[vcpkg baseline] Fix baseline errors (#12067)

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

9 files changed, 165 insertions, 26 deletions

diff --git a/ports/apr/CONTROL b/ports/apr/CONTROL
index 9786e3d9f..607f6c4d4 100644
--- a/ports/apr/CONTROL
+++ b/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
diff --git a/ports/apr/portfile.cmake b/ports/apr/portfile.cmake
index ede0eb9fc..b3ede1a1d 100644
--- a/ports/apr/portfile.cmake
+++ b/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
diff --git a/ports/paraview/CONTROL b/ports/paraview/CONTROL
index e22b8f385..5f1631462 100644
--- a/ports/paraview/CONTROL
+++ b/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

diff --git a/ports/paraview/fix-using-hdf5.patch b/ports/paraview/fix-using-hdf5.patch
new file mode 100644
index 000000000..7d547e77e
--- /dev/null
+++ b/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;

diff --git a/ports/paraview/portfile.cmake b/ports/paraview/portfile.cmake
index 97c6d7670..4e706453c 100644
--- a/ports/paraview/portfile.cmake
+++ b/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_static_plugins.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

         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 

-#but require additional patching in paraview to make it work. 

+#The following two dependencies should probably be their own port

+#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 

-        VisIt_Build.patch        

+    PATCHES

+        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()
\ No newline at end of file
+endif()

diff --git a/ports/vtk/CONTROL b/ports/vtk/CONTROL
index 412869822..0e494fe6d 100644
--- a/ports/vtk/CONTROL
+++ b/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
diff --git a/ports/vtk/fix-using-hdf5.patch b/ports/vtk/fix-using-hdf5.patch
new file mode 100644
index 000000000..834ab15e9
--- /dev/null
+++ b/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 {
diff --git a/ports/vtk/portfile.cmake b/ports/vtk/portfile.cmake
index ecc9176ce..09c997f7a 100644
--- a/ports/vtk/portfile.cmake
+++ b/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
 )
 
diff --git a/scripts/ci.baseline.txt b/scripts/ci.baseline.txt
index e15f0a6fb..598dd3d72 100644
--- a/scripts/ci.baseline.txt
+++ b/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

-xmsh:arm-uwp=fail

-xmsh:x64-uwp=fail

-xmsh:x64-windows=fail

-xmsh:x64-windows-static=fail

-xmsh:x86-windows=fail

-xmsh:x64-linux=ignore

+# The xmsh upstream repository is gone, if we find no replacement before

+# 2021-01-01 we will remove the port outright.

+xmsh:arm-uwp=skip

+xmsh:arm64-windows=skip

+xmsh:x64-linux=skip

+xmsh:x64-osx=skip

+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