gentoo resync : 07.01.2022

9 files changed, 157 insertions, 186 deletions

diff --git a/sci-libs/silo/files/silo-4.10.2-mpiposix.patch b/sci-libs/silo/files/silo-4.10.2-mpiposix.patch
deleted file mode 100644
index 30a3f910b196..000000000000
--- a/sci-libs/silo/files/silo-4.10.2-mpiposix.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- src/hdf5_drv/silo_hdf5.c.orig	2017-07-28 08:52:09.026638768 +0200
-+++ src/hdf5_drv/silo_hdf5.c	2017-07-28 09:00:12.306635882 +0200
-@@ -4752,18 +4752,19 @@
-         }
- 
-         /* default HDF5 mpi drivers */
--        case DB_FILE_OPTS_H5_DEFAULT_MPIP:
--        {
--#ifdef H5_HAVE_PARALLEL
--            h5status |= H5Pset_fapl_mpiposix(retval, MPI_COMM_SELF, TRUE);
--#else
--            H5Pclose(retval);
--            return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
--#endif
--            break;
--        }
-+//        case DB_FILE_OPTS_H5_DEFAULT_MPIP:
-+//        {
-+//#ifdef H5_HAVE_PARALLEL
-+//            h5status |= H5Pset_fapl_mpiposix(retval, MPI_COMM_SELF, TRUE);
-+//#else
-+//            H5Pclose(retval);
-+//            return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
-+//#endif
-+//            break;
-+//        }
- 
-         case DB_FILE_OPTS_H5_DEFAULT_MPIO:
-+	case DB_FILE_OPTS_H5_DEFAULT_MPIP:
-         {
- #ifdef H5_HAVE_PARALLEL
-             MPI_Info info;
-@@ -5069,15 +5070,15 @@
-                     if ((p = DBGetOption(opts, DBOPT_H5_MPIP_NO_GPFS_HINTS)))
-                         use_gpfs_hints = FALSE;
- 
--                    if (vfd == DB_H5VFD_MPIO)
-+//                    if (vfd == DB_H5VFD_MPIO)
-                     {
-                         h5status |= H5Pset_fapl_mpio(retval, mpi_comm, mpi_info);
-                         if (created_info) MPI_Info_free(&mpi_info);
-                     }
--                    else
--                    {
--                        h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm, use_gpfs_hints);
--                    }
-+//                    else
-+//                    {
-+//                        h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm, use_gpfs_hints);
-+//                    }
- #else 
-                     H5Pclose(retval);
-                     return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
diff --git a/sci-libs/silo/files/silo-4.10.2-qt5.patch b/sci-libs/silo/files/silo-4.10.2-qt5.patch
deleted file mode 100644
index 1e1fe8803a37..000000000000
--- a/sci-libs/silo/files/silo-4.10.2-qt5.patch
+++ /dev/null
@@ -1,44 +0,0 @@
---- tools/silex/SiloFile.h.orig	2018-01-24 11:01:23.354705068 +0100
-+++ tools/silex/SiloFile.h	2018-01-24 11:01:34.843705761 +0100
-@@ -61,6 +61,8 @@
- #include <vector>
- using std::vector;
- 
-+#define toAscii toLatin1
-+
- // ****************************************************************************
- //  Class:  SiloDir
- //
---- tools/silex/main.cpp.orig	2018-01-24 11:02:21.201708556 +0100
-+++ tools/silex/main.cpp	2018-01-24 11:02:34.146709336 +0100
-@@ -58,7 +58,7 @@
- #include <cstdlib>
- 
- #ifndef Q_WS_MACX
--#include "qwindowsstyle.h"
-+//#include "qwindowsstyle.h"
- #endif
- #include "qfiledialog.h"
- #include "qstring.h"
-@@ -91,7 +91,7 @@
-     QApplication::setColorSpec(QApplication::ManyColor);
-     QApplication a(argc, argv);
- #ifndef Q_WS_MACX
--    a.setStyle(new QWindowsStyle);
-+//    a.setStyle(new QWindowsStyle);
- #endif
-     Explorer *w = 0;
-     if (argc > 1)
---- tools/silex/SiloView.cpp.orig	2018-01-24 11:03:13.775711725 +0100
-+++ tools/silex/SiloView.cpp	2018-01-24 11:03:30.032712706 +0100
-@@ -109,8 +109,8 @@
-         dirTreeView->OpenRootDir();
-         dirView->Set(silo->root);
- 
--        dirTreeView->header()->setResizeMode(QHeaderView::Interactive);
--        dirView->header()->setResizeMode(QHeaderView::Interactive);
-+        dirTreeView->header()->setSectionResizeMode(QHeaderView::Interactive);
-+        dirView->header()->setSectionResizeMode(QHeaderView::Interactive);
-     }
- }
- 
diff --git a/sci-libs/silo/files/silo-4.10.2-qtlibs.patch b/sci-libs/silo/files/silo-4.10.2-qtlibs.patch
deleted file mode 100644
index ecd5297c281f..000000000000
--- a/sci-libs/silo/files/silo-4.10.2-qtlibs.patch
+++ /dev/null
@@ -1,78 +0,0 @@
---- configure.orig	2018-01-24 10:50:10.458664501 +0100
-+++ configure	2018-01-24 10:50:42.967666461 +0100
-@@ -27541,7 +27541,7 @@
-         ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p |
-                      sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`"
-       fi
--      ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+      ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-     else
-       # Use cached value or do search, starting with suggestions from
-       # the command line
-@@ -27615,7 +27615,7 @@
-       ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p |
-                    sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`"
-     fi
--    ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+    ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-   else
-     # There is no valid definition for $QTDIR as Trolltech likes to see it
-     ax_qt_dir=
-@@ -27627,7 +27627,7 @@
-         ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p |
-                      sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`"
-       fi
--      ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+      ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-     else
-       # Normally, when there is no traditional Trolltech installation,
-       # the library is installed in a place where the linker finds it
-@@ -27645,10 +27645,10 @@
-       # See if we find the library without any special options.
