[med-svn] [gubbins] 01/04: Imported Upstream version 1.4.4

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository gubbins.

commit 4448f22099607021b2d172ece62cec65d1d17c65
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 9 17:06:48 2015 +0100

    Imported Upstream version 1.4.4
---
 VERSION                |  2 +-
 configure.ac           | 17 ++++++++++++++---
 src/Makefile.am        |  8 +++++---
 tests/helper_methods.c |  6 +++---
 4 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/VERSION b/VERSION
index 428b770..1c99cf0 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.4.3
+1.4.4
diff --git a/configure.ac b/configure.ac
index eff27a5..673f5a7 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,12 +1,22 @@
-AC_INIT([gubbins], m4_esyscmd([tr -d '\n' < VERSION]), [aidan at ontologyengineering.org], [$(PACKAGE_NAME)$(AC_PACKAGE_VERSION)], [https://github.com/sanger-pathogens/gubbins])
+AC_INIT([gubbins], m4_esyscmd([tr -d '\n' < VERSION]), [gubbins at sanger.ac.uk], [$(PACKAGE_NAME)$(AC_PACKAGE_VERSION)], [https://github.com/sanger-pathogens/gubbins])
 
-AM_INIT_AUTOMAKE([foreign tar-pax])
+AM_INIT_AUTOMAKE([foreign tar-pax subdir-objects])
 AC_CONFIG_SRCDIR([configure.ac])
 AC_CONFIG_HEADERS([config.h])
 
 # Add our own macro dir, so we can check for PTHREAD
 AC_CONFIG_MACRO_DIR([m4])
 
+AC_CANONICAL_HOST
+
+case $host_os in
+	*linux*)
+		HOST_OS=linux
+		;;
+	*) ;;
+esac
+AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux])
+
 AC_PROG_LIBTOOL
 AC_PROG_CC
 AC_PROG_CXX
@@ -16,6 +26,7 @@ AX_PTHREAD
 
 # Ensure zlib is available
 PKG_CHECK_MODULES([zlib], [zlib])
+AC_CHECK_HEADERS([zlib.h math.h])
 
 # Check for Python
 AM_PATH_PYTHON([3.0],
@@ -28,4 +39,4 @@ AM_PATH_PYTHON([3.0],
 AC_CONFIG_FILES([Makefile src/Makefile release/Makefile python/Makefile])
 AC_OUTPUT
 
-AC_CHECK_HEADERS([zlib.h math.h])
+
diff --git a/src/Makefile.am b/src/Makefile.am
index 9982933..3100236 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,4 +1,3 @@
-
 # ship these headers in the "make dist" target
 EXTRA_DIST = Newickform.h alignment_file.h block_tab_file.h string_cat.h branch_sequences.h fasta_of_snp_sites.h gff_file.h gubbins.h kseq.h parse_phylip.h parse_vcf.h phylip_of_snp_sites.h seqUtil.h snp_searching.h snp_sites.h tree_statistics.h tree_scaling.h vcf.h
 
@@ -18,7 +17,6 @@ libgubbins_la_LIBADD = -lm
 #libPyGubbins_la_CPPFLAGS = $(PYTHON_CPPFLAGS)
 #libPyGubbins_la_LIBADD = $(PYTHON_LDFLAGS) -lboost_python libgubbins.la -lz -lm
 
-
 # "make check" target
 TESTS = $(check_PROGRAMS)
 check_PROGRAMS = run_all_tests
@@ -32,4 +30,8 @@ run_all_tests_SOURCES = \
 	../tests/helper_methods.c \
 	../tests/run_all_tests.c
 run_all_tests_CFLAGS = -I../tests $(PTHREAD_CFLAGS)
-run_all_tests_LDADD = -lcheck libgubbins.la -lz -lm $(PTHREAD_LDFLAGS) -lrt
+run_all_tests_LDADD = -lcheck libgubbins.la -lz -lm $(PTHREAD_LDFLAGS)
+
+if HOST_LINUX
+run_all_tests_LDADD += -lrt
+endif
diff --git a/tests/helper_methods.c b/tests/helper_methods.c
index 914dc84..258d731 100644
--- a/tests/helper_methods.c
+++ b/tests/helper_methods.c
@@ -23,14 +23,14 @@ int compare_files(char expected_output_filename[],char actual_output_filename[]
   fseek(expected_output_fh, 0L, SEEK_END);
   numbytes = ftell(expected_output_fh);
   fseek(expected_output_fh, 0L, SEEK_SET);	
-  expected_buffer = (char*)calloc(numbytes, sizeof(char));	
+  expected_buffer = (char*)calloc(numbytes +1, sizeof(char));	
   fread(expected_buffer, sizeof(char), numbytes, expected_output_fh);
   fclose(expected_output_fh);
   
   fseek(actual_output_fh, 0L, SEEK_END);
   numbytes = ftell(actual_output_fh);
   fseek(actual_output_fh, 0L, SEEK_SET);	
-  actual_buffer = (char*)calloc(numbytes, sizeof(char));	
+  actual_buffer = (char*)calloc(numbytes +1, sizeof(char));	
   fread(actual_buffer, sizeof(char), numbytes, actual_output_fh);
   fclose(actual_output_fh);
   
@@ -137,4 +137,4 @@ int cp(const char *to, const char *from)
 
     errno = saved_errno;
     return -1;
-}
\ No newline at end of file
+}

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gubbins.git