[vcpkg baseline] Fix baseline errors (#12067)

Co-authored-by: Billy Robert O'Neal III <bion@microsoft.com>

ports/apr/CONTROL

@@ -1,5 +1,5 @@
 Source: apr
-Version: 1.7.0
+Version: 1.7.0-1
 Homepage: https://apr.apache.org/
 Description: The Apache Portable Runtime (APR) is a C library that forms a system portability layer that covers many operating systems.
 Supports: !uwp

ports/apr/portfile.cmake

@@ -76,6 +76,13 @@ else()
 
     vcpkg_install_make()
 
+    vcpkg_replace_string(${CURRENT_PACKAGES_DIR}/debug/lib/pkgconfig/apr-1.pc
+        "-lapr-\${APR_MAJOR_VERSION}" "-lapr-1"
+    )
+    vcpkg_replace_string(${CURRENT_PACKAGES_DIR}/lib/pkgconfig/apr-1.pc
+        "-lapr-\${APR_MAJOR_VERSION}" "-lapr-1"
+    )
+    vcpkg_fixup_pkgconfig(SYSTEM_LIBRARIES pthread rt dl)
 endif()
 
 # Handle copyright

ports/paraview/CONTROL

@@ -1,5 +1,5 @@
 Source: paraview
-Version: 5.8.0
+Version: 5.8.0-1
 Homepage: https://www.paraview.org/
 Description: VTK-based Data Analysis and Visualization Application
 Build-Depends: vtk[core,paraview], protobuf, cgns, boost-core, boost-format, boost-algorithm

