update to netcdf-4.6.3, from martin@ taking maintainer, various feedback

from landry@ and myself, ok with Tom Knienieder (outgoing maintainer)

math/netcdf/Makefile

@@ -1,45 +1,58 @@
-# $OpenBSD: Makefile,v 1.33 2018/10/28 07:31:29 bentley Exp $ 
+# $OpenBSD: Makefile,v 1.34 2019/03/13 20:27:40 sthen Exp $
 
-BROKEN-powerpc=	fails to build
-BROKEN-hppa =	fails to configure
+# let's give it a chance?
+#BROKEN-powerpc=	fails to build
+#BROKEN-hppa =	fails to configure
 
 COMMENT=	library for machine-independent, array-oriented data access
 
-DISTNAME=	netcdf-3.6.2
-REVISION =	7
+V=		4.6.3
+NAME=		netcdf
+DISTNAME=	${NAME}-c-${V}
+PKGNAME=	${NAME}-${V}
+
 CATEGORIES=	math
 
-SHARED_LIBS=	netcdf		4.0 \
-		netcdff		4.0 \
-		netcdf_c++	4.0
+SHARED_LIBS=	netcdf		5.0 # 4.0
 
 HOMEPAGE=	http://www.unidata.ucar.edu/software/netcdf/
 
-MAINTAINER=	Tom Knienieder <tom@knienieder.com>
-MODULES =	fortran
-MODFORTRAN_COMPILER = g77
-BUILD_DEPENDS =	${MODFORTRAN_BUILD_DEPENDS}
+MAINTAINER=	Martin Reindl <martin@catai.org>
 
-# BSD-like
+# BSD
 PERMIT_PACKAGE_CDROM=	Yes
 
-WANTLIB=		c m ${COMPILER_LIBCXX}
+WANTLIB=		c m z pthread
+WANTLIB+=		curl crypto nghttp2 ssl
+WANTLIB+=		hdf5 hdf5_hl
+
+LIB_DEPENDS =		net/curl \
+			math/hdf5
+
+TEST_DEPENDS=		shells/bash \
+			textproc/gdiff
 
 COMPILER =		base-clang ports-gcc base-gcc
 
 MASTER_SITES=		ftp://ftp.unidata.ucar.edu/pub/netcdf/
 
 CONFIGURE_STYLE= 	gnu
-CONFIGURE_ENV=		CPPFLAGS="-Df2cFortran"
+CONFIGURE_ENV+=		LDFLAGS="-L${LOCALBASE}/lib" \
+			CPPFLAGS="-I${LOCALBASE}/include"
+
 CONFIGURE_ARGS+=	--enable-shared \
-			--disable-f90
+			--disable-doxygen \
+			--enable-netcdf-4 \
+			--enable-dap \
+			--prefix=${PREFIX}
 
 USE_GMAKE=		Yes
 SEPARATE_BUILD=		Yes
 
+# https://github.com/Unidata/netcdf-c/issues/1347#issuecomment-467633543
+# "Actually, I did not intend the .so files in netcdf-c/plugins to be
+# installed. They are intended only for testing and examples"
 post-install:
-	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/netcdf
-	@cd ${WRKSRC}/man && ${INSTALL_DATA} *.txt *.pdf \
-		${PREFIX}/share/doc/netcdf
+	rm ${PREFIX}/lib/lib{bzip2,misc}.{a,la,so}
 
