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Bug 233297 - [science overlay] sci-libs/hdf5-1.8.3 version bump
Summary: [science overlay] sci-libs/hdf5-1.8.3 version bump
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High enhancement (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords: InOverlay
Depends on:
Blocks:
 
Reported: 2008-07-29 17:26 UTC by Darren Dale
Modified: 2009-08-18 21:15 UTC (History)
7 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
minor changes to hdf5-1.6.7.ebuild (hdf5-1.8.1.patch,462 bytes, patch)
2008-09-28 09:13 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff
gcc4.3 patch (hdf5-1.8.1-gcc4.3.patch,274 bytes, patch)
2008-09-28 09:14 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff
Mpich2 patch (hdf5-1.8.1-mpich2.patch,538 bytes, patch)
2008-09-28 09:15 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff
hdf5-1.8.2.ebuild (hdf5-1.8.2.ebuild,7.77 KB, text/plain)
2008-11-19 00:10 UTC, Matthias Langer
Details
As suggested in #11 (hdf5-1.8.2-gcc4.3.3.patch,413 bytes, patch)
2009-03-21 13:46 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff
Patch to hdf5-1.8.2.ebuild (hdf5-1.8.2.patch,998 bytes, patch)
2009-03-21 13:51 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff
As suggested in #14 (hdf5-1.8.2-gcc4.3.3.patch,962 bytes, patch)
2009-03-21 17:12 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff

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Description Darren Dale 2008-07-29 17:26:21 UTC
hdf5-1.8.1 was released on May 29, 2008. Could this version please be added to portage? It would be nice if openmpi could be supported, instead of defaulting to mpich2.



Reproducible: Always

Steps to Reproduce:
Comment 1 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2008-09-28 09:13:47 UTC
Created attachment 166659 [details, diff]
minor changes to hdf5-1.6.7.ebuild

I have only added new patches since there were some slight differences in the code. This required to change ${PN} => ${P}
Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2008-09-28 09:14:49 UTC
Created attachment 166661 [details, diff]
gcc4.3 patch
Comment 3 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2008-09-28 09:15:48 UTC
Created attachment 166663 [details, diff]
Mpich2 patch
Comment 4 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2008-09-28 09:18:21 UTC
Compiled and tested on:
Portage 2.1.4.4 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.25-gentoo-r7 x86_64)
=================================================================
System uname: 2.6.25-gentoo-r7 x86_64 AMD Opteron(tm) Processor 246
Timestamp of tree: Mon, 22 Sep 2008 07:34:01 +0000

with sys-cluster/mpich2-1.0.7
Comment 5 Matthias Langer 2008-11-19 00:10:39 UTC
Created attachment 172333 [details]
hdf5-1.8.2.ebuild

This ebuild, which I have attached completely for convenience, is almost the same as the one for 1.8.1. The changes are:

* The gcc-4.3 patch is no longer applied (the patch doesn't work any more; i guess this has been fixed upstream, but i've not verified that yet).

* The USE flags "threads" and "fortran" are now mutually exclusive (otherwise configure dies anyway).

Please note that I've only roughly verified that this ebuild works for me on amd64 with USE="fortran ssl zlib -cxx -debug -mpi -szip -threads -tools".
Comment 6 Darren Dale 2009-01-12 16:04:30 UTC
I tried using the 1.8.2 ebuild with USE="ssl szip threads zlib -cxx -debug -fortran* -mpi -tools" (I also renamed the mpich2 patch to 1.8.2, was this correct?), and got the following error :

make[2]: Entering directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform'
test -z "/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c 'h5perf_serial' '/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5perf_serial'
libtool: install: /usr/bin/install -c .libs/h5perf_serial /var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5perf_serial
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform'
make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform'
!!! dosed: /var/tmp/portage/sci-libs/hdf5-1.8.2/image/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5cc does not exist
 *
 * ERROR: sci-libs/hdf5-1.8.2 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_install
 *             environment, line 3250:  Called die
 * The specific snippet of code:
 *       dosed "s/SHLIB:-no/SHLIB:-yes/g" "${D}"usr/bin/h5cc || die "dosed failed"
 *  The die message:
 *   dosed failed
 *
 * If you need support, post the topmost build error, and the call stack if relevant.
 * A complete build log is located at '/var/log/portage/sci-libs:hdf5-1.8.2:20090112-155556.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.8.2/temp/environment'.
 * This ebuild is from an overlay: '/usr/local/portage/'
 *
 * QA Notice: file does not exist:
 *
 *      dosed: /var/tmp/portage/sci-libs/hdf5-1.8.2/image/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5cc does not exist

my emerge --info:

