upgrade to 1.0.6

PR:		106849
Submitted by:	maintainer

8 files changed, 60 insertions, 27 deletions

diff --git a/science/cdo/Makefile b/science/cdo/Makefile
index e1cc978f3874..9f720b425e32 100644
--- a/science/cdo/Makefile
+++ b/science/cdo/Makefile
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	cdo
-PORTVERSION=	1.0.2
+PORTVERSION=	1.0.6
 CATEGORIES=	science
 MASTER_SITES=	http://www.mpimet.mpg.de/fileadmin/software/cdo/ \
 		http://sunpoet.net/distfiles/
@@ -20,6 +20,7 @@ GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--program-transform-name=""
 CONFIGURE_ENV=	CC="${CC}" \
 		CFLAGS="${CFLAGS} -I${LOCALBASE}/include ${PTHREAD_CFLAGS}" \
+		CPPFLAGS="${CPPFLAGS} -I${LOCALBASE}/include" \
 		LDFLAGS="${LDFLAGS} -L${LOCALBASE}/lib ${PTHREAD_LIBS}"
 
 PLIST_FILES=	bin/cdo
@@ -27,8 +28,6 @@ PLIST_FILES=	bin/cdo
 OPTIONS=	HDF5	"HDF5 support" off \
 		NETCDF	"NETCDF support" off
 
-.include <bsd.port.pre.mk>
-
 .if defined(WITH_HDF5)
 CONFIGURE_ARGS+=	--with-hdf5=${LOCALBASE}
 LIB_DEPENDS+=		hdf5.0:${PORTSDIR}/science/hdf5
@@ -39,8 +38,4 @@ CONFIGURE_ARGS+=	--with-netcdf=${LOCALBASE}
 LIB_DEPENDS+=		netcdf.1:${PORTSDIR}/science/netcdf
 .endif
 
-.if ${OSVERSION} <= 600000 
-EXTRA_PATCHES+=	"${PATCHDIR}/extra-patch-freebsd5-pthread"
-.endif
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/science/cdo/distinfo b/science/cdo/distinfo
index 2826a0baef22..3e8a8cf11b48 100644
--- a/science/cdo/distinfo
+++ b/science/cdo/distinfo
@@ -1,3 +1,3 @@
-MD5 (cdo-1.0.2.tar.gz) = c8bbdfdb1ca43fb58a0c403c8208b9d0
-SHA256 (cdo-1.0.2.tar.gz) = 41dd4e63c1f5e7927942da132d03b681ccced0cfe931258d19dbfad41c6a9699
-SIZE (cdo-1.0.2.tar.gz) = 1560719
+MD5 (cdo-1.0.6.tar.gz) = 4d27edf8c576cab34eacf358073456d1
+SHA256 (cdo-1.0.6.tar.gz) = aaf22308a446942bac9158f631ca749cd91d33e4985cca4f6e7c6cf37b474ec5
+SIZE (cdo-1.0.6.tar.gz) = 2279653
diff --git a/science/cdo/files/patch-src-cdo.c b/science/cdo/files/patch-src-cdo.c
deleted file mode 100644
index c488e335a891..000000000000
--- a/science/cdo/files/patch-src-cdo.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/cdo.c.orig	Tue Sep 12 14:50:14 2006
-+++ src/cdo.c	Mon Dec  4 17:38:55 2006
-@@ -663,7 +663,7 @@
-       fprintf(stderr, "FLT_EVAL_METHOD     = %d\n", FLT_EVAL_METHOD);
- #endif
- #if defined (FP_FAST_FMA)
--      fprintf(stderr, "FP_FAST_FMA         = %d\n", FP_FAST_FMA);
-+      fprintf(stderr, "FP_FAST_FMA         = defined\n");
- #endif
-       fprintf(stderr, "\n");
- 
diff --git a/science/cdo/files/extra-patch-freebsd5-pthread b/science/cdo/files/patch-src-cdo_pthread.c
index 0cf7364580af..34cddbdf3abe 100644
--- a/science/cdo/files/extra-patch-freebsd5-pthread
+++ b/science/cdo/files/patch-src-cdo_pthread.c
@@ -1,13 +1,13 @@
 --- src/cdo_pthread.c.orig	Wed Mar 22 22:04:18 2006
-+++ src/cdo_pthread.c	Mon Dec  4 11:46:11 2006
++++ src/cdo_pthread.c	Mon Dec 18 10:01:00 2006
 @@ -32,8 +32,10 @@
  {
  #if  defined  (HAVE_LIBPTHREAD)
    pthread_attr_t attr;
-+/*
++#if __FreeBSD_version >= 600000
    pthread_mutexattr_t m_attr;
    pthread_condattr_t c_attr;
-+*/
++#endif
  
