From 21267fef74ca2d12acdaf4569e38d0e1e0080f60 Mon Sep 17 00:00:00 2001 From: Alec Wysoker Date: Thu, 14 Mar 2024 13:41:49 -0400 Subject: [PATCH] Change from Imports to Suggests --- src/R/packages/DropSeq.dropulation/DESCRIPTION | 3 ++- src/R/packages/DropSeq.dropulation/NAMESPACE | 1 - .../DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R | 3 ++- src/R/packages/DropSeq.dropulation/README.md | 4 ++++ 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/src/R/packages/DropSeq.dropulation/DESCRIPTION b/src/R/packages/DropSeq.dropulation/DESCRIPTION index 25b1194d..5ae86704 100644 --- a/src/R/packages/DropSeq.dropulation/DESCRIPTION +++ b/src/R/packages/DropSeq.dropulation/DESCRIPTION @@ -4,7 +4,8 @@ Title: Tools for analyzing Dropulation data Version: 3.0.0 Date: 2024-03-13 Imports: graphics, utils, stats, data.table,RColorBrewer,vegan, gridExtra, - ggplot2,ggrepel,purrr,stringr,scales,DropSeq.utilities + ggplot2,ggrepel,purrr,stringr,scales +Suggests: DropSeq.utilities Remotes: github::broadinstitute/Drop-seq/src/R/packages/DropSeq.utilities Author: Jim Nemesh Maintainer: McCarroll Lab diff --git a/src/R/packages/DropSeq.dropulation/NAMESPACE b/src/R/packages/DropSeq.dropulation/NAMESPACE index 69068461..6d870db2 100644 --- a/src/R/packages/DropSeq.dropulation/NAMESPACE +++ b/src/R/packages/DropSeq.dropulation/NAMESPACE @@ -4,7 +4,6 @@ export(censusSeqQC) export(donorAssignmentQC) export(estimateDoubletRatePoissonDistribution) export(estimateEmptyCount) -import(DropSeq.utilities) import(RColorBrewer) import(data.table) import(ggplot2) diff --git a/src/R/packages/DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R b/src/R/packages/DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R index 210af8e8..54e00359 100644 --- a/src/R/packages/DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R +++ b/src/R/packages/DropSeq.dropulation/R/DonorAssignmentStandardAnalysis.R @@ -602,7 +602,8 @@ writeSummaryStats<-function (summaryStats, outSummaryStatsFile) { #' @param outCellBarcodesFile cell barcodes for donors in the experiment (optional) #' @param anonymizeDonors If set to true, donor IDs are changed to DONOR_1, DONOR_2, etc. Purely for sharing #' visualizations of not-yet-public data. -#' @import grDevices graphics utils stats data.table RColorBrewer DropSeq.utilities vegan +#' @import grDevices graphics utils stats data.table RColorBrewer vegan +#' @suggest DropSeq.utilities #' @export donorAssignmentQC<-function (expName="", likelihoodSummaryFile, doubletLikelihoodFile, dgeSummaryFile=NULL, dgeRawSummaryFile=NULL, readsPerCellFile=NULL, censusFile=NULL, expectedSamplesFile, outFileLikelyDonors=NULL, outDonorToCellMap=NULL, outPDF=NULL, diff --git a/src/R/packages/DropSeq.dropulation/README.md b/src/R/packages/DropSeq.dropulation/README.md index 4486f9f5..d9cd38bc 100644 --- a/src/R/packages/DropSeq.dropulation/README.md +++ b/src/R/packages/DropSeq.dropulation/README.md @@ -19,3 +19,7 @@ It is not recommended to install the latest version of DropSeq.dropulation from # install.packages("devtools") devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.dropulation") ``` + +Note that dependent package DropSeq.utilities is Suggests: rather than Imports: in order +to make it less likely that a user will install a possibly-unstable version of that package +rather than a released version. \ No newline at end of file