Patch
#+begin_src sh
--- CMakeLists.txt.orig 2023-02-01 23:55:18.171758209 +0100
+++ CMakeLists.txt 2023-02-01 23:07:43.945491855 +0100
@@ -23,25 +23,25 @@
set (VCFEVAL_AVAILABLE 0)
endif()
-execute_process(
- COMMAND ${CMAKE_SOURCE_DIR}/external/make_dependencies.sh
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
- RESULT_VARIABLE EXTERNAL_SUCCESS)
-
-if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
- message(FATAL_ERROR "Building external dependencies has failed")
-endif()
-
-set(Boost_USE_STATIC_LIBS ON) # only find static libs
-set(Boost_USE_MULTITHREADED ON)
-set(Boost_USE_STATIC_RUNTIME ON)
+#execute_process(
+# COMMAND ${CMAKE_SOURCE_DIR}/external/make_dependencies.sh
+# WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+# RESULT_VARIABLE EXTERNAL_SUCCESS)
+
+#if(NOT "${EXTERNAL_SUCCESS}" STREQUAL "0")
+# message(FATAL_ERROR "Building external dependencies has failed")
+#endif()
+
+#set(Boost_USE_STATIC_LIBS ON) # only find static libs
+#set(Boost_USE_MULTITHREADED ON)
+#set(Boost_USE_STATIC_RUNTIME ON)
# un-break library finding
-set(Boost_NO_BOOST_CMAKE ON)
-set(Boost_NO_SYSTEM_PATHS ON)
+#set(Boost_NO_BOOST_CMAKE ON)
+#set(Boost_NO_SYSTEM_PATHS ON)
-set(BOOST_ROOT ${CMAKE_BINARY_DIR})
-message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
+#set(BOOST_ROOT ${CMAKE_BINARY_DIR})
+#message("Using our own Boost, which was built at ${HAPLOTYPES_SOURCE_DIR}/external/boost_install")
find_package(Boost 1.55.0 COMPONENTS thread iostreams regex unit_test_framework filesystem system program_options REQUIRED)
include_directories(${Boost_INCLUDE_DIRS})
#+end_src
2. Echec de la compilation
/Home/Users/apraga/source/source/src/c++/lib/tools/Roc.cpp: In member function 'roc::Level roc::Roc::getTotals(uint64_t) const':
/Home/Users/apraga/source/source/src/c++/lib/tools/Roc.cpp:178:27: error: 'numeric_limits' is not a member of 'std'
178 | last.level = std::numeric_limits<double>::quiet_NaN();
| ^~~~~~~~~~~~~~ |
| |
Patch Roc.cpp
#+begin_src diff
--- src/c++/lib/tools/Roc.cpp.orig 2023-02-01 23:52:50.514230141 +0100
+++ src/c++/lib/tools/Roc.cpp 2023-02-01 23:52:52.729223136 +0100
@@ -34,6 +34,9 @@
*/
#include "helpers/Roc.hh"
+#include <stdexcept>
+#include <limits>
+
2. Patch Roc.cpp pour avoir numeric_limits ( error: 'numeric_limits' is not a member of 'std')
3. ajout de flags de link (essai, error)
set(ZLIB_LIBRARIES -lz -lbz2 -lcurl -lcrypto -llzma)
4. Changer les appels à print en print() dans le code python et suppression de quelques import
[nix-shell:~/source]$ sed -i.orig 's/print \"\(.*\)"/print(\1)/' src/python/*.py
**** TODO Version avec rtg-tools