 .include <bsd.port.mk>

math/netcdf/distinfo

@@ -1,2 +1,2 @@
-SHA256 (netcdf-3.6.2.tar.gz) = /qp2c/Np5ftX/MUUJuK+aUIo3cwUH8P9IDmSaftrkxE=
-SIZE (netcdf-3.6.2.tar.gz) = 5312882
+SHA256 (netcdf-c-4.6.3.tar.gz) = M1/fFtdTH0MK115zLtGpo/yDrT75H7M6cBGaVV3VQVw=
+SIZE (netcdf-c-4.6.3.tar.gz) = 5961248

math/netcdf/patches/patch-cxx_ncvalues_cpp

@@ -1,13 +0,0 @@
-$OpenBSD: patch-cxx_ncvalues_cpp,v 1.1 2018/10/28 07:31:29 bentley Exp $
-
-Index: cxx/ncvalues.cpp
---- cxx/ncvalues.cpp.orig
-+++ cxx/ncvalues.cpp
-@@ -10,6 +10,7 @@
- #include <config.h>
- #include <iostream>
- #include <string>
-+#include <cstring>
- 
- #include "ncvalues.h"
- 

math/netcdf/patches/patch-dap4_test_test_data_sh

@@ -0,0 +1,32 @@
+$OpenBSD: patch-dap4_test_test_data_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: dap4_test/test_data.sh
+--- dap4_test/test_data.sh.orig
++++ dap4_test/test_data.sh
+@@ -21,8 +21,8 @@ for f in $F ; do
+     fi
+     ${NCDUMP} ./results_test_data/${f}.nc > ./results_test_data/${f}.d4d
+     if test "x${TEST}" = x1 ; then
+-	if ! diff -wBb ${BASELINE}/${f}.d4d ./results_test_data/${f}.d4d ; then
+-	    failure "diff -wBb ${BASELINE}/${f}.d4d ./results_test_data/${f}.d4d"
++	if ! gdiff -wBb ${BASELINE}/${f}.d4d ./results_test_data/${f}.d4d ; then
++	    failure "gdiff -wBb ${BASELINE}/${f}.d4d ./results_test_data/${f}.d4d"
+ 	fi
+     elif test "x${RESET}" = x1 ; then
+ 	echo "${f}:"
+@@ -77,13 +77,13 @@ if test "x${CDLDIFF}" = x1 ; then
+       echo "Not found: ${CDLTESTFILES}/${STEM}.cdl"
+       continue
+     fi
+-    echo "diff -wBb ${CDLTESTFILES}/${STEM}.cdl ./results_test_data/${f}.d4d"
++    echo "gdiff -wBb ${CDLTESTFILES}/${STEM}.cdl ./results_test_data/${f}.d4d"
+     rm -f ./b1 ./b2 ./r1 ./r2
+     trim ${CDLTESTFILES}/${STEM}.cdl ./b1
+     trim ./results_test_data/${f}.d4d ./r1
+     baseclean b1 b2
+     resultclean r1 r2
+-    if ! diff -wBb ./b2 ./r2 ; then
++    if ! gdiff -wBb ./b2 ./r2 ; then
+ 	failure "${f}"
+     fi
+   done

math/netcdf/patches/patch-dap4_test_test_meta_sh

@@ -0,0 +1,32 @@
+$OpenBSD: patch-dap4_test_test_meta_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: dap4_test/test_meta.sh
+--- dap4_test/test_meta.sh.orig
++++ dap4_test/test_meta.sh
+@@ -34,8 +34,8 @@ for f in ${F} ; do
+     fi
+     ${NCDUMP} ${DUMPFLAGS} -h ./results_test_meta/${f} > ./results_test_meta/${f}.d4m
+     if test "x${TEST}" = x1 ; then
+-	if ! diff -wBb ${BASELINE}/${f}.d4m ./results_test_meta/${f}.d4m ; then
+-	    failure "diff -wBb ${BASELINE}/${f}.ncdump ./results_test_meta/${f}.d4m"
++	if ! gdiff -wBb ${BASELINE}/${f}.d4m ./results_test_meta/${f}.d4m ; then
++	    failure "gdiff -wBb ${BASELINE}/${f}.ncdump ./results_test_meta/${f}.d4m"
+ 	fi
+     elif test "x${RESET}" = x1 ; then
+ 	echo "${f}:" 
+@@ -45,12 +45,12 @@ done
+ 
+ if test "x${CDLDIFF}" = x1 ; then
+   for f in $CDL ; do
+-    echo "diff -wBb ${CDLTESTFILES}/${f}.cdl ./results_test_meta/${f}.d4m"
++    echo "gdiff -wBb ${CDLTESTFILES}/${f}.cdl ./results_test_meta/${f}.d4m"
+     rm -f ./tmp
+     cat ${CDLTESTFILES}/${f}.cdl \
+     cat >./tmp
+-    echo diff -wBbu ./tmp ./results_test_meta/${f}.d4m
+-    if ! diff -wBbu ./tmp ./results_test_meta/${f}.d4m ; then
++    echo gdiff -wBbu ./tmp ./results_test_meta/${f}.d4m
++    if ! gdiff -wBbu ./tmp ./results_test_meta/${f}.d4m ; then
+ 	failure "${f}" 
+     fi
+   done

