From 4e5bd0461a7de0a5af295c4d7c36b9e8da4f27a7 Mon Sep 17 00:00:00 2001
From: Joe Zhu <sha.joe.zhu@gmail.com>
Date: Mon, 23 Dec 2024 00:31:01 +0800
Subject: [PATCH] update

---
 Makefile.am                     |  2 +-
 src/codeCogs/asympt_expn.h      |  6 +++---
 src/codeCogs/errorfn.h          |  2 +-
 src/codeCogs/errorfnc.h         |  6 +++---
 src/codeCogs/errorfnc_exp.h     |  2 +-
 src/codeCogs/gamma.h            |  4 ++--
 src/codeCogs/log_gamma.h        |  2 +-
 src/codeCogs/logbeta.h          | 10 +++++-----
 src/codeCogs/loggammasum.h      |  2 +-
 src/codeCogs/stirling.h         |  2 +-
 tests/test-coverage-coverall.sh |  6 +++---
 11 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 84d1fc7e..c1870bbe 100755
--- a/Makefile.am
+++ b/Makefile.am
@@ -16,7 +16,7 @@ TESTS = unit_tests io_unit_tests
 check_PROGRAMS = unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
 PROG = DEPLOID
 
-common_flags = -std=c++17 -Isrc/ -Isrc/vcf/src/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\" -Wall  -Wextra
+common_flags = -std=c++17 -Isrc/ -Isrc/codeCogs/ -Isrc/vcf/src/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\" -Wall  -Wextra
 
 common_LDADD = -lz
 
diff --git a/src/codeCogs/asympt_expn.h b/src/codeCogs/asympt_expn.h
index 55a8fd1c..a5491164 100755
--- a/src/codeCogs/asympt_expn.h
+++ b/src/codeCogs/asympt_expn.h
@@ -18,9 +18,9 @@
 #include <assert.h>
 
 #include <math.h>
-#include "src/codeCogs/xsub_ln_add1.h"
-#include "src/codeCogs/errorfnc.h"
-#include "src/codeCogs/errorfnc_exp.h"
+#include "xsub_ln_add1.h"
+#include "errorfnc.h"
+#include "errorfnc_exp.h"
 
 namespace Maths
 {
diff --git a/src/codeCogs/errorfn.h b/src/codeCogs/errorfn.h
index 7be45d67..dc66d273 100755
--- a/src/codeCogs/errorfn.h
+++ b/src/codeCogs/errorfn.h
@@ -14,7 +14,7 @@
 #define MATHS_SPECIAL_ERRORFN_H
 
 #include <assert.h>
-#include "src/codeCogs/poly_eval.h"
+#include "poly_eval.h"
 
 namespace Maths
 {
diff --git a/src/codeCogs/errorfnc.h b/src/codeCogs/errorfnc.h
index bbbf5aa2..b1084e4d 100755
--- a/src/codeCogs/errorfnc.h
+++ b/src/codeCogs/errorfnc.h
@@ -24,9 +24,9 @@
 #endif
 #endif
 
-#include "src/codeCogs/expx2.h"
-#include "src/codeCogs/errorfnc_exp.h"
-#include "src/codeCogs/errorfn.h"
+#include "expx2.h"
+#include "errorfnc_exp.h"
+#include "errorfn.h"
 
 #define MINLOG -7.08396418532264106224E2
 
diff --git a/src/codeCogs/errorfnc_exp.h b/src/codeCogs/errorfnc_exp.h
index f384cb7f..998deaf8 100755
--- a/src/codeCogs/errorfnc_exp.h
+++ b/src/codeCogs/errorfnc_exp.h
@@ -24,7 +24,7 @@
 #endif
 #endif
 
-#include "src/codeCogs/poly_eval.h"
+#include "poly_eval.h"
 
 namespace Maths
 {
diff --git a/src/codeCogs/gamma.h b/src/codeCogs/gamma.h
index 39de0514..70cb84de 100755
--- a/src/codeCogs/gamma.h
+++ b/src/codeCogs/gamma.h
@@ -26,8 +26,8 @@
 
