From owner-freebsd-ports-bugs@FreeBSD.ORG Wed Nov 19 07:10:02 2008 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 2BB751065677 for ; Wed, 19 Nov 2008 07:10:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 04BA58FC23 for ; Wed, 19 Nov 2008 07:10:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id mAJ7A1u1011326 for ; Wed, 19 Nov 2008 07:10:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id mAJ7A1cq011325; Wed, 19 Nov 2008 07:10:01 GMT (envelope-from gnats) Resent-Date: Wed, 19 Nov 2008 07:10:01 GMT Resent-Message-Id: <200811190710.mAJ7A1cq011325@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Wen Heping Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id CBE7A10656FB for ; Wed, 19 Nov 2008 07:09:12 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id B86938FC13 for ; Wed, 19 Nov 2008 07:09:12 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.3/8.14.3) with ESMTP id mAJ79CRJ025310 for ; Wed, 19 Nov 2008 07:09:12 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.3/8.14.3/Submit) id mAJ79CeY025309; Wed, 19 Nov 2008 07:09:12 GMT (envelope-from nobody) Message-Id: <200811190709.mAJ79CeY025309@www.freebsd.org> Date: Wed, 19 Nov 2008 07:09:12 GMT From: Wen Heping To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/128988: [New Port]science/hdf5-18:Hierarchical Data Format library (from NCSA) X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 19 Nov 2008 07:10:02 -0000 >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 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 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 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: