Bug 153419 – coot-0.1.2 can't find clipper

• Status: RESOLVED WORKSFORME
• Product: Gentoo Linux

[Description Klaas Decanniere 2006-10-30 02:04:15 UTC]

probably something simple, but I'm not sure yet how to go and fix this myself  in the ebuild environment.
(I might regret this later on, but I noticed that the maintainer feels a bit lonely - I could probably be coached/convinced into helping to maintain some (protein) crystallography packages)


emerge quits with this error when trying to install coot-0.1.2 (0.1.2-pre-something seems fine):

checking for Clipper... no
Error locating Clipper

!!! Please attach the following file when filing a report to bugs.gentoo.org:
!!! /var/tmp/portage/coot-0.1.2/work/coot-0.1.2/config.log

!!! ERROR: sci-chemistry/coot-0.1.2 failed.
Call stack:
  ebuild.sh, line 1546:   Called dyn_compile
  ebuild.sh, line 937:   Called src_compile
  coot-0.1.2.ebuild, line 72:   Called econf '--includedir=${prefix}/include/coot' '--with-gtkcanvas-prefix=/usr' '--with-clipper-prefix=/usr' '--with-mmdb-prefix=/usr' '--with-ssmlib-prefix=/usr' '--with-guile=/usr' '--with-python=/usr'
  ebuild.sh, line 540:   Called die

!!! econf failed
!!! If you need support, post the topmost build error, and the call stack if relevant.


And emerge --info gives:
Portage 2.1.1-r1 (default-linux/x86/2006.1, gcc-4.1.1, glibc-2.4-r3, 2.6.17-gentoo-r8 i686)
=================================================================
System uname: 2.6.17-gentoo-r8 i686 Transmeta(tm) Crusoe(tm) Processor TM5800
Gentoo Base System version 1.12.5
Last Sync: Mon, 30 Oct 2006 09:20:01 +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:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
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="i686-pc-linux-gnu"
CFLAGS="-O3 -march=i686 -pipe -mpreferred-stack-boundary=2 -falign-functions=0 -falign-jumps=0 -falign-loops=0"
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"
CXXFLAGS="-O3 -march=i686 -pipe -mpreferred-stack-boundary=2 -falign-functions=0 -falign-jumps=0 -falign-loops=0"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://ftp.belnet.be/mirror/rsync.gentoo.org/gentoo/ ftp://ftp.belnet.be/mirror/rsync.gentoo.org/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://ftp.join.uni-muenster.de/pub/linux/distributions/gentoo http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo ftp://ftp.snt.utwente.nl/pub/os/linux/gentoo ftp://mirror.scarlet-internet.nl/pub/gentoo "
LINGUAS="en nl fr de"
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.europe.gentoo.org/gentoo-portage"
USE="x86 X acpi alsa berkdb bitmap-fonts bzip2 cli cracklib crypt cups dlloader dri dvd dvdr elibc_glibc emacs fftw fortran gdbm gif gpm iconv input_devices_keyboard input_devices_mouse ipv6 isdnlog jpeg kernel_linux ldap libg++ linguas_de linguas_en linguas_fr linguas_nl mime mmx mp3 ncurses nls nptl nptlonly nsplugin pam pcre perl png ppds pppd python readline reflection rt73usb session smartcard spl ssl tcpd tiff truetype truetype-fonts type1-fonts udev unicode userland_GNU video_cards_fbdev video_cards_nv video_cards_nvidia video_cards_vesa wifi win32codecs xinerama xorg zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 Donnie Berkholz (RETIRED) 2006-10-30 08:41:35 UTC]

Gotta read the output more carefully. =)

!!! Please attach the following file when filing a report to bugs.gentoo.org:
!!! /var/tmp/portage/coot-0.1.2/work/coot-0.1.2/config.log

Also the output of `qlist ccp4 | grep clipper`, `qlist ccp4 | grep clipper | grep 'lib/.*so$' | xargs ldd` and `qlist -I -v ccp4` would be helpful to ensure you've got the clipper libraries and they aren't broken.