math/netcdf/patches/patch-dap4_test_test_parse_sh

@@ -0,0 +1,27 @@
+$OpenBSD: patch-dap4_test_test_parse_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: dap4_test/test_parse.sh
+--- dap4_test/test_parse.sh.orig
++++ dap4_test/test_parse.sh
+@@ -20,18 +20,18 @@ for f in $F ; do
+ 	failure "${f}"
+     fi
+     if test "x${TEST}" = x1 ; then
+-	if ! diff -wBb ${BASELINE}/${f}.d4p ./results_test_parse/${f}.d4p ; then
++	if ! gdiff -wBb ${BASELINE}/${f}.d4p ./results_test_parse/${f}.d4p ; then
+ 	    failure "${f}"
+ 	fi
+     elif test "x${DIFF}" = x1 ; then
+-	echo "diff -wBb ${DMRTESTFILES}/${f}.dmr ./results_test_parse/${f}.d4p"
++	echo "gdiff -wBb ${DMRTESTFILES}/${f}.dmr ./results_test_parse/${f}.d4p"
+ 	rm -f ./tmp
+ 	cat ./results_test_parse/${f}.d4p \
+ 	| sed -e '/<Dimensions>/d' -e '/<Types>'/d -e '/<Variables>'/d -e '/<Groups>'/d \
+ 	| sed -e '/<\/Dimensions>/d' -e '/<\/Types>'/d -e '/<\/Variables>'/d -e '/<\/Groups>'/d  \
+ 	| sed -e '/_edu.ucar.opaque.size/,+2d' \
+ 	| cat > ./tmp
+-	if ! diff -wBb ${DMRTESTFILES}/${f}.dmr ./tmp ; then
++	if ! gdiff -wBb ${DMRTESTFILES}/${f}.dmr ./tmp ; then
+ 	    failure "${f}" 
+ 	fi
+     elif test "x${RESET}" = x1 ; then

math/netcdf/patches/patch-dap4_test_test_raw_sh

@@ -0,0 +1,27 @@
+$OpenBSD: patch-dap4_test_test_raw_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: dap4_test/test_raw.sh
+--- dap4_test/test_raw.sh.orig
++++ dap4_test/test_raw.sh
+@@ -51,8 +51,8 @@ for f in $F ; do
+         failure "${URL}"
+     fi
+     if test "x${TEST}" = x1 ; then
+-	if ! diff -wBb ${BASELINERAW}/${f}.dmp ${builddir}/results_test_raw/${f}.dmp ; then
+-	    failure "diff ${f}.dmp"
++	if ! gdiff -wBb ${BASELINERAW}/${f}.dmp ${builddir}/results_test_raw/${f}.dmp ; then
++	    failure "gdiff ${f}.dmp"
+ 	fi
+     elif test "x${RESET}" = x1 ; then
+ 	echo "${f}:"
+@@ -60,8 +60,8 @@ for f in $F ; do
+     elif test "x${DIFF}" = x1 ; then
+ 	echo "hdrtest: ${f}"
+ 	baseclean
+-        if ! diff -wBb ${BASELINERAW}/${f}.dmp ${BASELINE}/${f}.ncdump ; then
+-          failure diff -wBb ${BASELINERAW}/${f}.dmp ${BASELINE}/${f}.ncdump
++        if ! gdiff -wBb ${BASELINERAW}/${f}.dmp ${BASELINE}/${f}.ncdump ; then
++          failure gdiff -wBb ${BASELINERAW}/${f}.dmp ${BASELINE}/${f}.ncdump
+ 	fi
+     fi
+ done