Portage 2.1.6.4 (default/linux/amd64/2008.0/desktop, gcc-4.3.2, glibc-2.9_p20081201-r1, 2.6.28-gentoo x86_64)
=================================================================                                            
System uname: Linux-2.6.28-gentoo-x86_64-Dual_Core_AMD_Opteron-tm-_Processor_275-with-gentoo-2.0.0           
Timestamp of tree: Mon, 12 Jan 2009 12:10:01 +0000                                                           
app-shells/bash:     3.2_p48                                                                                 
dev-java/java-config: 1.3.7-r1, 2.1.6-r1                                                                     
dev-lang/python:     2.6.1                                                                                   
dev-util/cmake:      2.6.2                                                                                   
sys-apps/baselayout: 2.0.0                                                                                   
sys-apps/openrc:     0.4.1-r1                                                                                
sys-apps/sandbox:    1.3.2                                                                                   
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.19
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.28-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="collision-protect distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="en en_US"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/layman/soor-overlay /usr/local/portage/layman/devnull /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow X aac acl acpi alsa amd64 apache2 atlas avahi bash-completion berkdb blas bluetooth bookmarks branding bzip2 cairo cblas cdr cli cracklib crypt ctype cups dbus dirac doc dri dvd dvdr dvdread eds emacs emboss encode esd evo examples f77 fam fftw firefox foomativdb fortran gdbm gfortran gif gimpprint glitz gpm gstreamer gtk hal iconv imagemagick imap isdnlog ivman java jpeg jpeg2k kde kdrive kpathsea lapack latex ldap libnotify lzo mad mdnsresponder-compat midi mikmod mime mmap mmx mozbranding mozilla mozsvg mp3 mpeg mplayer mudflap multilib multislot mysql ncurses newspr nptl nptlonly nsplugin ogg opengl openmp oss pam pcre pdf perl pertty pic png postgres ppds pppd python qt3 qt3support qt4 quicktime readline reflection rss samba sdl session spell spl sse sse2 ssl startup-notification subversion svg symlink sysfs tcltk tcpd tetex threads tiff tk transparency truetype ubuntu umfpack unicode usb v4l v4l2 vorbis webdav winbind xcomposite xfs xft xml xorg xulrunner xv zeroconf zlib" ALSA_CARDS="ali5451 als4000 atiixpatiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US" USERLAND="GNU" VIDEO_CARDS="nvidia vga nv"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 7 Arthur Magill 2009-01-22 19:15:49 UTC
See bug 255070 - I had the same problem with 1.6.7, I fixed by changing {D} to {ROOT} in src_install. I'm not sure if this is a sensible way to fix, but it works ;-)

The clue is in the path:

/var/tmp/portage/sci-libs/hdf5-1.8.2/image/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5cc

Notice that /var/tmp/portage/sci-libs/hdf5-X.Y.Z/image is repeated twice. I don't understand why this ebuild works for some people though?
Comment 8 Darren Dale 2009-01-30 21:05:02 UTC
I have a new error cropping up when I try to install using gcc-4.3.3 and portage-2.2_rc23:

