remove part of XML dep

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for Mass Spectrometry and Proteomics
-Version: 2.29.2
+Version: 2.29.3
 Description: MSnbase provides infrastructure for manipulation,
              processing and visualisation of mass spectrometry and
              proteomics data, ranging from raw to quantitative and
@@ -94,9 +94,9 @@ Imports:
     digest,
     lattice,
     ggplot2,
-    XML,
     scales,
     MASS,
+    XML,
     Rcpp
 Suggests:
     testthat,
@@ -170,7 +170,6 @@ Collate:
     'functions-addIdentificationData.R'
     'functions-mzR.R'
     'functions-plotting.R'
-    'header.R'
     'hmap.R'
     'iPQF.R'
     'iTRAQ4.R'

NAMESPACE

@@ -25,8 +25,7 @@ importFrom(MsCoreUtils, closest, rbindFill,
            impute_matrix, normalize_matrix,
            robustSummary, medianPolish,
            formatRt)
-importFrom(XML, xmlInternalTreeParse, getDefaultNamespace, xpathApply,
-           xmlAttrs)
+importFrom(XML, xmlParse, xpathSApply)
 importFrom(graphics, abline, axis, grid, legend, lines, points, text,
            barplot, layout, par, matplot, mtext)
 importFrom(stats, ave, median, medpolish, quantile, reorder, setNames,

NEWS.md

@@ -1,5 +1,9 @@
 # MSnbase 2.29
 
+## MSnbase 2.29.3
+
+- Remove XML dependency.
+
 ## MSnbase 2.29.2
 
 - Use fragmentation functions from PSMatch.

tests/testthat/test_MSnExp.R

@@ -377,14 +377,6 @@ test_that("phenoData<- on MSnExp works", {
     expect_equal(phenoData(im), pd_2)
 })
 
-test_that("injection time", {
-    f <- msdata::proteomics(full.names = TRUE,
-                            pattern = "MS3TMT10_01022016_32917-33481.mzML.gz")
-    it1 <- MSnbase:::injectionTimeFromFile1(f) ## in millisecs
-    it2 <- fData(readMSData(f, mode = "onDisk"))$injectionTime ## in millisecs
-    expect_equal(it1, it2)
-})
-
 test_that("chromatogram,MSnExp works", {
     inMem <- microtofq_in_mem_ms1
     ## Reduce here the tests. Most of the tests are performed in