math/netcdf/patches/patch-dap4_test_test_remote_sh

@@ -0,0 +1,16 @@
+$OpenBSD: patch-dap4_test_test_remote_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: dap4_test/test_remote.sh
+--- dap4_test/test_remote.sh.orig
++++ dap4_test/test_remote.sh
+@@ -77,8 +77,8 @@ for f in $F ; do
+         failure "${URL}"
+     fi
+     if test "x${TEST}" = x1 ; then
+-	if ! diff -wBb "${BASELINEREM}/${f}.dmp" "${builddir}/results_test_remote/${f}.dmp" ; then
+-	    failure "diff ${f}.dmp"
++	if ! gdiff -wBb "${BASELINEREM}/${f}.dmp" "${builddir}/results_test_remote/${f}.dmp" ; then
++	    failure "gdiff ${f}.dmp"
+ 	fi
+     elif test "x${RESET}" = x1 ; then
+ 	echo "${f}:" 

math/netcdf/patches/patch-libdispatch_dfile_c

@@ -0,0 +1,13 @@
+$OpenBSD: patch-libdispatch_dfile_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: libdispatch/dfile.c
+--- libdispatch/dfile.c.orig
++++ libdispatch/dfile.c
+@@ -32,7 +32,6 @@
+ #ifdef HAVE_STDIO_H
+ #include <stdio.h>
+ #endif
+-extern int fileno(FILE*);
+ 
+ #include "ncdispatch.h"
+ #include "netcdf_mem.h"

math/netcdf/patches/patch-libdispatch_dparallel_c

@@ -0,0 +1,13 @@
+$OpenBSD: patch-libdispatch_dparallel_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: libdispatch/dparallel.c
+--- libdispatch/dparallel.c.orig
++++ libdispatch/dparallel.c
+@@ -10,7 +10,6 @@
+ #ifdef HAVE_STDIO_H
+ #include <stdio.h>
+ #endif
+-extern int fileno(FILE*);
+ 
+ /**
+ Create a netCDF file for parallel I/O.

math/netcdf/patches/patch-nc_test4_tst_camrun_c

@@ -0,0 +1,17 @@
+$OpenBSD: patch-nc_test4_tst_camrun_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: nc_test4/tst_camrun.c
+--- nc_test4/tst_camrun.c.orig
++++ nc_test4/tst_camrun.c
+@@ -685,10 +685,10 @@ get_mem_used2(int *mem_used)
+       fscanf(pf, "%u %u %u %u %u %u", &size, &resident, &share,
+ 	     &text, &lib, &data);
+       *mem_used = (data * page_size) / MEGABYTE;
++      fclose(pf);
+    }
+    else
+       *mem_used = -1;
+-  fclose(pf);
+ }
+ 
+ int

math/netcdf/patches/patch-ncdap_test_tst_remote3_sh

@@ -0,0 +1,11 @@
+$OpenBSD: patch-ncdap_test_tst_remote3_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncdap_test/tst_remote3.sh
+--- ncdap_test/tst_remote3.sh.orig
++++ ncdap_test/tst_remote3.sh
+@@ -1,4 +1,4 @@
+-#!/bin/bash
++#!/usr/local/bin/bash
+ 
+ if test "x$SETX" = x1 ; then set -x ; fi
+ 