mv -f .deps/overhead.Tpo .deps/overhead.Po                                                                                        
/bin/sh ../libtool --tag=CC   --mode=link gcc  -O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -Wlogical-op -Wvla -O -fomit-frame-pointer -finline-functions  -Wl,-O1 -o overhead overhead.o ../src/libhdf5.la -lpthread -lz -lm   
libtool: link: gcc -O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -Wlogical-op -Wvla -O -fomit-frame-pointer -finline-functions -Wl,-O1 -o .libs/overhead overhead.o  ../src/.libs/libhdf5.so -lpthread -lz -lm                   
gcc -DHAVE_CONFIG_H -I. -I../src -I../src -I../test -I../tools/lib  -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE    -DNDEBUG -UH5_DEBUG_API  -O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -Wlogical-op -Wvla -O -fomit-frame-pointer -finline-functions -MT zip_perf.o -MD -MP -MF .deps/zip_perf.Tpo -c -o zip_perf.o zip_perf.c                                                                                                                 
zip_perf.c: In function 'error':                                                                                                  
zip_perf.c:186: warning: function might be possible candidate for 'printf' format attribute                                       
zip_perf.c: In function 'write_file':                                                                                             
zip_perf.c:248: warning: conversion to 'uLongf' from 'int' may change the sign of the result                                      
zip_perf.c: In function 'get_unique_name':                                                                                        
zip_perf.c:329: warning: passing argument 1 of 'strcat' discards qualifiers from pointer target type                              
zip_perf.c:334: warning: passing argument 1 of 'strcat' discards qualifiers from pointer target type                              
zip_perf.c:337: warning: request for implicit conversion from 'void *' to 'char *' not permitted in C++                           
zip_perf.c: In function 'fill_with_random_data':                                                                                  
zip_perf.c:456: warning: conversion to 'long unsigned int' from 'ssize_t' may change the sign of the result                       
zip_perf.c:466: warning: conversion to 'uLongf' from 'int' may change the sign of the result                                      
zip_perf.c: In function 'do_write_test':                                                                                          
zip_perf.c:532: warning: conversion to 'long unsigned int' from 'ssize_t' may change the sign of the result                       
zip_perf.c: In function 'fill_with_random_data':
/usr/include/bits/fcntl2.h:45: warning: will never be executed
/usr/include/bits/fcntl2.h:49: warning: will never be executed
/usr/include/bits/fcntl2.h:51: warning: will never be executed
/usr/include/bits/fcntl2.h:57: warning: will never be executed
/usr/include/bits/fcntl2.h:60: warning: will never be executed
/usr/include/bits/fcntl2.h:58: warning: will never be executed
zip_perf.c: In function 'do_write_test':
/usr/include/bits/fcntl2.h:45: warning: will never be executed
/usr/include/bits/fcntl2.h:45: warning: will never be executed
/usr/include/bits/fcntl2.h:57: warning: will never be executed
/usr/include/bits/fcntl2.h:60: warning: will never be executed
/usr/include/bits/fcntl2.h:58: warning: will never be executed
/usr/include/bits/fcntl2.h:51: warning: will never be executed
/usr/include/bits/fcntl2.h:57: warning: will never be executed
/usr/include/bits/fcntl2.h:60: warning: will never be executed
/usr/include/bits/fcntl2.h:58: warning: will never be executed
/usr/include/bits/fcntl2.h:54: warning: will never be executed
zip_perf.c: In function 'error':
zip_perf.c:181: warning: function might be possible candidate for attribute 'noreturn'
zip_perf.c: In function 'main':
/usr/include/bits/unistd.h:39: warning: will never be executed
/usr/include/bits/unistd.h:42: warning: will never be executed
/usr/include/bits/unistd.h:43: warning: will never be executed
/usr/include/bits/unistd.h:40: warning: will never be executed
/usr/include/bits/string3.h:82: warning: will never be executed
In function 'open',
    inlined from 'do_write_test' at zip_perf.c:552,
    inlined from 'main' at zip_perf.c:653:
/usr/include/bits/fcntl2.h:51: error: call to '__open_missing_mode' declared with attribute error: open with O_CREAT in second argument needs 3 arguments
zip_perf.c:69:1: warning: macro "GZ_SUFFIX" is not used
zip_perf.c:50:1: warning: macro "SET_BINARY_MODE" is not used
zip_perf.c:91:1: warning: macro "BUFLEN" is not used
zip_perf.c:72:1: warning: macro "SUFFIX_LEN" is not used
zip_perf.c:92:1: warning: macro "MAX_NAME_LEN" is not used
make[2]: *** [zip_perf.o] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform'
make[1]: *** [all-local] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2'
make: *** [all-recursive] Error 1
 *
 * ERROR: sci-libs/hdf5-1.8.2 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_compile
 *             environment, line 3232:  Called die
 * The specific snippet of code:
 *       make || die "make failed";
 *  The die message:
 *   make failed
 *
 * If you need support, post the topmost build error, and the call stack if relevant.
 * A complete build log is located at '/var/log/portage/sci-libs:hdf5-1.8.2:20090130-205200.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.8.2/temp/environment'.
 * This ebuild is from an overlay named 'local': '/usr/local/portage/'




