Date: Wed, 19 Nov 2008 07:09:12 GMT From: Wen Heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/128988: [New Port]science/hdf5-18:Hierarchical Data Format library (from NCSA) Message-ID: <200811190709.mAJ79CeY025309@www.freebsd.org> Resent-Message-ID: <200811190710.mAJ7A1cq011325@freefall.freebsd.org>
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>Number: 128988
>Category: ports
>Synopsis: [New Port]science/hdf5-18:Hierarchical Data Format library (from NCSA)
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Wed Nov 19 07:10:01 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator: Wen Heping
>Release: FreeBSD-8.0 Current
>Organization:
ChangAn Middle School
>Environment:
FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Sep 21 18:56:51 HKT 2008 root@fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386
>Description:
HDF5 is a completely new Hierarchical Data Format product consisting of a
data format specification and a supporting library implementation. HDF5 is
designed to address some of the limitations of the older HDF product and to
address current and anticipated requirements of modern systems and
applications.
HDF5 includes the following improvements.
- A new file format designed to address some of the deficiencies of HDF4.x,
particularly the need to store larger files and more objects per file.
- A simpler, more comprehensive data model that includes only two basic
structures: a multidimensional array of record structures, and a grouping
structure.
- A simpler, better-engineered library and API, with improved support for
parallel I/O, threads, and other requirements imposed by modern systems
and applications.
WWW: http://hdf.ncsa.uiuc.edu/HDF5/
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# hdf5-18
# hdf5-18/pkg-plist
# hdf5-18/pkg-descr
# hdf5-18/distinfo
# hdf5-18/Makefile
# hdf5-18/files
# hdf5-18/files/patch-src-H5FDdirect.c
#
echo c - hdf5-18
mkdir -p hdf5-18 > /dev/null 2>&1
echo x - hdf5-18/pkg-plist
sed 's/^X//' >hdf5-18/pkg-plist << 'c1d3ded362f9db49cb10a7e1d8ab4523'
Xbin/h5mkgrp
Xbin/h5copy
Xbin/h5stat
Xbin/h5perf_serial
Xbin/gif2h5
Xbin/h52gif
Xbin/h5c++
Xbin/h5cc
Xbin/h5debug
Xbin/h5diff
Xbin/h5dump
X%%FORTRAN%%bin/h5fc
Xbin/h5import
Xbin/h5jam
Xbin/h5ls
Xbin/h5redeploy
Xbin/h5repack
Xbin/h5repart
Xbin/h5unjam
Xinclude/hdf5_hl.h
Xinclude/H5ACpublic.h
Xinclude/H5AbstractDs.h
Xinclude/H5Apublic.h
Xinclude/H5ArrayType.h
Xinclude/H5AtomType.h
Xinclude/H5Attribute.h
Xinclude/H5Classes.h
Xinclude/H5CommonFG.h
Xinclude/H5CompType.h
Xinclude/H5Cpp.h
Xinclude/H5CppDoc.h
Xinclude/H5Cpublic.h
Xinclude/H5DataSet.h
Xinclude/H5DataSpace.h
Xinclude/H5DataType.h
Xinclude/H5DcreatProp.h
Xinclude/H5Dpublic.h
Xinclude/H5DSpublic.h
Xinclude/H5DxferProp.h
Xinclude/H5EnumType.h
Xinclude/H5Epubgen.h
Xinclude/H5Epublic.h
Xinclude/H5Exception.h
Xinclude/H5FDcore.h
Xinclude/H5FDdirect.h
Xinclude/H5FDfamily.h
Xinclude/H5FDlog.h
Xinclude/H5FDmpi.h
Xinclude/H5FDmpio.h
Xinclude/H5FDmpiposix.h
Xinclude/H5FDmulti.h
Xinclude/H5FDpublic.h
Xinclude/H5FDsec2.h
Xinclude/H5FDstdio.h
Xinclude/H5FaccProp.h
Xinclude/H5FcreatProp.h
Xinclude/H5File.h
Xinclude/H5FloatType.h
Xinclude/H5Fpublic.h
Xinclude/H5Gpublic.h
Xinclude/H5Group.h
Xinclude/H5IdComponent.h
Xinclude/H5IMpublic.h
Xinclude/H5Include.h
Xinclude/H5IntType.h
Xinclude/H5Ipublic.h
Xinclude/H5Library.h
Xinclude/H5LTpublic.h
Xinclude/H5Lpublic.h
Xinclude/H5MMpublic.h
Xinclude/H5Object.h
Xinclude/H5Opublic.h
Xinclude/H5PTpublic.h
Xinclude/H5PacketTable.h
Xinclude/H5Ppublic.h
Xinclude/H5PredType.h
Xinclude/H5PropList.h
