libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -O2 -pipe -MT time.lo -MD -MP -MF .deps/time.Tpo -c time.cpp -o time.o >/dev/null 2>&1 mv -f .deps/time.Tpo .deps/time.Plo /bin/sh ../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -O2 -pipe -MT update_e_from_d.lo -MD -MP -MF .deps/update_e_from_d.Tpo -c -o update_e_from_d.lo update_e_from_d.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -O2 -pipe -MT update_e_from_d.lo -MD -MP -MF .deps/update_e_from_d.Tpo -c update_e_from_d.cpp -fPIC -DPIC -o .libs/update_e_from_d.o update_e_from_d.cpp: In member function 'void meep::fields_chunk::update_e_from_d()': update_e_from_d.cpp:91: error: 'memcpy' was not declared in this scope make[3]: *** [update_e_from_d.lo] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-physics/meep-0.10.1/work/meep-0.10.1/src' make[2]: *** [all] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-physics/meep-0.10.1/work/meep-0.10.1/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-physics/meep-0.10.1/work/meep-0.10.1' make: *** [all] Error 2 * * ERROR: sci-physics/meep-0.10.1 failed. Portage 2.1.4.4 (default-linux/amd64/2007.0, gcc-4.3.1, glibc-2.8_p20080602-r0, 2.6.25.1 x86_64) ================================================================= System uname: 2.6.25.1 x86_64 Dual-Core AMD Opteron(tm) Processor 2212 HE Timestamp of tree: Tue, 17 Jun 2008 20:45:01 +0000 app-shells/bash: 3.2_p39 dev-lang/python: 2.5.2-r4 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.2.5 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.62 sys-devel/automake: 1.10.1-r1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.4 virtual/os-headers: 2.6.25-r4 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="buildpkg distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://216.165.129.134/gentoo http://gentoo.mirrors.tds.net/gentoo http://gentoo.osuosl.org/" LANG="en_US" 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" SYNC="rsync://208.71.112.51/gentoo-portage" USE="X acl amd64 berkdb cli cracklib crypt cups dri fortran gcj gdbm gpm iconv ipv6 isdnlog midi mmx mudflap ncurses nls nptl nptlonly objc openmp pam pcre perl pppd python readline reflection session spl sse sse2 ssl tcpd unicode xorg 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 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 evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="vga" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
[cite] Portage 2.1.4.4 (default-linux/amd64/2007.0, gcc-4.3.1, glibc-2.8_p20080602-r0, 2.6.25.1 x86_64) [/cite] I think this is a glibc-2.8 bug. Compiles fine on my box with glibc-2.6. However tests fail. Do you want to handle this together or should I file a new bug? BR, Dustin Portage 2.1.4.4 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo_dazuko-patch-r8-stable x86_64) ================================================================= System uname: 2.6.24-gentoo_dazuko-patch-r8-stable x86_64 Intel(R) Core(TM)2 Duo CPU T8100 @ 2.10GHz Timestamp of tree: Fri, 27 Jun 2008 07:15:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.5.2-r5 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r2 sys-devel/automake: 1.4_p6, 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/bin/mygenkernel /usr/sbin/run-crons /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache collision-protect distlocks fixpackages metadata-transfer multilib-strict parallel-fetch sandbox sfperms strict test unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="ftp://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://pandemonium.tiscali.de/pub/gentoo/ ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/ ftp://gd.tuwien.ac.at/opsys/linux/gentoo/ ftp://gentoo.inode.at/source/" LINGUAS="en de" MAKEOPTS="-j7" PKGDIR="/home/ftp/binpkg/" PORTAGE_COMPRESS="" PORTAGE_RSYNC_EXTRA_OPTS="--timeout=500" 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/alon-barlev /usr/local/portage/layman/haskell /usr/local/portage/layman/sunrise /usr/local/portage/layman/science /usr/local/portage/layman/connectical-contrib /usr/local/portage/layman/synce /usr/local/portage/modified /usr/local/portage/own" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac aalib accessibility acl acpi alsa amd64 amr amrnb amrr amrwb apm async audacious audiofile bash-completion berkdb bindist bl bluetooth branding bzip2 cairo cardbus cjk cli cpudetection cracklib crypt css ctype cups dbus dga divx dri dts dvd dvdr dvdread eds encode evo exif expat extensions fam fbcon fbcondecor fbsplash ffmpeg flac foomaticdb force-cgi-redirect fortran ftp gd gdbm gedit gif gimp glade glibc-omitfp glitz gmedia gmp gnutls gphoto2 gs gsm gtk gtkhtml guile hddtemp hdf5 iconv icq icu idn ieee1394 imagemagick imap imlib iproute2 ipw4965 isdnlog jack java javascript jikes jpeg jpeg2k kerberos keyscrub kpathsea laptop latex lcms ldap libcaca libnotify libwww live lm_sensors logrotate loop-aes lzo mad memlimit midi mikmod mime mmx mmxext