-       # Don't add top $LIBS permanently yet
-       ax_save_LIBS="$LIBS"
--      LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+      LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-       ax_qt_LIBS="$LIBS"
-       ax_save_CXXFLAGS="$CXXFLAGS"
--      CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui"
-+      CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui -I$ax_qt_include_dir/QtWidgets -fPIC"
-       cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
- _ACEOF
-@@ -27706,7 +27706,7 @@
-         # That did not work. Try the multi-threaded version
-         echo "Non-critical error, please neglect the above." >&5
-         ax_qt_lib=qt-mt
--        LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+        LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-         cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
- _ACEOF
-@@ -27764,7 +27764,7 @@
-           # That did not work. Try the OpenGL version
-           echo "Non-critical error, please neglect the above." >&5
-           ax_qt_lib=qt-gl
--          LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+          LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-           cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
- _ACEOF
-@@ -27847,7 +27847,7 @@
-               fi
-             done
-             # Try with that one
--            LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-+            LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQt5Core -lQt5Gui -lQt5Widgets -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS"
-             cat >conftest.$ac_ext <<_ACEOF
- /* confdefs.h.  */
- _ACEOF
-@@ -27955,7 +27955,7 @@
-     fi # all $ax_qt_* are set
-   fi   # $have_qt reflects the system status
-   if test x"$have_qt" = xyes; then
--    QT_CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui"
-+    QT_CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui -I$ax_qt_include_dir/QtWidgets -fPIC"
-     if test x"$ax_qt_lib" = xqt-mt; then
-         QT_CXXFLAGS="$QT_CXXFLAGS -DQT_THREAD_SUPPORT"
-     fi
diff --git a/sci-libs/silo/files/silo-4.10.2-tests.patch b/sci-libs/silo/files/silo-4.10.2-tests.patch
deleted file mode 100644
index 2e0a52191d0e..000000000000
--- a/sci-libs/silo/files/silo-4.10.2-tests.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- tests/Makefile.in.old	2014-07-24 07:25:53.464381420 +0200
-+++ tests/Makefile.in	2014-07-24 07:26:14.951048323 +0200
-@@ -169,7 +169,7 @@
- 	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
- 	$(ioperf_stdio_la_LDFLAGS) $(LDFLAGS) -o $@
- rocket_silo_la_LIBADD =
--am_rocket_silo_la_OBJECTS = rocket_silo.lo
-+am_rocket_silo_la_OBJECTS = rocket_silo.lo ../src/.libs/libsilo.la
- rocket_silo_la_OBJECTS = $(am_rocket_silo_la_OBJECTS)
- rocket_silo_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
- 	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
diff --git a/sci-libs/silo/files/silo-4.11-autoreconf.patch b/sci-libs/silo/files/silo-4.11-autoreconf.patch
new file mode 100644
index 000000000000..371b346e921c
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11-autoreconf.patch
@@ -0,0 +1,35 @@
+Author: Alastair McKinstry <mckinstry@debian.org>
+Description: Fixes needed for autoreconf to work on Debian
+ When autoreconf is run, VL_LIB_READLINE is lost from aclocal, so included in config/
+ Also include AX_CHECK_COMPLER_FLAG() which is not in autoconf (just autoconf-archive)
+ AX_CHECK_COMPILER_FLAGS() is obsolete
+Last-Updated: 2021-01-14
+Forwarded: no
+Link: https://sources.debian.org/patches/silo-llnl/4.11-2/autoreconf.patch/
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -195,6 +195,8 @@
+ dnl This allows multiple src-dir builds within one host.