  #if defined (PTHREAD_KEYS_MAX)
    fprintf(stderr, "PTHREAD_KEYS_MAX    = %d\n", PTHREAD_KEYS_MAX);
@@ -15,7 +15,7 @@
    print_pthread_attr("Default pthread attr", &attr);
    pthread_attr_destroy(&attr);
  
-+/*
++#if __FreeBSD_version >= 600000
    pthread_mutexattr_init(&m_attr);
    print_pthread_mutexattr("Default pthread mutexattr", &m_attr);
    pthread_mutexattr_destroy(&m_attr);
@@ -23,7 +23,7 @@
    pthread_condattr_init(&c_attr);
    print_pthread_condattr("Default pthread condattr ", &c_attr);
    pthread_condattr_destroy(&c_attr);
-+*/
++#endif
  
    fprintf(stderr, "\n");
  #endif
diff --git a/science/cdo/files/patch-src-config.h.in b/science/cdo/files/patch-src-config.h.in
new file mode 100644
index 000000000000..792cca69a62d
--- /dev/null
+++ b/science/cdo/files/patch-src-config.h.in
@@ -0,0 +1,11 @@
+--- src/config.h.in.orig	Wed Dec 13 21:30:19 2006
++++ src/config.h.in	Mon Dec 18 10:41:13 2006
+@@ -1,5 +1,8 @@
+ /* src/config.h.in.  Generated from configure.ac by autoheader.  */
+ 
++#include <unistd.h>
++#include <sys/param.h>
++
+ /* Compiler */
+ #undef COMPILER
+ 
diff --git a/science/cdo/files/patch-src-pthread_debug.c b/science/cdo/files/patch-src-pthread_debug.c
new file mode 100644
index 000000000000..accba3d44423
--- /dev/null
+++ b/science/cdo/files/patch-src-pthread_debug.c
@@ -0,0 +1,18 @@
+--- src/pthread_debug.c.orig	Mon Dec  4 16:11:40 2006
++++ src/pthread_debug.c	Mon Dec 18 10:01:00 2006
+@@ -77,6 +77,7 @@
+ }
+ 
+ 
++#if __FreeBSD_version >= 600000
+ void print_pthread_mutexattr(const char *caller,  pthread_mutexattr_t *m_attr)
+ {
+   int protocol, kind, pshared;
+@@ -107,6 +108,7 @@
+   POUT2(caller, pshared, PTHREAD_PROCESS_SHARED, PTHREAD_PROCESS_PRIVATE);
+ #endif
+ }
++#endif
+ 
+ 
+ int PTHREAD_Debug = 0;
diff --git a/science/cdo/files/patch-src-pthread_debug.h b/science/cdo/files/patch-src-pthread_debug.h
new file mode 100644
index 000000000000..ac134fe9be35
--- /dev/null
+++ b/science/cdo/files/patch-src-pthread_debug.h
@@ -0,0 +1,13 @@
+--- src/pthread_debug.h.orig	Wed Feb 15 21:22:38 2006
++++ src/pthread_debug.h	Mon Dec 18 10:01:00 2006
+@@ -15,8 +15,10 @@
+ void Pthread_cond_wait(const char *caller, pthread_cond_t *cond, pthread_mutex_t *mutex);
+ 
+ void print_pthread_attr(const char *caller, pthread_attr_t *attr);
++#if __FreeBSD_version >= 600000
+ void print_pthread_mutexattr(const char *caller,  pthread_mutexattr_t *m_attr);
+ void print_pthread_condattr(const char *caller, pthread_condattr_t *c_attr);
++#endif
+ 
+ 
+ #define  pthread_create(a, b, c, d)    Pthread_create(func, a, b, c, d)
diff --git a/science/cdo/pkg-message b/science/cdo/pkg-message
new file mode 100644
index 000000000000..9fcc65b65a4d
--- /dev/null
+++ b/science/cdo/pkg-message
@@ -0,0 +1,7 @@
+In CDO version 1.0.6, three new environment variables were introduced:
+- CDO_DISABLE_HISTORY:
+  If set to 1, the netCDF history attribute of input datasets is not used.
+- CDO_DISABLE_FILESUFFIX:
+  If set to 1, file suffix (.grb, .nc, ...) will not be added to the output file name of split*.
+- IGNORE_ATT_COORDINATES:
+  If set to 1, netCDF variable attribute "coordinates" will be ignored.