Added library dependencies iherited from use of HDF5 on NCBI Cobalt including the need for the Intel Compiler's C runtime. This will need to be cleaned up so that Cobalt specific dependencies don't pollute the baseline. Also changed compiler flag from using GNU99 standards to pure C99 for possibility of using the Intel Compiler. Note that Intel's icc accepts gnu99 but then doesn't implement it properly since it does not accept the C99 syntax of declaring variables in for loops even though GNU99 implies C99.

2 files changed, 8 insertions, 6 deletions

diff --git a/configure.ac b/configure.ac
index f45958c..59c5f36 100644
--- a/configure.ac
+++ b/configure.ac
@@ -12,14 +12,12 @@ AC_CONFIG_FILES([
 ################
 
 AC_SEARCH_LIBS([H5Fcreate],[hdf5],[],
-[AC_MSG_ERROR(The HDF5 libraries are needed to build the system.)])
+[AC_MSG_ERROR(The HDF5 libraries are needed to build the system.)],
+[-lirc -lmpi -lz -lsz])
 
 AC_SEARCH_LIBS([H5TBmake_table],[hdf5_hl],[],
 [AC_MSG_ERROR(The HDF5 libraries are needed to build the system.)],
-[-lhdf5])
-
-AC_CHECK_HEADERS([mpi.h],[],
-[AC_MSG_ERROR(The MPI headers are needed to build the system.)])
+[-lirc -lhdf5 -lmpi -lz -lsz])
 
 AC_CHECK_HEADERS([hdf5.h],[],
 [AC_MSG_ERROR(The HDF5 headers are needed to build the system.)])
diff --git a/src/Makefile.am b/src/Makefile.am
index adc9e8d..752c0fe 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -10,6 +10,8 @@ aggregator_SOURCES = \
         model/blast_scores_data_init.c \
         model/sequence_data_init.c
 
+aggregator_LDADD = -lirc -lmpi -lsz -lz
+
 updator_SOURCES = \
         updator.c \
         assign/assign_protein_type.c \
@@ -19,6 +21,8 @@ updator_SOURCES = \
         model/gi_type_data_init.c \
         model/sequence_data_init.c
 
+updator_LDADD = -lirc -lmpi -lsz -lz
+
 noinst_HEADERS = \
         assign/assign_protein_type.h \
         error/check_error.h \
@@ -33,4 +37,4 @@ noinst_HEADERS = \
         model/sequence_data.h \
         model/sequence_data_init.h
 
-AM_CFLAGS = -Wall -std=gnu99
+AM_CFLAGS = -Wall -std=c99