Bug 389743 – sci-biology/rebase-1111 with USE=emboss fails to install

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Walter Meinl 2011-11-06 18:35:13 UTC]

>>> Emerging (1 of 1) sci-biology/rebase-1111
 * rebase-1111.tar.xz RMD160 SHA1 SHA256 size ;-) ...                    [ ok ]
>>> Unpacking source...
>>> Unpacking rebase-1111.tar.xz to /var/tmp/portage/sci-biology/rebase-1111/work
>>> Source unpacked in /var/tmp/portage/sci-biology/rebase-1111/work
>>> Preparing source in /var/tmp/portage/sci-biology/rebase-1111/work/rebase-1111 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/rebase-1111/work/rebase-1111 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/rebase-1111/work/rebase-1111 ...

 * Indexing Rebase for usage with EMBOSS.

   EMBOSS An error in rebaseextract.c at line 178:
Invalid withrefm file
 * ERROR: sci-biology/rebase-1111 failed (compile phase):
 *   Indexing Rebase failed.
 * 
 * Call stack:
 *     ebuild.sh, line  91:  Called src_compile
 *   environment, line 201:  Called die
 * The specific snippet of code:
 *           EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} -protofile proto.${MY_PV} -equivalences || die "Indexing Rebase failed.";
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/rebase-1111',
 * the complete build log and the output of 'emerge -pqv =sci-biology/rebase-1111'.
 * The complete build log is located at '/var/log/portage/sci-biology:rebase-1111:20111106-182829.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/rebase-1111/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/rebase-1111/work/rebase-1111'

The culprit seems to be the withrefm file. When I look in the rebase-1111.tar.xz file it contains several size 0 files amongst them withrefm.txt and withrefm.111
Size of withrefm.txt (and .111) on the NEB ftp server is 2464 kb.

[Comment 1 Patricio Jeraldo 2011-11-09 18:25:37 UTC]

(In reply to comment #0) 
> The culprit seems to be the withrefm file. When I look in the
> rebase-1111.tar.xz file it contains several size 0 files amongst them
> withrefm.txt and withrefm.111
> Size of withrefm.txt (and .111) on the NEB ftp server is 2464 kb.

That seems to be the case. To test this, I made a new tarball with the files from the FTP server, and it seems to have emerged properly.

I'm leaning towards a packing mistake, and a simple repack should fix the problem.

Patricio

[Comment 2 Justin Lecher (RETIRED) 2011-11-10 19:48:16 UTC]

mmh thats bad. I will fix that tomorrow.

[Comment 3 Justin Lecher (RETIRED) 2011-11-11 13:32:45 UTC]

Should be fixed now