# emerge --info                                                
Portage 2.2_rc23 (default/linux/amd64/2008.0/desktop, gcc-4.3.3, glibc-2.9_p20081201-r1, 2.6.28-gentoo-r1 x86_64)
=================================================================
System uname: Linux-2.6.28-gentoo-r1-x86_64-Dual_Core_AMD_Opteron-tm-_Processor_275-with-gentoo-2.0.0
Timestamp of tree: Fri, 30 Jan 2009 18:30:01 +0000
app-shells/bash:     3.2_p48
dev-java/java-config: 1.3.7-r1, 2.1.7
dev-lang/python:     2.6.1
dev-util/cmake:      2.6.2-r1
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.4.2
sys-apps/sandbox:    1.3.3
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.19
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.28-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="collision-protect distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch userpriv"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="en en_US"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/layman/soor-overlay /usr/local/portage/layman/devnull /usr/local/portage/layman/science /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow X aac acl acpi alsa amd64 apache2 atlas avahi bash-completion berkdb blas bluetooth bookmarks branding bzip2 cairo cblas cdr cli cracklib crypt ctype cups dbus dirac doc dri dvd dvdr dvdread eds emacs emboss encode esd evo examples f77 fam fftw firefox foomativdb fortran gdbm gfortran gif gimpprint glitz gpm gstreamer gtk hal iconv imagemagick imap isdnlog ivman java jpeg jpeg2k kde kdrive kpathsea lapack latex ldap libnotify lzo mad mdnsresponder-compat midi mikmod mime mmap mmx mozbranding mozilla mozsvg mp3 mpeg mplayer mudflap multilib multislot mysql ncurses newspr nptl nptlonly nsplugin ogg opengl openmp oss pam pcre pdf perl pertty pic png postgres ppds pppd python qt3 qt3support qt4 quicktime readline reflection rss samba sdl session spell spl sse sse2 ssl startup-notification subversion svg symlink sysfs tcltk tcpd tetex threads tiff tk transparency truetype ubuntu umfpack unicode usb v4l v4l2 vorbis webdav webkit winbind xcomposite xfs xft xml xorg xulrunner xv zeroconf zlib" ALSA_CARDS="ali5451 als4000atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US" USERLAND="GNU" VIDEO_CARDS="nvidia vga nv"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 9 Darren Dale 2009-02-05 21:23:01 UTC
(In reply to comment #8)
> In function 'open',
>     inlined from 'do_write_test' at zip_perf.c:552,
>     inlined from 'main' at zip_perf.c:653:
> /usr/include/bits/fcntl2.h:51: error: call to '__open_missing_mode' declared
> with attribute error: open with O_CREAT in second argument needs 3 arguments

This fcntl2.h problem has hit a couple other packages, for example bug #257139
Comment 10 Darren Dale 2009-03-05 18:58:33 UTC
(In reply to comment #9)
> (In reply to comment #8)
> > In function 'open',
> >     inlined from 'do_write_test' at zip_perf.c:552,
> >     inlined from 'main' at zip_perf.c:653:
> > /usr/include/bits/fcntl2.h:51: error: call to '__open_missing_mode' declared
> > with attribute error: open with O_CREAT in second argument needs 3 arguments
> 
> This fcntl2.h problem has hit a couple other packages, for example bug #257139
> 

This O_CREAT issue was resolved in davfs2, the resolution and patch can be found in bug #257823
Comment 11 Darren Dale 2009-03-14 14:58:13 UTC
(In reply to comment #10)
> 
> This O_CREAT issue was resolved in davfs2, the resolution and patch can be
> found in bug #257823
> 

This change allowed me to compile:

$ diff -r perform/zip_perf.c.old perform/zip_perf.c
552c552
<         output = open(filename, O_RDWR | O_CREAT);
---
>         output = open(filename, O_RDWR | O_CREAT, S_IRWXU);
Comment 12 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2009-03-21 13:46:47 UTC
Created attachment 185734 [details, diff]
As suggested in #11
Comment 13 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2009-03-21 13:51:53 UTC
Created attachment 185736 [details, diff]
Patch to hdf5-1.8.2.ebuild

Covers all the remarks from the discussion. Tested on:
Portage 2.2_rc23 (default/linux/amd64/2008.0, gcc-4.3.3, glibc-2.9_p20081201-r2, 2.6.28-gentoo-r2 x86_64)
=================================================================
Comment 14 Darren Dale 2009-03-21 15:45:23 UTC
(In reply to comment #13)
> Created an attachment (id=185736) [edit]
> Patch to hdf5-1.8.2.ebuild
> 
> Covers all the remarks from the discussion. Tested on:
> Portage 2.2_rc23 (default/linux/amd64/2008.0, gcc-4.3.3,
> glibc-2.9_p20081201-r2, 2.6.28-gentoo-r2 x86_64)
> =================================================================
> 

Did you run the test suite? It may be necessary to patch ./config/gnu-flags file in the HDF5 source code and setting PROD_CFLAGS from "-O" to "-O0". dt_arith conversion tests can fail with gcc, as discussed at http://www.hdfgroup.org/HDF5/release/known_problems5.html.

