Now BUILD_FOR_DEPLOYMENT works. ish.

CMakeLists.txt

@@ -21,10 +21,12 @@ project(spell_qtl)
 #INCLUDE(pandocology)
 
 find_package(Boost 1.55.0 REQUIRED)
-set(CMAKE_CONFIGURATION_TYPES Debug Release CACHE TYPE INTERNAL FORCE)
+#set(CMAKE_CONFIGURATION_TYPES Debug Release CACHE INTERNAL FORCE)
 
 set(CMAKE_VERBOSE_MAKEFILE ON)
 
+set(BUILD_FOR_DEPLOYMENT FALSE CACHE BOOL "Link against static libc++ and use minimal symbol version where possible")
+
 MESSAGE(STATUS "CMAKE VERSION ${CMAKE_VERSION}")
 MESSAGE(STATUS "${CMAKE_CURRENT_SOURCE_DIR}")
 
@@ -70,6 +72,14 @@ include_directories(AFTER ${CMAKE_SOURCE_DIR}/include/ ${CMAKE_SOURCE_DIR}/inclu
 include_directories(SYSTEM /usr/include ${Boost_INCLUDE_DIRS} ${EXPAT_INCLUDE_DIR} ${X2C_INCLUDE_DIR})
 include_directories(AFTER /usr/include ${Boost_INCLUDE_DIRS} ${EXPAT_INCLUDE_DIR} ${X2C_INCLUDE_DIR})
 
+if(${BUILD_FOR_DEPLOYMENT})
+    set(libstdcpp ${CMAKE_BINARY_DIR}/libstdc++.a)
+else(${BUILD_FOR_DEPLOYMENT})
+    set(libstdcpp "")
+endif(${BUILD_FOR_DEPLOYMENT})
+
+MESSAGE(STATUS "libstdcpp = ${libstdcpp}")
+
 set(SPELL_PEDIGREE_SRC
         src/static_data.cc
         src/pedigree/main.cc
@@ -89,13 +99,66 @@ set(SPELL_QTL_SRC
         src/computations/basic_data.cc src/computations/probabilities.cc src/computations/model.cc src/computations/frontends.cc
 )
 
-add_executable(spell-pedigree ${SPELL_PEDIGREE_SRC})
-add_executable(spell-marker ${SPELL_MARKER_SRC})
-add_executable(spell-qtl ${SPELL_QTL_SRC})
+MESSAGE(STATUS "spell-pedigree src = ${SPELL_PEDIGREE_SRC}")
+
+
+#get_cmake_property(_variableNames VARIABLES)
+#foreach (_variableName ${_variableNames})
+#    message(STATUS "${_variableName}=${${_variableName}}")
+#endforeach()
+
+if(${BUILD_FOR_DEPLOYMENT})
+    add_executable(spell-pedigree ${SPELL_PEDIGREE_SRC} ${libstdcpp})
+    add_executable(spell-marker ${SPELL_MARKER_SRC})
+    add_executable(spell-qtl ${SPELL_QTL_SRC} ${libstdcpp})
+    add_custom_command(OUTPUT glibc.h libstdc++.a COMMAND ${CMAKE_SOURCE_DIR}/deploy/make_old_libc_header.sh WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
+    add_custom_command(OUTPUT libgmp.a COMMAND ${CMAKE_SOURCE_DIR}/deploy/compile_gmp.sh ${CMAKE_BINARY_DIR}/glibc.h ${CMAKE_BINARY_DIR} WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/deploy)
+    add_custom_target(glibc.h)
+    #add_custom_target(stdc++ ${CMAKE_BINARY_DIR}/libstdc++.a)
+    #add_library(stdc++ INTERFACE IMPORTED)
+    #set_property(TARGET stdc++ PROPERTY INTERFACE_LINK_LIBRARIES ${CMAKE_BINARY_DIR}/libstdc++.a)
+
+    add_library(gmp INTERFACE IMPORTED)
+    add_custom_target(pouet ALL DEPENDS ${CMAKE_BINARY_DIR}/libgmp.a)
+    #set_property(TARGET gmp PROPERTY INTERFACE_LINK_LIBRARIES ${CMAKE_BINARY_DIR}/libgmp.a)
+    #set_target_properties(stdc++ PROPERTIES LINKER_LANGUAGE CXX)
+    #set_target_properties(gmp PROPERTIES LINKER_LANGUAGE C)
+    #add_dependencies(gmp stdc++)
+    #set_source_files_properties(${CMAKE_BINARY_DIR}/libgmp.a PROPERTIES GENERATED TRUE)
+    #set_source_files_properties(${libstdcpp} PROPERTIES GENERATED TRUE)
+    #set_source_files_properties(${CMAKE_BINARY_DIR}/libstdc++.a PROPERTIES EXTERNAL_OBJECT TRUE GENERATED TRUE)
+    
+    SET_SOURCE_FILES_PROPERTIES(${SPELL_PEDIGREE_SRC} ${SPELL_MARKER_SRC} ${SPELL_QTL_SRC}
+            PROPERTIES
+            OBJECT_DEPENDS glibc.h
+            COMPILE_FLAGS "-include ${CMAKE_BINARY_DIR}/glibc.h -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=0")
+
+    #add_dependencies(stdc++ libstdc++.a)
+    #add_dependencies(gmp libgmp.a)
+    add_dependencies(spell-pedigree glibc.h)
+    add_dependencies(spell-marker glibc.h pouet)
+    add_dependencies(spell-qtl glibc.h)
+
+    MESSAGE(STATUS " PROUT ${libstdcpp}")
+    
+    set(CMAKE_EXE_LINKER_FLAGS "-include ${CMAKE_BINARY_DIR}/glibc.h -rdynamic -static-libgcc")
+
+    target_link_libraries(spell-marker ${libstdcpp} ${CMAKE_BINARY_DIR}/libgmp.a)
+    target_link_libraries(spell-qtl ${libstdcpp})
+    target_link_libraries(spell-pedigree ${libstdcpp})
+    
+    #list(APPEND spell-pedigree_SRC "${CMAKE_BINARY_DIR}/libstdc++.a")
+    #list(APPEND spell-qtl_SRC "${CMAKE_BINARY_DIR}/libstdc++.a")
+    #list(APPEND spell-marker_SRC "${CMAKE_BINARY_DIR}/libstdc++.a")
+else()
+    add_executable(spell-pedigree ${SPELL_PEDIGREE_SRC})
+    add_executable(spell-marker ${SPELL_MARKER_SRC})
+    add_executable(spell-qtl ${SPELL_QTL_SRC})
+    set(CMAKE_EXE_LINKER_FLAGS "-rdynamic")
+endif()
 
 target_link_libraries(spell-marker dl gmp)
-target_link_libraries(spell-qtl expat dl)
-set(CMAKE_EXE_LINKER_FLAGS "-rdynamic")
+target_link_libraries(spell-qtl expat dl rt)
 
 SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
 

deploy/compile_gmp.sh

+#!/bin/bash
+
+PATH_TO_GLIBC_H=$1
+OUTPUT_PATH=$2
+
+cd gmp
+
+# fetch GMP
+cd gmp-6.1.2 || (curl https://gmplib.org/download/gmp/gmp-6.1.2.tar.xz -o - | xz -d | tar xf - && cd gmp-6.1.2)
+
+# cleanup and configure
+[ -f Makefile ] && make clean
+
+CFLAGS="-include $PATH_TO_GLIBC_H" ./configure --disable-shared --enable-fake-cpuid --enable-fat
+
+# build
+make
+
+# deploy lib
+cp .libs/libgmp.a $OUTPUT_PATH

deploy/make_old_libc_header.sh

+#!/bin/bash
+LIBCPP=/usr/lib/gcc/x86_64-linux-gnu/5/libstdc++.a
+maxver=2.9
+headerf=${1:-glibc.h}
+set -e
+for lib in libc.so.6 libm.so.6 libpthread.so.0 libdl.so.2 libresolv.so.2 librt.so.1; do
+objdump -T /lib/x86_64-linux-gnu/$lib
+done | awk -v maxver=${maxver} -vheaderf=${headerf} -vredeff=${headerf}.redef -f <(cat <<'EOF'
+BEGIN {
+split(maxver, ver, /\./)
+limit_ver = ver[1] * 10000 + ver[2]*100 + ver[3]
+}
+/GLIBC_/ {
+gsub(/\(|\)/, "",$(NF-1))
+split($(NF-1), ver, /GLIBC_|\./)
+vers = ver[2] * 10000 + ver[3]*100 + ver[4]
+if (vers > 0) {
+    if (symvertext[$(NF)] != $(NF-1))
+        count[$(NF)]++
+    if (vers <= limit_ver && vers > symvers[$(NF)]) {
+        symvers[$(NF)] = vers
+        symvertext[$(NF)] = $(NF-1)
+    }
+}
+}
+END {
+for (s in symvers) {
+    if (count[s] > 1) {
+        printf("__asm__(\".symver %s,%s@%s\");\n", s, s, symvertext[s]) > headerf
+        printf("%s %s@%s\n", s, s, symvertext[s]) > redeff
+    }
+}
+}
+EOF
+)
+sort ${headerf} -o ${headerf}
+objcopy --redefine-syms=${headerf}.redef $LIBCPP libstdc++.a
+rm ${headerf}.redef