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authorVincent Legoll <vincent.legoll@gmail.com>2020-05-04 00:39:36 +0200
committerLudovic Courtès <ludo@gnu.org>2020-05-04 10:26:52 +0200
commit06ed1dba359aeb70f6da908ca5672c541c714ab1 (patch)
tree0d56a87637253234f5413ed770c96edc2a94231c /gnu/packages/patches
parentfeba2c97514b142e356a4927640a78b3cd21d327 (diff)
gnu: Add gromacs.
* gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r--gnu/packages/patches/gromacs-tinyxml2.patch67
1 files changed, 67 insertions, 0 deletions
diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch
new file mode 100644
index 0000000000..cc7d7459a8
--- /dev/null
+++ b/gnu/packages/patches/gromacs-tinyxml2.patch
@@ -0,0 +1,67 @@
+Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs
+build.
+
+This patch fixes three issues:
+
+- cmake now errors out if using multiple target_link_libraries with mixed styles
+ of signatures.
+
+- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the
+ new API: document.ErrorStr() & tinyxml2::XML_SUCCESS.
+
+Those fixes will be submitted for inclusion to upstream, but may not be suitable
+there as long as they still keep the old version bundled.
+
+First hunk has already been requested for merging. Third is in discussion. Second
+will only be sent if third is OK'ed.
+
+diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt
+--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200
++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200
+@@ -73,7 +73,7 @@
+
+ if(HAVE_TINYXML2)
+ include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR})
+- target_link_libraries(testutils ${TinyXML2_LIBRARIES})
++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES})
+ else()
+ include_directories(BEFORE SYSTEM "../external/tinyxml2")
+ endif()
+diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp
+--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200
++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200
+@@ -206,21 +206,12 @@
+ document.LoadFile(path.c_str());
+ if (document.Error())
+ {
+- const char* errorStr1 = document.GetErrorStr1();
+- const char* errorStr2 = document.GetErrorStr2();
++ const char* errorStr = document.ErrorStr();
+ std::string errorString("Error was ");
+- if (errorStr1)
+- {
+- errorString += errorStr1;
+- }
+- if (errorStr2)
+- {
+- errorString += errorStr2;
+- }
+- if (!errorStr1 && !errorStr2)
+- {
++ if (errorStr)
++ errorString += errorStr;
++ else
+ errorString += "not specified.";
+- }
+ GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n."
+ + errorString + "\n"));
+ }
+@@ -371,7 +362,7 @@
+ XMLElementPtr rootElement = createRootElement(&document);
+ createChildElements(rootElement, rootEntry);
+
+- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR)
++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS)
+ {
+ GMX_THROW(TestException("Reference data saving failed in " + path));
+ }