Here is the code that needs to be modified:

     gcc-3.[0-4]*|gcc-4.[0123]*)
        # The optimization level is reduced for gcc 3.* and 4.* due to problems
        # with code generation for src/H5Tconv.c with the -O2 & -O3
        # optimization levels (which shows up as failures for various integer
        # types -> long long conversions in the test/dtypes test). Perhaps
        # later versions of gcc will fix this bug... - QAK - 2003/10/20
        PROD_CFLAGS="-O0"
        ;;
Comment 15 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2009-03-21 17:12:34 UTC
Created attachment 185749 [details, diff]
As suggested in #14

(In reply to comment #13)
No I didn't, but when I did, I got the error you'd reported. New patch fixes it.
Comment 16 Darren Dale 2009-03-24 14:55:37 UTC
(In reply to comment #15)
> Created an attachment (id=185749) [edit]
> As suggested in #14
> 
> (In reply to comment #13)
> No I didn't, but when I did, I got the error you'd reported. New patch fixes
> it.
> 

Works for me. Thank you for all your effort on this ebuild.
Comment 17 Darren Dale 2009-05-12 13:06:25 UTC
hdf-1.8.3 has been released. This new version does not require the changes contained in hdf5-1.8.2-gcc4.3.3.patch. It does, however, include a bugfix, I think for compression filters, which required changes to downstream packages like pytables and h5py (both of which have already implemented the changes in their development branches, but have not made new releases at the time of this writing).
Comment 18 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2009-05-12 14:40:09 UTC
(In reply to comment #17)
> hdf-1.8.3 has been released. This new version does not require the changes
> contained in hdf5-1.8.2-gcc4.3.3.patch. It does, however, include a bugfix, I
> think for compression filters, which required changes to downstream packages
> like pytables and h5py (both of which have already implemented the changes in
> their development branches, but have not made new releases at the time of this
> writing).

I've been doing some cleaning in this ebuild. Can anyone explain me why lines:
	    mv "${ROOT}"usr/bin/h5pfc "${ROOT}"usr/bin/h5fc
	    mv "${ROOT}"usr/bin/h5pcc "${ROOT}"usr/bin/h5cc
are necessary??
Nothing in portage really depends on those wrappers...
Comment 19 Sébastien Fabbro (RETIRED) gentoo-dev 2009-06-24 16:52:31 UTC
Hi,

I've been working on a tree candidate for hdf5-1.8.3, since the current 1.6.7 ebuild is very buggy. Lots of patches and ebuild cleaning. Please test the one in the science overlay against other packages and with different use flags combination. Report (and patches welcome) here! The plan is to push it to the tree in a couple weeks.

Thanks
Comment 20 Peter Alexander 2009-06-24 20:09:56 UTC
(In reply to comment #19)
> Hi,
> 
> I've been working on a tree candidate for hdf5-1.8.3, since the current 1.6.7
> ebuild is very buggy. Lots of patches and ebuild cleaning. Please test the one
> in the science overlay against other packages and with different use flags
> combination. Report (and patches welcome) here! The plan is to push it to the
> tree in a couple weeks.
> 
> Thanks
> 


Thank you very much for this effort. 

hdf5-1.8.3 from the science overlay fails for me... first with my normal CFLAGS/LDFLAGS and then with out any at all (only default). 

Below, the following are provided: 1) Use flags 2) emerge --info (showing gentoo default CFLAGS/LDFLAGS) 3) Build log 4) automake.out

1) 
[ebuild  N    ] sci-libs/hdf5-1.8.3  USE="examples ssl threads zlib -cxx -fortran -mpi -szip