ports/paraview/fix-using-hdf5.patch

@@ -0,0 +1,105 @@
+diff --git a/databases/readers/M3DC1/avtM3DC1FileFormat.C b/databases/readers/M3DC1/avtM3DC1FileFormat.C
+index 642be7e..d044b87 100644
+--- a/databases/readers/M3DC1/avtM3DC1FileFormat.C
++++ b/databases/readers/M3DC1/avtM3DC1FileFormat.C
+@@ -2051,10 +2051,10 @@ avtM3DC1FileFormat::linkIterator(hid_t locId, const char* name,
+   switch (linfo->type) {
+     case H5L_TYPE_HARD: {
+ 
+-      H5O_info_t objinfo;
++      H5O_info1_t objinfo;
+ 
+       /* Stat the object */
+-      if(H5Oget_info_by_name(locId, name, &objinfo, H5P_DEFAULT) < 0) {
++      if(H5Oget_info_by_name1(locId, name, &objinfo, H5P_DEFAULT) < 0) {
+         debug5 << "visitLinks() - unable to open object with name " <<name <<std::endl;
+         debug5 << "visitLinks() - this object and all children will be dropped." <<std::endl;
+         return 0;
+@@ -2103,7 +2103,7 @@ avtM3DC1FileFormat::linkIterator(hid_t locId, const char* name,
+       targbuf = NULL;
+       
+       // Get info of the linked object.
+-      H5O_info_t objinfo;
++      H5O_info1_t objinfo;
+       hid_t obj_id = H5Oopen(locId, name, H5P_DEFAULT);
+       
+       if (obj_id < 0) {
+@@ -2113,7 +2113,7 @@ avtM3DC1FileFormat::linkIterator(hid_t locId, const char* name,
+       }
+ 
+       //Test-open the linked object
+-      if (H5Oget_info (obj_id, &objinfo) < 0) {
++      if (H5Oget_info1(obj_id, &objinfo) < 0) {
+         debug5 << "visitLinks() - unable to open external object " <<name <<std::endl;
+         debug5 << "visitLinks() - this object and all children will be dropped." <<std::endl;
+         return 0;
+diff --git a/databases/readers/Pixie/avtPixieFileFormat.C b/databases/readers/Pixie/avtPixieFileFormat.C
+index 6532b4e..ff56604 100644
+--- a/databases/readers/Pixie/avtPixieFileFormat.C
++++ b/databases/readers/Pixie/avtPixieFileFormat.C
+@@ -1979,10 +1979,10 @@ avtPixieFileFormat::VisitLinks(hid_t locId, const char* name,
+   switch (linfo->type) {
+     case H5L_TYPE_HARD: {
+ 
+-      H5O_info_t objinfo;
++      H5O_info1_t objinfo;
+ 
+       /* Stat the object */
+-      if(H5Oget_info_by_name(locId, name, &objinfo, H5P_DEFAULT) < 0) {
++      if(H5Oget_info_by_name1(locId, name, &objinfo, H5P_DEFAULT) < 0) {
+         debug5 << "visitLinks() - unable to open object with name " <<name <<std::endl;
+         debug5 << "visitLinks() - this object and all children will be dropped." <<std::endl;
+         return 0;
+@@ -2031,7 +2031,7 @@ avtPixieFileFormat::VisitLinks(hid_t locId, const char* name,
+       targbuf = NULL;
+       
+       // Get info of the linked object.
+-      H5O_info_t objinfo;
++      H5O_info1_t objinfo;
+       hid_t obj_id = H5Oopen(locId, name, H5P_DEFAULT);
+       
+       if (obj_id < 0) {
+@@ -2041,7 +2041,7 @@ avtPixieFileFormat::VisitLinks(hid_t locId, const char* name,
+       }
+ 
+       //Test-open the linked object
+-      if (H5Oget_info (obj_id, &objinfo) < 0) {
++      if (H5Oget_info1(obj_id, &objinfo) < 0) {
+         debug5 << "visitLinks() - unable to open external object " <<name <<std::endl;
+         debug5 << "visitLinks() - this object and all children will be dropped." <<std::endl;
+         return 0;
+diff --git a/databases/readers/Vs/VsFilter.C b/databases/readers/Vs/VsFilter.C
+index c6caba6..b95f424 100644
+--- a/databases/readers/Vs/VsFilter.C
++++ b/databases/readers/Vs/VsFilter.C
+@@ -60,10 +60,10 @@ int VsFilter::visitLinks(hid_t locId, const char* name,
+   switch (linfo->type) {
+     case H5L_TYPE_HARD: {
+ 
+-      H5O_info_t objinfo;
++      H5O_info1_t objinfo;
+ 
+       /* Stat the object */
+-      if(H5Oget_info_by_name(locId, name, &objinfo, H5P_DEFAULT) < 0) {
++      if(H5Oget_info_by_name1(locId, name, &objinfo, H5P_DEFAULT) < 0) {
+         VsLog::errorLog() <<"VsFilter::visitLinks() - unable to open object with name " <<name <<std::endl;
+         VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
+         return 0;
+@@ -112,7 +112,7 @@ int VsFilter::visitLinks(hid_t locId, const char* name,
+       targbuf = NULL;
+       
+       // Get info of the linked object.
+-      H5O_info_t objinfo;
++      H5O_info1_t objinfo;
+ #ifndef H5_USE_16_API
+       hid_t obj_id = H5Oopen(locId, name, H5P_DEFAULT);
+ #else
+@@ -126,7 +126,7 @@ int VsFilter::visitLinks(hid_t locId, const char* name,
+       }
+ 
+       //Test-open the linked object
+-      if (H5Oget_info (obj_id, &objinfo) < 0) {
++      if (H5Oget_info1(obj_id, &objinfo) < 0) {
+         VsLog::errorLog() <<"VsFilter::visitLinks() - unable to open external object " <<name <<std::endl;
+         VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
+         return 0;

ports/paraview/portfile.cmake

@@ -1,7 +1,7 @@
 set(VERSION 5.8)
 
 vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS
-    "cuda"         PARAVIEW_USE_CUDA            #untested; probably only affects internal VTK build so it does nothing here 
+    "cuda"         PARAVIEW_USE_CUDA            #untested; probably only affects internal VTK build so it does nothing here
     "all_modules"  PARAVIEW_BUILD_ALL_MODULES   #untested
     "mpi"          PARAVIEW_USE_MPI             #untested
     "vtkm"         PARAVIEW_USE_VTKM
@@ -18,8 +18,8 @@ vcpkg_from_github(
         paraview_build.patch
         remove_duplicates.patch # Missed something in the above patch
         cgns.patch
-        qt_plugin.patch # Remove with Qt version > 5.14 
+        qt_plugin.patch # Remove with Qt version > 5.14
-        qt_static_plugins.patch # Remove with Qt version > 5.14 
+        qt_static_plugins.patch # Remove with Qt version > 5.14
         python_include.patch
         python_wrapper.patch
 )
@@ -28,8 +28,8 @@ if(VCPKG_LIBRARY_LINKAGE STREQUAL "static")
     list(APPEND VisItPatches removedoublesymbols.patch)
 endif()
 
-#The following two dependencies should probably be their own port 
+#The following two dependencies should probably be their own port
-#but require additional patching in paraview to make it work. 
+#but require additional patching in paraview to make it work.
 
 #Get VisItBridge Plugin
 vcpkg_from_gitlab(
@@ -38,8 +38,9 @@ vcpkg_from_gitlab(
     REPO paraview/visitbridge
     REF c2605b5c3115bc4869c76a0d8bfdd8939b59f283
     SHA512 6d2c1d6e1cd345547926938451755e7a8be5dabd89e18a2ceb419db16c5b29f354554a5130eb365b7e522d655370fd4766953813ff530c06e4851fe26104ce58
-    PATCHES 
+    PATCHES
-        VisIt_Build.patch        
+        VisIt_Build.patch
+        fix-using-hdf5.patch
         #removeunusedsymbols.patch # These also get remove in master of ParaView
         ${VisItPatches}
 )
@@ -61,7 +62,7 @@ if("python" IN_LIST FEATURES)
         -DPython3_FIND_REGISTRY=NEVER
         "-DPython3_EXECUTABLE:PATH=${PYTHON3}" # Required by more than one feature
         )
-  
+
     #VTK_PYTHON_SITE_PACKAGES_SUFFIX should be set to the install dir of the site-packages
 endif()
 
@@ -75,15 +76,15 @@ vcpkg_configure_cmake(
         -DVTK_MODULE_ENABLE_ParaView_qttesting=YES
         -DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION:BOOL=OFF
         -DPARAVIEW_USE_QTHELP:BOOL=OFF
-        
+
         #A little bit of help in finding the boost headers
         "-DBoost_INCLUDE_DIR:PATH=${CURRENT_INSTALLED_DIR}/include"
-    
+
         # Workarounds for CMake issues
         -DHAVE_SYS_TYPES_H=0    ## For some strange reason the test first succeeds and then fails the second time around
-        -DWORDS_BIGENDIAN=0     ## Tests fails in VisItCommon.cmake for some unknown reason this is just a workaround since most systems are little endian. 
+        -DWORDS_BIGENDIAN=0     ## Tests fails in VisItCommon.cmake for some unknown reason this is just a workaround since most systems are little endian.
         ${ADDITIONAL_OPTIONS}
-       
+
         #-DPARAVIEW_ENABLE_FFMPEG:BOOL=OFF
 )
 if(CMAKE_HOST_UNIX)
@@ -113,7 +114,7 @@ set(TOOLS   paraview
             smTestDriver
             vtkProcessXML
             vtkWrapClientServer)
-            
+
 foreach(tool ${TOOLS})
     # Remove debug tools
     set(filename ${CURRENT_PACKAGES_DIR}/debug/bin/${tool}${VCPKG_TARGET_EXECUTABLE_SUFFIX})
@@ -128,7 +129,7 @@ foreach(tool ${TOOLS})
     if(EXISTS ${filename})
         file(REMOVE ${filename})
     endif()
-    
+
     # Move release tools
     set(filename ${CURRENT_PACKAGES_DIR}/bin/${tool}${VCPKG_TARGET_EXECUTABLE_SUFFIX})
     if(EXISTS ${filename})
@@ -156,7 +157,7 @@ if(VCPKG_LIBRARY_LINKAGE STREQUAL "static")
             file(RENAME "${CURRENT_PACKAGES_DIR}/debug/bin/${name}" "${CURRENT_PACKAGES_DIR}/debug/lib/${name}")
         endif()
     endmacro()
-    
+
     set(to_move Lib paraview-${VERSION} paraview-config)
     foreach(name ${to_move})
         move_bin_to_lib(${name})
@@ -170,4 +171,4 @@ if(VCPKG_LIBRARY_LINKAGE STREQUAL "static")
     endforeach()
 