math/netcdf/patches/patch-ncdap_test_tst_urls_sh

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncdap_test_tst_urls_sh,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncdap_test/tst_urls.sh
+--- ncdap_test/tst_urls.sh.orig
++++ ncdap_test/tst_urls.sh
+@@ -8,7 +8,7 @@
+ # Define various sets of test targets
+ 
+ # Figure our dst server; if none, then just stop
+-DTS=`${execdir}/findtestserver dap2 dts`
++DTS=`./findtestserver dap2 dts`
+ if test "x$DTS" = "x" ; then
+ echo "WARNING: Cannot locate test server for dts"
+ exit 1

math/netcdf/patches/patch-ncgen3_ncgen_l

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncgen3_ncgen_l,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncgen3/ncgen.l
+--- ncgen3/ncgen.l.orig
++++ ncgen3/ncgen.l
+@@ -25,8 +25,6 @@
+    We include lexical definitions for all three, but use the second version.
+ */
+ 
+-extern int fileno(FILE*);
+-
+ /* lex specification for tokens for ncgen */
+ 
+ /* Fill value used by ncdump from version 2.4 and later.  Should match

math/netcdf/patches/patch-ncgen3_ncgen_y

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncgen3_ncgen_y,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncgen3/ncgen.y
+--- ncgen3/ncgen.y.orig
++++ ncgen3/ncgen.y
+@@ -19,8 +19,6 @@ static char SccsId[] = "$Id: ncgen.y,v 1.34 2010/03/31
+ #include        "ncgen.h"
+ #include	"genlib.h"	/* for grow_darray() et al */
+ 
+-extern int fileno(FILE*);
+-
+ typedef struct Symbol {		/* symbol table entry */
+ 	char    	*name;
+ 	struct Symbol   *next;

math/netcdf/patches/patch-ncgen3_ncgentab_c

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncgen3_ncgentab_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncgen3/ncgentab.c
+--- ncgen3/ncgentab.c.orig
++++ ncgen3/ncgentab.c
+@@ -84,8 +84,6 @@ static char SccsId[] = "$Id: ncgen.y,v 1.34 2010/03/31
+ #include        "ncgen.h"
+ #include	"genlib.h"	/* for grow_darray() et al */
+ 
+-extern int fileno(FILE*);
+-
+ typedef struct Symbol {		/* symbol table entry */
+ 	char    	*name;
+ 	struct Symbol   *next;

math/netcdf/patches/patch-ncgen3_ncgenyy_c

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncgen3_ncgenyy_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncgen3/ncgenyy.c
+--- ncgen3/ncgenyy.c.orig
++++ ncgen3/ncgenyy.c
+@@ -865,8 +865,6 @@ char *ncgtext;
+    We include lexical definitions for all three, but use the second version.
+ */
+ 
+-extern int fileno(FILE*);
+-
+ /* lex specification for tokens for ncgen */
+ 
+ /* Fill value used by ncdump from version 2.4 and later.  Should match

math/netcdf/patches/patch-ncgen_ncgen_1

@@ -1,14 +0,0 @@
-$OpenBSD: patch-ncgen_ncgen_1,v 1.1 2017/05/08 13:31:58 schwarze Exp $
-
-Index: ncgen/ncgen.1
---- ncgen/ncgen.1.orig
-+++ ncgen/ncgen.1
-@@ -339,7 +339,7 @@ are all acceptable \fIfloat\fP constants:
- -2.0f
- 3.14159265358979f	// will be truncated to less precision
- 1.f
--.1f
-+\&.1f
- .fi
- .RE
- .LP

math/netcdf/patches/patch-ncgen_ncgen_l

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncgen_ncgen_l,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncgen/ncgen.l
+--- ncgen/ncgen.l.orig
++++ ncgen/ncgen.l
+@@ -38,8 +38,6 @@
+ #include "ncgen.h"
+ #include "ncgeny.h"
+ 
+-EXTERNL int fileno(FILE*);
+-
+ #define FILL_STRING "_"
+ #define XDR_INT32_MIN (-2147483647-1)
+ #define XDR_INT32_MAX 2147483647

