Fix check-bioc.yml

.Rbuildignore

@@ -0,0 +1,5 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^\.travis\.yml$
+^LICENSE\.md$

.gitignore

@@ -1,5 +1,4 @@
 .RData
-.Rbuildignore
 .Rhistory
 .Rproj.user
 *.Rproj

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: RMassBank
 Title: Workflow to process tandem MS files and build MassBank records
-Version: 3.22.1
+Version: 3.22.2
 Authors@R: c(
     person("RMassBank at Eawag", , , "massbank@eawag.ch", role = "cre"),
     person("Michael A.", "Stravs", , "michael.stravs@eawag.ch", role = "aut",
@@ -27,7 +27,8 @@ Description: Workflow to process tandem MS files and build MassBank
     of compound information from Internet databases, and export to
     MassBank records.
 License: Artistic-2.0
-Depends:
+Depends: 
+    R (>= 4.1.0),
     Rcpp
 Imports:
     assertthat,
@@ -51,6 +52,7 @@ Imports:
     readr,
     rjson,
     S4Vectors,
+    stringr,
     tibble,
     tidyselect,
     webchem,
@@ -71,7 +73,7 @@ VignetteBuilder:
 biocViews: ImmunoOncology, Bioinformatics, MassSpectrometry, Metabolomics,
     Software
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 SystemRequirements: OpenBabel
 Collate: 
     'alternateAnalyze.R'

NAMESPACE

@@ -176,6 +176,7 @@ import(rcdk)
 import(readJDX)
 import(readr)
 import(rjson)
+import(stringr)
 import(tibble)
 import(yaml)
 importFrom(Biobase,"classVersion<-")

R/createMassBank.R

@@ -732,7 +732,7 @@ gatherData <- function(id)
 	# Get the api key from the settings
 	ccte_api_key = getOption("RMassBank")$settings$ccte_api_key
 
-	if(!is.null(api_key)) {
+	if(!is.null(ccte_api_key)) {
 	  dtxsid <- getDTXSID(key = inchikey_split, api_key = ccte_api_key)
 
 	  if(is.null(dtxsid)){

R/webAccess.R

@@ -791,7 +791,7 @@ getPcSDF <- function(query, from = "smiles"){
 #' Retrieves ChemSpider CSID from UK RSC for a search term.
 #'
 #' Requires a valid API key
-#' @usage getCSID(key, api_key)
+#' @usage getCSID(key, identifier, api_key)
 #' @param key ID to be converted
 #' @param identifier identifier (name, inchikey)
 #' @param api_key API key for ChemSpider (to be created on the developer site)
@@ -804,7 +804,7 @@ getPcSDF <- function(query, from = "smiles"){
 #' \url{https://developer.rsc.org/api-reference#}
 #' @examples
 #' \dontrun{
-#' getDTXSID(key = "MKXZASYAUGDDCJ-NJAFHUGGSA-N", identifier = "InChIKey", api_key = "your key")
+#' getDTXSID(key = "MKXZASYAUGDDCJ-NJAFHUGGSA-N", identifier = "InChIKey", api_key = "your RCS API key")
 #' }
 #' @export
 getCSID <- function(key, identifier, api_key)

R/zzz.R

@@ -1,56 +1,57 @@
-# Central import section
-
-#' @importFrom assertthat assert_that has_args
-#' @importFrom Biobase isVersioned isCurrent classVersion<- classVersion
-#' @importFrom ChemmineR smiles2sdf validSDF write.SDF
-#' @importFrom data.table fread fwrite
-#' @import digest
-#' @importFrom dplyr rename_with select
-#' @import glue
-#' @import httr
-#' @import httr2
-#' @import logger
-#' @importFrom methods setGeneric setMethod
-#' @import mzR
-#' @import rcdk
-#' @import Rcpp
-#' @import readJDX
-#' @import readr
-#' @import rjson
-#' @import S4Vectors
-#' @importFrom stats lm loess median predict smooth.spline
-#' @import tibble
-#' @importFrom tidyselect everything
-#' @importFrom utils URLencode capture.output data flush.console 
-#' @importFrom utils packageVersion read.csv read.csv2 setTxtProgressBar
-#' @importFrom utils str txtProgressBar type.convert write.csv write.table
-#' @importFrom utils globalVariables
-#' @importFrom webchem cir_query
-#' @import XML
-#' @import yaml
-
-
-.onLoad <- function(libname, pkgname) {
-  RMassBank.env <<- new.env()
-  RMassBank.env$ReadAnnotation <- FALSE
-  RMassBank.env$testnumber <- 1
-  ## new variables
-  RMassBank.env$verbose.output <- FALSE
-  RMassBank.env$export.invalid <- FALSE
-  RMassBank.env$export.molfiles <- TRUE
-  RMassBank.env$strictMsMsSpectraSelection <- FALSE
-
-  mb <- list()
-  attach(RMassBank.env)
-}
-
-utils::globalVariables(c("cpdID",
-                         "isotopes",
-                         "mzCalc",
-                         "...1",
-                         "occurrenceMatrix",
-                         "c.msmsWSspecs",
-                         "mass.calc",
-                         "updateObjectFromSlots"))
-
-
+# Central import section
+
+#' @importFrom assertthat assert_that has_args
+#' @importFrom Biobase isVersioned isCurrent classVersion<- classVersion
+#' @importFrom ChemmineR smiles2sdf validSDF write.SDF
+#' @importFrom data.table fread fwrite
+#' @import digest
+#' @importFrom dplyr rename_with select
+#' @import glue
+#' @import httr
+#' @import httr2
+#' @import logger
+#' @importFrom methods setGeneric setMethod
+#' @import mzR
+#' @import rcdk
+#' @import Rcpp
+#' @import readJDX
+#' @import readr
+#' @import rjson
+#' @import S4Vectors
+#' @importFrom stats lm loess median predict smooth.spline
+#' @import stringr
+#' @import tibble
+#' @importFrom tidyselect everything
+#' @importFrom utils URLencode capture.output data flush.console
+#' @importFrom utils packageVersion read.csv read.csv2 setTxtProgressBar
+#' @importFrom utils str txtProgressBar type.convert write.csv write.table
+#' @importFrom utils globalVariables
+#' @importFrom webchem cir_query
+#' @import XML
+#' @import yaml
+
+
+.onLoad <- function(libname, pkgname) {
+  RMassBank.env <<- new.env()
+  RMassBank.env$ReadAnnotation <- FALSE
+  RMassBank.env$testnumber <- 1
+  ## new variables
+  RMassBank.env$verbose.output <- FALSE
+  RMassBank.env$export.invalid <- FALSE
+  RMassBank.env$export.molfiles <- TRUE
+  RMassBank.env$strictMsMsSpectraSelection <- FALSE
+
+  mb <- list()
+  attach(RMassBank.env)
+}
+
+utils::globalVariables(c("cpdID",
+                         "isotopes",
+                         "mzCalc",
+                         "...1",
+                         "occurrenceMatrix",
+                         "c.msmsWSspecs",
+                         "mass.calc",
+                         "updateObjectFromSlots"))
+
+