The package tries to infinitely rebuild itself. It seems that the libraries libblast.so and libeinfo.so should normally be a part of the package (or at least get installed as dependencies), but they are not anywhere on the system. Reproducible: Always Steps to Reproduce: 1. emerge ncbi-tools++ 2. revdep-rebuild Actual Results: * Checking dynamic linking consistency [ 11% ] * broken /usr/bin/eutils_sample (requires libeinfo.so) [ 18% ] * broken /usr/bin/makembindex (requires libblast.so) [ 21% ] * broken /usr/bin/omssa2pepXML (requires libblast.so) * broken /usr/bin/omssacl (requires libblast.so) * broken /usr/bin/omssamerge (requires libblast.so) [ 29% ] * broken /usr/bin/srsearch (requires libblast.so) [ 33% ] * broken /usr/bin/update_omssamod (requires libblast.so) * broken /usr/bin/windowmasker (requires libblast.so) [ 100% ] * Generated new 3_broken.rr * Assigning files to packages * /usr/bin/eutils_sample -> sci-biology/ncbi-tools++ * /usr/bin/makembindex -> sci-biology/ncbi-tools++ * /usr/bin/omssa2pepXML -> sci-biology/ncbi-tools++ * /usr/bin/omssacl -> sci-biology/ncbi-tools++ * /usr/bin/omssamerge -> sci-biology/ncbi-tools++ * /usr/bin/srsearch -> sci-biology/ncbi-tools++ * /usr/bin/update_omssamod -> sci-biology/ncbi-tools++ * /usr/bin/windowmasker -> sci-biology/ncbi-tools++ Expected Results: Clean package I ran lafilefixer which does not fix the problem. Tried to emerge it with sqlite USE flag both on or off. The same behavior is encountered on computers with both Intel Core i7 and AMD K8 CPUs. Here is emerge --info: Portage 2.1.7.16 (default/linux/amd64/10.0, gcc-4.3.4, glibc-2.10.1-r1, 2.6.31-gentoo-r6 x86_64) ================================================================= System uname: Linux-2.6.31-gentoo-r6-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-1.12.13 Timestamp of tree: Tue, 23 Feb 2010 17:30:01 +0000 app-shells/bash: 4.0_p35 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.4 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc: 4.3.4 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA skype-eula dlj-1.1 PUEL" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /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="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" LINGUAS="en ru" 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="/usr/local/portage/layman/sunrise /usr/local/portage/layman/devnull" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl alsa amd64 bash-completion berkdb blas branding bzip2 ccda cdr cli cracklib crypt css cups cxx dbus djvu dri dvd dvdr emboss fontconfig fortran gdbm gif gpm gtk gzip hal iconv ipv6 jpeg jpeg2k lapack latex mmx modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly ogg opengl openmp pam pcre perl png pppd python readline reflection savedconfig session smp spell spl sse sse2 ssl svg sysfs tcpd tiff ubuntu unicode v4l v4l2 vcd vim-syntax xft xorg xv 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 evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en ru" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
It seems that the ncbi-tools++ ebuild intentionally removes these libraries: src_install() { emake install || die # File collisions with sci-biology/ncbi-tools rm -f "${D}"/usr/bin/{asn2asn,rpsblast,test_regexp} rm -f "${D}"/usr/$(get_libdir)/libblast.* # File collision with openrc. NCBI probably needs a subdirectory in /usr/lib rm -f "${D}"/usr/$(get_libdir)/libeinfo.* The package ncbi-tools has only the following files, /usr/lib64/libblast.a /usr/lib64/libblastapi.a /usr/lib64/libblastcompadj.a not libblast.so Would it be possible to add a --with-mt to the configure options, otherwise the blast cannot run using multiple threads
Thank you for reporting. Fix applied in sci-biology/ncbi-tools++-2009.05.15-r2 , please test. I am currently unable to set --with-mt, because the package fails to compile with gcc-4.4 when using that flag (but compiles fine with gcc-4.3). Please open a new bug for that issue. Patches are welcome - I currently don't have enough time to work on this issue.
Thanks, it works for me. There are no collisions with ncbi-tools-20090809-r1. I do not have openrc installed.
FYI: The latest revision enables --with-mt for multithreading support.