+ AC_PREFIX_DEFAULT("SILO_TOP_SRC_DIR")
+ 
++AC_PROG_F77
++
+ dnl
+ dnl Handle the python module right away to determine if we need shared libs.
+ dnl Ordinarily, we default to static libs
+@@ -618,10 +620,10 @@
+ # it is an argument to the -D argument. So, I think this is
+ # just totally bogus!
+ # Default to large file support
+-AX_CHECK_COMPILER_FLAGS("-D_LARGEFILE_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE_SOURCE";)
+-AX_CHECK_COMPILER_FLAGS("-D_LARGEFILE64_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE64_SOURCE";)
+-AX_CHECK_COMPILER_FLAGS("-D_FILE_OFFSET_BITS=64",CFLAGS="$CFLAGS -D_FILE_OFFSET_BITS=64";)
+-AX_CHECK_COMPILER_FLAGS("-Wdeclaration-after-statement",CFLAGS="$CFLAGS -Wdeclaration-after-statement";)
++AX_CHECK_COMPILE_FLAG("-D_LARGEFILE_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE_SOURCE";)
++AX_CHECK_COMPILE_FLAG("-D_LARGEFILE64_SOURCE",CFLAGS="$CFLAGS -D_LARGEFILE64_SOURCE";)
++AX_CHECK_COMPILE_FLAG("-D_FILE_OFFSET_BITS=64",CFLAGS="$CFLAGS -D_FILE_OFFSET_BITS=64";)
++AX_CHECK_COMPILE_FLAG("-Wdeclaration-after-statement",CFLAGS="$CFLAGS -Wdeclaration-after-statement";)
+ 
+ #
+ # Note: regardless of what the stuff above regarding large file support
diff --git a/sci-libs/silo/files/silo-4.11-hdf5.patch b/sci-libs/silo/files/silo-4.11-hdf5.patch
new file mode 100644
index 000000000000..6791a44aa2b1
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11-hdf5.patch
@@ -0,0 +1,46 @@
+Link: https://aur.archlinux.org/cgit/aur.git/tree/hdf5.patch?h=silo
+
+--- a/src/hdf5_drv/H5FDsilo.c	2021-09-11 01:22:52.000000000 +0300
++++ b/src/hdf5_drv/H5FDsilo.c	2021-11-25 00:37:06.685422949 +0200
+@@ -252,13 +252,13 @@
+         snprintf(msg, sizeof(msg), Msg "(errno=%d, \"%s\")",	\
+             Errno, strerror(Errno));					\
+     ret_value = Ret;							\
+-    H5Epush_ret(Func, Cls, Maj, Min, msg, Ret)				\
++    H5Epush_ret(Func, Cls, Maj, Min, msg, Ret);				\
+ }
+ #else
+ #define H5E_PUSH_HELPER(Func,Cls,Maj,Min,Msg,Ret,Errno)			\
+ {									\
+     ret_value = Ret;							\
+-    H5Epush_ret(Func, Cls, Maj, Min, Msg, Ret)				\
++    H5Epush_ret(Func, Cls, Maj, Min, Msg, Ret);				\
+ }
+ #endif
+ 
+@@ -1355,7 +1355,7 @@
+     assert(sizeof(hsize_t)<=8);
+     memcpy(p, &file->block_size, sizeof(hsize_t));
+     if (H5Tconvert(H5T_NATIVE_HSIZE, H5T_STD_U64LE, 1, buf+8, NULL, H5P_DEFAULT)<0)
+-        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1)
++        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1);
+ 
+     return 0;
+ }
+@@ -1383,14 +1383,14 @@
+ 
+     /* Make sure the name/version number is correct */
+     if (strcmp(name, "LLNLsilo"))
+-        H5Epush_ret(func, H5E_ERR_CLS, H5E_FILE, H5E_BADVALUE, "invalid silo superblock", -1)
++        H5Epush_ret(func, H5E_ERR_CLS, H5E_FILE, H5E_BADVALUE, "invalid silo superblock", -1);
+ 
+     buf += 8;
+     /* Decode block size */
+     assert(sizeof(hsize_t)<=8);
+     memcpy(x, buf, 8);
+     if (H5Tconvert(H5T_STD_U64LE, H5T_NATIVE_HSIZE, 1, x, NULL, H5P_DEFAULT)<0)
+-        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1)
++        H5Epush_ret(func, H5E_ERR_CLS, H5E_DATATYPE, H5E_CANTCONVERT, "can't convert superblock info", -1);
+     ap = (hsize_t*)x;
+     /*file->block_size = *ap; ignore stored value for now */
+ 
diff --git a/sci-libs/silo/files/silo-4.11-test-disable-largefile.patch b/sci-libs/silo/files/silo-4.11-test-disable-largefile.patch
