I ran across a stupid issue in ~x86 when trying to emerge sci-visualization/paraview-3.4.0. It seems that Utilities/hdf5/H5Zdeflate.c is missing zlib.h include. Patch in URL and attached. Reproducible: Always Steps to Reproduce: 1. unmask sci-visualization/paraview-3.4.0 on x86 2. emerge it
Created attachment 191593 [details, diff] patch that fixes compilation on x86
emerge --info and the build.log please.
emerge --info: Portage 2.2_rc33 (default/linux/x86/2008.0/desktop, gcc-4.3.2, glibc-2.8_p20080602-r1, 2.6.25-sabayon i686) ================================================================= System uname: Linux-2.6.25-sabayon-i686-Intel-R-_Xeon-R-_CPU_X3220_@_2.40GHz-with-glibc2.0 Timestamp of tree: Mon, 18 May 2009 06:30:17 +0000 distcc 3.0 i686-pc-linux-gnu [disabled] ccache version 2.4 [disabled] app-shells/bash: 3.2_p48-r1 dev-java/java-config: 1.3.7, 2.1.6-r1 dev-lang/python: 2.4.4-r15, 2.5.4-r2 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.6.3 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.3-r5 sys-apps/sandbox: 1.9 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r4 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-Os -march=i686 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/entropy /opt/glftpd/etc /opt/glftpd/ftp-data /opt/openfire/resources/security/ /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/share/config/kdm/ /usr/kde/3.5/shutdown /usr/kde/4.1/env /usr/kde/4.1/share/config /usr/kde/4.1/shutdown /usr/kde/4.2/env /usr/kde/4.2/share/config /usr/kde/4.2/shutdown /usr/lib/fax /usr/share/config /usr/share/xbmc/userdata /var/bind /var/lib/hsqldb /var/spool/fax/etc /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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/skel /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-Os -march=i686 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="collision-protect distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ ftp://mirror.leaseweb.com/gentoo/ ftp://mirror.muntinternet.net/pub/gentoo/ ftp://91.121.124.139/gentoo-distfiles/ http://mirror.switch.ch/ftp/mirror/gentoo/" LANG="en_US" LC_ALL="en_US" LDFLAGS="-Wl,-O1" LINGUAS="en en_US af ar az bg bn br bs ca cs cy da de el en_GB eo es et eu fa fi fr fy ga gl he hi hr hu is it ja kk km ko lt lv mk mn ms nb nds nl nn pa pl pt pt_BR ro ru rw se sk sl sr sr@Latn ss sv ta tg tr uk uz vi zh_CN zh_TW es_AR es_ES fy_NL ga_IE gu gu_IN nb_NO nn_NO pt_PT sv_SE zh" MAKEOPTS="-j2 -s " 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/sabayon /usr/local/portage/layman/enlightenment" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dfx 7Zip X a52 aac aalib accessibility acl acpi aiglx aim alsa arts artswrappersuid audiofile avahi berkdb bidi bluetooth bzip2 cairo cdda cddb cdr chm cjk cli config_wizard cpudetection cracklib crypt css cups dbox2 dbus dga dri dts dv dvb dvd dvdr dvdread dxr3 emboss encode extramodules fam fame fat ffmpeg fftw firefox flac flash foomatic-db fortran freetype gcj gdbm gif gimpprint gnutls gphoto2 gpm gs gsm gstreamer gtk hal hfs iconv icq ieee1394 imap inotify ipod ipv6 irc irda isdnlog jabber jack jfs jingle joystick jpeg kde kdeenablefinal kdehiddenvisibility kdeprefix kerberos kickoff kipi lame lcd ldap libnotify live lj lm_sensors logitech-mouse lzo mad mail midi mikmod mjpeg mmx mng mozdevelop mp3 mp3rtp mpeg msn mudflap musepack musicbrainz ncurses network new-login nls nptl nptlonly nsplugin ntfs ogg openal openexr opengl openmp pam pcmcia pcre pda pdf perl png povray ppds pppd pulseaudio python qt3support qt4 quicktime quotas rar rdesktop readline reflection reiserfs rss scanner sdl session slp sms speex spell spl ssl startup-notification stream svg sysfs tcpd theora tiff tracker truetype udev unicode usb v4l v4l2 visualization voice vorbis weather wifi win32codecs wmf x264 x86 xcb xfs xine xinerama xml xorg xpm xprint xulrunner xv xvid xvmc yahoo zeroconf