@@ -4,9 +4,12 @@ Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

 Version: 2.29.2

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

-Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,

-            Laurent Gatto <laurent.gatto@uclouvain.be>,

-            Qiakng Kou <qkou@umail.iu.edu>

+Authors@R: c(

+    person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")),

+    person("Laurent", "Gatto", email="laurent.gatto@uclouvain.be", role=c("aut")),

+    person("Qiakng", "Kou", email="qkou@umail.iu.edu", role=c("aut")),

+    person("David","Rauh",email="drauh@ipb-halle.de", role=c("ctb"))

+    )

 Description: mzR provides a unified API to the common file formats and

         parsers available for mass spectrometry data. It comes with a

         wrapper for the ISB random access parser for mass spectrometry

@@ -8,16 +8,16 @@

 //   Cedars Sinai Medical Center, Los Angeles, California  90048

 // Copyright 2008 Vanderbilt University - Nashville, TN 37232

 //

-// Licensed under the Apache License, Version 2.0 (the "License"); 

-// you may not use this file except in compliance with the License. 

-// You may obtain a copy of the License at 

+// Licensed under the Apache License, Version 2.0 (the "License");

+// you may not use this file except in compliance with the License.

+// You may obtain a copy of the License at

 //

 // http://www.apache.org/licenses/LICENSE-2.0

 //

-// Unless required by applicable law or agreed to in writing, software 

-// distributed under the License is distributed on an "AS IS" BASIS, 

-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 

-// See the License for the specific language governing permissions and 

+// Unless required by applicable law or agreed to in writing, software

+// distributed under the License is distributed on an "AS IS" BASIS,

+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

+// See the License for the specific language governing permissions and

 // limitations under the License.

 //

@@ -94,20 +94,6 @@ extern "C"

         PULONG ReturnLength

         );

-    struct SYSTEM_HANDLE {

-        ULONG ProcessID;

-        BYTE HandleType;

-        BYTE Flags;

-        USHORT Handle;

-        PVOID Object;

-        ACCESS_MASK GrantedAccess;

-    };

-

-    struct SYSTEM_HANDLE_INFORMATION {

-        ULONG HandleCount;

-        SYSTEM_HANDLE Handles[1];

-    };

-

     enum SECTION_INHERIT

     {

         ViewShare = 1,

@@ -154,6 +140,11 @@ extern "C"

     PVOID GetLibraryProcAddress(PSTR LibraryName, PSTR ProcName) {

         return GetProcAddress(GetModuleHandleA(LibraryName), ProcName);

     }

+

+    typedef struct __PUBLIC_OBJECT_TYPE_INFORMATION {

+      UNICODE_STRING TypeName;

+      ULONG Reserved[22];

+    } PUBLIC_OBJECT_TYPE_INFORMATION, *PPUBLIC_OBJECT_TYPE_INFORMATION;

 }

     int GetFileHandleTypeNumber(SYSTEM_HANDLE_INFORMATION* handleInfos)

@@ -170,15 +161,15 @@ extern "C"

         }

         map<int, int> handlesPerType;

-        for (size_t i = 0; i < handleInfos->HandleCount; ++i)

+        for (size_t i = 0; i < handleInfos->Count; ++i)

         {

-            if (handleInfos->Handles[i].ProcessID != currentProcessId)

+            if (handleInfos->Handle[i].OwnerPid != currentProcessId)

                 continue;

-            if (handleInfos->Handles[i].HandleType < 20) // this is not the File string you're looking for

+            if (handleInfos->Handle[i].ObjectType < 20) // this is not the File string you're looking for

                 continue;

-            const auto handle = reinterpret_cast<HANDLE>(handleInfos->Handles[i].Handle);

+            const auto handle = reinterpret_cast<HANDLE>(handleInfos->Handle[i].HandleValue);

             ULONG size;

             auto queryResult = NtQueryObject(handle, ObjectTypeInformation, typeInfoBytes.data(), typeInfoBytes.size(), &size);

             if (queryResult == STATUS_INFO_LENGTH_MISMATCH)

@@ -193,14 +184,15 @@ extern "C"

                 const auto type = std::wstring(typeInfo->TypeName.Buffer, typeInfo->TypeName.Length / sizeof(WCHAR));

                 if (type == fileType)

                     //return handleInfos->Handles[i].HandleType;

-                    ++handlesPerType[handleInfos->Handles[i].HandleType];

+                    ++handlesPerType[handleInfos->Handle[i].ObjectType];

             }

         }

         if (handlesPerType.empty())

             return 0;

-        auto typeMode = std::max_element(handlesPerType.begin(), handlesPerType.end(), [](const auto& a, const auto& b) { return a.second < b.second; });

+        auto typeMode = std::max_element(handlesPerType.begin(),

+                                         handlesPerType.end(), [](const std::pair<const int, int> a, const std::pair<const int, int> b) { return a.second < b.second; });

         return typeMode->first;

     }

@@ -368,16 +360,16 @@ PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath,

     wchar_t szPath[260];

     // iterate over every handle and close file handles that match the filepath

-    for (DWORD i = 0; i < pInfo->HandleCount; i++)

+    for (DWORD i = 0; i < pInfo->Count; i++)

     {

-        auto& handleInfo = pInfo->Handles[i];

-        if (handleInfo.ProcessID != currentProcessId)

+        auto& handleInfo = pInfo->Handle[i];

+        if (handleInfo.OwnerPid != currentProcessId)

             continue;

-        if (handleInfo.HandleType == fileHandleType)

+        if (handleInfo.ObjectType == fileHandleType)

         {

             szPath[0] = '\0';

-            if (!GetFileNameFromHandle((HANDLE)handleInfo.Handle, szPath, 260))

+            if (!GetFileNameFromHandle((HANDLE)handleInfo.HandleValue, szPath, 260))

             {

                 /*char messageBuffer[256];

                 memset(messageBuffer, 0, 256);

@@ -390,7 +382,7 @@ PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath,

             wchar_t* handlePath = szPath;

             if (bal::iends_with(handlePath, wideFilepathWithoutRoot.c_str()))

             {

-                if (!CloseHandle((HANDLE)handleInfo.Handle))

+                if (!CloseHandle((HANDLE)handleInfo.HandleValue))

                     fprintf(stderr, "[force_close_handles_to_filepath()] Error closing file handle.\n");

                 //else

                 //    fprintf(stderr, "[force_close_handles_to_filepath()] Closed file handle: " + gcnew String(handlePath));

@@ -402,7 +394,7 @@ PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath,

             SIZE_T viewSize = 1;

             PVOID viewBase = NULL;

-            NTSTATUS status = NtMapViewOfSection((HANDLE)handleInfo.Handle, currentProcessHandle, &viewBase, 0, 0, NULL, &viewSize, ViewShare, 0, PAGE_READONLY);

+            NTSTATUS status = NtMapViewOfSection((HANDLE)handleInfo.HandleValue, currentProcessHandle, &viewBase, 0, 0, NULL, &viewSize, ViewShare, 0, PAGE_READONLY);

             if (!NT_SUCCESS(status))

                 continue;

@@ -418,7 +410,7 @@ PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath,

             if (!bal::iends_with(wstring(mappedFilename.data()), wideFilename))

                 continue;

-            if (!CloseHandle((HANDLE)handleInfo.Handle))

+            if (!CloseHandle((HANDLE)handleInfo.HandleValue))

                 fprintf(stderr, "[force_close_handles_to_filepath()] Error closing section handle.\n");

             //else

             //    fprintf(stderr, "[force_close_handles_to_filepath()] Closed section handle.\n");