Bug 101667 – sci-biology/prosite-19.7: Died: Unknown qualifier -prositedir

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Martin Mokrejš 2005-08-07 11:58:14 UTC]

20:54:10 (241.45 KB/s) - `/usr/portage/distfiles/prosite-19.7.tar.bz2' saved
[3589984]

>>> md5 files   ;-) prosite-19.3.ebuild
>>> md5 files   ;-) prosite-18.49.ebuild
>>> md5 files   ;-) prosite-19.5.ebuild
>>> md5 files   ;-) prosite-19.0.ebuild
>>> md5 files   ;-) prosite-18.46.ebuild
>>> md5 files   ;-) prosite-19.7.ebuild
>>> md5 files   ;-) prosite-19.2.ebuild
>>> md5 files   ;-) prosite-18.48.ebuild
>>> md5 files   ;-) prosite-19.4.ebuild
>>> md5 files   ;-) prosite-19.6.ebuild
>>> md5 files   ;-) prosite-19.1.ebuild
>>> md5 files   ;-) prosite-18.47.ebuild
>>> md5 files   ;-) files/digest-prosite-19.0
>>> md5 files   ;-) files/digest-prosite-19.1
>>> md5 files   ;-) files/digest-prosite-19.2
>>> md5 files   ;-) files/digest-prosite-19.3
>>> md5 files   ;-) files/digest-prosite-19.4
>>> md5 files   ;-) files/digest-prosite-19.5
>>> md5 files   ;-) files/digest-prosite-19.6
>>> md5 files   ;-) files/digest-prosite-19.7
>>> md5 files   ;-) files/digest-prosite-18.46
>>> md5 files   ;-) files/digest-prosite-18.47
>>> md5 files   ;-) files/digest-prosite-18.48
>>> md5 files   ;-) files/digest-prosite-18.49
>>> md5 src_uri ;-) prosite-19.7.tar.bz2
>>> Unpacking source...
>>> Unpacking prosite-19.7.tar.bz2 to /var/tmp/portage/prosite-19.7/work
>>> Source unpacked.

 * Indexing PROSITE for usage with EMBOSS.
Died: Unknown qualifier -prositedir

!!! ERROR: sci-biology/prosite-19.7 failed.
!!! Function src_compile, Line 22, Exitcode 1
!!! Indexing PROSITE failed.
!!! If you need support, post the topmost build error, NOT this status message.


# emerge info
Portage 2.0.51.22-r2 (default-linux/x86/2005.0, gcc-3.4.4, glibc-2.3.5-r1,
2.6.13-rc5-git4 i686)
=================================================================
System uname: 2.6.13-rc5-git4 i686 Intel(R) Pentium(R) 4 CPU 3.00GHz
Gentoo Base System version 1.6.13
ccache version 2.4 [disabled]
dev-lang/python:     2.3.4-r1, 2.4.1-r1
sys-apps/sandbox:    1.2.11
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
sys-devel/binutils:  2.16.1
sys-devel/libtool:   1.5.18-r1
virtual/os-headers:  2.4.19-r1, 2.6.11-r2
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O3 -mmmx -msse -msse2 -fomit-frame-pointer -march=pentium4
-funroll-loops -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.3/env
/usr/kde/3.3/share/config /usr/kde/3.3/shutdown /usr/kde/3.4/env
/usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config
/usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /var/bind
/var/qmail/alias /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d"
CXXFLAGS="-O3 -mmmx -msse -msse2 -fomit-frame-pointer -march=pentium4
-funroll-loops -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distcc distlocks sandbox sfperms strict"
GENTOO_MIRRORS="ftp://ftp.muni.cz/pub/linux/gentoo http://gentoo.mirror.icd.hu/
http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/
http://gd.tuwien.ac.at/opsys/linux/gentoo/
ftp://ftp.tu-clausthal.de/pub/linux/gentoo/"
LINGUAS="cs cz en"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X Xaw3d aalib acpi adns alsa apache2 apm arts ati avcodec avi bidi
bitmap-fonts bonobo caca cdparanoia crypt cscope cups curl dba dga directfb
distcc divx divx4 divx4linux divx5 divx5linux dv dvb dvd dvdr dvdread eds emacs
emacs-w3 emboss encode esd ethereal evo f77 faac faad faad2 fam fame fbcon
ffmpeg flac flash foomaticdb fortran fvwm fvwm2 gb gd gdbm ggi gif gphoto2 gpm
gstreamer gtk gtk2 gtkhtml guile i8x0 icc imagemagick imlib imlib2 innodb java
jpeg junit lcms leim libg++ libwww live lpthread lzo lzw-tiff mad mcal mesa
mikmod mmx mmx2 motif mozilla mp3 mpeg mule mysql ncurses network nls nptl ogg
oggvorbis opengl oss pam pda pdflib perl php php4 plotutils png ppds pthread
pthreads python qt qtx quicktime readline rtc samba scanner sdl slp speex spell
sse sse2 ssl svga tcltk tcpd tetex tex theora thread threads tiff truetype
truetype-fonts type1-fonts unicode usb v4l v4l2 vorbis win32 winvidix wmf xine
xml xml2 xmms xosd xv xvid xvmc yv12 zeo zlib video_cards_radeon linguas_cs
linguas_cz linguas_en userland_GNU kernel_linux elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS



Reproducible: Always
Steps to Reproduce:
1.
2.
3.

[Comment 1 Jakub Moc (RETIRED) 2005-08-07 12:05:07 UTC]

I guess this is identical issue as in Bug 101650, please emerge sync and try again.

[Comment 2 Martin Mokrejš 2005-08-07 12:08:45 UTC]

Damn, is the bugzilla search case sensitive? :(( Sorry for the dupe.

[Comment 3 Jakub Moc (RETIRED) 2005-08-07 12:14:48 UTC]

(In reply to comment #2)
> Damn, is the bugzilla search case sensitive? :(( Sorry for the dupe.

Well, it should't be, but you need to prefix the search with ALL if you are
searching for duplicate bugs. However, the -prosite option is the new one, in
the supposedly fixed ebuild.

@ribosome - it this compatible only with emboss-3.0 or what's wrong here?

[Comment 4 Martin Mokrejš 2005-08-07 12:19:27 UTC]

BTW, I have sci-biology/emboss-2.10.0 installed. I have rsnced 30 minutes ago,
so I'll wait for the fix to get to my rsync server.

[Comment 5 Olivier Fisette (RETIRED) 2005-08-07 13:03:23 UTC]

Sorry, this was worse than I thought. I further modified the ebuild to require     
EMBOSS-3.0.0. Wait for an hour or so and the fix will propagate to your rsync 
server. 
     
Wish they documented these changes. That's what the changelog is for...     

[Comment 6 Martin Mokrejš 2005-08-09 14:50:17 UTC]

~x86 as now would do this on my host (the downgrade of emboss screws the rest):

# emerge -up world

These are the packages that I would merge, in order:

Calculating world dependencies ...done!
[ebuild     UD] sci-biology/emboss-2.10.0 [3.0.0] 
[ebuild     U ] sci-biology/embassy-phylip-3.57c-r1 [3.6b] 
[ebuild     U ] sci-biology/embassy-domainatrix-1.0.0-r1 [0.1.0] 
[ebuild  NS   ] www-apps/bugzilla-2.20_rc2  
[ebuild     U ] sci-chemistry/chemtool-1.6.7 [1.6.6] 
[ebuild     U ] x11-libs/qt-3.3.4-r7 [3.3.4-r6] 
[ebuild     U ] media-libs/imlib2-1.2.0.007-r1 [1.2.0.007] 
[ebuild     U ] dev-perl/XML-LibXML-1.58-r1 [1.58] 
[ebuild     U ] app-editors/vim-core-6.3.084-r1 [6.3.084] 
#

[Comment 7 Olivier Fisette (RETIRED) 2005-08-09 16:52:10 UTC]

Sorry, but I do not understand what the problem is.       
       
If I am not wrong about what I have done (that is not a given, though), one   
may currently use either the stable or testing branch of EMBOSS and the   
EMBASSY programs, but not mix the two; if you try, you will be told packages   
block each other.    
    
As for Prosite, any indexed version will be compatible with any     
version of EMBOSS. Indexing Prosite using the version of EMBOSS currently in     
the testing branch (3.0.0) will require using the version of Prosite currently     
in the testing branch. Indexing Prosite using the stable version of EMBOSS    
requires using the stable version of Prosite. Prosite ebuilds depend on the   
correct EMBOSS version. All this is reasonable, in my opinion, but I might    
have missed something.   
    
The "emerge" output you posted looks correct to me (if you use the stable    
branch). If you want to test EMBOSS 3.0.0 and the corresponding EMBASSY    
packages, I suggest you add all these packages (and Prosite) to your    
"/etc/portage/package.keywords" file.   
   
Please post feedback on this as soon as possible, as I want the transition to   
EMBOSS 3.0.0 to be as painless as possible. 

[Comment 8 Olivier Fisette (RETIRED) 2005-08-13 06:54:24 UTC]

This really ought to be fixed by now...