[med-svn] [indelible] 01/11: added build system and fix headers

[Fabian Klötzl]

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kloetzl-guest pushed a commit to branch master
in repository indelible.

commit 1293159cd6d5bde6e22a18e5553ad7f46c27cb3e
Author: Fabian Klötzl <fabian at kloetzl.info>
Date:   Mon Dec 21 13:50:01 2015 +0100

    added build system and fix headers
---
 .../patches/0001-added-headers-for-getpid-2.patch  | 21 +++++++++
 .../0002-added-auto-tools-build-system.patch       | 54 ++++++++++++++++++++++
 debian/patches/series                              |  2 +
 3 files changed, 77 insertions(+)

diff --git a/debian/patches/0001-added-headers-for-getpid-2.patch b/debian/patches/0001-added-headers-for-getpid-2.patch
new file mode 100644
index 0000000..cabe097
--- /dev/null
+++ b/debian/patches/0001-added-headers-for-getpid-2.patch
@@ -0,0 +1,21 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 21 Dec 2015 13:37:33 +0100
+Subject: added headers for getpid(2)
+
+---
+ src/indelible.cpp | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/indelible.cpp b/src/indelible.cpp
+index 46de883..75ce82a 100644
+--- a/src/indelible.cpp
++++ b/src/indelible.cpp
+@@ -123,6 +123,8 @@ int inspinvcount, corepinvcount;
+ #include <sstream>
+ #include <algorithm>
+ #include <map>
++#include <sys/types.h>
++#include <unistd.h>
+ 
+ #ifdef WINDOWS
+ 	#include "windows.h"
diff --git a/debian/patches/0002-added-auto-tools-build-system.patch b/debian/patches/0002-added-auto-tools-build-system.patch
new file mode 100644
index 0000000..0cc970e
--- /dev/null
+++ b/debian/patches/0002-added-auto-tools-build-system.patch
@@ -0,0 +1,54 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 21 Dec 2015 13:39:45 +0100
+Subject: added auto tools build system
+
+Upstream did not provide a makefile or any more advanced build system. Thus,
+I added files for autoconf and automake to help with the installation.
+---
+ Makefile.am  |  6 ++++++
+ configure.ac | 23 +++++++++++++++++++++++
+ 2 files changed, 29 insertions(+)
+ create mode 100644 Makefile.am
+ create mode 100644 configure.ac
+
+diff --git a/Makefile.am b/Makefile.am
+new file mode 100644
+index 0000000..ba9c4ba
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,6 @@
++bin_PROGRAMS= indelible
++indelible_SOURCES= src/indelible.cpp
++indelible_CPPFLAGS= -Isrc
++
++# The following files are #included by indelible.cpp
++EXTRA_indelible_SOURCES= src/control.cpp src/models.cpp src/paml.cpp src/randoms.cpp src/MersenneTwister.h
+diff --git a/configure.ac b/configure.ac
+new file mode 100644
+index 0000000..3d34e72
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,23 @@
++AC_INIT([indelible], [1.03])
++AM_INIT_AUTOMAKE([-Wall foreign])
++
++AC_PROG_CPP
++AC_PROG_CXX
++
++AC_LANG(C++)
++
++AC_CHECK_LIB([m],[cos])
++
++AC_TYPE_SIZE_T
++AC_TYPE_INT32_T
++AC_TYPE_UINT32_T
++AC_HEADER_STDBOOL
++
++AC_FUNC_MALLOC
++AC_CHECK_HEADERS([limits.h])
++AC_CHECK_FUNCS([floor pow sqrt])
++
++AC_CONFIG_FILES([
++ Makefile
++])
++AC_OUTPUT
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..028adcf
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+0001-added-headers-for-getpid-2.patch
+0002-added-auto-tools-build-system.patch

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