol = nrow(list.data[[1]]), dimnames = list(rownames = seq(ncol(list.data[[1]])), colnames = rownames(list.data[[1]]))), O_pi = matrix(0, nrow = ncol(list.data[[1]]), ncol = nrow(list.data[[1]]), dimnames = list(rownames = seq(ncol(list.data[[1]])), colnames = rownames(list.data[[1]]))), beta_mu = matrix(0, nrow = sdm.ncol, ncol = nrow(list.data[[1]]), dimnames = list(rownames = sdm.colnames, colnames = rownames(list.data[[1]]))), beta_pi = matrix(0, nrow = sdm.ncol, ncol = nrow(list.data[[1]]), dimnames = list(rownames = sdm.colnames, colnames = rownames(list.data[[1]]))), alpha_mu = matrix(0, nrow = 0, ncol = nrow(list.data[[1]]), dimnames = list(rownames = NULL, colnames = rownames(list.data[[1]]))), alpha_pi = matrix(0, nrow = 0, ncol = nrow(list.data[[1]]), dimnames = list(rownames = NULL, colnames = rownames(list.data[[1]]))), verbose = verbose): object 'parallelEnv' not found

parellelEnv variable is now available on Solaris OS.

diegommcc/digitalDLSorteR_dev documentation built on Nov. 3, 2024, 3:56 a.m.