new file mode 100644
index 000000000000..953453e12fe0
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11-test-disable-largefile.patch
@@ -0,0 +1,23 @@
+Author: Alastair McKinstry <mckinstry@debian.org>
+Description: Disable largefile test. Seems to fail on rounding error
+Forwarded: yes
+Last-Updated: 2011-06-09
+Link: https://sources.debian.org/patches/silo-llnl/4.11-2/test-disable-largefile.patch/
+
+--- a/tests/testsuite.at
++++ b/tests/testsuite.at
+@@ -324,10 +324,10 @@
+ AT_SETUP(xversion)
+ AT_CHECK(test -z "$BROWSER" -o "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND testxvers `pwd`,,ignore,ignore)
+ AT_CLEANUP
+-AT_SETUP(largefile)
+-AT_KEYWORDS(large)
+-AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND largefile,,ignore,ignore)
+-AT_CLEANUP
++#AT_SETUP(largefile)
++#AT_KEYWORDS(large)
++#AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND largefile,,ignore,ignore)
++#AT_CLEANUP
+ #AT_SETUP(memfile_simple)
+ #AT_CHECK(testall -small $STARGS,,ignore)
+ #AT_CHECK(test "$STARGS" != DB_HDF5 && exit 77 || $VALGRIND memfile_simple $STARGS,,ignore,ignore)
diff --git a/sci-libs/silo/files/silo-4.11-tests.patch b/sci-libs/silo/files/silo-4.11-tests.patch
new file mode 100644
index 000000000000..a093d318ded6
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11-tests.patch
@@ -0,0 +1,26 @@
+--- a/tests/Makefile.in
++++ b/tests/Makefile.in
+@@ -169,7 +169,7 @@
+ 	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+ 	$(ioperf_stdio_la_LDFLAGS) $(LDFLAGS) -o $@
+ rocket_silo_la_LIBADD =
+-am_rocket_silo_la_OBJECTS = rocket_silo.lo
++am_rocket_silo_la_OBJECTS = rocket_silo.lo ../src/.libs/libsiloh5.la
+ rocket_silo_la_OBJECTS = $(am_rocket_silo_la_OBJECTS)
+ rocket_silo_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
+ 	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
+
+Author: Alastair McKinstry <mckinstry@debian.org>
+Description: bash is needed to execute this testscript for test 62.
+Last-Updated: 2011-04-11
+Forwarded: no
+Link: https://sources.debian.org/patches/silo-llnl/4.11-2/testsuite-fix.patch/
+
+--- a/tests/testdtypes
++++ b/tests/testdtypes
+@@ -1,4 +1,4 @@
+-#!/bin/sh
++#!/bin/bash
+ 
+ # Copyright (C) 1994-2016 Lawrence Livermore National Security, LLC.
+ # LLNL-CODE-425250.
diff --git a/sci-libs/silo/files/silo-4.11-testsuite-python-write.patch b/sci-libs/silo/files/silo-4.11-testsuite-python-write.patch
new file mode 100644
index 000000000000..ac0bc859068a
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11-testsuite-python-write.patch
@@ -0,0 +1,27 @@
+Author: Alastair McKinstry <mckinstry@debian.org>
+Description: Python code seems to be broken. Disable test and inform upstream.
+Last-Updated: 2011-06-09
+Forwarded: yes
+Link: https://sources.debian.org/patches/silo-llnl/4.11-2/testsuite-python-write.patch/
+
+--- a/tests/test_write.py
++++ b/tests/test_write.py
+@@ -52,11 +52,13 @@
+ db = Silo.Create("foo.silo", "test file")
+ db.Write("t1", 12)
+ db.Write("t2", "hello")
+-db.Write("t3", (13,))
+-db.Write("t4", 14.5)
+-db.Write("t5", (1.2, 10))
+-db.Write("t6", (1.2, 10.2))
+-db.Write("t7", (10, 1.2))
++# Disable writes with floating point. Seem to break on python2.7
++# --amck, 2011-06-09
++#db.Write("t3", (13,))
++#db.Write("t4", 14.5)
++#db.Write("t5", (1.2, 10))
++#db.Write("t6", (1.2, 10.2))
++#db.Write("t7", (10, 1.2))
+ db.Write("t8", "a")
+ db.MkDir("a")
+ db.Write("a/t8", "x2")