try to resolve of the missing xsi namespace: Error in <globalEnvironment> -> snowfall_prallel_RPC_slave_node%&H00000000@172.17.0.3:41954 -> if_closure -> R_invoke$if_closure_internal -> "dasy_task"(&filepath, &workflow...)(&filepath, &workflow...)(&filepath, &workflow...) -> R_invoke$dasy_task -> "read_rawfile"(&file, "cache_enable" <- &opt_ca...)(&file, "cache_enable" <- &opt_ca...) -> R_invoke$read_rawfile -> R_invoke$else_branch_internal -> R_invoke$else_branch_internal -> "load_raw"(...)(...) -> R_invoke$load_raw -> "ms2_peaks"(...)(Call "open.mzpack"(&file)...) -> ms2_peaks -> "open.mzpack"(&file...)(&file...) -> open.mzpack

  1. Exception: class_name: scan, xml was dump at temp file: '/tmp/Rscript/error_xml_dump_58880b.xml', and previews of the invalid xml fragment: <?xml version="1.0" encoding="utf-16"?>

<scan num="204"
          scanType="Full"
          centroided="1"
          msLevel="2"
          peaksCount="0"
          polarity="+"
          retentionTime="PT18.313S"
          collisionEnergy="25"
          msInstrumentID="1">
      <precursorMz precursorScanNum="202" precursorIntensity="3132" activationMethod="CID">162.97729492</precursorMz>
      <peaks xsi:nil="true"
             compressionType="zlib"
             compressedLen="0"
             precision="64"
             byteOrder="network"
             contentType="m/z-int"></peaks>
</scan>

  2. InvalidOperationException: There is an error in XML document (13, 14).
  3. XmlException: 'xsi' is an undeclared prefix. Line 13, position 14.
  4. stackFrames:
   at Microsoft.VisualBasic.XmlExtensions.LoadFromXml(String xml, Type schema, Boolean throwEx, Boolean doNamespaceIgnorant, Type[] variants)
   at Microsoft.VisualBasic.Text.Xml.Linq.DeserializeHandler`1.LoadXml(String xml, Type[] variants)
   at Microsoft.VisualBasic.Text.Xml.Linq.Data.NodeInstanceBuilder[T](IEnumerable`1 nodes, String replaceXmlns, String xmlNode, Boolean ignoreError, Type[] variants)+MoveNext()
   at BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzXML.XML.LoadScans(String[] mzXML)+MoveNext()
   at BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache.ScanPopulator`1.PopulateValidScans(IEnumerable`1 scans)+MoveNext()
   at BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache.ScanPopulator`1.Load(IEnumerable`1 scans, Action`1 progress)+MoveNext()
   at System.Linq.Enumerable.<ToArray>g__EnumerableToArray|324_0[TSource](IEnumerable`1 source)
   at BioNovoGene.Analytical.MassSpectrometry.Assembly.Converter.LoadRawFileAuto(String xml, String tolerance, Double intocutoff, Action`1 progress, String prefer)
   at mzkit.MzWeb.openFromFile(String file, String prefer, Double da, Double noise_cutoff, Boolean verbose, Environment env)
   at mzkit.MzWeb.Open(Object file, Boolean verbose, Environment env)
   at System.RuntimeMethodHandle.InvokeMethod(ObjectHandleOnStack target, Void** arguments, ObjectHandleOnStack sig, BOOL isConstructor, ObjectHandleOnStack result)
   at System.RuntimeMethodHandle.InvokeMethod(ObjectHandleOnStack target, Void** arguments, ObjectHandleOnStack sig, BOOL isConstructor, ObjectHandleOnStack result)
   at System.Reflection.MethodBaseInvoker.InterpretedInvoke_Method(Object obj, IntPtr* args)
   at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span`1 copyOfArgs, BindingFlags invokeAttr)

   let ms2data as generic = Call "ms2_peaks"(Call "open.mzpack"(&file))
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

mzweb.R#_clr_interop::.open.mzpack at [mzkit, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null]:line &Hx0a04d799b
Daisy.call_function."open.mzpack"(&file...)(&file...) at rawfile.R:line 9
mzweb.R#_clr_interop::.ms2_peaks at [mzkit, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null]:line &Hx0becdc6ee
Daisy.call_function."ms2_peaks"(...)(Call "open.mzpack"(&file)...) at rawfile.R:line 9
Daisy.declare_function.R_invoke$load_raw at rawfile.R:line 7
Daisy.call_function."load_raw"(...)(...) at rawfile.R:line 25
unknown.unknown.R_invoke$else_branch_internal at n/a:line n/a
unknown.unknown.R_invoke$else_branch_internal at n/a:line n/a
Daisy.declare_function.R_invoke$read_rawfile at rawfile.R:line 5
Daisy.call_function."read_rawfile"(&file, "cache_enable" <- &opt_ca...)(&file, "cache_enable" <- &opt_ca...) at dasy_task.R:line 94
Daisy.declare_function.R_invoke$dasy_task at dasy_task.R:line 72
runSlaveNode.call_function."dasy_task"(&filepath, &workflow...)(&filepath, &workflow...)(&filepath, &workflow...) at daisy_parallel.R:line 34
unknown.unknown.R_invoke$if_closure_internal at n/a:line n/a
runSlaveNode.n/a.if_closure at daisy_parallel.R:line 25
unknown.unknown.snowfall_prallel_RPC_slave_node%&H00000000@172.17.0.3:41954 at n/a:line n/a
SMRUCC/R#.global.<globalEnvironment> at <globalEnvironment>:line n/a

Author: xieguigang

Microsoft.VisualBasic.Core/src/Text/Xml/Linq/DeserializeHandler.vb

@@ -118,7 +118,7 @@ Namespace Text.Xml.Linq
         ''' <returns></returns>
         Public Function LoadXml(xml As String, Optional variants As Type() = Nothing) As T
             Call sb.Clear()
-            Call sb.AppendLine("<?xml version=""1.0"" encoding=""utf-16""?>")
+            Call sb.AppendLine("<?xml version=""1.0"" encoding=""utf-16"" xmlns:xsi=""http://www.w3.org/2001/XMLSchema-instance""?>")
             Call sb.AppendLine(process(xml))
 
             If Not ReplaceXmlns.StringEmpty Then