x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -m64 -O3 -O2 -pipe -march=native -DNDEBUG -I/usr/include -Wl,-O1 -Wl,--as-needed -L/usr/lib -o bam2fastx -L/usr/lib bam2fastx.o ../src/libgc.a -lbam -lz -lz /usr/lib/libbam.so: undefined reference to `log' /usr/lib/libbam.so: undefined reference to `pow' /usr/lib/libbam.so: undefined reference to `sqrt' collect2: ld returned 1 exit status make[2]: *** [bam2fastx] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/tophat-1.3.2/work/tophat-1.3.2/src' # emerge --info =sci-biology/tophat-1.3.2 !!! Invalid PORTDIR_OVERLAY (not a dir): '/usr/local/portage' !!! Invalid PORTDIR_OVERLAY (not a dir): '/var/lib/layman' Portage 2.1.10.41 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.13-r4, 3.1.6-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.1.6-gentoo-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.1 Timestamp of tree: Sat, 28 Jan 2012 00:45:01 +0000 app-shells/bash: 4.2_p20 dev-lang/python: 2.7.2-r3, 3.1.4-r3 dev-util/cmake: 2.8.7-r1 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1 sys-apps/openrc: 0.9.8.2 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.11.2-r1 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.3-r2 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.1 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=native" DISTDIR="/mnt/external/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug 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="en cs cz" MAKEOPTS="-j5" 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="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X alsa amd64 amr apache apache2 berkdb bzip2 cairo cgi cli cracklib crypt cups cxx dbus device-mapper dri encode ffmpeg flac fontconfig fortran gd gdbm gnutls hal iconv id3tag innodb ipv6 java jce jpeg jpg kde ladspa laptop mad mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ogg opengl openmp openssl pam pcre perl php png policykit python qt3support qt4 readline server session sndfile sse sse2 ssl suexec svg sysfs syslog tcpd threads tiff truetype unicode usb wavpack xml 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 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" 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="en cs cz" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="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 # emerge -pqv =sci-biology/tophat-1.3.2 [ebuild N ] sci-biology/tophat-1.3.2 USE="bam"
Created attachment 300197 [details] build.log
I have sci-biology/samtools-0.1.18 freshly installed (a new computer install) and anyways, revdep-rebuild does not find anything wrong. # equery belongs /usr/lib/libbam.so * Searching for /usr/lib/libbam.so ... sci-biology/samtools-0.1.18 (/usr/lib64/libbam.so.1)
fixed, please test
Both sci-biology/tophat-1.3.3 and sci-biology/tophat-1.4.1 work, thanks.