math/netcdf/patches/patch-ncgen_ncgenl_c

@@ -0,0 +1,14 @@
+$OpenBSD: patch-ncgen_ncgenl_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: ncgen/ncgenl.c
+--- ncgen/ncgenl.c.orig
++++ ncgen/ncgenl.c
+@@ -1420,8 +1420,6 @@ char *yytext;
+ #include "ncgen.h"
+ #include "ncgeny.h"
+ 
+-EXTERNL int fileno(FILE*);
+-
+ #define FILL_STRING "_"
+ #define XDR_INT32_MIN (-2147483647-1)
+ #define XDR_INT32_MAX 2147483647

math/netcdf/patches/patch-oc2_ocdump_c

@@ -0,0 +1,14 @@
+$OpenBSD: patch-oc2_ocdump_c,v 1.1 2019/03/13 20:27:40 sthen Exp $
+
+Index: oc2/ocdump.c
+--- oc2/ocdump.c.orig
++++ oc2/ocdump.c
+@@ -10,8 +10,6 @@
+ #include <sys/stat.h>
+ #endif
+ 
+-extern int fileno(FILE*);
+-
+ #include "ocinternal.h"
+ #include "ocdebug.h"
+ 

math/netcdf/pkg/PLIST

@@ -1,36 +1,27 @@
-@comment $OpenBSD: PLIST,v 1.6 2015/03/16 18:07:50 naddy Exp $
+@comment $OpenBSD: PLIST,v 1.7 2019/03/13 20:27:40 sthen Exp $
+bin/nc-config
+@bin bin/nccopy
 @bin bin/ncdump
 @bin bin/ncgen
-include/ncvalues.h
+@bin bin/ncgen3
 include/netcdf.h
-include/netcdf.hh
-include/netcdf.inc
-include/netcdfcpp.h
+include/netcdf_aux.h
+include/netcdf_filter.h
+include/netcdf_mem.h
+include/netcdf_meta.h
+@comment lib/libbzip2.a
+@comment lib/libbzip2.la
+@comment lib/libbzip2.so
+@comment lib/libmisc.a
+@comment lib/libmisc.la
+@comment lib/libmisc.so
 lib/libnetcdf.a
 lib/libnetcdf.la
+lib/libnetcdf.settings
 @lib lib/libnetcdf.so.${LIBnetcdf_VERSION}
-lib/libnetcdf_c++.a
-lib/libnetcdf_c++.la
-@lib lib/libnetcdf_c++.so.${LIBnetcdf_c++_VERSION}
-lib/libnetcdff.a
-lib/libnetcdff.la
-@lib lib/libnetcdff.so.${LIBnetcdff_VERSION}
+lib/pkgconfig/netcdf.pc
+@man man/man1/nccopy.1
 @man man/man1/ncdump.1
 @man man/man1/ncgen.1
+@man man/man1/ncgen3.1
 @man man/man3/netcdf.3
-@man man/man3/netcdf_f77.3
-share/doc/netcdf/
-share/doc/netcdf/netcdf-c.pdf
-share/doc/netcdf/netcdf-c.txt
-share/doc/netcdf/netcdf-cxx.pdf
-share/doc/netcdf/netcdf-cxx.txt
-share/doc/netcdf/netcdf-f77.pdf
-share/doc/netcdf/netcdf-f77.txt
-share/doc/netcdf/netcdf-f90.pdf
-share/doc/netcdf/netcdf-f90.txt
-share/doc/netcdf/netcdf-install.pdf
-share/doc/netcdf/netcdf-install.txt
-share/doc/netcdf/netcdf-tutorial.pdf
-share/doc/netcdf/netcdf-tutorial.txt
-share/doc/netcdf/netcdf.pdf
-share/doc/netcdf/netcdf.txt