2) 
glacier ~ # emerge --info
Portage 2.2_rc33 (default/linux/x86/2008.0, gcc-4.3.2, glibc-2.8_p20080602-r1, 2.6.27-gentoo-r8 i686)
=================================================================                                    
System uname: Linux-2.6.27-gentoo-r8-i686-Intel-R-_Pentium-R-_4_CPU_3.60GHz-with-glibc2.0            
Timestamp of tree: Tue, 23 Jun 2009 23:00:01 +0000                                                   
ccache version 2.4 [enabled]                                                                         
app-shells/bash:     3.2_p39                                                                         
dev-java/java-config: 2.1.7                                                                          
dev-lang/python:     2.4.4-r13, 2.5.4-r2                                                             
dev-python/pycrypto: 2.0.1-r6                                                                        
dev-util/ccache:     2.4-r7                                                                          
dev-util/cmake:      2.6.4                                                                           
sys-apps/baselayout: 1.12.11.1                                                                       
sys-apps/sandbox:    2.0                                                                             
sys-devel/autoconf:  2.13, 2.63                                                                      
sys-devel/automake:  1.5, 1.7.9-r1, 1.9.6-r2, 1.10.2                                                 
sys-devel/binutils:  2.18-r3                                                                         
sys-devel/gcc-config: 1.4.1                                                                          
sys-devel/libtool:   1.5.26                                                                          
virtual/os-headers:  2.6.27-r2                                                                       
ACCEPT_KEYWORDS="x86"                                                                                
CBUILD="i686-pc-linux-gnu"                                                                           
CFLAGS="-O2 -march=i686 -pipe"                                                                       
CHOST="i686-pc-linux-gnu"                                                                            
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/4.2/env /usr/kde/4.2/share/config /usr/kde/4.2/shutdown /usr/kde/live/env /usr/kde/live/share/config /usr/kde/live/shutdown /usr/share/config"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O2 -march=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="ccache distlocks fixpackages metadata-transfer parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch userpriv usersandbox"
GENTOO_MIRRORS="http://open-systems.ufl.edu/mirrors/gentoo http://www.gtlib.gatech.edu/pub/gentoo http://gentoo.osuosl.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/layman/qting-edge /usr/local/portage/layman/berkano /usr/local/portage/layman/kde-testing /usr/local/portage/layman/travlr /usr/local/portage/layman/science"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X alsa bash-completion bzip2 cdr cli cracklib dbus dvd fftw fortran glib gpm iconv isdnlog java6 jpeg jpeg2k kde lapack latex midi mmx mudflap ncurses nptl nptlonly nsplugin nvidia openmp pam pcre perl png pppd python qt4 readline realmedia reflection sasl session spl sse sse2 sse3 ssl svga sysfs tcpd tetex threads umfpack unicode wmp x86 xinerama xorg xvmc zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nvidia"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

3)
glacier ~ # cat /var/log/portage/sci-libs:hdf5-1.8.3:20090624-195143.log
>>> Unpacking source...                                                 
>>> Unpacking hdf5-1.8.3.tar.gz to /var/tmp/portage/sci-libs/hdf5-1.8.3/work
>>> Source unpacked in /var/tmp/portage/sci-libs/hdf5-1.8.3/work            
>>> Preparing source in /var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3 ...
 * Applying hdf5-1.8.3-as-needed.patch ...                                                                          [ ok ]
 * Applying hdf5-1.8.3-includes.patch ...                                                                           [ ok ]
 * Applying hdf5-1.8.3-gnutools.patch ...                                                                           [ ok ]
 * Applying hdf5-1.8.3-noreturn.patch ...                                                                           [ ok ]
 * Applying hdf5-1.8.3-destdir.patch ...                                                                            [ ok ]
 * Applying hdf5-1.8.3-signal.patch ...                                                                             [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3' ...
 * Running aclocal ...                                                                                              [ ok ]
 * Running autoconf ...                                                                                             [ ok ]
 * Running autoheader ...                                                                                           [ ok ]
 * Running automake --add-missing --copy --foreign ...                                                              [ !! ]

 * Failed Running automake !
 *
 * Include in your bugreport the contents of:
 *
 *   /var/tmp/portage/sci-libs/hdf5-1.8.3/temp/automake.out

 *
 * ERROR: sci-libs/hdf5-1.8.3 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_prepare
 *             environment, line 2681:  Called eautoreconf
 *             environment, line  869:  Called eautomake
 *             environment, line  842:  Called autotools_run_tool 'automake' '--add-missing' '--copy' '--foreign'
 *             environment, line  354:  Called die
 * The specific snippet of code:
 *           die "Failed Running $1 !";
 *  The die message:
 *   Failed Running automake !
 *
 * If you need support, post the topmost build error, and the call stack if relevant.
 * A complete build log is located at '/var/log/portage/sci-libs:hdf5-1.8.3:20090624-195143.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.8.3/temp/environment'.
 * This ebuild is from an overlay named 'science': '/usr/local/portage/layman/science/'



THE REST IS CONTINUED IN THE NEXT COMMENT

Comment 21 Peter Alexander 2009-06-24 20:11:17 UTC
(In reply to comment #20)
> (In reply to comment #19)
> 
> 
> THE REST IS CONTINUED IN THE NEXT COMMENT
> 

