Bug 154545 – sci-biology/mafft cannot run - MAFFT_BINARIES is not set

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description dawe 2006-11-09 02:52:32 UTC]

Hi, after installing mafft (sci-biology/mafft) it cannot run since $MAFFT_BINARIES is not set.

$ mafft

correctly installed?
mafft binaries have to be installed in $MAFFT_BINARIES
or the /usr/local/lib/mafft directory.

As a workaroud I added

export MAFFT_BINARIES=/usr/bin

in my /etc/profile, nevertheless should be corrected the ebuild to add the proper environmental variable.

# emerge --info
Portage 2.1.2_pre3-r5 (default-linux/x86/no-nptl, gcc-4.1.1, glibc-2.5-r0, 2.6.18-gentoo-r1smp i686)
=================================================================
System uname: 2.6.18-gentoo-r1smp i686 Intel(R) Xeon(TM) CPU 3.06GHz
Gentoo Base System version 1.12.5
Last Sync: Sat, 21 Oct 2006 13:20:01 +0000
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.60
sys-devel/automake:  1.6.3, 1.7.9-r1, 1.9.6-r2, 1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="x86 X apm arts berkdb bitmap-fonts cli cracklib crypt cups dlloader dri eds elibc_glibc emboss encode foomaticdb fortran gdbm gif gpm gstreamer gtk gtk2 imlib input_devices_evdev input_devices_keyboard input_devices_mouse ipv6 isdnlog jpeg kde kernel_linux ldap libg++ libwww mad mikmod motif mp3 mpeg mysql ncurses nls ogg opengl oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts userland_GNU video_cards_apm video_cards_ark video_cards_ati video_cards_chips video_cards_cirrus video_cards_cyrix video_cards_dummy video_cards_fbdev video_cards_glint video_cards_i128 video_cards_i740 video_cards_i810 video_cards_imstt video_cards_mga video_cards_neomagic video_cards_nsc video_cards_nv video_cards_rendition video_cards_s3 video_cards_s3virge video_cards_savage video_cards_siliconmotion video_cards_sis video_cards_sisusb video_cards_tdfx video_cards_tga video_cards_trident video_cards_tseng video_cards_v4l video_cards_vesa video_cards_vga video_cards_via video_cards_vmware video_cards_voodoo vorbis xml xmms xorg xv zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Donnie Berkholz (RETIRED) 2006-11-09 06:52:47 UTC]

Fixed in -r1, thanks!