zlib" ALSA_CARDS="emu10k1x darla20 darla24 emu10k1 gina20 gina24 hdsp hdspm ice1712 indigo indigoio layla20 layla24 mia mixart mona pcxhr rme32 rme96 sb16 sbawe sscape usbusx2y vx222 usb-usx2y" 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" APACHE2_MPMS="prefork" CAMERAS="agfa_cl20 casio_qv dimagev dimera3500 kodak_dc120 kodak_dc210 kodak_dc240 kodak_dc3200 kodak_ez200 konica_qm150 panasonic_coolshot panasonic_dc1000 panasonic_dc1580 panasonic_l859 polaroid_pdc320 polaroid_pdc640 polaroid_pdc700 ricoh_g3 sipix_blink sipix_blink2 sipix_web2 sony_dscf1 sony_dscf55 toshiba_pdrm11 adc65 aox barbie canon clicksmart310 digigr8 digita directory enigma13 fuji gsmart300 hp215 iclick jamcam jd11 konica largan lg_gsm mars mustek pccam300 pccam600 ptp2 ricoh samsung sierra smal sonix soundvision spca50x sq905 stv0674 stv0680 sx330z template" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse void" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US af ar az bg bn br bs ca cs cy da de el en_GB eo es et eu fa fi fr fy ga gl he hi hr hu is it ja kk km ko lt lv mk mn ms nb nds nl nn pa pl pt pt_BR ro ru rw se sk sl sr sr@Latn ss sv ta tg tr uk uz vi zh_CN zh_TW es_AR es_ES fy_NL ga_IE gu gu_IN nb_NO nn_NO pt_PT sv_SE zh" LIRC_DEVICES="audio audio_alsa" USERLAND="GNU" VIDEO_CARDS="fbdev vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 191626 [details] build log
Hi Fabio, Thanks much for your report. Something doesn't seem quite right. The offending file H5Zdeflate.c should only be built when the internal hdf5 implementation is used and in this case the macro H5_HAVE_ZLIB_H should be defined supplying the zlib declarations in hdf5_zlib.h. Hence, zlib.h link in your patch should not be needed. Does this problem persists for you? Everything works fine on all my machines. Best, Markus
Hey Markus, thanks for the reply. Actually, it's still an issue here on our 32bit build server. Just let me know what info you need. emerge --info: Portage 2.2_rc33 (default/linux/x86/2008.0/desktop, gcc-4.4.1, glibc-2.10.1-r0, 2.6.25-sabayon i686) ================================================================= System uname: Linux-2.6.25-sabayon-i686-Intel-R-_Xeon-R-_CPU_X3220_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 23 Jul 2009 07:00:02 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] ccache version 2.4 [disabled] app-shells/bash: 4.0_p24 dev-java/java-config: 1.3.7-r1, 2.1.8-r1 dev-lang/python: 2.4.6, 2.5.4-r3, 2.6.2-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.6.4-r1 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r5 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/entropy /opt/glftpd/etc /opt/glftpd/ftp-data /opt/openfire/resources/security/ /usr/kde/3.5/share/config/kdm/ /usr/lib/fax /usr/share/config /usr/share/xbmc/userdata /var/bind /var/lib/hsqldb /var/spool/fax/etc /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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/skel /etc/splash /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="collision-protect distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ ftp://mirror.leaseweb.com/gentoo/ ftp://mirror.muntinternet.net/pub/gentoo/ ftp://91.121.124.139/gentoo-distfiles/ http://mirror.switch.ch/ftp/mirror/gentoo/" LANG="en_US" LC_ALL="en_US" LDFLAGS="-Wl,-O1,--as-needed" LINGUAS="en en_US af ar az bg bn br bs ca cs cy da de el en_GB eo es et eu fa fi fr fy ga gl he hi hr hu is it ja kk km ko lt lv mk mn ms nb nds nl nn pa pl pt pt_BR ro ru rw se sk sl sr sr@Latn ss sv ta tg tr uk uz vi zh_CN zh_TW es_AR es_ES fy_NL ga_IE gu gu_IN nb_NO nn_NO pt_PT sv_SE zh" MAKEOPTS="-j2 -s " 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/enlightenment /usr/local/portage/layman/sabayon /usr/local/portage/layman/kde-testing" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="7Zip X a52 aac aalib accessibility acl acpi aiglx aim alsa artswrappersuid