CONTINUED FROM COMMENT #20

4)
glacier ~ # cat /var/tmp/portage/sci-libs/hdf5-1.8.3/temp/automake.out
***** automake *****                                                  
***** PWD: /var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3       
***** automake --add-missing --copy --foreign                         

configure.in:2684: warning: AC_CACHE_VAL(hdf5_mpi_complex_derived_datatype_works, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                         
../../lib/autoconf/general.m4:1974: AC_CACHE_VAL is expanded from...                                                      
configure.in:2684: the top level                                                                                          
configure.in:2703: warning: AC_CACHE_VAL(hdf5_mpi_special_collective_io_works, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                            
configure.in:2703: the top level                                                                                          
configure.in:2832: warning: AC_CACHE_VAL(hdf5_direct_io, ...): suspicious cache-id, must contain _cv_ to be cached        
configure.in:2832: the top level                                                                                          
configure.in:2992: warning: AC_CACHE_VAL(hdf5_ldouble_to_integer_works, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                                   
configure.in:2992: the top level                                                                                          
configure.in:3142: warning: AC_CACHE_VAL(hdf5_fp_to_ullong_accurate, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                                      
configure.in:3142: the top level                                                                                          
configure.in:3179: warning: AC_CACHE_VAL(hdf5_fp_to_ullong_right_maximum, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                                 
configure.in:3179: the top level                                                                                          
configure.in:3224: warning: AC_CACHE_VAL(hdf5_ldouble_to_uint_accurate, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                                   
configure.in:3224: the top level                                                                                          
configure.in:3426: warning: AC_CACHE_VAL(hdf5_ldouble_to_llong_accurate, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                                  
configure.in:3426: the top level                                                                                          
configure.in:3487: warning: AC_CACHE_VAL(hdf5_llong_to_ldouble_correct, ...): suspicious cache-id, must contain _cv_ to be cached                                                                                                                   
configure.in:3487: the top level                                                                                          
c++/src/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined                                                   
c++/src/Makefile.am:28:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'                                   
c++/src/Makefile.am:28:   to `configure.in' and run `aclocal' and `autoconf' again.                                       
c++/src/Makefile.am:28:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure                                            
c++/src/Makefile.am:28:   its definition is in aclocal's search path.                                                     
fortran/src/Makefile.am:32: Libtool library used but `LIBTOOL' is undefined                                               
fortran/src/Makefile.am:32:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'                               
fortran/src/Makefile.am:32:   to `configure.in' and run `aclocal' and `autoconf' again.                                   
fortran/src/Makefile.am:32:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
fortran/src/Makefile.am:32:   its definition is in aclocal's search path.
fortran/test/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined
fortran/test/Makefile.am:28:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
fortran/test/Makefile.am:28:   to `configure.in' and run `aclocal' and `autoconf' again.
fortran/test/Makefile.am:28:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
fortran/test/Makefile.am:28:   its definition is in aclocal's search path.
hl/c++/src/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined
hl/c++/src/Makefile.am:28:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
hl/c++/src/Makefile.am:28:   to `configure.in' and run `aclocal' and `autoconf' again.
hl/c++/src/Makefile.am:28:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
hl/c++/src/Makefile.am:28:   its definition is in aclocal's search path.
hl/fortran/src/Makefile.am:30: Libtool library used but `LIBTOOL' is undefined
hl/fortran/src/Makefile.am:30:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
hl/fortran/src/Makefile.am:30:   to `configure.in' and run `aclocal' and `autoconf' again.
hl/fortran/src/Makefile.am:30:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
hl/fortran/src/Makefile.am:30:   its definition is in aclocal's search path.
hl/src/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined
hl/src/Makefile.am:28:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
hl/src/Makefile.am:28:   to `configure.in' and run `aclocal' and `autoconf' again.
hl/src/Makefile.am:28:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
hl/src/Makefile.am:28:   its definition is in aclocal's search path.
src/Makefile.am:33: Libtool library used but `LIBTOOL' is undefined
src/Makefile.am:33:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
src/Makefile.am:33:   to `configure.in' and run `aclocal' and `autoconf' again.
src/Makefile.am:33:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
src/Makefile.am:33:   its definition is in aclocal's search path.
test/Makefile.am:71: Libtool library used but `LIBTOOL' is undefined
test/Makefile.am:71:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
test/Makefile.am:71:   to `configure.in' and run `aclocal' and `autoconf' again.
test/Makefile.am:71:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
test/Makefile.am:71:   its definition is in aclocal's search path.
tools/lib/Makefile.am:27: Libtool library used but `LIBTOOL' is undefined
tools/lib/Makefile.am:27:   The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL'
tools/lib/Makefile.am:27:   to `configure.in' and run `aclocal' and `autoconf' again.
tools/lib/Makefile.am:27:   If `AC_PROG_LIBTOOL' is in `configure.in', make sure
tools/lib/Makefile.am:27:   its definition is in aclocal's search path.
Comment 22 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2009-06-24 20:44:15 UTC
(In reply to comment #20)
                      