Xinclude/H5Rpublic.h
Xinclude/H5Spublic.h
Xinclude/H5StrType.h
Xinclude/H5TBpublic.h
Xinclude/H5Tpublic.h
Xinclude/H5VarLenType.h
Xinclude/H5Zpublic.h
Xinclude/H5api_adpt.h
Xinclude/H5pubconf.h
Xinclude/H5public.h
Xinclude/H5version.h
Xinclude/hdf5.h
X%%FORTRAN%%include/h5a.mod
X%%FORTRAN%%include/h5d.mod
X%%FORTRAN%%include/h5e.mod
X%%FORTRAN%%include/h5f.mod
X%%FORTRAN%%include/h5fortran_flags.mod
X%%FORTRAN%%include/h5fortran_types.mod
X%%FORTRAN%%include/h5g.mod
X%%FORTRAN%%include/h5global.mod
X%%FORTRAN%%include/h5i.mod
X%%FORTRAN%%include/h5lib.mod
X%%FORTRAN%%include/h5p.mod
X%%FORTRAN%%include/h5r.mod
X%%FORTRAN%%include/h5s.mod
X%%FORTRAN%%include/h5t.mod
X%%FORTRAN%%include/h5z.mod
X%%FORTRAN%%include/hdf5.mod
X%%FORTRAN%%include/h5_dble_interface.mod
X%%FORTRAN%%include/h5o.mod
X%%FORTRAN%%include/h5l.mod
X%%FORTRAN%%include/h5tb.mod
X%%FORTRAN%%include/h5lt.mod
X%%FORTRAN%%include/h5im.mod
X%%FORTRAN%%lib/libhdf5_fortran.so
X%%FORTRAN%%lib/libhdf5_fortran.so.0
X%%FORTRAN%%lib/libhdf5hl_fortran.so
X%%FORTRAN%%lib/libhdf5hl_fortran.so.0
X%%FORTRAN%%lib/libhdf5hl_fortran.la
X%%FORTRAN%%lib/libhdf5hl_fortran.a
Xlib/libhdf5_cpp.so
Xlib/libhdf5_cpp.so.0
Xlib/libhdf5_hl_cpp.so
Xlib/libhdf5_hl_cpp.so.0
Xlib/libhdf5_hl_cpp.la
Xlib/libhdf5_hl_cpp.a
Xlib/libhdf5.a
Xlib/libhdf5.la
Xlib/libhdf5.settings
Xlib/libhdf5.so
Xlib/libhdf5.so.6
Xlib/libhdf5_cpp.a
Xlib/libhdf5_cpp.la
X%%FORTRAN%%lib/libhdf5_fortran.a
X%%FORTRAN%%lib/libhdf5_fortran.la
Xlib/libhdf5_hl.a
Xlib/libhdf5_hl.la
Xlib/libhdf5_hl.so
Xlib/libhdf5_hl.so.0
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Attributes.txt
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.am
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile.in
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_attribute.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_chunk_read.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_compound.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_drivers.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_dtransform.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_elink_unix2win.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_extend_write.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_extlink.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_group.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_interm_group.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_mount.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_read.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_ref2reg.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_reference.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_select.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_shared_mesg.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h5_write.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ph5example.c
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/testh5cc.sh
X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/testh5cc.sh.in
X%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
c1d3ded362f9db49cb10a7e1d8ab4523
echo x - hdf5-18/pkg-descr
sed 's/^X//' >hdf5-18/pkg-descr << 'cfa9f4b507716a89e5883f4b122a423b'
XHDF5 is a completely new Hierarchical Data Format product consisting of a
Xdata format specification and a supporting library implementation. HDF5 is
Xdesigned to address some of the limitations of the older HDF product and to
Xaddress current and anticipated requirements of modern systems and
Xapplications.
X
XHDF5 includes the following improvements.