audiofile avahi bash-completion berkdb bidi bluetooth bzip2 cairo cdda cddb cdr chm cjk cli config_wizard cpudetection cracklib crypt css cups dbox2 dbus dga dri dts dv dvb dvd dvdr dvdread dxr3 emboss encode extramodules fam fame fat ffmpeg fftw firefox flac flash foomatic-db fortran freetype gcj gdbm gif gimpprint gmp gnutls gphoto2 gpm gs gsm gstreamer gtk hal hfs iconv icq ieee1394 imap inotify ipod ipv6 irc irda isdnlog jabber jack jfs jingle joystick jpeg kde kdeenablefinal kdehiddenvisibility kerberos kipi lame lcd ldap libnotify live lj lm_sensors logitech-mouse lzo mad mail matroska midi mikmod mjpeg mmx mng mozdevelop mp3 mp3rtp mpeg msn mudflap musepack musicbrainz ncurses network new-login nls nptl nptlonly nsplugin ntfs ogg openal openexr opengl openmp pam pcmcia pcre pda pdf perl png policykit povray ppds pppd pulseaudio python qt3support qt4 quicktime quotas rar rdesktop readline reflection reiserfs rss scanner sdl session slp sms speex spell spl ssl startup-notification stream svg sysfs tcpd theora tiff tracker truetype udev unicode usb v4l v4l2 visualization voice vorbis weather wifi win32codecs wmf x264 x86 xcb xfs xine xinerama xml xorg xpm xprint xulrunner xv xvid xvmc yahoo zeroconf zlib" ALSA_CARDS="emu10k1x darla20 darla24 emu10k1 gina20 gina24 hdsp hdspm ice1712 indigo indigoio layla20 layla24 mia mixart mona pcxhr rme32 rme96 sb16 sbawe sscape usbusx2y vx222 usb-usx2y" 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" APACHE2_MPMS="prefork" CAMERAS="agfa_cl20 casio_qv dimagev dimera3500 kodak_dc120 kodak_dc210 kodak_dc240 kodak_dc3200 kodak_ez200 konica_qm150 panasonic_coolshot panasonic_dc1000 panasonic_dc1580 panasonic_l859 polaroid_pdc320 polaroid_pdc640 polaroid_pdc700 ricoh_g3 sipix_blink sipix_blink2 sipix_web2 sony_dscf1 sony_dscf55 toshiba_pdrm11 adc65 aox barbie canon clicksmart310 digigr8 digita directory enigma13 fuji gsmart300 hp215 iclick jamcam jd11 konica largan lg_gsm mars mustek pccam300 pccam600 ptp2 ricoh samsung sierra smal sonix soundvision spca50x sq905 stv0674 stv0680 sx330z template" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse void" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US af ar az bg bn br bs ca cs cy da de el en_GB eo es et eu fa fi fr fy ga gl he hi hr hu is it ja kk km ko lt lv mk mn ms nb nds nl nn pa pl pt pt_BR ro ru rw se sk sl sr sr@Latn ss sv ta tg tr uk uz vi zh_CN zh_TW es_AR es_ES fy_NL ga_IE gu gu_IN nb_NO nn_NO pt_PT sv_SE zh" LIRC_DEVICES="audio audio_alsa" USERLAND="GNU" VIDEO_CARDS="fbdev vesa radeonhd" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Hi Fabio, I've just added paraview-3.6.1 to portage and, hopefully, the issue you are having will be gone. Please feel free to re-open this bug should there still be the same issue with 3.6.1. cheers, Markus
Still the same issue with paraview 3.6.1. Sorry ;) !
Created attachment 199550 [details] sci-visualization/paraview-3.6.1 build.log
Quite strange! From your build directory, could you please post the following files Utilities/hdf5/hdf5_zlib.h Utilities/hdf5/H5pubconf.h CMakeCache.txt Thanks, Markus
Hey Markus, sorry for the delay, please find them attached.
Created attachment 200927 [details] requested CMakeCache.txt requested CMakeCache.txt
Created attachment 200928 [details] requested H5pubconf.h requested H5pubconf.h
Created attachment 200929 [details] requested hdf5_zlib.h requested hdf5_zlib.h
Thanks! I'll have a look at this over the weekend. Markus
This is a very odd issue - cmake detects zlib.h just fine at the top level //Path to a file. ZLIB_INCLUDE_DIR:PATH=/usr/include but then fails to pick it up when configuring hdf5. This is a shot in the dark, but could you try adding the following line to your ebuild (somewhere among the other lines) and see if that helps CMAKE_VARIABLES="${CMAKE_VARIABLES} -DHDF5_ZLIB_INCLUDE_DIRS:PATH=/usr/include" Thanks, Markus
Not in the tree anymore
