'emerge atlas' fails with: ... make[4]: `clib.grd' is up to date. make[4]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/interfaces/lapack/C2F/src' make[3]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/interfaces/lapack/C2F/src' cd /var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/src/auxil/ ; make ptlib make[3]: Entering directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/src/auxil' gcc -o ATL_ptflushcache.o -c -DL2SIZE=4194304 -I/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/include -I/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS//include -I/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_UNKNOWNx86 -DATL_CPUMHZ=1333 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632 -DWALL -DATL_FULL_LAPACK -DATL_NCPU=2 -O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe -fPIC -m32 /var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS//src/auxil/ATL_ptflushcache.c In file included from /var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS//include/atlas_threads.h:14:0, from /var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS//src/auxil/ATL_ptflushcache.c:33: /var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/include/atlas_tsumm.h:1:0: error: unterminated #ifndef make[3]: *** [ATL_ptflushcache.o] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/src/auxil' make[2]: *** [IBuildPtlibs0] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared/bin' DONE STAGE 5-1-0 at 13:09 ATLAS install complete. Examine ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details. make[1]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared' make clean make[1]: Entering directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared' rm -f *.o x* config?.out *core* make[1]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.41/work/ATLAS_shared' make -j1 libclapack.a rm -rf clapack libclapack.a mkdir clapack cd clapack ; ar x ../liblapack.a rm -f clapack/*f77wrap* clapack/*C2F* ar r libclapack.a clapack/ATL_* clapack/clapack_* ar: creating libclapack.a rm -rf clapack make -j1 libptclapack.a make: *** No rule to make target `libptlapack.a', needed by `libptclapack.a'. Stop. * ERROR: sci-libs/atlas-3.9.41 failed (compile phase): * emake failed Reproducible: Always root@inspironM12:/root(8)# emerge --info =sci-libs/atlas-3.9.41 Portage 2.1.10.7 (default/linux/x86/10.0/desktop, gcc-4.5.2, glibc-2.13-r4, 2.6.39-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-2.6.39-gentoo-i686-Intel-R-_Atom-TM-_CPU_Z520_@_1.33GHz-with-gentoo-2.0.3 Timestamp of tree: Fri, 22 Jul 2011 02:00:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2, 3.2 dev-util/cmake: 2.8.5-r2::science dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.0.3 sys-apps/openrc: 0.8.3-r1 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1-r1 sys-devel/binutils: 2.21.1 sys-devel/gcc: 4.5.2 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 2.6.38 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo java-overlay science x11 bicatali x-portage x-cpan g-octave ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" 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-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/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" CXXFLAGS="-O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j1" 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="/var/lib/layman/java-overlay /var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/bicatali /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d a52 aac abiword acl acpi admin afs alsa ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus declarative dell designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago garmin gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp mudflap musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 x86 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" ALSA_CARDS="intel8x0" 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 cgid 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" CALLIGRA_FEATURES="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="psb intel vesa" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root@inspironM12:/root(9)# emerge -pqv =sci-libs/atlas-3.9.41 [ebuild N ] sci-libs/atlas-3.9.41 USE="doc fortran lapack threads -static-libs"
Created attachment 280813 [details] bzip2ed /var/tmp/portage/sci-libs/atlas-3.9.41/temp/build.log
try with 3.9.46 just bumped. if it still fails, report upstream, since it looks like a specific non-gentoo bug
sci-libs/atlas-3.9.46 works for me.
let's close it then.
Please open the bug again. Some libraries fail to link to atlas-3.9.46 on systems with ATOM processors, e.g. sci-libs/cholmod-1.7.3-r1 and sci-libs/umfpack-5.5.1 fails to configure with: checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for sgemm_ in -lf77blas -lm -latlas ... no checking for sgemm_... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -lblas... no checking for sgemm_ in -lmkl... no checking for sgemm_... (cached) no checking for sgemm_ in -lcxml... no checking for sgemm_ in -ldxml... no checking for sgemm_ in -lscs... no checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) no checking for sgemm_ in -lblas... (cached) no configure: error: Cannot find blas libraries In config.log I find: configure:15039: i686-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed conftest.c -lf77blas -lm -latlas -lm -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.2 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../.. -lgfortran -lm >&5 /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_thread_free' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_join_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_free_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_wait_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_signal_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_thread_init' collect2: ld returned 1 exit status ... Then I find that the size of /usr/lib/libatlas.so.3 on the system with the ATOM CPU is with 3258008 Bytes less than the half of the size on a system with an Core(TM)2 CPU (6961488 Bytes). Is this to expect. I already emerged twice atlas-3.9.46 on the system with the ATOM CPU and have not observed any error. What could I else do?
It seems me that the current issue does not fit to description of the bug, therefore I opened a new Bug 377391 about problems of some libraries with sci-libs/atlas-3.9.46.
