Bugzilla Bug 208462

These two sequence analysis programs have 13 programs in /usr/bin in common.

Reproducible: Always

Steps to Reproduce:
1. emerge sci-biology/hmmer sci-biology/qrna
2.
3.

Actual Results:  
>>> Emerging (1 of 1) sci-biology/qrna-2.0.3c to /
>>> Extracting info
>>> Extracting qrna-2.0.3c
* checking 142 files for package collisions
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at http://bugs.gentoo.org unless you report exactly which
 * two packages install the same file(s). Once again, please do NOT file
 * a bug report unless you have completely understood the above message.
 * 
 * package sci-biology/qrna-2.0.3c NOT merged
 * 
 * Detected file collision(s):
 * 
 *      /usr/bin/shuffle
 *      /usr/bin/afetch
 *      /usr/bin/alistat
 *      /usr/bin/compalign
 *      /usr/bin/compstruct
 *      /usr/bin/revcomp
 *      /usr/bin/seqsplit
 *      /usr/bin/seqstat
 *      /usr/bin/sfetch
 *      /usr/bin/sindex
 *      /usr/bin/sreformat
 *      /usr/bin/translate
 *      /usr/bin/weight
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * sci-biology/hmmer-2.3.2-r2
 *      /usr/bin/shuffle
 *      /usr/bin/afetch
 *      /usr/bin/alistat
 *      /usr/bin/compalign
 *      /usr/bin/compstruct
 *      /usr/bin/revcomp
 *      /usr/bin/seqsplit
 *      /usr/bin/seqstat
 *      /usr/bin/sfetch
 *      /usr/bin/sindex
 *      /usr/bin/sreformat
 *      /usr/bin/translate
 *      /usr/bin/weight

I've emailed the Eddy lab to see what they say about this.

Here's what Eddy said:

Hi Jeff,

Those are all programs in our SQUID library (some Linux distributions
have called it bioSQUID to avoid name clashes). Both HMMER and QRNA
also include SQUID, and both install SQUID executables by default.

So those programs are identical, modulo version differences.  They're
small utilities for manipulating biosequence info.

Because SQUID was poorly version controlled, I think you might need to
use the release dates of your HMMER and QRNA distros to determine
which version is more recent.

also, not sure which web page you were trying to access (maybe one of
our old St. Louis pages; we moved in 2006), but QRNA is still
available on the web:
  http://selab.janelia.org/software.html#qrna
and
  ftp://selab.janelia.org/pub/software/qrna/

best,
Sean


So I guess I'll have to see which SQUID is newer and install that one, while
leaving the other out. I've got to do some housework (sheetrock, ugh!), but
I'll be thinking of ways to handle this.
Suggestions welcome!!

I guess I'd just decide once and for all which of sci-biology/hmmer or 
sci-biology/qrna is in charge of installing the executables and then
make sure that the other one doesn't install them as well.

Best,
Markus

That's what I was thinking... pick the one that installs the newest squid and
roll with it... making sure it stays that way in subsequent releases.

Hi Jeff,

Any news one this one? Unfortunately, I don't know
the packages very well otherwise I'd take care of
it.

Thanks,
Markus

Whoops! I forgot about this one. I'll commit a fix in the next day or two.
Thanks Markus

I disabled installing the squid02 stuff from qrna and added hmmer as a
dependency. Hopefully that'll make eveyone happy :)
Thanks,
Jeff