Emerge fails during src_compile. sci-libs/hdf5-1.6.2 instead works out of the box. I am attaching the build.log.
Created attachment 191760 [details] Build log
please attach ouput of emerge --info
Ans output of emerge -vp sci-libs/hdf5
Oh sorry I forgot to attach those: davide@kerr ~ $ emerge --info Portage 2.1.6.11 (default/linux/amd64/2008.0/desktop, gcc-4.3.2, glibc-2.8_p20080602-r1, 2.6.28-gentoo-r5 x86_64) ================================================================= System uname: Linux-2.6.28-gentoo-r5-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9450_@_2.66GHz-with-glibc2.2.5 Timestamp of tree: Sat, 16 May 2009 18:00:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p39 dev-lang/python: 2.5.4-r2 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.2-r1 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.6-r2 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="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=core2 -pipe" 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" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/init.d /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=core2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y" FEATURES="buildpkg ccache distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" FFLAGS="-O2 -march=core2 -pipe" GENTOO_MIRRORS="ftp://gentoo.imj.fr/pub/gentoo/ ftp://mirror.leaseweb.com/gentoo/ ftp://gd.tuwien.ac.at/opsys/linux/gentoo/ http://de-mirror.org/distro/gentoo/" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="en it" MAKEOPTS="-j6" 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/mine /usr/local/portage/layman/science /usr/local/portage/layman/sunrise" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl acpi alsa amd64 bash-completion berkdb bzip2 cairo cdr cli cracklib crypt cups dbus dri dvd dvdr dvdread eds emboss encode fam ffmpeg firefox fortran ftp gdbm gif gnome gphoto2 gpm gstreamer gtk hal iconv imagemagick ipv6 isdnlog jpeg lapack latex ldap libnotify mad midi mikmod mmx mp3 mpeg msn mudflap multilib ncurses nptl nptlonly ogg opengl openmp pam pcre pdf perl png ppds pppd python quicktime readline reflection samba sdl session spell spl sqlite sse sse2 ssl ssse3 startup-notification svg sysfs tcpd tiff truetype unicode usb vim-syntax vorbis xcomposite xml xorg xulrunner xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp 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 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" LINGUAS="en it" USERLAND="GNU" VIDEO_CARDS="radeon vesa" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS davide@kerr ~ $ emerge -pv hdf5 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-libs/hdf5-1.6.4 [1.6.2] USE="ssl zlib -debug -hlapi% -mpi% -static -szip% -threads" 0 kB
same for me, but version 1.6.7 works. Perhaps you should try this one. see bug 245715
same for me on x86_64 (see attached build.log and emergeinfo)
Created attachment 192484 [details] failed build log
Created attachment 192486 [details] emerge --info
(In reply to comment #6) > same for me on x86_64 (see attached build.log and emergeinfo) > some explanation: emerge sci-libs/hdf5 -pv These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/hdf5-1.6.4 USE="ssl threads zlib -debug -hlapi -mpi -static -szip" 0 kB Previously, ebuild was merged fine with gcc-4.1.2.
Created attachment 193655 [details, diff] fix byte order detection problem at: H5detect: ./H5detect.c:848: fix_order: Assertion `0 == n / 2' failed. ------------H5detect.c------------- 845: /* 846: * Bi-endian machines like VAX. 847: */ 848: assert(0 == n / 2); 849: if (mesg) *mesg = "VAX"; 850: for (i = 0; i < n; i += 2) { 851: perm[i] = (n - 2) - i; 852: perm[i + 1] = (n - 1) - i; 853: } -----------H5detect.c------------- i think that n should be even, assert must look like: assert(0 == n % 2);
Created attachment 193659 [details] ebuild to build with H5detect.c.patch and hdf5-gcc4.3.3-fix.patch
Same problem here. Can this problem be fixed in portage? Or should =sci-libs/hdf5-1.6.4 be HARD MASKED, as it FTBFS?
hdf5-1.6.4 seems to have a few issues for me as well. It would probably best if we try to stabilize a later version. Candidates would either be 1.6.7 which seems to compile fine and pass the tests or perhaps even 1.8.* (I haven't checked if all stable packages depending on hdf5 can deal with 1.8* yet). Thanks, Markus
Hi, I'm also getting compile errors here for =sci-libs/hdf5-1.6.4. =================== *snip* =================== [...] H5Tconv.c:3788: warning: dereferencing pointer 'd.263' does break strict-aliasing rules H5Tconv.c:3788: note: initialized from here H5Tconv.c: In function 'H5T_conv_schar_short': H5Tconv.c:3755: warning: dereferencing pointer 'd.244' does break strict-aliasing rules H5Tconv.c:3755: note: initialized from here H5Tconv.c:3755: warning: dereferencing pointer 'd.244' does break strict-aliasing rules H5Tconv.c:3755: note: initialized from here mv -f H5Tconv.o H5Tconv.lo make[2]: Leaving directory `/var/tmp/paludis/sci-libs-hdf5-1.6.4/work/hdf5-1.6.4/src' make[1]: Leaving directory `/var/tmp/paludis/sci-libs-hdf5-1.6.4/work/hdf5-1.6.4' make[1]: *** [lib] Error 1 make: *** [all] Error 2 /usr/libexec/paludis/utils/emake: emake returned error 2 !!! ERROR in sci-libs/hdf5-1.6.4::gentoo: !!! In src_compile at line 3722 !!! emake failed [...] =================== *snap* =================== These compilation problems did not occur for 1.6.7. The problem is that I need an installation of the 1.6 series b/c a (non-portage) library that I use links against it and hasn't been updated to the 1.8 API yet. Cheers, Nico
(In reply to comment #14) > The problem is that I need an installation of the 1.6 series b/c a > (non-portage) library that I use links against it and hasn't been updated to > the 1.8 API yet. Please note that anything requiring hdf5-1.6.x can be built with the 1.8 library by compiling with the -D H5_USE_16_API option (unless your HDF5 1.8 library was configured with the --disable-deprecated-symbols option). Best regards, Kacper Kowalik
> library by compiling with the -D H5_USE_16_API option (unless your HDF5 1.8 That's good to know, thanks! Anyway, I just renamed sci-libs/hdf5-1.6.4 to sci-libs/hdf5-1.6.10 and things work and compile fine here on amd64. Cheers, Nico
Removed from tree
