lastfixes

NAMESPACE

@@ -567,7 +567,8 @@ importMethodsFrom("Spectra", "precursorMz")
 importMethodsFrom("Spectra", "$")
 importMethodsFrom("Spectra", "uniqueMsLevels")
 importMethodsFrom("Spectra", "backendBpparam")
-importFrom("Spectra", "MsBackendMemory", "dataStorageBasePath")
+importFrom("Spectra", "MsBackendMemory", "dataStorageBasePath",
+           "dataStorageBasePath<-")
 
 ## MsExperiment things
 importClassesFrom("MsExperiment", "MsExperiment")

R/PlainTextParam.R

@@ -169,7 +169,7 @@ setMethod("storeResults",
 setMethod("loadResults",
           signature(object = "MsExperiment",
                     param = "PlainTextParam"),
-          function(object, param, spectraFilePath){
+          function(object, param, spectraFilePath = character()){
               res <- .load_msexperiment(path = param@path,
                                         spectraFilePath = spectraFilePath)
               validObject(res)
@@ -183,8 +183,7 @@ setMethod("loadResults",
                     param = "PlainTextParam"),
           function(object, param, spectraFilePath){
               res <- callNextMethod()
-              res <- .load_xcmsexperiment(res, path = param@path,
-                                          spectraFilePath = spectraFilePath) # not sure if the spectraFilePath is necessary here
+              res <- .load_xcmsexperiment(res, path = param@path)
               validObject(res)
               res
           }
@@ -207,7 +206,6 @@ setMethod("loadResults",
     else stop("No \"sample_data.txt\" file found in ", path)
     fl <- file.path(path, "spectra_files.txt")
     if (file.exists(fl)){
-        spec <- spectra(fl)
         sf <- .import_spectra_files(fl, spectraFilePath = spectraFilePath)
         res <- readMsExperiment(spectraFiles = sf, sampleData = sd)
         fl <- file.path(path, "spectra_processing_queue.json")

R/RDataParam.R

@@ -84,11 +84,15 @@ setMethod("storeResults",
 setMethod("loadResults",
           signature(object = "XcmsExperiment",
                     param = "RDataParam"),
-          function(object, param, spectraFilePath){
-              res <- load(file = param@fileName)
+          function(object, param, spectraFilePath = character()){
+              env <- new.env()
+              load(file = param@fileName, envir = env)
+              res <- get(ls(env)[1], envir = env)
               if (!length(spectraFilePath) == 0 &&
-                  inherits(s@backend, "MsBackendMzR"))
+                  inherits(spectra(res)@backend, "MsBackendMzR")) {
                   dataStorageBasePath(spectra(res)) <- spectraFilePath
+              }
+
               res
           }
 )

tests/testthat/test_PlainTextParam.R

@@ -32,9 +32,8 @@ test_that("storeResults,PlainTextParam,XcmsExperiment works", {
     expect_true(file.exists(file.path(param@path, "feature_definitions.txt")))
     expect_true(file.exists(file.path(param@path, "feature_peak_index.txt")))
     pth = file.path(tempdir(), "test2")
-    param <- PlainTextParam(path = pth, spectraExport = FALSE)
+    param <- PlainTextParam(path = pth)
     storeResults(xmse_full, param = param)
-    expect_false(file.exists(file.path(param@path, "spectra_files.txt")))
 })
 
 test_that("loadResults, PlainTextParam works", {