mng motif mp2 mp3 mp4 mpeg mudflap multilib musepack ncurses nls nntp nptl nptlonly nsplugin nvidia ogg opengl openmp pam pch pcmcia pcre pda pdf perl plotutils png posix ppds pppd print python quicktime readline realmedia reflection rtsp ruby rubytests samba sasl sdl server session simplexml slang sndfile soap sockets speex spell spl sse sse2 ssl ssse3 stream suhosin svg swat syslog tcpd tetex tga theora threads tiff truetype unicode usb userlocales v4l v4l2 vcd vim-syntax vim-with-x vorbis wifi winbind wma wmf wmp wxwindows x264 xanim xine xinetd xml xorg xpm xsl xulrunner xv xvid xvmc zlib" ALSA_CARDS="hda-intel mpu401" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter 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" CAMERAS="fuji ptp2" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en de" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS_FLAGS
Hi guys, Thanks much for the note! Let's just leave it at this bug. I'll have a look at it later. Thanks, Markus
Created attachment 158647 [details] Build log with tests failing (In reply to comment #2) > Thanks much for the note! Let's just leave it > at this bug. I'll have a look at it later. For completeness since you want to do it in this bug.
The gcc-4.3 compile issue (not glibc related) reported originally should be fixed now. Unfortunately, I can not reproduce the test failures since all pass fine for me on both amd64 and x86 using gcc-4.3.1. Have you tried if using a more recent gcc works for you? Thanks, Markus
(In reply to comment #4) > The gcc-4.3 compile issue (not glibc related) reported originally > should be fixed now. Unfortunately, I can not reproduce the > test failures since all pass fine for me on both amd64 and x86 using > gcc-4.3.1. Have you tried if using a more recent gcc works > for you? > > Thanks, > Markus > No, I have not. Unfortunately, this is a production machine and I won't update it to a more recent gcc version until this becomes stable.
(In reply to comment #5) > (In reply to comment #4) > > The gcc-4.3 compile issue (not glibc related) reported originally > > should be fixed now. Unfortunately, I can not reproduce the > > test failures since all pass fine for me on both amd64 and x86 using > > gcc-4.3.1. Have you tried if using a more recent gcc works > > for you? > > > > Thanks, > > Markus > > > No, I have not. Unfortunately, this is a production machine and I won't update > it to a more recent gcc version until this becomes stable. > All test pass here even with gcc-4.1.2, so, unfortunately, there's not much I can do at this point unless you can somehow track this down some more. You may also want to get in touch with upstream since they likely have a much better idea of what the issue could be. Best, Markus
> All test pass here even with gcc-4.1.2, so, unfortunately, there's not > much I can do at this point unless you can somehow track this down > some more. You may also want to get in touch with upstream since > they likely have a much better idea of what the issue could be. > Hi Markus, I've check in upstream mailing list. There are others having the same way but upstream cannot reproduce the problem either. However, there was a hint concerning the blas implementation. The guy having the same failure like me used blas-reference as did I. Upstream tested however with blas-atlas so I emerged this over night. This morning, I was able to reproduce the failure with blas-reference again, then switched with eselect to blas-atlas threads. With that tests succeeded correctly. So either there is a buggy blas-reference or the test is not compatible. Hope this helps to track it down. Since the test fails, I am pretty sure that meep does not work correctly with blas-reference. Could you explicitely RDEPEND="!sci-libs/blas-reference" on it or does this break something? BR, Dustin
(In reply to comment #7) > Since the test fails, I am pretty sure that meep does not work correctly with > blas-reference. Could you explicitely RDEPEND="!sci-libs/blas-reference" on it > or does this break something? > > BR, > Dustin > Hi Dustin, Thanks a lot for tracking this down and blas-reference indeed seems to cause trouble in this regard. It is probably an issue with the test or meep itself so lets hope upstream will take a look at it. I am not sure if there is a really clean way to handle this. There's no way we can enforce a certain blas-implementation after the package is compiled so a warning is probably the best we can do. For now, I'll have the ebuild explicitly depend on blas-atlas and display a warning to the user if a blas implementation other than blas-atlas is selected. Hopefully, that sounds like an acceptable solution for the time being. Best, Markus
With meep-0.20.3, blas-reference worked for me. Do you confirm this as well?
I can confirm this. I re-compiled meep-0.20.3 with blas-reference eselected and all tests passed fine. BR, Dustin
Thanks, I removed 0.10.3. Now closing.
