diff --git a/DESCRIPTION b/DESCRIPTION index 8bc12f9..2f6921d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,7 +8,9 @@ Maintainer: Karan Uppal Description: xMSannotator includes functions for metabolite annotation using HMDB, KEGG, LipidMaps, T3DB, and ChemSpider. The package also includes utilites for querying KEGG using the REST interface. License: GPL2.0 LazyLoad: no +Depends: R (>= 3.5.0) Imports: + methods, XML, R2HTML, WGCNA, @@ -28,10 +30,11 @@ Imports: limma, tidyr, foreach, - magrittr, - dataCompareR + magrittr Suggests: covr, - testthat (>= 3.0.0) + testthat (>= 3.0.0), + dataCompareR, + patrick Config/testthat/edition: 3 RoxygenNote: 7.1.1 diff --git a/NAMESPACE b/NAMESPACE index 1210fb5..783d9d3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -20,16 +20,24 @@ export(group_by_rt_histv2) export(multilevelannotation) export(multilevelannotationstep2) export(overlapmzchild) +export(remove_water_adducts) export(replace_with_module) import(WGCNA) import(dplyr) import(dynamicTreeCut) import(flashClust) +import(methods) import(plyr) import(snow) import(tidyr) +import(utils) importFrom(Rdisop,getMolecule) importFrom(foreach,"%do%") importFrom(foreach,"%dopar%") importFrom(foreach,foreach) +importFrom(grDevices,dev.off) +importFrom(grDevices,pdf) +importFrom(graphics,hist) +importFrom(graphics,par) +importFrom(graphics,plot) importFrom(magrittr,"%>%") diff --git a/R/get_chemscorev1.6.71.R b/R/get_chemscorev1.6.71.R index 24d5f1b..ed66299 100644 --- a/R/get_chemscorev1.6.71.R +++ b/R/get_chemscorev1.6.71.R @@ -148,6 +148,7 @@ compute_score <- function(adduct_weights, cur_adducts_with_isotopes) { return(score[1]) } +#' @export remove_water_adducts <- function(curformula, mchemicaldata) { numoxygen <- check_element(curformula, "O") water_adducts <- c("M+H-H2O", "M+H-2H2O", "M-H2O-H") diff --git a/R/multilevelannotation.R b/R/multilevelannotation.R index 8f062c4..6cdb73c 100644 --- a/R/multilevelannotation.R +++ b/R/multilevelannotation.R @@ -47,6 +47,10 @@ call_multilevelannotationstep2 <- function(arg1, } } +#' @import utils +#' @import methods +#' @importFrom graphics hist par plot +#' @importFrom grDevices dev.off pdf #' @import flashClust #' @import dynamicTreeCut #' @import WGCNA diff --git a/conda/environment-dev.yml b/conda/environment-dev.yml index 9a12307..3b30080 100644 --- a/conda/environment-dev.yml +++ b/conda/environment-dev.yml @@ -5,7 +5,7 @@ channels: - defaults - r dependencies: - - r-base + - r-base >=3.5.0 - boost-cpp - r-biocmanager - r-rsqlite