X - A new file format designed to address some of the deficiencies of HDF4.x,
X particularly the need to store larger files and more objects per file.
X - A simpler, more comprehensive data model that includes only two basic
X structures: a multidimensional array of record structures, and a grouping
X structure.
X - A simpler, better-engineered library and API, with improved support for
X parallel I/O, threads, and other requirements imposed by modern systems
X and applications.
X
XWWW: http://hdf.ncsa.uiuc.edu/HDF5/
cfa9f4b507716a89e5883f4b122a423b
echo x - hdf5-18/distinfo
sed 's/^X//' >hdf5-18/distinfo << 'd34aad5b87fbe6798a4940bfc335dec7'
XMD5 (hdf5-1.8.2.tar.gz) = af92ef65ef495dbd205131574ad4eee1
XSHA256 (hdf5-1.8.2.tar.gz) = 795db1a98cd4effde3309efbbc118e1f5ae112369c1202f3f74dba4654bfbaf5
XSIZE (hdf5-1.8.2.tar.gz) = 7094386
d34aad5b87fbe6798a4940bfc335dec7
echo x - hdf5-18/Makefile
sed 's/^X//' >hdf5-18/Makefile << '1ea0f40a7f989eab3e8253f27f526c32'
X# New ports collection makefile for: hdf5-18
X# Date created: Nov 20, 2008
X# Whom: Wen Heping <wenheping@gmail.com>
X#
X# $FreeBSD$
X#
X
XPORTNAME= hdf5
XPORTVERSION= 1.8.2
XCATEGORIES= science archivers graphics
XMASTER_SITES= ftp://ftp.hdfgroup.org/HDF5/current/src/
X
XMAINTAINER= wenheping@gmail.com
XCOMMENT= Hierarchical Data Format library (from NCSA)
X
XCONFLICTS= hdf5-1.6.*
X
XUSE_LDCONFIG= yes
XGNU_CONFIGURE= yes
XCONFIGURE_ARGS= --disable-debug \
X --enable-cxx \
X --enable-instrument \
X --enable-production \
X --enable-strict-format-checks \
X --with-pthread=/usr \
X --with-ssl=/usr \
X --with-zlib=/usr
X
X.include <bsd.port.pre.mk>
X
X.if defined(WITH_FORTRAN)
XUSE_FORTRAN= yes
XCONFIGURE_ENV+= F9X=${FC}
XCONFIGURE_ARGS+= --enable-fortran
XPLIST_SUB+= FORTRAN=""
X.else
XPLIST_SUB+= FORTRAN="@comment "
X.endif
X
X.if ${ARCH} == "sparc64"
XBROKEN= Does not compile on ${ARCH}
X.endif
X
Xpost-patch:
X @${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
X @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags
X
Xpost-install:
X.if !defined(NOPORTEXAMPLES)
X @${MKDIR} ${EXAMPLESDIR}
X ${INSTALL_DATA} ${WRKSRC}/examples/* ${EXAMPLESDIR}
X.endif
X
X.for i in gif2h5 h52gif h5debug h5diff h5dump h5import h5jam h5ls h5repack h5repart h5unjam
X @${STRIP_CMD} ${PREFIX}/bin/${i}
X.endfor
X
Xregression-test: build
X @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE} check
X
X.include <bsd.port.post.mk>
1ea0f40a7f989eab3e8253f27f526c32
echo c - hdf5-18/files
mkdir -p hdf5-18/files > /dev/null 2>&1
echo x - hdf5-18/files/patch-src-H5FDdirect.c
sed 's/^X//' >hdf5-18/files/patch-src-H5FDdirect.c << 'd53e4f06f0eb5ef17dfc5960db9a23ee'
X--- src/H5FDdirect.c.orig 2008-09-24 22:02:07.000000000 +0800
X+++ src/H5FDdirect.c 2008-09-24 22:02:38.000000000 +0800
X@@ -29,6 +29,8 @@
X * this file. */
X /* #define _XOPEN_SOURCE 600 */
X
X+#define O_DIRECT 0x00010000
X+
X #include "H5private.h" /* Generic Functions */
X #include "H5Eprivate.h" /* Error handling */
X #include "H5Fprivate.h" /* File access */
d53e4f06f0eb5ef17dfc5960db9a23ee
exit
>Release-Note:
>Audit-Trail:
>Unformatted:
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