> sys-devel/libtool:  1.5.26                                                     
seems to be the problem. Ebuild works for me (libtool-2.2.6a) 
Comment 23 Peter Alexander 2009-06-24 21:13:30 UTC
(In reply to comment #22)
> (In reply to comment #20)
> 
> > sys-devel/libtool:  1.5.26                                                     
> seems to be the problem. Ebuild works for me (libtool-2.2.6a) 
> 

Thank you. 
libtool-2.2.6a allowed me to build succesfully. 
I was able to use my custom CFLAGS/LDFLAGS with out problem.
Comment 24 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2009-06-25 15:07:05 UTC
(In reply to comment #19)

Firstly, let me thank you for your effort of putting hdf5-1.8.3 to science overlay!
As for the problems I have encountered so far:
hdf5-1.8 needs >=szip-2. It fails with current stable version (1.1-r1), but compiles with szip-2.1.
Comment 25 Darren Dale 2009-06-30 14:24:14 UTC
emerge fails with the examples use flag enabled:

make -j5 DESTDIR=/var/tmp/portage/sci-libs/hdf5-1.8.3/image/ install-examples                
+ for d in examples                                                                          
+ cd examples                                                                                
+ make install-examples                                                                      
make[1]: Entering directory `/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3/examples'  
+ /usr/bin/install -c -m 644 ./h5_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                               
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_read.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                                
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_extend_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                        
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_chunk_read.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                          
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_compound.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                            
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_group.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                               
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_select.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                              
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_attribute.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                           
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_mount.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                               
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_reference.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                           
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_drivers.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                             
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_extlink.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                             
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_elink_unix2win.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.                                                      
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory                               
+ exit 1                                                                                     
+ /usr/bin/install -c -m 644 ./h5_ref2reg.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory
+ exit 1
+ /usr/bin/install -c -m 644 ./h5_shared_mesg.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory
+ exit 1
+ /usr/bin/install -c -m 644 ./ph5example.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.
/usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory
+ exit 1
make[1]: *** [install-examples] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3/examples'
+ exit 1
make: *** [install-examples] Error 1
 *
 * ERROR: sci-libs/hdf5-1.8.3 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_install
 *             environment, line 2793:  Called die
 * The specific snippet of code:
 *           emake DESTDIR="${D}" install-examples || die "emake install examples failed";
 *  The die message:
 *   emake install examples failed


If I disable the examples use flag, emerge is successful.
Comment 26 Darren Dale 2009-07-01 13:59:53 UTC
After emerging hdf5 on ~amd64 with gcc-4.4 and USE="szip threads zlib -cxx -examples -fortran -mpi", I installed h5py-1.2 and observed a number of test failures, all of the tests of h5py.h5d failed with the same DatatypeError, for example:

======================================================================
ERROR: test_create_offset (h5py.tests.test_h5d.TestH5D)               
----------------------------------------------------------------------
Traceback (most recent call last):                                    
  File "/home/share/packages/h5py-1.2.0/h5py/tests/test_h5d.py", line 41, in setUp
    self.dset = h5d.open(self.fid, "CompoundChunked")                             
  File "/home/share/packages/h5py-1.2.0/h5py/_sync.py", line 88, in wrap          
    return func(*args, **kwds)                                                    
  File "h5d.pyx", line 78, in h5py.h5d.open (h5py/h5d.c:1391)                     
DatatypeError: Incorrect array datatype version (Datatype: Wrong version number)


I ran "emerge -C hdf5" and then installed hdf5-1.8.3 manually with:

./configure --prefix=/usr/local --enable-threadsafe --with-zlib=/usr --with-pthread=/usr
make
sudo make install

Then I ran the h5py tests again and this time they all passed. Does anyone know what the ebuild is doing differently?
Comment 27 Sébastien Fabbro (RETIRED) gentoo-dev 2009-08-18 21:15:55 UTC
Now in portage tree.