[Comment 2 Klaas Decanniere 2006-10-30 09:44:24 UTC]

Created attachment 100805 [details]
coot-0.1.2/work/coot-0.1.2/config.log

[Comment 3 Klaas Decanniere 2006-10-30 09:45:35 UTC]

Created attachment 100807 [details]
qlist ccp4 | grep clipper

[Comment 4 Klaas Decanniere 2006-10-30 09:47:20 UTC]

Created attachment 100808 [details]
qlist ccp4 | grep clipper | grep 'lib/.*so' | xargs ldd

[Comment 5 Klaas Decanniere 2006-10-30 09:48:04 UTC]

Created attachment 100809 [details]
qlist -I -v ccp4

[Comment 6 Donnie Berkholz (RETIRED) 2006-10-30 10:20:14 UTC]

Simple enough ...
/usr/lib/gcc/i686-pc-linux-gnu/4.1.1/../../../../i686-pc-linux-gnu/bin/ld: cannot find -lrfftw

Do you have fftw-2 installed? It should have been pulled in by ccp4.

qlist -I -v fftw
qlist fftw | grep rfftw

[Comment 7 Klaas Decanniere 2006-10-30 11:40:05 UTC]

(In reply to comment #6)


> Do you have fftw-2 installed? It should have been pulled in by ccp4.
> 
> qlist -I -v fftw

sci-libs/fftw-2.1.5-r1

> qlist fftw | grep rfftw
> 

/usr/lib/libsrfftw_threads.la
/usr/lib/libsrfftw_threads.so.2.0.7
/usr/lib/libsrfftw_threads.so.2
/usr/lib/libdrfftw_threads.la
/usr/lib/libsrfftw_threads.a
/usr/lib/libdrfftw_threads.a
/usr/lib/libdrfftw_threads.so.2.0.7
/usr/include/drfftw.h
/usr/include/srfftw.h
/usr/include/srfftw_threads.h
/usr/include/drfftw_threads.h
/usr/lib/libsrfftw_threads.so
/usr/lib/libdrfftw_threads.so
/usr/lib/libdrfftw_threads.so.2
/usr/include/rfftw.h
/usr/include/rfftw_threads.h
/usr/lib/librfftw_threads.so
/usr/lib/librfftw.so

There seemed to be a version mismatch, so I re-emerged fftw-2.1.5-r1 just to be sure (without actually changing anything, except starting the bread maker and adding cupsd to the default runlevel). 
I now get more libraries: 

/usr/lib/librfftw_threads.so
/usr/lib/libsrfftw_threads.la
/usr/lib/libsrfftw_threads.so
/usr/lib/libdrfftw.a
/usr/lib/libsrfftw_threads.so.2.0.7
/usr/lib/libsrfftw.a
/usr/lib/libdrfftw.so.2.0.7
/usr/lib/libsrfftw_threads.so.2
/usr/lib/libdrfftw_threads.la
/usr/lib/libdrfftw_threads.so
/usr/lib/libsrfftw.la
/usr/lib/libsrfftw_threads.a
/usr/lib/libsrfftw.so.2.0.7
/usr/lib/libdrfftw.so.2
/usr/lib/libdrfftw_threads.so.2
/usr/lib/libdrfftw_threads.a
/usr/lib/libdrfftw.la
/usr/lib/libdrfftw.so
/usr/lib/libdrfftw_threads.so.2.0.7
/usr/include/rfftw.h
/usr/include/rfftw_threads.h
/usr/include/drfftw.h
/usr/include/srfftw.h
/usr/include/srfftw_threads.h
/usr/include/drfftw_threads.h
/usr/lib/libsrfftw.so.2
/usr/lib/libsrfftw.so
/usr/lib/librfftw.so


Right now, coot is compiling. 
:-)

don't know why, though.

Thanks,

Klaas

[Comment 8 Donnie Berkholz (RETIRED) 2006-10-30 13:14:06 UTC]

OK, some kind of bug apparently fixed now, so we'll just close this.

[Comment 9 Donnie Berkholz (RETIRED) 2006-10-30 13:19:21 UTC]

Please catch me on IRC or drop an email regarding helping with xtal packages.