Updated description and import/export statements

DESCRIPTION

@@ -8,7 +8,9 @@ Maintainer: Karan Uppal <kuppal2@emory.edu>
 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

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,"%>%")

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")

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

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