From 85a72bb0e02ed23ed1d1cc28b4787359a8a762a9 Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Fri, 3 May 2024 09:13:12 +0000 Subject: [PATCH 1/3] fix for gcc13 --- gatb-core/thirdparty/kff-cpp-api/kff_io.hpp | 1 + 1 file changed, 1 insertion(+) diff --git a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp index 5a265661..881eada1 100644 --- a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp +++ b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp @@ -10,6 +10,7 @@ * */ +#include #include #include #include From 43425a1abe1448c5ab804f186174212d437af871 Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Fri, 3 May 2024 09:21:11 +0000 Subject: [PATCH 2/3] attempt 2 --- gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in | 1 + 1 file changed, 1 insertion(+) diff --git a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in index a4c5e14d..a0b2b51b 100644 --- a/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in +++ b/gatb-core/thirdparty/kff-cpp-api/kff_io.hpp.in @@ -10,6 +10,7 @@ * */ +#include #include #include #include From 4dffb1a995583aafefa1a1d576f18baea040a71e Mon Sep 17 00:00:00 2001 From: Francois Gindraud Date: Tue, 21 May 2024 16:45:30 +0200 Subject: [PATCH 3/3] Short term fix for undefined function While trying to compile for ARM Mac, got the following error in hdf5: /Users/runner/work/kissplice-ci-clone/kissplice-ci-clone/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Odeprec.c:141:8: error: call to undeclared function 'H5CX_set_apl'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] if(H5CX_set_apl(&lapl_id, H5P_CLS_LACC, loc_id, FALSE) < 0) ^ /Users/runner/work/kissplice-ci-clone/kissplice-ci-clone/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Odeprec.c:195:8: error: call to undeclared function 'H5CX_set_apl'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] if(H5CX_set_apl(&lapl_id, H5P_CLS_LACC, loc_id, FALSE) < 0) ^ /Users/runner/work/kissplice-ci-clone/kissplice-ci-clone/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Odeprec.c:322:8: error: call to undeclared function 'H5CX_set_apl'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] if(H5CX_set_apl(&lapl_id, H5P_CLS_LACC, loc_id, FALSE) < 0) ^ The long term fix is to use an up to date hdf5 (making it an external dependency ?). In the meantime add a header including the missing declaration. --- gatb-core/thirdparty/hdf5/src/H5Odeprec.c | 1 + 1 file changed, 1 insertion(+) diff --git a/gatb-core/thirdparty/hdf5/src/H5Odeprec.c b/gatb-core/thirdparty/hdf5/src/H5Odeprec.c index 33ed7874..0c924789 100644 --- a/gatb-core/thirdparty/hdf5/src/H5Odeprec.c +++ b/gatb-core/thirdparty/hdf5/src/H5Odeprec.c @@ -32,6 +32,7 @@ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ #include "H5Eprivate.h" /* Error handling */ #include "H5Opkg.h" /* Object headers */