 #include <math.h>
 #include <float.h>
-#include "src/codeCogs/poly_eval.h"
-#include "src/codeCogs/stirling.h"
+#include "poly_eval.h"
+#include "stirling.h"
 
 #define MAXNUM 1.79769313486231570815E308
 #define PI 3.141592653589793238
diff --git a/src/codeCogs/log_gamma.h b/src/codeCogs/log_gamma.h
index 1bcfcf48..7380dcb7 100755
--- a/src/codeCogs/log_gamma.h
+++ b/src/codeCogs/log_gamma.h
@@ -15,7 +15,7 @@
 #define MATHS_SPECIAl_GAMMA_LOG_GAMMA_H
 
 #include <cmath>
-#include "src/codeCogs/machine_epsilon.h"
+#include "machine_epsilon.h"
 
 #define D1      -0.5772156649015328605195174
 #define D2      0.4227843350984671393993777
diff --git a/src/codeCogs/logbeta.h b/src/codeCogs/logbeta.h
index c6a4a1bd..a1f48ebe 100755
--- a/src/codeCogs/logbeta.h
+++ b/src/codeCogs/logbeta.h
@@ -15,11 +15,11 @@
 #define MATHS_SPECIAL_GAMMA_LOGBETA_H
 
 #include <math.h>
-#include "src/codeCogs/ln_add1.h"
-#include "src/codeCogs/log_gamma.h"
-#include "src/codeCogs/loggammasum.h"
-#include "src/codeCogs/loggammafrac.h"
-#include "src/codeCogs/asympt_expn.h"
+#include "ln_add1.h"
+#include "log_gamma.h"
+#include "loggammasum.h"
+#include "loggammafrac.h"
+#include "asympt_expn.h"
 
 namespace Maths
 {
diff --git a/src/codeCogs/loggammasum.h b/src/codeCogs/loggammasum.h
index 0afe10c5..d2c84c50 100755
--- a/src/codeCogs/loggammasum.h
+++ b/src/codeCogs/loggammasum.h
@@ -16,7 +16,7 @@
 
 #include <assert.h>
 #include <math.h>
-#include "src/codeCogs/log_gamma.h"
+#include "log_gamma.h"
 
 namespace Maths
 {
diff --git a/src/codeCogs/stirling.h b/src/codeCogs/stirling.h
index f8e985e8..ac36b253 100755
--- a/src/codeCogs/stirling.h
+++ b/src/codeCogs/stirling.h
@@ -16,7 +16,7 @@
 
 #include <math.h>
 #include <float.h>
-#include "src/codeCogs/poly_eval.h"
+#include "poly_eval.h"
 
 namespace Maths
 {
diff --git a/tests/test-coverage-coverall.sh b/tests/test-coverage-coverall.sh
index 84c415b1..1239c88b 100755
--- a/tests/test-coverage-coverall.sh
+++ b/tests/test-coverage-coverall.sh
@@ -4,8 +4,8 @@
 make -mj
 
 # Generate html report
-lcov --base-directory . --directory . --zerocounters -q
+lcov --ignore-errors empty --base-directory . --directory . --zerocounters -q
 make check -mj
-lcov --base-directory . --directory . -c -o coverage/lcov.info
+lcov --ignore-errors empty --base-directory . --directory . -c -o coverage/lcov.info
 # --rc lcov_branch_coverage=1 option will turn on branch check
-lcov --remove coverage/lcov.info "/usr*" "src/codeCogs/*" "src/random/*" "src/export/*" "src/gzstream/*" "tests/unittest/*" -o coverage/lcov.info # remove output for external libraries
+lcov --ignore-errors empty --remove coverage/lcov.info "/usr*" "src/codeCogs/*" "src/vcf/*" "src/lasso/*" "src/export/*" "src/gzstream/*" "tests/unittest/*" -o coverage/lcov.info # remove output for external libraries