'emerge -v apbs' fails with: ... checking for strcasecmp... yes checking for --disable-tools... no configure: tools will be compiled checking for --with-blas... -lblas configure: checking blas using -lblas checking for dscal in -lblas... no configure: error: BLAS libraries or headers missing: exiting on error! !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-chemistry/apbs-1.3-r1/work/apbs-1.3-source/config.log * ERROR: sci-chemistry/apbs-1.3-r1 failed (configure phase): Reproducible: Always Actual Results: root@orca:/usr/local/portage(228)# emerge --info =sci-chemistry/apbs-1.3-r1 Portage 2.1.10.3 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r2, 2.6.39-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.39-gentoo-r1-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-2.0.3 Timestamp of tree: Thu, 30 Jun 2011 07:00:01 +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: 2.8.4-r1 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: 4.4.5, 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-r2 Repositories: gentoo x11 java-overlay sunrise science bicatali x-portage x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb" 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-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/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="-march=native -O2 -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="-j9" 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/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/science /var/lib/layman/bicatali /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative 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 gcj 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 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate 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 multilib 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 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 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" 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" USERLAND="GNU" VIDEO_CARDS="nv nouveau 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@orca:/usr/local/portage(229)# emerge -pqv =sci-chemistry/apbs-1.3-r1 [ebuild N ] sci-chemistry/apbs-1.3-r1 USE="arpack doc openmp python tools -fetk -mpi"
Created attachment 278671 [details] /var/tmp/portage/sci-chemistry/apbs-1.3-r1/work/apbs-1.3-source/config.log
Shame on me. Consider it to be fixed within an hour.
After some 'emerge --sync' it still fails for me.
which error? still configure? Could you attach some log please?
Almost the same error as before: root@orca:/root(2)# emerge -pvuDN world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] sci-chemistry/apbs-1.3-r1 USE="arpack doc openmp python tools -fetk -mpi" 0 kB root@orca:/root(3)# emerge -vuDN world These are the packages that would be merged, in order: ... checking for strcasecmp... yes checking for --disable-tools... no configure: tools will be compiled checking for --with-blas... -lptf77blas -lm -latlas -lpthread configure: checking blas using -lptf77blas -lm -latlas -lpthread checking for dscal in -lblas... no configure: error: BLAS libraries or headers missing: exiting on error!
Created attachment 279013 [details] /var/tmp/portage/sci-chemistry/apbs-1.3-r1/work/apbs-1.3-source/config.log
Okay, that buildsystem is crappy. On my system libblas.so is present although I use atlas. But the configure check tests -lblas and not the libs passed with configure. Leter on it uses the correct one. Please sync and test. If it works the bug can be closed.
+ 07 Jul 2011; Justin Lecher <jlec@gentoo.org> apbs-1.3-r1.ebuild: + Fix for atlas detection as blas implementation +
fixed?
Fixed!
Created attachment 280209 [details] /var/tmp/portage/sci-chemistry/apbs-1.3-r1/temp/build.log Still failed to build. Using atlas from bicatali overlay.
okay lets see
could please check the output of grep lblas /usr/lib/*.la
(In reply to comment #13) > could please check the output of > > grep lblas /usr/lib/*.la $ grep lblas /usr/lib/*.la /usr/lib/libapbs.la:dependency_libs=' -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0/../../.. -L/var/tmp/portage/sci-chemistry/apbs-1.3-r1/work/apbs-1.3-source/contrib/lib -L/usr/lib64 -lgfortran -lblas -lgomp -lrt -lmaloc -lreadline -lm -lz' /usr/lib/libapbsmainroutines.la:dependency_libs=' -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.0/../../.. -L../src/aaa_lib/.libs/ -L/usr/lib64 -L/var/tmp/portage/sci-chemistry/apbs-1.3-r1/work/apbs-1.3-source/contrib/lib -lapbs -lgfortran -lgomp -lmaloc -lblas -lrt -lreadline -lm -lz' So, I do "emerge -C apbs" and then it was build successfully. Thanks.
fixed in 1.3-r2. Actually there was a bug in the buildsystem which was corercted now.