     file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/bin ${CURRENT_PACKAGES_DIR}/debug/bin)
-endif()
+endif()

ports/vtk/CONTROL

@@ -1,5 +1,5 @@
 Source: vtk
-Version: 9.0-3
+Version: 9.0-4
 Description: Software system for 3D computer graphics, image processing, and visualization
 Homepage: https://github.com/Kitware/VTK
 Build-Depends: zlib, libpng, tiff, libxml2, jsoncpp, glew, freetype, expat, hdf5[core], libjpeg-turbo, proj4, lz4, liblzma, libtheora, eigen3, double-conversion, pugixml, libharu[notiffsymbols], sqlite3, netcdf-c, utfcpp, libogg, pegtl-2

ports/vtk/fix-using-hdf5.patch

@@ -0,0 +1,22 @@
+diff --git a/ThirdParty/h5part/vtkh5part/src/H5Part.c b/ThirdParty/h5part/vtkh5part/src/H5Part.c
+index 228d246..41af04d 100644
+--- a/ThirdParty/h5part/vtkh5part/src/H5Part.c
++++ b/ThirdParty/h5part/vtkh5part/src/H5Part.c
+@@ -2092,7 +2092,7 @@ _H5Part_iteration_operator2 (
+     case H5L_TYPE_HARD: {
+ 
+       H5O_info_t objinfo;
+-      if( H5Oget_info_by_name( group_id, member_name, &objinfo, H5P_DEFAULT ) < 0 ) {
++      if( H5Oget_info_by_name1( group_id, member_name, &objinfo, H5P_DEFAULT ) < 0 ) {
+ 	return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name );
+       }
+ 
+@@ -2142,7 +2142,7 @@ _H5Part_iteration_operator2 (
+           if ( obj_id < 0 ) {
+ 	    return (herr_t)HANDLE_H5G_OPEN_ERR ( member_name );
+           }
+-          else if ( H5Oget_info ( obj_id, &objinfo ) < 0 ) {
++          else if ( H5Oget_info1 ( obj_id, &objinfo ) < 0 ) {
+ 	    return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name );
+           }
+           else {

ports/vtk/portfile.cmake

@@ -101,6 +101,7 @@ vcpkg_from_github(
         pythonwrapper.patch # Required by ParaView to Wrap required classes
         NoUndefDebug.patch # Required to link against correct Python library depending on build type. 
         python_debug.patch
+        fix-using-hdf5.patch
         # Last patch TODO: Patch out internal loguru
 )
 

scripts/ci.baseline.txt

@@ -1965,13 +1965,16 @@ xerces-c:x64-uwp=fail
 xeus:x64-linux=ignore
 xmlsec:arm-uwp=fail
 xmlsec:x64-uwp=fail
-xmsh:arm64-windows=fail
+# The xmsh upstream repository is gone, if we find no replacement before
-xmsh:arm-uwp=fail
+# 2021-01-01 we will remove the port outright.
-xmsh:x64-uwp=fail
+xmsh:arm-uwp=skip
-xmsh:x64-windows=fail
+xmsh:arm64-windows=skip
-xmsh:x64-windows-static=fail
+xmsh:x64-linux=skip
-xmsh:x86-windows=fail
+xmsh:x64-osx=skip
-xmsh:x64-linux=ignore
+xmsh:x64-uwp=skip
+xmsh:x64-windows-static=skip
+xmsh:x64-windows=skip
+xmsh:x86-windows=skip
 xtensor-io:x64-uwp=ignore
 x-plane:arm64-windows=fail
 x-plane:arm-uwp=fail