Bug 152114 – sci-biology/ncbi-tools emerge fails

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Nick Fankhauser 2006-10-20 06:53:21 UTC]

I get this error when trying to emerge sci-biology/ncbi-tools:

i386-pc-linux-gnu-gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -O2 -march=pentium4m -pipe -c -O2 -march=pentium4m -pipe  -I../include -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF ncbithr.c
cp -p ncbithr.o ../lib
make: *** No rule to make target `ncbibs.o', needed by `libncbi.a'.  Stop.
Fatal error building NCBI core libraries.
Please be sure that you have X11 and Motif libraries installed.
The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful.

I have x11 and motif installed. I also tried lesstif. I tried with all optimizing CFLAGS turned off (like j1 instead of j2) and it's still the same error.

Here is make emerge --info:
thinkpad # emerge --info
Portage 2.1.1 (default-linux/x86/no-nptl, gcc-4.1.1, glibc-2.3.6-r4, 2.6.17-gentoo-r8 i686)
=================================================================
System uname: 2.6.17-gentoo-r8 i686 Genuine Intel(R) CPU           T2400  @ 1.83GHz
Gentoo Base System version 1.12.5
Last Sync: Thu, 19 Oct 2006 11:00:01 +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:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r76
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i386-pc-linux-gnu"
CFLAGS="-O2 -march=pentium4m -pipe"
CHOST="i386-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-O2 -march=pentium4m -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="ftp://mirror.switch.ch/mirror/gentoo/ http://mirror.switch.ch/mirror/gentoo/ ftp://ftp.solnet.ch/mirror/Gentoo"
LINGUAS=""
MAKEOPTS="-j2"
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"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X alsa apache2 apm arts asf avi berkdb bitmap-fonts bzip2 cli cracklib crypt cups dlloader dri eds elibc_glibc emboss encode exif fam ffmpeg flac foomaticdb fortran gd gdbm gif gnome gphoto2 gpm gstreamer gtk gtk2 hal i810 imagemagick imap imlib input_devices_keyboard input_devices_mouse intel isdnlog java jpeg kde kernel_linux libg++ libwww mad mikmod motif mp3 mpeg mysql ncurses nls nsplugin ogg opengl oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection sdl session spell spl ssl svg tcpd tetex truetype truetype-fonts type1-fonts unicode usb userland_GNU video_cards_i810 video_cards_vesa vorbis win32codecs wxwindows xml xmms xorg xv xvid zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 Nick Fankhauser 2006-10-20 07:10:30 UTC]

I also tried with the -X use flag and it didn't help.

[Comment 2 Jeffrey Gardner (RETIRED) 2006-10-20 12:55:21 UTC]

which version are you trying to install?

[Comment 3 Nick Fankhauser 2006-10-20 13:15:37 UTC]

(In reply to comment #2)
> which version are you trying to install?
> 

stable i386:
sci-biology/ncbi-tools-20050605 

[Comment 4 Olivier Fisette (RETIRED) 2006-10-22 10:31:53 UTC]

Hi Nick,

Can you please test if the latest version (20060507) fixes your problem?

[Comment 5 Ian Tegebo 2006-10-25 20:56:12 UTC]

I ran into the same problem that Nick and followed a similar path.  I've unmasked ncbi-tools and have gotten beyond the initial error from sci-biology/ncbi-tools-20050605 using sci-biology/ncbi-tools-20060507.  I'll post with the results.

[Comment 6 Ian Tegebo 2006-10-25 21:05:29 UTC]

(In reply to comment #5)
> I'll post with the results.
20060507 built just fine for me.  I did:
echo 'sci-biology/ncbi-tools ~x86' >> /etc/portage/package.mask
sudo emerge -va '>sci-biology/ncbi-tools-20050605'

[Comment 7 Nick Fankhauser 2006-10-26 02:34:15 UTC]

Yes, the latest ~i386 version fixes this problem here.

[Comment 8 Olivier Fisette (RETIRED) 2006-10-26 06:37:55 UTC]

Thanks for reporting. Arch teams are in the process of stabilising the newest ncbi-tools version (bug #152292).

[Comment 9 Olivier Fisette (RETIRED) 2006-12-10 11:15:27 UTC]

This should be solved now that a more recent version is stable on x86. Thanks for your feedback.